bims-ginsta Biomed News
on Genome instability
Issue of 2024–08–25
twenty-one papers selected by
Jinrong Hu, National University of Singapore
  1. Retinoic acid induces human gastruloids with posterior embryo-like structures.
  2. Compression-dependent microtubule reinforcement enables cells to navigate confined environments.
  3. Condensate interfacial forces reposition DNA loci and probe chromatin viscoelasticity.
  4. A liquid-like coat mediates chromosome clustering during mitotic exit.
  5. Mechanisms of minor pole-mediated spindle bipolarization in human oocytes.
  6. Coordination of force-generating actin-based modules stabilizes and remodels membranes in vivo.
  7. Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics.
  8. Mechanoresponsive regulation of myogenesis by the force-sensing transcriptional regulator Tono.
  9. The desmosome-intermediate filament system facilitates mechanotransduction at adherens junctions for epithelial homeostasis.
  10. Dynamic regulation of tissue fluidity controls skin repair during wound healing.
  11. Stem cells tightly regulate dead cell clearance to maintain tissue fitness.
  12. Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cells.
  13. Rapid phagosome isolation enables unbiased multiomic analysis of human microglial phagosomes.
  14. Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules.
  15. Mouse models to investigate in situ cell fate decisions induced by p53.
  16. NAC guides a ribosomal multienzyme complex for nascent protein processing.
  17. Hallmarks of regeneration.
  18. Lysosomes drive the piecemeal removal of mitochondrial inner membrane.
  19. Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression.
  20. RNA sequestration in P-bodies sustains myeloid leukaemia.
  21. In-depth analysis of transcriptomes in ovarian cortical follicles from children and adults reveals interfollicular heterogeneity.
  1. Nat Cell Biol. 2024 Aug 20.
    Retinoic acid induces human gastruloids with posterior embryo-like structures.
    Nobuhiko Hamazaki, Wei Yang, Connor A Kubo, Chengxiang Qiu, Beth K Martin, Riddhiman K Garge, Samuel G Regalado, Eva K Nichols, Sriram Pendyala, Nicholas Bradley, Douglas M Fowler, Choli Lee, Riza M Daza, Sanjay Srivatsan, Jay Shendure.
      Gastruloids are a powerful in vitro model of early human development. However, although elongated and composed of all three germ layers, human gastruloids do not morphologically resemble post-implantation human embryos. Here we show that an early pulse of retinoic acid (RA), together with later Matrigel, robustly induces human gastruloids with posterior embryo-like morphological structures, including a neural tube flanked by segmented somites and diverse cell types, including neural crest, neural progenitors, renal progenitors and myocytes. Through in silico staging based on single-cell RNA sequencing, we find that human RA-gastruloids progress further than other human or mouse embryo models, aligning to E9.5 mouse and CS11 cynomolgus monkey embryos. We leverage chemical and genetic perturbations of RA-gastruloids to confirm that WNT and BMP signalling regulate somite formation and neural tube length in the human context, while transcription factors TBX6 and PAX3 underpin presomitic mesoderm and neural crest, respectively. Looking forward, RA-gastruloids are a robust, scalable model for decoding early human embryogenesis.
    DOI:  https://doi.org/10.1038/s41556-024-01487-8
  2. Nat Cell Biol. 2024 Aug 19.
    Compression-dependent microtubule reinforcement enables cells to navigate confined environments.
    Robert J Ju, Alistair D Falconer, Christanny J Schmidt, Marco A Enriquez Martinez, Kevin M Dean, Reto P Fiolka, David P Sester, Max Nobis, Paul Timpson, Alexis J Lomakin, Gaudenz Danuser, Melanie D White, Nikolas K Haass, Dietmar B Oelz, Samantha J Stehbens.
      Cells migrating through complex three-dimensional environments experience considerable physical challenges, including tensile stress and compression. To move, cells need to resist these forces while also squeezing the large nucleus through confined spaces. This requires highly coordinated cortical contractility. Microtubules can both resist compressive forces and sequester key actomyosin regulators to ensure appropriate activation of contractile forces. Yet, how these two roles are integrated to achieve nuclear transmigration in three dimensions is largely unknown. Here, we demonstrate that compression triggers reinforcement of a dedicated microtubule structure at the rear of the nucleus by the mechanoresponsive recruitment of cytoplasmic linker-associated proteins, which dynamically strengthens and repairs the lattice. These reinforced microtubules form the mechanostat: an adaptive feedback mechanism that allows the cell to both withstand compressive force and spatiotemporally organize contractility signalling pathways. The microtubule mechanostat facilitates nuclear positioning and coordinates force production to enable the cell to pass through constrictions. Disruption of the mechanostat imbalances cortical contractility, stalling migration and ultimately resulting in catastrophic cell rupture. Our findings reveal a role for microtubules as cellular sensors that detect and respond to compressive forces, enabling movement and ensuring survival in mechanically demanding environments.
    DOI:  https://doi.org/10.1038/s41556-024-01476-x
  3. Cell. 2024 Aug 14. pii: S0092-8674(24)00828-6. [Epub ahead of print]
    Condensate interfacial forces reposition DNA loci and probe chromatin viscoelasticity.
