bims-ginsta Biomed News
on Genome instability
Issue of 2024–02–25
forty-six papers selected by
Jinrong Hu, National University of Singapore
  1. The spindle protein CKAP2 regulates microtubule dynamics and ensures faithful chromosome segregation.
  2. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization.
  3. Identification of a motif in TPX2 that regulates spindle architecture in Xenopus egg extracts.
  4. Aberrant cortex contractions impact mammalian oocyte quality.
  5. Tissue-specific compensatory mechanisms maintain tissue architecture and body size independent of cell size in polyploid zebrafish.
  6. UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER.
  7. Imaging and Analysis of Drosophila Neural Stem Cell Asymmetric Division.
  8. JAK-STAT-dependent contact between follicle cells and the oocyte controls Drosophila anterior-posterior polarity and germline development.
  9. Structure of mavacamten-free human cardiac thick filaments within the sarcomere by cryoelectron tomography.
  10. Stalled translation by mitochondrial stress upregulates a CNOT4-ZNF598 ribosomal quality control pathway important for tissue homeostasis.
  11. Modified histone peptides uniquely tune the material properties of HP1α condensates.
  12. Mouse oocytes sequester aggregated proteins in degradative super-organelles.
  13. Increases in cyclin A/Cdk activity and in PP2A-B55 inhibition by FAM122A are key mitosis-inducing events.
  14. Single-molecule tracking reveals the functional allocation, in vivo interactions, and spatial organization of universal transcription factor NusG.
  15. Regulation of long-range BMP gradients and embryonic polarity by propagation of local calcium-firing activity.
  16. Hallmarks of totipotent and pluripotent stem cell states.
  17. ZNF692 regulates nucleolar morphology by interacting with NPM1 and modifying its self-assembly properties.
  18. Endothelial to mesenchymal transition: at the axis of cardiovascular health and disease.
  19. Oncogenic c-Myc induces replication stress by increasing cohesins chromatin occupancy in a CTCF-dependent manner.
  20. An emerging paradigm in epigenetic marking: coordination of transcription and replication.
  21. Contractility drives the spatio-temporal coordination of morphogenesis and cell fate in hair follicles.
  22. Genetic drivers of heterogeneity in type 2 diabetes pathophysiology.
  23. Stem cell migration drives lung repair in living mice.
  24. Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression.
  25. Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility.
  26. The CNK-HYP scaffolding complex promotes RAF activation by enhancing KSR-MEK interaction.
  27. Poly(ADP-ribosyl)ation of TIMELESS limits DNA replication stress and promotes stalled fork protection.
  28. Transcription factor exchange enables prolonged transcriptional bursts.
  29. Serine mistranslation induces the integrated stress response without accumulation of uncharged tRNAs.
  30. SIRT7 regulates NUCKS1 chromatin binding to elicit metabolic and inflammatory gene expression in senescence and liver aging.
  31. Local and global changes in cell density induce reorganisation of 3D packing in a proliferating epithelium.
  32. ATG5 attenuates inflammatory signaling in mouse embryonic stem cells to control differentiation.
  33. WNT signalling control by KDM5C during development affects cognition.
  34. DNA satellite and chromatin organization at mouse centromeres and pericentromeres.
  35. The zonula adherens matura redefines the apical junction of intestinal epithelia.
  36. mTORC1 activity oscillates throughout the cell cycle promoting mitotic entry and differentially influencing autophagy induction.
  37. Temporal dynamics of BMP/Nodal ratio drive tissue-specific gastrulation morphogenesis.
  38. The origin recognition complex requires chromatin tethering by a hypervariable intrinsically disordered region that is functionally conserved from sponge to man.
  39. IL-10 constrains sphingolipid metabolism to limit inflammation.
  40. Investigating Heterogeneous Cell-Cycle Progression Using Single-Cell Imaging Approaches.
  41. A SPLICS reporter reveals [Formula: see text]-synuclein regulation of lysosome-mitochondria contacts which affects TFEB nuclear translocation.
  42. A mutational atlas for Parkin proteostasis.
  43. Single molecule imaging of the central dogma reveals myosin-2A gene expression is regulated by contextual translational buffering.
  44. Mast Cells in Cardiac Remodeling: Focus on the Right Ventricle.
  45. Nr5a2 ensures inner cell mass formation in mouse blastocyst.
  46. Spatially resolved transcriptome of the aging mouse brain.
  1. Proc Natl Acad Sci U S A. 2024 Feb 27. 121(9): e2318782121
    The spindle protein CKAP2 regulates microtubule dynamics and ensures faithful chromosome segregation.
    Lia Mara Gomes Paim, Azriel Abraham Lopez-Jauregui, Thomas S McAlear, Susanne Bechstedt.
      Regulation of microtubule dynamics by microtubule-associated proteins (MAPs) is essential for mitotic spindle assembly and chromosome segregation. Altered microtubule dynamics, particularly increased microtubule growth rates, were found to be a contributing factor for the development of chromosomal instability, which potentiates tumorigenesis. The MAP XMAP215/CKAP5 is the only known microtubule growth factor, and whether other MAPs regulate microtubule growth in cells is unclear. Our recent in vitro reconstitution experiments have demonstrated that Cytoskeleton-Associated Protein 2 (CKAP2) increases microtubule nucleation and growth rates, and here, we find that CKAP2 is also an essential microtubule growth factor in cells. By applying CRISPR-Cas9 knock-in and knock-out (KO) as well as microtubule plus-end tracking live cell imaging, we show that CKAP2 is a mitotic spindle protein that ensures faithful chromosome segregation by regulating microtubule growth. Live cell imaging of endogenously labeled CKAP2 showed that it localizes to the spindle during mitosis and rapidly shifts its localization to the chromatin upon mitotic exit before being degraded. Cells lacking CKAP2 display reduced microtubule growth rates and an increased proportion of chromosome segregation errors and aneuploidy that may be a result of an accumulation of kinetochore-microtubule misattachments. Microtubule growth rates and chromosome segregation fidelity can be rescued upon ectopic CKAP2 expression in KO cells, revealing a direct link between CKAP2 expression and microtubule dynamics. Our results unveil a role of CKAP2 in regulating microtubule growth in cells and provide a mechanistic explanation for the oncogenic potential of CKAP2 misregulation.
    Keywords:  chromosome segregation; kinetochore; microtubule dynamics; mitosis; spindle
    DOI:  https://doi.org/10.1073/pnas.2318782121
  2. Nat Phys. 2024 ;20(2): 310-321
    Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization.
    Silvia Caballero-Mancebo, Rushikesh Shinde, Madison Bolger-Munro, Matilda Peruzzo, Gregory Szep, Irene Steccari, David Labrousse-Arias, Vanessa Zheden, Jack Merrin, Andrew Callan-Jones, Raphaël Voituriez, Carl-Philipp Heisenberg.
      Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole-a protuberance of the zygote's vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces.
    Keywords:  Biological physics; Biophysics
    DOI:  https://doi.org/10.1038/s41567-023-02302-1
  3. bioRxiv. 2024 Feb 11. pii: 2024.02.10.579770. [Epub ahead of print]
    Identification of a motif in TPX2 that regulates spindle architecture in Xenopus egg extracts.
    Guadalupe E Pena, Xiao Zhou, Lauren Slevin, Christopher Brownlee, Rebecca Heald.
      A bipolar spindle composed of microtubules and many associated proteins functions to segregate chromosomes during cell division in all eukaryotes, yet spindle size and architecture varies dramatically across different species and cell types. Targeting protein for Xklp2 (TPX2) is one candidate factor for modulating spindle microtubule organization through its roles in branching microtubule nucleation, activation of the mitotic kinase Aurora A, and association with the kinesin-5 (Eg5) motor. Here we identify a conserved nuclear localization sequence (NLS) motif, 123 KKLK 126 in X. laevis TPX2, which regulates astral microtubule formation and spindle pole morphology in Xenopus egg extracts. Addition of recombinant TPX2 with this sequence mutated to AALA dramatically increased spontaneous formation of microtubule asters and recruitment of phosphorylated Aurora A, pericentrin, and Eg5 to meiotic spindle poles. We propose that TPX2 is a linchpin spindle assembly factor whose regulation contributes to the recruitment and activation of multiple microtubule polymerizing and organizing proteins, generating distinct spindle architectures.
    DOI:  https://doi.org/10.1101/2024.02.10.579770
  4. Dev Cell. 2024 Feb 20. pii: S1534-5807(24)00047-9. [Epub ahead of print]
    Aberrant cortex contractions impact mammalian oocyte quality.
    Elvira Nikalayevich, Gaëlle Letort, Ghislain de Labbey, Elena Todisco, Anastasia Shihabi, Hervé Turlier, Raphaël Voituriez, Mohamed Yahiatene, Xavier Pollet-Villard, Metello Innocenti, Melina Schuh, Marie-Emilie Terret, Marie-Hélène Verlhac.
      The cortex controls cell shape. In mouse oocytes, the cortex thickens in an Arp2/3-complex-dependent manner, ensuring chromosome positioning and segregation. Surprisingly, we identify that mouse oocytes lacking the Arp2/3 complex undergo cortical actin remodeling upon division, followed by cortical contractions that are unprecedented in mammalian oocytes. Using genetics, imaging, and machine learning, we show that these contractions stir the cytoplasm, resulting in impaired organelle organization and activity. Oocyte capacity to avoid polyspermy is impacted, leading to a reduced female fertility. We could diminish contractions and rescue cytoplasmic anomalies. Similar contractions were observed in human oocytes collected as byproducts during IVF (in vitro fertilization) procedures. These contractions correlate with increased cytoplasmic motion, but not with defects in spindle assembly or aneuploidy in mice or humans. Our study highlights a multiscale effect connecting cortical F-actin, contractions, and cytoplasmic organization and affecting oocyte quality, with implications for female fertility.
    DOI:  https://doi.org/10.1016/j.devcel.2024.01.027
  5. Dev Biol. 2024 Feb 20. pii: S0012-1606(24)00025-3. [Epub ahead of print]
    Tissue-specific compensatory mechanisms maintain tissue architecture and body size independent of cell size in polyploid zebrafish.
    C D Small, T J Benfey, B D Crawford.
      Genome duplications and ploidy transitions have occurred in nearly every major taxon of eukaryotes, but they are far more common in plants than in animals. Due to the conservation of the nuclear:cytoplasmic volume ratio increased DNA content results in larger cells. In plants, polyploid organisms are larger than diploids as cell number remains relatively constant. Conversely, vertebrate body size does not correlate with cell size and ploidy as vertebrates compensate for increased cell size to maintain tissue architecture and body size. This has historically been explained by a simple reduction in cell number that matches the increase in cell size maintaining body size as ploidy increases, but here we show that the compensatory mechanisms that maintain body size in triploid zebrafish are tissue-specific: A) erythrocytes respond in the classical pattern with a reduced number of larger erythrocytes in circulation, B) muscle, a tissue comprised of polynucleated muscle fibers, compensates by reducing the number of larger nuclei such that myofiber and myotome size in unaffected by ploidy, and C) vascular tissue compensates by thickening blood vessel walls, possibly at the expense of luminal diameter. Understanding the physiological implications of ploidy on tissue function requires a detailed description of the specific mechanisms of morphological compensation occurring in each tissue to understand how ploidy changes affect development and physiology.
    Keywords:  Cell size; Morphogenesis; Muscle development; N:C ratio; Patterning; Polyploidy; Tissue architecture; Vascular development; Whole genome duplication; Zebrafish
    DOI:  https://doi.org/10.1016/j.ydbio.2024.02.005
  6. Nature. 2024 Feb 21.
    UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER.
    Paul A DaRosa, Ivan Penchev, Samantha C Gumbin, Francesco Scavone, Magda Wąchalska, Joao A Paulo, Alban Ordureau, Joshua J Peter, Yogesh Kulathu, J Wade Harper, Thomas Becker, Roland Beckmann, Ron R Kopito.
      Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour1. UFM1 is a UBL that predominantly modifies a single lysine residue on a single ribosomal protein, uL24 (also called RPL26), on ribosomes at the cytoplasmic surface of the endoplasmic reticulum (ER)2,3. UFM1 conjugation (UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER3,4. Neither the molecular mechanism by which the UFMylation machinery achieves such precise target selection nor how this ribosomal modification promotes 60S rescue is known. Here we show that ribosome UFMylation in vivo occurs on free 60S and we present sequential cryo-electron microscopy snapshots of the heterotrimeric UFM1 E3 ligase (E3(UFM1)) engaging its substrate uL24. E3(UFM1) binds the L1 stalk, empty transfer RNA-binding sites and the peptidyl transferase centre through carboxy-terminal domains of UFL1, which results in uL24 modification more than 150 Å away. After catalysing UFM1 transfer, E3(UFM1) remains stably bound to its product, UFMylated 60S, forming a C-shaped clamp that extends all the way around the 60S from the transfer RNA-binding sites to the polypeptide tunnel exit. Our structural and biochemical analyses suggest a role for E3(UFM1) in post-termination release and recycling of the large ribosomal subunit from the ER membrane.
    DOI:  https://doi.org/10.1038/s41586-024-07073-0
  7. Methods Mol Biol. 2024 ;2740 229-242
    Imaging and Analysis of Drosophila Neural Stem Cell Asymmetric Division.
    Anne-Marie Berisha, Gregory Eot-Houllier, Régis Giet.
      Cell division is a conserved process among eukaryotes. It is designed to segregate chromosomes into future daughter cells and involves a complex rearrangement of the cytoskeleton, including microtubules and actin filaments. An additional level of complexity is present in asymmetric dividing stem cells because cytoskeleton elements are also regulated by polarity cues. The neural stem cell system of the fruit fly represents a simple model to dissect the mechanisms that control cytoskeleton reorganization during asymmetric division. In this chapter, we propose to describe protocols that allow accurate analysis of microtubule reorganization during cell division in this model.
    Keywords:  Asymmetric cell division; Central nervous system; Chromosomes; Drosophila; Indirect immunofluorescence; Live imaging; Microscopy; Microtubule; Neural stem cells
    DOI:  https://doi.org/10.1007/978-1-0716-3557-5_14
  8. Nat Commun. 2024 Feb 22. 15(1): 1627
    JAK-STAT-dependent contact between follicle cells and the oocyte controls Drosophila anterior-posterior polarity and germline development.
    Charlotte Mallart, Sophie Netter, Fabienne Chalvet, Sandra Claret, Antoine Guichet, Jacques Montagne, Anne-Marie Pret, Marianne Malartre.
      The number of embryonic primordial germ cells in Drosophila is determined by the quantity of germ plasm, whose assembly starts in the posterior region of the oocyte during oogenesis. Here, we report that extending JAK-STAT activity in the posterior somatic follicular epithelium leads to an excess of primordial germ cells in the future embryo. We show that JAK-STAT signaling is necessary for the differentiation of approximately 20 specialized follicle cells maintaining tight contact with the oocyte. These cells define, in the underlying posterior oocyte cortex, the anchoring of the germ cell determinant oskar mRNA. We reveal that the apical surface of these posterior anchoring cells extends long filopodia penetrating the oocyte. We identify two JAK-STAT targets in these cells that are each sufficient to extend the zone of contact with the oocyte, thereby leading to production of extra primordial germ cells. JAK-STAT signaling thus determines a fixed number of posterior anchoring cells required for anterior-posterior oocyte polarity and for the development of the future germline.
    DOI:  https://doi.org/10.1038/s41467-024-45963-z
  9. Proc Natl Acad Sci U S A. 2024 Feb 27. 121(9): e2311883121
    Structure of mavacamten-free human cardiac thick filaments within the sarcomere by cryoelectron tomography.
    Liang Chen, Jun Liu, Hosna Rastegarpouyani, Paul M L Janssen, Jose R Pinto, Kenneth A Taylor.
      Heart muscle has the unique property that it can never rest; all cardiomyocytes contract with each heartbeat which requires a complex control mechanism to regulate cardiac output to physiological requirements. Changes in calcium concentration regulate the thin filament activation. A separate but linked mechanism regulates the thick filament activation, which frees sufficient myosin heads to bind the thin filament, thereby producing the required force. Thick filaments contain additional nonmyosin proteins, myosin-binding protein C and titin, the latter being the protein that transmits applied tension to the thick filament. How these three proteins interact to control thick filament activation is poorly understood. Here, we show using 3-D image reconstruction of frozen-hydrated human cardiac muscle myofibrils lacking exogenous drugs that the thick filament is structured to provide three levels of myosin activation corresponding to the three crowns of myosin heads in each 429Å repeat. In one crown, the myosin heads are almost completely activated and disordered. In another crown, many myosin heads are inactive, ordered into a structure called the interacting heads motif. At the third crown, the myosin heads are ordered into the interacting heads motif, but the stability of that motif is affected by myosin-binding protein C. We think that this hierarchy of control explains many of the effects of length-dependent activation as well as stretch activation in cardiac muscle control.
    Keywords:  cMyBP-C; myosin; striated muscle; titin; vertebrates
    DOI:  https://doi.org/10.1073/pnas.2311883121
  10. Nat Commun. 2024 Feb 22. 15(1): 1637
    Stalled translation by mitochondrial stress upregulates a CNOT4-ZNF598 ribosomal quality control pathway important for tissue homeostasis.
    Ji Geng, Shuangxi Li, Yu Li, Zhihao Wu, Sunil Bhurtel, Suman Rimal, Danish Khan, Rani Ohja, Onn Brandman, Bingwei Lu.
      Translational control exerts immediate effect on the composition, abundance, and integrity of the proteome. Ribosome-associated quality control (RQC) handles ribosomes stalled at the elongation and termination steps of translation, with ZNF598 in mammals and Hel2 in yeast serving as key sensors of translation stalling and coordinators of downstream resolution of collided ribosomes, termination of stalled translation, and removal of faulty translation products. The physiological regulation of RQC in general and ZNF598 in particular in multicellular settings is underexplored. Here we show that ZNF598 undergoes regulatory K63-linked ubiquitination in a CNOT4-dependent manner and is upregulated upon mitochondrial stresses in mammalian cells and Drosophila. ZNF598 promotes resolution of stalled ribosomes and protects against mitochondrial stress in a ubiquitination-dependent fashion. In Drosophila models of neurodegenerative diseases and patient cells, ZNF598 overexpression aborts stalled translation of mitochondrial outer membrane-associated mRNAs, removes faulty translation products causal of disease, and improves mitochondrial and tissue health. These results shed lights on the regulation of ZNF598 and its functional role in mitochondrial and tissue homeostasis.