    Amy R Strom, Yoonji Kim, Hongbo Zhao, Yi-Che Chang, Natalia D Orlovsky, Andrej Košmrlj, Cornelis Storm, Clifford P Brangwynne.
      Biomolecular condensates assemble in living cells through phase separation and related phase transitions. An underappreciated feature of these dynamic molecular assemblies is that they form interfaces with other cellular structures, including membranes, cytoskeleton, DNA and RNA, and other membraneless compartments. These interfaces are expected to give rise to capillary forces, but there are few ways of quantifying and harnessing these forces in living cells. Here, we introduce viscoelastic chromatin tethering and organization (VECTOR), which uses light-inducible biomolecular condensates to generate capillary forces at targeted DNA loci. VECTOR can be utilized to programmably reposition genomic loci on a timescale of seconds to minutes, quantitatively revealing local heterogeneity in the viscoelastic material properties of chromatin. These synthetic condensates are built from components that naturally form liquid-like structures in living cells, highlighting the potential role for native condensates to generate forces and do work to reorganize the genome and impact chromatin architecture.
    Keywords:  biomolecular condensates; capillary forces; nuclear mechanics; programmable genome organization
    DOI:  https://doi.org/10.1016/j.cell.2024.07.034
  4. Mol Cell. 2024 Aug 08. pii: S1097-2765(24)00620-8. [Epub ahead of print]
    A liquid-like coat mediates chromosome clustering during mitotic exit.
    Alberto Hernandez-Armendariz, Valerio Sorichetti, Yuki Hayashi, Zuzana Koskova, Andreas Brunner, Jan Ellenberg, Anđela Šarić, Sara Cuylen-Haering.
      The individualization of chromosomes during early mitosis and their clustering upon exit from cell division are two key transitions that ensure efficient segregation of eukaryotic chromosomes. Both processes are regulated by the surfactant-like protein Ki-67, but how Ki-67 achieves these diametric functions has remained unknown. Here, we report that Ki-67 radically switches from a chromosome repellent to a chromosome attractant during anaphase in human cells. We show that Ki-67 dephosphorylation during mitotic exit and the simultaneous exposure of a conserved basic patch induce the RNA-dependent formation of a liquid-like condensed phase on the chromosome surface. Experiments and coarse-grained simulations support a model in which the coalescence of chromosome surfaces, driven by co-condensation of Ki-67 and RNA, promotes clustering of chromosomes. Our study reveals how the switch of Ki-67 from a surfactant to a liquid-like condensed phase can generate mechanical forces during genome segregation that are required for re-establishing nuclear-cytoplasmic compartmentalization after mitosis.
    Keywords:  Ki-67; RNA; anaphase; capillary forces; chromosome; mitosis; phase separation; phosphorylation; surface condensation; surfactant
    DOI:  https://doi.org/10.1016/j.molcel.2024.07.022
  5. Science. 2024 Aug 23. 385(6711): eado1022
    Mechanisms of minor pole-mediated spindle bipolarization in human oocytes.
    Tianyu Wu, Yuxi Luo, Meiling Zhang, Biaobang Chen, Xingzhu Du, Hao Gu, Siyuan Xie, Zhiqi Pan, Ran Yu, Ruiqi Hai, Xiangli Niu, Guimin Hao, Liping Jin, Juanzi Shi, Xiaoxi Sun, Yanping Kuang, Wen Li, Qing Sang, Lei Wang.
      Spindle bipolarization, the process of a microtubule mass transforming into a bipolar spindle, is a prerequisite for accurate chromosome segregation. In contrast to mitotic cells, the process and mechanism of spindle bipolarization in human oocytes remains unclear. Using high-resolution imaging in more than 1800 human oocytes, we revealed a typical state of multipolar intermediates that form during spindle bipolarization and elucidated the mechanism underlying this process. We found that the minor poles formed in multiple kinetochore clusters contribute to the generation of multipolar intermediates. We further determined the essential roles of HAUS6, KIF11, and KIF18A in spindle bipolarization and identified mutations in these genes in infertile patients characterized by oocyte or embryo defects. These results provide insights into the physiological and pathological mechanisms of spindle bipolarization in human oocytes.
    DOI:  https://doi.org/10.1126/science.ado1022
  6. J Cell Biol. 2024 Nov 04. pii: e202401091. [Epub ahead of print]223(11):
    Coordination of force-generating actin-based modules stabilizes and remodels membranes in vivo.
    Marco Heydecker, Akiko Shitara, Desu Chen, Duy T Tran, Andrius Masedunskas, Muhibullah S Tora, Seham Ebrahim, Mark A Appaduray, Jorge Luis Galeano Niño, Abhishek Bhardwaj, Kedar Narayan, Edna C Hardeman, Peter W Gunning, Roberto Weigert.