    DOI:  https://doi.org/10.1038/s41467-024-45525-3
  11. bioRxiv. 2024 Feb 09. pii: 2024.02.07.579285. [Epub ahead of print]
    Modified histone peptides uniquely tune the material properties of HP1α condensates.
    Priyasha Deshpande, Emily Prentice, Alfredo Vidal Ceballos, Patrizia Casaccia, Shana Elbaum-Garfinkle.
      Biomolecular condensates have emerged as a powerful new paradigm in cell biology with broad implications to human health and disease, particularly in the nucleus where phase separation is thought to underly elements of chromatin organization and regulation. Specifically, it has been recently reported that phase separation of heterochromatin protein 1alpha (HP1α) with DNA contributes to the formation of condensed chromatin states. HP1α localization to heterochromatic regions is mediated by its binding to specific repressive marks on the tail of histone H3, such as trimethylated lysine 9 on histone H3 (H3K9me3). However, whether epigenetic marks play an active role in modulating the material properties of HP1α and dictating emergent functions of its condensates, remains only partially understood. Here, we leverage a reductionist system, comprised of modified and unmodified histone H3 peptides, HP1α and DNA to examine the contribution of specific epigenetic marks to phase behavior of HP1α. We show that the presence of histone peptides bearing the repressive H3K9me3 is compatible with HP1α condensates, while peptides containing unmodified residues or bearing the transcriptional activation mark H3K4me3 are incompatible with HP1α phase separation. In addition, inspired by the decreased ratio of nuclear H3K9me3 to HP1α detected in cells exposed to uniaxial strain, using fluorescence microscopy and rheological approaches we demonstrate that H3K9me3 histone peptides modulate the dynamics and network properties of HP1α condensates in a concentration dependent manner. These data suggest that HP1α-DNA condensates are viscoelastic materials, whose properties may provide an explanation for the dynamic behavior of heterochromatin in cells in response to mechanostimulation.
    Statement of significance: The organization of genomic information in eukaryotic cells necessitates compartmentalization into functional domains allowing for the expression of cell identity-specific genes, while repressing genes related to alternative fates. Heterochromatin hosts these transcriptionally silent regions of the genome - which ensure the stability of cell identity -and is characterized by repressive histone marks (H3K9m3) and other specialized proteins (HP1a), recently shown to phase separate with DNA. We show that HP1a forms condensates with DNA which persist in the presence of H3K9me3 peptides. The viscoelastic nature of these condensates depend on H3K9me3:HP1 ratios, which are modulated by mechanical strain in cells. Thus, phase separation may explain the dynamic behavior of heterochromatin in cells, in response to mechanostimulation.
    DOI:  https://doi.org/10.1101/2024.02.07.579285
  12. Cell. 2024 Feb 09. pii: S0092-8674(24)00068-0. [Epub ahead of print]
    Mouse oocytes sequester aggregated proteins in degradative super-organelles.
    Gabriele Zaffagnini, Shiya Cheng, Marion C Salzer, Barbara Pernaute, Juan Manuel Duran, Manuel Irimia, Melina Schuh, Elvan Böke.
      Oocytes are among the longest-lived cells in the body and need to preserve their cytoplasm to support proper embryonic development. Protein aggregation is a major threat for intracellular homeostasis in long-lived cells. How oocytes cope with protein aggregation during their extended life is unknown. Here, we find that mouse oocytes accumulate protein aggregates in specialized compartments that we named endolysosomal vesicular assemblies (ELVAs). Combining live-cell imaging, electron microscopy, and proteomics, we found that ELVAs are non-membrane-bound compartments composed of endolysosomes, autophagosomes, and proteasomes held together by a protein matrix formed by RUFY1. Functional assays revealed that in immature oocytes, ELVAs sequester aggregated proteins, including TDP-43, and degrade them upon oocyte maturation. Inhibiting degradative activity in ELVAs leads to the accumulation of protein aggregates in the embryo and is detrimental for embryo survival. Thus, ELVAs represent a strategy to safeguard protein homeostasis in long-lived cells.
    Keywords:  RUFY1; embryo; female fertility; lysosomal acidification; membraneless organelles; oocyte; oocyte quality; protein aggregation; proteostasis; super-organelles
    DOI:  https://doi.org/10.1016/j.cell.2024.01.031
  13. EMBO J. 2024 Feb 20.
    Increases in cyclin A/Cdk activity and in PP2A-B55 inhibition by FAM122A are key mitosis-inducing events.
    Benjamin Lacroix, Suzanne Vigneron, Jean Claude Labbé, Lionel Pintard, Corinne Lionne, Gilles Labesse, Anna Castro, Thierry Lorca.
      Entry into mitosis has been classically attributed to the activation of a cyclin B/Cdk1 amplification loop via a partial pool of this kinase becoming active at the end of G2 phase. However, how this initial pool is activated is still unknown. Here we discovered a new role of the recently identified PP2A-B55 inhibitor FAM122A in triggering mitotic entry. Accordingly, depletion of the orthologue of FAM122A in C. elegans prevents entry into mitosis in germline stem cells. Moreover, data from Xenopus egg extracts strongly suggest that FAM122A-dependent inhibition of PP2A-B55 could be the initial event promoting mitotic entry. Inhibition of this phosphatase allows subsequent phosphorylation of early mitotic substrates by cyclin A/Cdk, resulting in full cyclin B/Cdk1 and Greatwall (Gwl) kinase activation. Subsequent to Greatwall activation, Arpp19/ENSA become phosphorylated and now compete with FAM122A, promoting its dissociation from PP2A-B55 and taking over its phosphatase inhibition role until the end of mitosis.
    Keywords:  Arpp19; Cyclin A.; FAM122A; Mitosis; PP2A-B55
    DOI:  https://doi.org/10.1038/s44318-024-00054-z
  14. Mol Cell. 2024 Feb 14. pii: S1097-2765(24)00092-3. [Epub ahead of print]
    Single-molecule tracking reveals the functional allocation, in vivo interactions, and spatial organization of universal transcription factor NusG.
    Hafez El Sayyed, Oliver J Pambos, Mathew Stracy, Max E Gottesman, Achillefs N Kapanidis.
      During transcription elongation, NusG aids RNA polymerase by inhibiting pausing, promoting anti-termination on rRNA operons, coupling transcription with translation on mRNA genes, and facilitating Rho-dependent termination. Despite extensive work, the in vivo functional allocation and spatial distribution of NusG remain unknown. Using single-molecule tracking and super-resolution imaging in live E. coli cells, we found NusG predominantly in a chromosome-associated population (binding to RNA polymerase in elongation complexes) and a slowly diffusing population complexed with the 30S ribosomal subunit; the latter provides a "30S-guided" path for NusG into transcription elongation. Only ∼10% of NusG is fast diffusing, with its mobility suggesting non-specific interactions with DNA for >50% of the time. Antibiotic treatments and deletion mutants revealed that chromosome-associated NusG participates mainly in rrn anti-termination within phase-separated transcriptional condensates and in transcription-translation coupling. This study illuminates the multiple roles of NusG and offers a guide on dissecting multi-functional machines via in vivo imaging.
    Keywords:  liquid-liquid phase separation; rrn anti-termination; single-molecule tracking; transcription elongation; transcription-translation coupling
    DOI:  https://doi.org/10.1016/j.molcel.2024.01.025
  15. Nat Commun. 2024 Feb 17. 15(1): 1463
    Regulation of long-range BMP gradients and embryonic polarity by propagation of local calcium-firing activity.
    Hyung Chul Lee, Nidia M M Oliveira, Cato Hastings, Peter Baillie-Benson, Adam A Moverley, Hui-Chun Lu, Yi Zheng, Elise L Wilby, Timothy T Weil, Karen M Page, Jianping Fu, Naomi Moris, Claudio D Stern.
      Many amniote vertebrate species including humans can form identical twins from a single embryo, but this only occurs rarely. It has been suggested that the primitive-streak-forming embryonic region emits signals that inhibit streak formation elsewhere but the signals involved, how they are transmitted and how they act has not been elucidated. Here we show that short tracks of calcium firing activity propagate through extraembryonic tissue via gap junctions and prevent ectopic primitive streak formation in chick embryos. Cross-regulation of calcium activity and an inhibitor of primitive streak formation (Bone Morphogenetic Protein, BMP) via NF-κB and NFAT establishes a long-range BMP gradient spanning the embryo. This mechanism explains how embryos of widely different sizes can maintain positional information that determines embryo polarity. We provide evidence for similar mechanisms in two different human embryo models and in Drosophila, suggesting an ancient evolutionary origin.
    DOI:  https://doi.org/10.1038/s41467-024-45772-4
  16. Cell Stem Cell. 2024 Feb 13. pii: S1934-5909(24)00039-0. [Epub ahead of print]
    Hallmarks of totipotent and pluripotent stem cell states.
    Peng Du, Jun Wu.
      Though totipotency and pluripotency are transient during early embryogenesis, they establish the foundation for the development of all mammals. Studying these in vivo has been challenging due to limited access and ethical constraints, particularly in humans. Recent progress has led to diverse culture adaptations of epiblast cells in vitro in the form of totipotent and pluripotent stem cells, which not only deepen our understanding of embryonic development but also serve as invaluable resources for animal reproduction and regenerative medicine. This review delves into the hallmarks of totipotent and pluripotent stem cells, shedding light on their key molecular and functional features.
    Keywords:  formative pluripotency; intermediate pluripotency; naive pluripotency; pluripotency; pluripotent stem cells; primed pluripotency; totipotency; totipotent stem cells
    DOI:  https://doi.org/10.1016/j.stem.2024.01.009
  17. J Biol Chem. 2024 Feb 19. pii: S0021-9258(24)00149-2. [Epub ahead of print] 105773
    ZNF692 regulates nucleolar morphology by interacting with NPM1 and modifying its self-assembly properties.
    Isabella N Brown, Arlene Levario, Chunhui Jiang, Weronika Stachera, Enrique Rodriguez, Yi-Heng Hao, Jeffrey B Woodruff, M Carmen Lafita-Navarro, Maralice Conacci-Sorrell.
      The nucleolus, a membraneless organelle, is responsible for ribosomal RNA transcription, ribosomal RNA processing, and ribosome assembly. Nucleolar size and number are indicative of a cell's protein synthesis rate and proliferative capacity, and abnormalities in the nucleolus have been linked to neurodegenerative diseases and cancer. In this study, we demonstrated that the nucleolar protein ZNF692 directly interacts with nucleophosmin 1 (NPM1). Knocking down ZNF692 resulted in the nucleolar redistribution of NPM1 in ring-like structures and reduced protein synthesis. Purified NPM1 forms spherical condensates in vitro but mixing it with ZNF692 produces irregular condensates more closely resembling living cell nucleoli. Our findings indicate that ZNF692, by interacting with NPM1, plays a critical role in regulating nucleolar architecture and function in living cells.
    Keywords:  NPM1; ZNF692; condensates; nucleolus; protein assembly
    DOI:  https://doi.org/10.1016/j.jbc.2024.105773
  18. Cardiovasc Res. 2024 Feb 22. pii: cvae021. [Epub ahead of print]
    Endothelial to mesenchymal transition: at the axis of cardiovascular health and disease.
    Ignacio Fernando Hall, Franceska Kishta, Yang Xu, Andrew H Baker, Jason C Kovacic.
      Endothelial cells (ECs) line the luminal surface of blood vessels and play a major role in vascular (patho)-physiology by acting as a barrier, sensing circulating factors and intrinsic/extrinsic signals. ECs have the capacity to undergo endothelial-to-mesenchymal transition (EndMT), a complex differentiation process with key roles both during embryonic development and in adulthood. EndMT can contribute to EC activation and dysfunctional alterations associated with maladaptive tissue responses in human disease. During EndMT, ECs progressively undergo changes leading to expression of mesenchymal markers while repressing EC lineage-specific traits. This phenotypic and functional switch is considered to largely exist in a continuum, being characterized by a gradation of transitioning stages. In this report, we discuss process plasticity and potential reversibility and the hypothesis that different EndMT-derived cell populations may play a different role in disease progression or resolution. In addition, we review advancements in the EndMT field, current technical challenges, as well as therapeutic options and opportunities in the context of cardiovascular biology.
    Keywords:  Cellular plasticity and heterogeneity; Development; Endothelial cell biology; Endothelial-to-mesenchymal transition (EndMT); Human disease; Therapeutic options
    DOI:  https://doi.org/10.1093/cvr/cvae021
  19. Nat Commun. 2024 Feb 21. 15(1): 1579
    Oncogenic c-Myc induces replication stress by increasing cohesins chromatin occupancy in a CTCF-dependent manner.
    Silvia Peripolli, Leticia Meneguello, Chiara Perrod, Tanya Singh, Harshil Patel, Sazia T Rahman, Koshiro Kiso, Peter Thorpe, Vincenzo Calvanese, Cosetta Bertoli, Robertus A M de Bruin.
      Oncogene-induced replication stress is a crucial driver of genomic instability and one of the key events contributing to the onset and evolution of cancer. Despite its critical role in cancer, the mechanisms that generate oncogene-induced replication stress remain not fully understood. Here, we report that an oncogenic c-Myc-dependent increase in cohesins on DNA contributes to the induction of replication stress. Accumulation of cohesins on chromatin is not sufficient to cause replication stress, but also requires cohesins to accumulate at specific sites in a CTCF-dependent manner. We propose that the increased accumulation of cohesins at CTCF site interferes with the progression of replication forks, contributing to oncogene-induced replication stress. This is different from, and independent of, previously suggested mechanisms of oncogene-induced replication stress. This, together with the reported protective role of cohesins in preventing replication stress-induced DNA damage, supports a double-edge involvement of cohesins in causing and tolerating oncogene-induced replication stress.
    DOI:  https://doi.org/10.1038/s41467-024-45955-z
  20. Transcription. 2024 Feb 20. 1-16
    An emerging paradigm in epigenetic marking: coordination of transcription and replication.
    Tyler K Fenstermaker, Svetlana Petruk, Alexander Mazo.
      DNA replication and RNA transcription both utilize DNA as a template and therefore need to coordinate their activities. The predominant theory in the field is that in order for the replication fork to proceed, transcription machinery has to be evicted from DNA until replication is complete. If that does not occur, these machineries collide, and these collisions elicit various repair mechanisms which require displacement of one of the enzymes, often RNA polymerase, in order for replication to proceed. This model is also at the heart of the epigenetic bookmarking theory, which implies that displacement of RNA polymerase during replication requires gradual re-building of chromatin structure, which guides recruitment of transcriptional proteins and resumption of transcription. We discuss these theories but also bring to light newer data that suggest that these two processes may not be as detrimental to one another as previously thought. This includes findings suggesting that these processes can occur without fork collapse and that RNA polymerase may only be transiently displaced during DNA replication. We discuss potential mechanisms by which RNA polymerase may be retained at the replication fork and quickly rebind to DNA post-replication. These discoveries are important, not only as new evidence as to how these two processes are able to occur harmoniously but also because they have implications on how transcriptional programs are maintained through DNA replication. To this end, we also discuss the coordination of replication and transcription in light of revising the current epigenetic bookmarking theory of how the active gene status can be transmitted through S phase.
    Keywords:  RNA polymerase II; epigenetic bookmarking; nascent chromatin; transcription memory; transcription post-replication; transcription-replication conflicts
    DOI:  https://doi.org/10.1080/21541264.2024.2316965
  21. Nat Cell Biol. 2024 Feb 23.
    Contractility drives the spatio-temporal coordination of morphogenesis and cell fate in hair follicles.
      
    DOI:  https://doi.org/10.1038/s41556-024-01371-5
  22. Nature. 2024 Feb 19.
    Genetic drivers of heterogeneity in type 2 diabetes pathophysiology.
    VA Million Veteran Program
      Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes1,2 and molecular mechanisms that are often specific to cell type3,4. Here, to characterize the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study data from 2,535,601 individuals (39.7% not of European ancestry), including 428,452 cases of T2D. We identify 1,289 independent association signals at genome-wide significance (P < 5 × 10-8) that map to 611 loci, of which 145 loci are, to our knowledge, previously unreported. We define eight non-overlapping clusters of T2D signals that are characterized by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type-specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial cells and enteroendocrine cells. We build cluster-specific partitioned polygenic scores5 in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care.
    DOI:  https://doi.org/10.1038/s41586-024-07019-6
  23. Dev Cell. 2024 Feb 14. pii: S1534-5807(24)00074-1. [Epub ahead of print]
    Stem cell migration drives lung repair in living mice.
    Maurizio Chioccioli, Shuyu Liu, Sumner Magruder, Aleksandra Tata, Lucia Borriello, John E McDonough, Arvind Konkimalla, Sang-Hun Kim, Jessica Nouws, David G Gonzalez, Brian Traub, Xianjun Ye, Tao Yang, David R Entenberg, Smita Krishnaswamy, Caroline E Hendry, Naftali Kaminski, Purushothama Rao Tata, Maor Sauler.
      Tissue repair requires a highly coordinated cellular response to injury. In the lung, alveolar type 2 cells (AT2s) act as stem cells to replenish both themselves and alveolar type 1 cells (AT1s); however, the complex orchestration of stem cell activity after injury is poorly understood. Here, we establish longitudinal imaging of AT2s in murine intact tissues ex vivo and in vivo in order to track their dynamic behavior over time. We discover that a large fraction of AT2s become motile following injury and provide direct evidence for their migration between alveolar units. High-resolution morphokinetic mapping of AT2s further uncovers the emergence of distinct motile phenotypes. Inhibition of AT2 migration via genetic depletion of ArpC3 leads to impaired regeneration of AT2s and AT1s in vivo. Together, our results establish a requirement for stem cell migration between alveolar units and identify properties of stem cell motility at high cellular resolution.
    DOI:  https://doi.org/10.1016/j.devcel.2024.02.003
  24. bioRxiv. 2024 Feb 08. pii: 2024.02.06.579062. [Epub ahead of print]
    Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression.
    James Lee, Leman Simpson, Yi Li, Samuel Becker, Fan Zou, Xin Zhang, Lu Bai.
      Some transcription factors (TFs) can form liquid-liquid phase separated (LLPS) condensates. However, the functions of these TF condensates in 3D genome organization and gene regulation remain elusive. In response to methionine (met) starvation, budding yeast TF Met4 and a few co-activators, including Met32, induce a set of genes involved in met biosynthesis. Here, we show that the endogenous Met4 and Met32 form co-localized puncta-like structures in yeast nuclei upon met depletion. Recombinant Met4 and Met32 form mixed droplets with LLPS properties in vitro . In relation to chromatin, Met4 puncta co-localize with target genes, and at least a subset of these target genes are clustered in 3D in a Met4-dependent manner. A MET3pr -GFP reporter inserted near several native Met4 binding sites becomes co-localized with Met4 puncta and displays enhanced transcriptional activity. A Met4 variant with a partial truncation of an intrinsically disordered region (IDR) shows less puncta formation, and this mutant selectively reduces the reporter activity near Met4 binding sites to the basal level. Overall, these results support a model where Met4 and co-activators form condensates to bring multiple target genes into a vicinity with higher local TF concentrations, which facilitates a strong response to methionine depletion.
    DOI:  https://doi.org/10.1101/2024.02.06.579062
  25. Nat Chem. 2024 Feb 21.
    Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility.
    Ushnish Rana, Ke Xu, Amal Narayanan, Mackenzie T Walls, Athanassios Z Panagiotopoulos, José L Avalos, Clifford P Brangwynne.
      Endogenous biomolecular condensates, composed of a multitude of proteins and RNAs, can organize into multiphasic structures with compositionally distinct phases. This multiphasic organization is generally understood to be critical for facilitating their proper biological function. However, the biophysical principles driving multiphase formation are not completely understood. Here we use in vivo condensate reconstitution experiments and coarse-grained molecular simulations to investigate how oligomerization and sequence interactions modulate multiphase organization in biomolecular condensates. We demonstrate that increasing the oligomerization state of an intrinsically disordered protein results in enhanced immiscibility and multiphase formation. Interestingly, we find that oligomerization tunes the miscibility of intrinsically disordered proteins in an asymmetric manner, with the effect being more pronounced when the intrinsically disordered protein, exhibiting stronger homotypic interactions, is oligomerized. Our findings suggest that oligomerization is a flexible biophysical mechanism that cells can exploit to tune the internal organization of biomolecular condensates and their associated biological functions.
    DOI:  https://doi.org/10.1038/s41557-024-01456-6
  26. Nat Struct Mol Biol. 2024 Feb 22.
    The CNK-HYP scaffolding complex promotes RAF activation by enhancing KSR-MEK interaction.
    Pierre Maisonneuve, Malha Sahmi, Fanny Bergeron-Labrecque, Xianjie Iris Ma, Juliette Queguiner, Geneviève Arseneault, Martin Lefrançois, Igor Kurinov, Rémi Fronzes, Frank Sicheri, Marc Therrien.
      The RAS-MAPK pathway regulates cell proliferation, differentiation and survival, and its dysregulation is associated with cancer development. The pathway minimally comprises the small GTPase RAS and the kinases RAF, MEK and ERK. Activation of RAF by RAS is notoriously intricate and remains only partially understood. There are three RAF isoforms in mammals (ARAF, BRAF and CRAF) and two related pseudokinases (KSR1 and KSR2). RAS-mediated activation of RAF depends on an allosteric mechanism driven by the dimerization of its kinase domain. Recent work on human RAFs showed that MEK binding to KSR1 promotes KSR1-BRAF heterodimerization, which leads to the phosphorylation of free MEK molecules by BRAF. Similar findings were made with the single Drosophila RAF homolog. Here we show that the fly scaffold proteins CNK and HYP stabilize the KSR-MEK interaction, which in turn enhances RAF-KSR heterodimerization and RAF activation. The cryogenic electron microscopy structure of the minimal KSR-MEK-CNK-HYP complex reveals a ring-like arrangement of the CNK-HYP complex allowing CNK to simultaneously engage KSR and MEK, thus stabilizing the binary interaction. Together, these results illuminate how CNK contributes to RAF activation by stimulating the allosteric function of KSR and highlight the diversity of mechanisms impacting RAF dimerization as well as the regulatory potential of the KSR-MEK interaction.
    DOI:  https://doi.org/10.1038/s41594-024-01233-6
  27. Cell Rep. 2024 Feb 22. pii: S2211-1247(24)00173-6. [Epub ahead of print]43(3): 113845
    Poly(ADP-ribosyl)ation of TIMELESS limits DNA replication stress and promotes stalled fork protection.
    Julie Rageul, Natalie Lo, Amy L Phi, Jinal A Patel, Jennifer J Park, Hyungjin Kim.
      Poly(ADP-ribosyl)ation (PARylation), catalyzed mainly by poly(ADP-ribose) polymerase (PARP)1, is a key posttranslational modification involved in DNA replication and repair. Here, we report that TIMELESS (TIM), an essential scaffold of the replisome, is PARylated, which is linked to its proteolysis. TIM PARylation requires recognition of auto-modified PARP1 via two poly(ADP-ribose)-binding motifs, which primes TIM for proteasome-dependent degradation. Cells expressing the PARylation-refractory TIM mutant or under PARP inhibition accumulate TIM at DNA replication forks, causing replication stress and hyper-resection of stalled forks. Mechanistically, aberrant engagement of TIM with the replicative helicase impedes RAD51 loading and protection of reversed forks. Accordingly, defective TIM degradation hypersensitizes BRCA2-deficient cells to replication damage. Our study defines TIM as a substrate of PARP1 and elucidates how the control of replisome remodeling by PARylation is linked to stalled fork protection. Therefore, we propose a mechanism of PARP inhibition that impinges on the DNA replication fork instability caused by defective TIM turnover.
    Keywords:  BRCA1/2; CP: Molecular biology; DNA replication stress; PARP1; PTUbL; TIMELESS; poly(ADP-ribosyl)ation; replication fork reversal; replisome; ubiquitin-proteasome
    DOI:  https://doi.org/10.1016/j.celrep.2024.113845
  28. Mol Cell. 2024 Feb 09. pii: S1097-2765(24)00056-X. [Epub ahead of print]
    Transcription factor exchange enables prolonged transcriptional bursts.
    Wim Pomp, Joseph V W Meeussen, Tineke L Lenstra.
      Single-molecule imaging inside living cells has revealed that transcription factors (TFs) bind to DNA transiently, but a long-standing question is how this transient binding is related to transcription activation. Here, we devised a microscopy method to simultaneously measure transient TF binding at a single locus and the effect of these binding events on transcription. We show that DNA binding of the yeast TF Gal4 activates transcription of a target gene within a few seconds, with at least ∼20% efficiency and with a high initiation rate of ∼1 RNA/s. Gal4 DNA dissociation decreases transcription rapidly. Moreover, at a gene with multiple binding sites, individual Gal4 molecules only rarely stay bound throughout the entire burst but instead frequently exchange during a burst to increase the transcriptional burst duration. Our results suggest a mechanism for enhancer regulation in more complex eukaryotes, where TF cooperativity and exchange enable robust and responsive transcription regulation.
    Keywords:  DNA binding kinetics; cooperativity; single-molecule imaging; transcription factor; transcriptional bursting
    DOI:  https://doi.org/10.1016/j.molcel.2024.01.020
  29. bioRxiv. 2024 Feb 08. pii: 2024.02.04.578812. [Epub ahead of print]
    Serine mistranslation induces the integrated stress response without accumulation of uncharged tRNAs.
    Hong Zhang, Jiqiang Ling.
      Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that support robust and accurate protein synthesis. A rapidly expanding number of studies show that mutations in aaRSs lead to multiple human diseases, including neurological disorders and cancer. Much remains unknown about how aaRS mutations impact human health. In particular, how aminoacylation errors affect stress responses and fitness in eukaryotic cells remains poorly understood. The integrated stress response (ISR) is an adaptive mechanism in response to multiple stresses. However, chronic activation of the ISR contributes to the development of multiple diseases (e.g., neuropathies). Here we show that Ser misincorporation into Ala and Thr codons, resulting from aaRS editing defects or mutations in tRNAs, constitutively active the ISR. Such activation does not appear to depend on the accumulation of uncharged tRNAs, implicating that Ser mistranslation may lead to ribosome stalling and collision.
    DOI:  https://doi.org/10.1101/2024.02.04.578812
  30. bioRxiv. 2024 Feb 08. pii: 2024.02.05.578810. [Epub ahead of print]
    SIRT7 regulates NUCKS1 chromatin binding to elicit metabolic and inflammatory gene expression in senescence and liver aging.
    Khoa Tran, Michael Gilbert, Berta N Vazquez, Alessandro Ianni, Benjamin A Garcia, Alejandro Vaquero, Shelley Berger.
      Sirtuins, a class of highly conserved histone/protein deacetylases, are heavily implicated in senescence and aging. The regulation of sirtuin proteins is tightly controlled both transcriptionally and translationally and via localization within the cell. While Sirtiun proteins are implicated with aging, how their levels are regulated during aging across cell types and eliciting tissue specific age-related cellular changes is unclear. Here, we demonstrate that SIRT7 is targeted for degradation during senescence and liver aging. To uncover the significance of SIRT7 loss, we performed proteomics analysis and identified a new SIRT7 interactor, the HMG box protein NUCKS1. We found that the NUCKS1 transcription factor is recruited onto chromatin during senescence and this is mediated by SIRT7 loss. Further, depletion of NUCKS1 delayed senescence upon DNA damage leading to reduction of inflammatory gene expression. Examination of NUCKS1 transcriptional regulation during senescence revealed gene targets of transcription factors NFKB1, RELA, and CEBPβ. Consistently, in both Sirt7 KO mouse liver and in naturally aged livers, Nucks1 was recruited to chromatin. Further, Nucks1 was bound at promoters and enhancers of age-related genes, including transcription factor Rela, and, moreover, these bound sites had increased accessibility during aging. Overall, our results uncover NUCKS1 as a novel interactor of SIRT7, and show that loss of SIRT7 during senescence and liver aging promotes NUCKS1 chromatin binding to regulate metabolic and inflammatory genes.
    DOI:  https://doi.org/10.1101/2024.02.05.578810
  31. bioRxiv. 2024 Feb 08. pii: 2024.02.08.579268. [Epub ahead of print]
    Local and global changes in cell density induce reorganisation of 3D packing in a proliferating epithelium.
    Vanessa Barone, Antonio Tagua, Jesus Á Andrés-San Román, Amro Hamdoun, Juan Garrido-García, Deirdre C Lyons, Luis M Escudero.
      Tissue morphogenesis is intimately linked to the changes in shape and organisation of individual cells. In curved epithelia, cells can intercalate along their own apicobasal axes adopting a shape named "scutoid" that allows energy minimization in the tissue. Although several geometric and biophysical factors have been associated with this 3D reorganisation, the dynamic changes underlying scutoid formation in 3D epithelial packing remain poorly understood. Here we use live-imaging of the sea star embryo coupled with deep learning-based segmentation, to dissect the relative contributions of cell density, tissue compaction, and cell proliferation on epithelial architecture. We find that tissue compaction, which naturally occurs in the embryo, is necessary for the appearance of scutoids. Physical compression experiments identify cell density as the factor promoting scutoid formation at a global level. Finally, the comparison of the developing embryo with computational models indicates that the increase in the proportion of scutoids is directly associated with cell divisions. Our results suggest that apico-basal intercalations appearing just after mitosis may help accommodate the new cells within the tissue. We propose that proliferation in a compact epithelium induces 3D cell rearrangements during development.
    Summary statement: The study uses sea star embryogenesis as a model of a proliferating epithelium to highlight how cell division induces 3D cell rearrangements during development.
    DOI:  https://doi.org/10.1101/2024.02.08.579268
  32. Dev Cell. 2024 Feb 14. pii: S1534-5807(24)00046-7. [Epub ahead of print]
    ATG5 attenuates inflammatory signaling in mouse embryonic stem cells to control differentiation.
    Sheng Li, Jin Sun, Bo-Wen Zhang, Lu Yang, Ying-Cui Wan, Bei-Bei Chen, Nan Xu, Qian-Ru Xu, Juan Fan, Jia-Ni Shang, Rui Li, Chen-Ge Yu, Yan Xi, Su Chen.
      Attenuated inflammatory response is a property of embryonic stem cells (ESCs). However, the underlying mechanisms are unclear. Moreover, whether the attenuated inflammatory status is involved in ESC differentiation is also unknown. Here, we found that autophagy-related protein ATG5 is essential for both attenuated inflammatory response and differentiation of mouse ESCs and that attenuation of inflammatory signaling is required for mouse ESC differentiation. Mechanistically, ATG5 recruits FBXW7 to promote ubiquitination and proteasome-mediated degradation of β-TrCP1, resulting in the inhibition of nuclear factor κB (NF-κB) signaling and inflammatory response. Moreover, differentiation defects observed in ATG5-depleted mouse ESCs are due to β-TrCP1 accumulation and hyperactivation of NF-κB signaling, as loss of β-TrCP1 and inhibition of NF-κB signaling rescued the differentiation defects. Therefore, this study reveals a previously uncharacterized mechanism maintaining the attenuated inflammatory response in mouse ESCs and further expands the understanding of the biological roles of ATG5.
    Keywords:  ATG5; FBXW7; NF-κB signaling; embryonic stem cells; inflammatory response; β-TrCP1
    DOI:  https://doi.org/10.1016/j.devcel.2024.01.026
  33. Nature. 2024 Feb 21.
    WNT signalling control by KDM5C during development affects cognition.
    Violetta Karwacki-Neisius, Ahram Jang, Engin Cukuroglu, Albert Tai, Alan Jiao, Danilo Predes, Joon Yoon, Emily Brookes, Jiekai Chen, Aimee Iberg, Florian Halbritter, Katrin Õunap, Jozef Gecz, Thorsten M Schlaeger, Shannan Ho Sui, Jonathan Göke, Xi He, Maria K Lehtinen, Scott L Pomeroy, Yang Shi.
      Although KDM5C is one of the most frequently mutated genes in X-linked intellectual disability1, the exact mechanisms that lead to cognitive impairment remain unknown. Here we use human patient-derived induced pluripotent stem cells and Kdm5c knockout mice to conduct cellular, transcriptomic, chromatin and behavioural studies. KDM5C is identified as a safeguard to ensure that neurodevelopment occurs at an appropriate timescale, the disruption of which leads to intellectual disability. Specifically, there is a developmental window during which KDM5C directly controls WNT output to regulate the timely transition of primary to intermediate progenitor cells and consequently neurogenesis. Treatment with WNT signalling modulators at specific times reveal that only a transient alteration of the canonical WNT signalling pathway is sufficient to rescue the transcriptomic and chromatin landscapes in patient-derived cells and to induce these changes in wild-type cells. Notably, WNT inhibition during this developmental period also rescues behavioural changes of Kdm5c knockout mice. Conversely, a single injection of WNT3A into the brains of wild-type embryonic mice cause anxiety and memory alterations. Our work identifies KDM5C as a crucial sentinel for neurodevelopment and sheds new light on KDM5C mutation-associated intellectual disability. The results also increase our general understanding of memory and anxiety formation, with the identification of WNT functioning in a transient nature to affect long-lasting cognitive function.
    DOI:  https://doi.org/10.1038/s41586-024-07067-y
  34. Genome Biol. 2024 Feb 20. 25(1): 52
    DNA satellite and chromatin organization at mouse centromeres and pericentromeres.
    Jenika Packiaraj, Jitendra Thakur.
       BACKGROUND: Centromeres are essential for faithful chromosome segregation during mitosis and meiosis. However, the organization of satellite DNA and chromatin at mouse centromeres and pericentromeres is poorly understood due to the challenges of assembling repetitive genomic regions.
    RESULTS: Using recently available PacBio long-read sequencing data from the C57BL/6 strain, we find that contrary to the previous reports of their homogeneous nature, both centromeric minor satellites and pericentromeric major satellites exhibit a high degree of variation in sequence and organization within and between arrays. While most arrays are continuous, a significant fraction is interspersed with non-satellite sequences, including transposable elements. Using chromatin immunoprecipitation sequencing (ChIP-seq), we find that the occupancy of CENP-A and H3K9me3 chromatin at centromeric and pericentric regions, respectively, is associated with increased sequence enrichment and homogeneity at these regions. The transposable elements at centromeric regions are not part of functional centromeres as they lack significant CENP-A enrichment. Furthermore, both CENP-A and H3K9me3 nucleosomes occupy minor and major satellites spanning centromeric-pericentric junctions and a low yet significant amount of CENP-A spreads locally at centromere junctions on both pericentric and telocentric sides. Finally, while H3K9me3 nucleosomes display a well-phased organization on major satellite arrays, CENP-A nucleosomes on minor satellite arrays are poorly phased. Interestingly, the homogeneous class of major satellites also phase CENP-A and H3K27me3 nucleosomes, indicating that the nucleosome phasing is an inherent property of homogeneous major satellites.
    CONCLUSIONS: Our findings reveal that mouse centromeres and pericentromeres display a high diversity in satellite sequence, organization, and chromatin structure.
    Keywords:  CENP-A; Constitutive heterochromatin; H3K9me3; Long-read sequencing; Repetitive DNA; Transposable elements
    DOI:  https://doi.org/10.1186/s13059-024-03184-z
  35. Proc Natl Acad Sci U S A. 2024 Feb 27. 121(9): e2316722121
    The zonula adherens matura redefines the apical junction of intestinal epithelia.
    Pierre Mangeol, Dominique Massey-Harroche, Michael Sebbagh, Fabrice Richard, André Le Bivic, Pierre-François Lenne.
      Cell-cell apical junctions of epithelia consist of multiprotein complexes that organize as belts regulating cell-cell adhesion, permeability, and mechanical tension: the tight junction (zonula occludens), the zonula adherens (ZA), and the macula adherens. The prevailing dogma is that at the ZA, E-cadherin and catenins are lined with F-actin bundles that support and transmit mechanical tension between cells. Using super-resolution microscopy on human intestinal biopsies and Caco-2 cells, we show that two distinct multiprotein belts are basal of the tight junctions as the intestinal epithelia mature. The most apical is populated with nectins/afadin and lined with F-actin; the second is populated with E-cad/catenins. We name this dual-belt architecture the zonula adherens matura. We find that the apical contraction apparatus and the dual-belt organization rely on afadin expression. Our study provides a revised description of epithelial cell-cell junctions and identifies a module regulating the mechanics of epithelia.
    Keywords:  actin cytoskeleton; adhesive complexes; epithelial cells; small intestine; zonula adherens
    DOI:  https://doi.org/10.1073/pnas.2316722121
  36. bioRxiv. 2024 Feb 07. pii: 2024.02.06.579216. [Epub ahead of print]
    mTORC1 activity oscillates throughout the cell cycle promoting mitotic entry and differentially influencing autophagy induction.
    Jay N Joshi, Ariel D Lerner, Frank Scallo, Alexandra N Grumet, Paul Matteson, James H Millonig, Alexander J Valvezan.
      Mechanistic Target of Rapamycin Complex 1 (mTORC1) is a master metabolic regulator that stimulates anabolic cell growth while suppressing catabolic processes such as autophagy. mTORC1 is active in most, if not all, proliferating eukaryotic cells. However, it remains unclear whether and how mTORC1 activity changes from one cell cycle phase to another. Here we tracked mTORC1 activity through the complete cell cycle and uncover oscillations in its activity. We find that mTORC1 activity peaks in S and G2, and is lowest in mitosis and G1. We further demonstrate that multiple mechanisms are involved in controlling this oscillation. The interphase oscillation is mediated through the TSC complex, an upstream negative regulator of mTORC1, but is independent of major known regulatory inputs to the TSC complex, including Akt, Mek/Erk, and CDK4/6 signaling. By contrast, suppression of mTORC1 activity in mitosis does not require the TSC complex, and instead involves CDK1-dependent control of the subcellular localization of mTORC1 itself. Functionally, we find that in addition to its well-established role in promoting progression through G1, mTORC1 also promotes progression through S and G2, and is important for satisfying the Wee1- and Chk1-dependent G2/M checkpoint to allow entry into mitosis. We also find that low mTORC1 activity in G1 sensitizes cells to autophagy induction in response to partial mTORC1 inhibition or reduced nutrient levels. Together these findings demonstrate that mTORC1 is differentially regulated throughout the cell cycle, with important phase-specific functional consequences in proliferating cells.
    DOI:  https://doi.org/10.1101/2024.02.06.579216
  37. bioRxiv. 2024 Feb 07. pii: 2024.02.06.579243. [Epub ahead of print]
    Temporal dynamics of BMP/Nodal ratio drive tissue-specific gastrulation morphogenesis.
    Alyssa A Emig, Megan Hansen, Sandra Grimm, Cristian Coarfa, Nathan D Lord, Margot Kossmann Williams.
      Anteroposterior (AP) elongation of the vertebrate body plan is driven by convergence and extension (C&E) gastrulation movements in both the mesoderm and neuroectoderm, but how or whether molecular regulation of C&E differs between tissues remains an open question. Using a zebrafish explant model of AP axis extension, we show that C&E of the neuroectoderm and mesoderm can be uncoupled ex vivo , and that morphogenesis of individual tissues results from distinct morphogen signaling dynamics. Using precise temporal manipulation of BMP and Nodal signaling, we identify a critical developmental window during which high or low BMP/Nodal ratios induce neuroectoderm- or mesoderm-driven C&E, respectively. Increased BMP activity similarly enhances C&E specifically in the ectoderm of intact zebrafish gastrulae, highlighting the in vivo relevance of our findings. Together, these results demonstrate that temporal dynamics of BMP and Nodal morphogen signaling activate distinct morphogenetic programs governing C&E gastrulation movements within individual tissues.
    SUMMARY STATEMENT: Using zebrafish embryo and explant models, we demonstrate that temporal dynamics of morphogen signaling ratios distinguish between tissue-specific morphogenetic programs during vertebrate body plan formation.
    DOI:  https://doi.org/10.1101/2024.02.06.579243
  38. Nucleic Acids Res. 2024 Feb 21. pii: gkae122. [Epub ahead of print]
    The origin recognition complex requires chromatin tethering by a hypervariable intrinsically disordered region that is functionally conserved from sponge to man.
    Olubu A Adiji, Brendan S McConnell, Matthew W Parker.
      The first step toward eukaryotic genome duplication is loading of the replicative helicase onto chromatin. This 'licensing' step initiates with the recruitment of the origin recognition complex (ORC) to chromatin, which is thought to occur via ORC's ATP-dependent DNA binding and encirclement activity. However, we have previously shown that ATP binding is dispensable for the chromatin recruitment of fly ORC, raising the question of how metazoan ORC binds chromosomes. We show here that the intrinsically disordered region (IDR) of fly Orc1 is both necessary and sufficient for recruitment of ORC to chromosomes in vivo and demonstrate that this is regulated by IDR phosphorylation. Consistently, we find that the IDR confers the ORC holocomplex with ATP-independent DNA binding activity in vitro. Using phylogenetic analysis, we make the surprising observation that metazoan Orc1 IDRs have diverged so markedly that they are unrecognizable as orthologs and yet we find that these compositionally homologous sequences are functionally conserved. Altogether, these data suggest that chromatin is recalcitrant to ORC's ATP-dependent DNA binding activity, necessitating IDR-dependent chromatin tethering, which we propose poises ORC to opportunistically encircle nucleosome-free regions as they become available.
    DOI:  https://doi.org/10.1093/nar/gkae122
  39. Nature. 2024 Feb 21.
    IL-10 constrains sphingolipid metabolism to limit inflammation.
    Autumn G York, Mathias H Skadow, Joonseok Oh, Rihao Qu, Quan D Zhou, Wei-Yuan Hsieh, Walter K Mowel, J Richard Brewer, Eleanna Kaffe, Kevin J Williams, Yuval Kluger, Stephen T Smale, Jason M Crawford, Steven J Bensinger, Richard A Flavell.
      Interleukin-10 (IL-10) is a key anti-inflammatory cytokine that can limit immune cell activation and cytokine production in innate immune cell types1. Loss of IL-10 signalling results in life-threatening inflammatory bowel disease in humans and mice-however, the exact mechanism by which IL-10 signalling subdues inflammation remains unclear2-5. Here we find that increased saturated very long chain (VLC) ceramides are critical for the heightened inflammatory gene expression that is a hallmark of IL-10 deficiency. Accordingly, genetic deletion of ceramide synthase 2 (encoded by Cers2), the enzyme responsible for VLC ceramide production, limited the exacerbated inflammatory gene expression programme associated with IL-10 deficiency both in vitro and in vivo. The accumulation of saturated VLC ceramides was regulated by a decrease in metabolic flux through the de novo mono-unsaturated fatty acid synthesis pathway. Restoring mono-unsaturated fatty acid availability to cells deficient in IL-10 signalling limited saturated VLC ceramide production and the associated inflammation. Mechanistically, we find that persistent inflammation mediated by VLC ceramides is largely dependent on sustained activity of REL, an immuno-modulatory transcription factor. Together, these data indicate that an IL-10-driven fatty acid desaturation programme rewires VLC ceramide accumulation and aberrant activation of REL. These studies support the idea that fatty acid homeostasis in innate immune cells serves as a key regulatory node to control pathologic inflammation and suggests that 'metabolic correction' of VLC homeostasis could be an important strategy to normalize dysregulated inflammation caused by the absence of IL-10.
    DOI:  https://doi.org/10.1038/s41586-024-07098-5
  40. Methods Mol Biol. 2024 ;2740 263-273
    Investigating Heterogeneous Cell-Cycle Progression Using Single-Cell Imaging Approaches.
    Hee Won Yang.
      Investigating cell-cycle progression has been challenging due to the complex interconnectivity of regulatory processes and inherent cell-to-cell heterogeneity, which often require synchronization procedures. However, recent advancements in cell-cycle sensors and single-cell imaging techniques have turned this heterogeneity into an advantage for investigating the molecular mechanisms underlying diverse responses. This has led to significant progress in our understanding of cell-cycle regulation. In this paper, we present a comprehensive live single-cell imaging workflow that leverages cutting-edge live-cell sensors. These advanced single-cell imaging procedures provide promising opportunities for elucidating the molecular mechanisms underpinnings of heterogeneous responses in cell-cycle progression.
    Keywords:  Cell-cycle sensors; Cell-to-cell heterogeneity; Single-cell imaging
    DOI:  https://doi.org/10.1007/978-1-0716-3557-5_16
  41. Nat Commun. 2024 Feb 19. 15(1): 1516
    A SPLICS reporter reveals [Formula: see text]-synuclein regulation of lysosome-mitochondria contacts which affects TFEB nuclear translocation.
    Flavia Giamogante, Lucia Barazzuol, Francesca Maiorca, Elena Poggio, Alessandra Esposito, Anna Masato, Gennaro Napolitano, Alessio Vagnoni, Tito Calì, Marisa Brini.
      Mitochondrial and lysosomal activities are crucial to maintain cellular homeostasis: optimal coordination is achieved at their membrane contact sites where distinct protein machineries regulate organelle network dynamics, ions and metabolites exchange. Here we describe a genetically encoded SPLICS reporter for short- and long- juxtapositions between mitochondria and lysosomes. We report the existence of narrow and wide lysosome-mitochondria contacts differently modulated by mitophagy, autophagy and genetic manipulation of tethering factors. The overexpression of α-synuclein (α-syn) reduces the apposition of mitochondria/lysosomes membranes and affects their privileged Ca2+ transfer, impinging on TFEB nuclear translocation. We observe enhanced TFEB nuclear translocation in α-syn-overexpressing cells. We propose that α-syn, by interfering with mitochondria/lysosomes tethering impacts on local Ca2+ regulated pathways, among which TFEB mediated signaling, and in turn mitochondrial and lysosomal function. Defects in mitochondria and lysosome represent a common hallmark of neurodegenerative diseases: targeting their communication could open therapeutic avenues.
    DOI:  https://doi.org/10.1038/s41467-024-46007-2
  42. Nat Commun. 2024 Feb 20. 15(1): 1541
    A mutational atlas for Parkin proteostasis.
    Lene Clausen, Vasileios Voutsinos, Matteo Cagiada, Kristoffer E Johansson, Martin Grønbæk-Thygesen, Snehal Nariya, Rachel L Powell, Magnus K N Have, Vibe H Oestergaard, Amelie Stein, Douglas M Fowler, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen.
      Proteostasis can be disturbed by mutations affecting folding and stability of the encoded protein. An example is the ubiquitin ligase Parkin, where gene variants result in autosomal recessive Parkinsonism. To uncover the pathological mechanism and provide comprehensive genotype-phenotype information, variant abundance by massively parallel sequencing (VAMP-seq) is leveraged to quantify the abundance of Parkin variants in cultured human cells. The resulting mutational map, covering 9219 out of the 9300 possible single-site amino acid substitutions and nonsense Parkin variants, shows that most low abundance variants are proteasome targets and are located within the structured domains of the protein. Half of the known disease-linked variants are found at low abundance. Systematic mapping of degradation signals (degrons) reveals an exposed degron region proximal to the so-called "activation element". This work provides examples of how missense variants may cause degradation either via destabilization of the native protein, or by introducing local signals for degradation.
    DOI:  https://doi.org/10.1038/s41467-024-45829-4
  43. bioRxiv. 2024 Feb 18. pii: 2024.02.11.579797. [Epub ahead of print]
    Single molecule imaging of the central dogma reveals myosin-2A gene expression is regulated by contextual translational buffering.
    O'Neil Wiggan, Timothy J Stasevich.
      While protein homeostasis is a hallmark of gene regulation, unraveling the hidden regulatory mechanisms that maintain homeostasis is difficult using traditional methods. To confront this problem, we CRISPR engineered a human cell line with multiple tags in the endogenous MYH9 gene, which encodes the essential and ubiquitous myosin-2A cytoskeletal motor. Using these cells, we imaged MYH9 transcription, translation, and mature mRNA and protein in distinct colors, enabling a full dissection of the central dogma. Our data show that MYH9 transcription is upregulated in an SRF-dependent manner in response to cytoskeletal cues and that MYH9 translation can either buffer or match the transcriptional response depending on context. Upon knockdown of actin-depolymerizing proteins like cofilin, translation efficiency drops by a factor of two to buffer strong transcriptional upregulation, likely to help prevent excessive myosin activity. In contrast, following serum stimulation, translation matches the transcriptional response to readily reestablish steady state. Our results identify contextual translational buffering as an important regulatory mechanism driving stable MYH9 expression. They also demonstrate the power and broad applicability of our cell line, which can now be used to accurately quantify central dogma dynamics in response to diverse forms of cellular perturbations.
    DOI:  https://doi.org/10.1101/2024.02.11.579797
  44. J Cardiovasc Dev Dis. 2024 Feb 04. pii: 54. [Epub ahead of print]11(2):
    Mast Cells in Cardiac Remodeling: Focus on the Right Ventricle.
    Argen Mamazhakypov, Abdirashit Maripov, Akpay S Sarybaev, Ralph Theo Schermuly, Akylbek Sydykov.
      In response to various stressors, cardiac chambers undergo structural remodeling. Long-term exposure of the right ventricle (RV) to pressure or volume overload leads to its maladaptive remodeling, associated with RV failure and increased mortality. While left ventricular adverse remodeling is well understood and therapeutic options are available or emerging, RV remodeling remains underexplored, and no specific therapies are currently available. Accumulating evidence implicates the role of mast cells in RV remodeling. Mast cells produce and release numerous inflammatory mediators, growth factors and proteases that can adversely affect cardiac cells, thus contributing to cardiac remodeling. Recent experimental findings suggest that mast cells might represent a potential therapeutic target. This review examines the role of mast cells in cardiac remodeling, with a specific focus on RV remodeling, and explores the potential efficacy of therapeutic interventions targeting mast cells to mitigate adverse RV remodeling.
    Keywords:  cardiac remodeling; mast cells; right ventricle
    DOI:  https://doi.org/10.3390/jcdd11020054
  45. Cell Rep. 2024 Feb 21. pii: S2211-1247(24)00168-2. [Epub ahead of print]43(3): 113840
    Nr5a2 ensures inner cell mass formation in mouse blastocyst.
    Yanhua Zhao, Meiting Zhang, Jiqiang Liu, Xinglin Hu, Yuchen Sun, Xingwei Huang, Jingyu Li, Lei Lei.
      Recent studies have elucidated Nr5a2's role in activating zygotic genes during early mouse embryonic development. Subsequent research, however, reveals that Nr5a2 is not critical for zygotic genome activation but is vital for the gene program between the 4- and 8-cell stages. A significant gap exists in experimental evidence regarding its function during the first lineage differentiation's pivotal period. In this study, we observed that approximately 20% of embryos developed to the blastocyst stage following Nr5a2 ablation. However, these blastocysts lacked inner cell mass (ICM), highlighting Nr5a2's importance in first lineage differentiation. Mechanistically, using RNA sequencing and CUT&Tag, we found that Nr5a2 transcriptionally regulates ICM-specific genes, such as Oct4, to establish the pluripotent network. Interference with or overexpression of Nr5a2 in single blastomeres of 2-cell embryos can alter the fate of daughter cells. Our results indicate that Nr5a2 works as a doorkeeper to ensure ICM formation in mouse blastocyst.
    Keywords:  CP: Developmental biology; CP: Stem cell research; ICM; Nr5a2; Oct4; ZGA; inner cell mass; the first lineage differentiation; zygotic genome activation
    DOI:  https://doi.org/10.1016/j.celrep.2024.113840
  46. Aging Cell. 2024 Feb 19. e14109
    Spatially resolved transcriptome of the aging mouse brain.
    Cheng Wu, Tianxiang Tu, Mingzhe Xie, Yiting Wang, Biao Yan, Yajun Gong, Jiayi Zhang, Xiaolai Zhou, Zhi Xie.
      Brain aging is associated with cognitive decline, memory loss and many neurodegenerative disorders. The mammalian brain has distinct structural regions that perform specific functions. However, our understanding in gene expression and cell types within the context of the spatial organization of the mammalian aging brain is limited. Here we generated spatial transcriptomic maps of young and old mouse brains. We identified 27 distinguished brain spatial domains, including layer-specific subregions that are difficult to dissect individually. We comprehensively characterized spatial-specific changes in gene expression in the aging brain, particularly for isocortex, the hippocampal formation, brainstem and fiber tracts, and validated some gene expression differences by qPCR and immunohistochemistry. We identified aging-related genes and pathways that vary in a coordinated manner across spatial regions and parsed the spatial features of aging-related signals, providing important clues to understand genes with specific functions in different brain regions during aging. Combined with single-cell transcriptomics data, we characterized the spatial distribution of brain cell types. The proportion of immature neurons decreased in the DG region with aging, indicating that the formation of new neurons is blocked. Finally, we detected changes in information interactions between regions and found specific pathways were deregulated with aging, including classic signaling WNT and layer-specific signaling COLLAGEN. In summary, we established a spatial molecular atlas of the aging mouse brain (http://sysbio.gzzoc.com/Mouse-Brain-Aging/), which provides important resources and novel insights into the molecular mechanism of brain aging.
    Keywords:  aging; brain; cell types; gene expression; spatial transcriptome
    DOI:  https://doi.org/10.1111/acel.14109
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