      Membrane remodeling drives a broad spectrum of cellular functions, and it is regulated through mechanical forces exerted on the membrane by cytoplasmic complexes. Here, we investigate how actin filaments dynamically tune their structure to control the active transfer of membranes between cellular compartments with distinct compositions and biophysical properties. Using intravital subcellular microscopy in live rodents we show that a lattice composed of linear filaments stabilizes the granule membrane after fusion with the plasma membrane and a network of branched filaments linked to the membranes by Ezrin, a regulator of membrane tension, initiates and drives to completion the integration step. Our results highlight how the actin cytoskeleton tunes its structure to adapt to dynamic changes in the biophysical properties of membranes.
    DOI:  https://doi.org/10.1083/jcb.202401091
  7. Nat Rev Mol Cell Biol. 2024 Aug 21.
    Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics.
    Gunsagar S Gulati, Jeremy Philip D'Silva, Yunhe Liu, Linghua Wang, Aaron M Newman.
      Single-cell transcriptomics has broadened our understanding of cellular diversity and gene expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has emerged as a tool to contextualize single cells in multicellular neighbourhoods and to identify spatially recurrent phenotypes, or ecotypes. These technologies have generated vast datasets with targeted-transcriptome and whole-transcriptome profiles of hundreds to millions of cells. Such data have provided new insights into developmental hierarchies, cellular plasticity and diverse tissue microenvironments, and spurred a burst of innovation in computational methods for single-cell analysis. In this Review, we discuss recent advancements, ongoing challenges and prospects in identifying and characterizing cell states and multicellular neighbourhoods. We discuss recent progress in sample processing, data integration, identification of subtle cell states, trajectory modelling, deconvolution and spatial analysis. Furthermore, we discuss the increasing application of deep learning, including foundation models, in analysing single-cell and spatial transcriptomics data. Finally, we discuss recent applications of these tools in the fields of stem cell biology, immunology, and tumour biology, and the future of single-cell and spatial transcriptomics in biological research and its translation to the clinic.
    DOI:  https://doi.org/10.1038/s41580-024-00768-2
  8. Curr Biol. 2024 Aug 14. pii: S0960-9822(24)01018-2. [Epub ahead of print]
    Mechanoresponsive regulation of myogenesis by the force-sensing transcriptional regulator Tono.
    Xu Zhang, Jerome Avellaneda, Maria L Spletter, Sandra B Lemke, Pierre Mangeol, Bianca H Habermann, Frank Schnorrer.
      Muscle morphogenesis is a multi-step program, starting with myoblast fusion, followed by myotube-tendon attachment and sarcomere assembly, with subsequent sarcomere maturation, mitochondrial amplification, and specialization. The correct chronological order of these steps requires precise control of the transcriptional regulators and their effectors. How this regulation is achieved during muscle development is not well understood. In a genome-wide RNAi screen in Drosophila, we identified the BTB-zinc-finger protein Tono (CG32121) as a muscle-specific transcriptional regulator. tono mutant flight muscles display severe deficits in mitochondria and sarcomere maturation, resulting in uncontrolled contractile forces causing muscle rupture and degeneration during development. Tono protein is expressed during sarcomere maturation and localizes in distinct condensates in flight muscle nuclei. Interestingly, internal pressure exerted by the maturing sarcomeres deforms the muscle nuclei into elongated shapes and changes the Tono condensates, suggesting that Tono senses the mechanical status of the muscle cells. Indeed, external mechanical pressure on the muscles triggers rapid liquid-liquid phase separation of Tono utilizing its BTB domain. Thus, we propose that Tono senses high mechanical pressure to adapt muscle transcription, specifically at the sarcomere maturation stages. Consistently, tono mutant muscles display specific defects in a transcriptional switch that represses early muscle differentiation genes and boosts late ones. We hypothesize that a similar mechano-responsive regulation mechanism may control the activity of related BTB-zinc-finger proteins that, if mutated, can result in uncontrolled force production in human muscle.
    Keywords:  BTB-zinc finger; Drosophila; development; mechanical pressure; mechanobiology; mitochondria; muscle; phase separation; sarcomere; transcription
    DOI:  https://doi.org/10.1016/j.cub.2024.07.079
  9. Curr Biol. 2024 Aug 09. pii: S0960-9822(24)01013-3. [Epub ahead of print]
    The desmosome-intermediate filament system facilitates mechanotransduction at adherens junctions for epithelial homeostasis.
    Bageshri Naimish Nanavati, Ivar Noordstra, Angela K O Lwin, John W Brooks, James Rae, Robert G Parton, Suzie Verma, Kinga Duszyc, Kathleen J Green, Alpha S Yap.
      Epithelial homeostasis can be critically influenced by how cells respond to mechanical forces, both local changes in force balance between cells and altered tissue-level forces.1 Coupling of specialized cell-cell adhesions to their cytoskeletons provides epithelia with diverse strategies to respond to mechanical stresses.2,3,4 Desmosomes confer tissue resilience when their associated intermediate filaments (IFs)2,3 stiffen in response to strain,5,6,7,8,9,10,11 while mechanotransduction associated with the E-cadherin apparatus12,13 at adherens junctions (AJs) actively modulates actomyosin by RhoA signaling. Although desmosomes and AJs make complementary contributions to mechanical homeostasis in epithelia,6,8 there is increasing evidence to suggest that these cytoskeletal-adhesion systems can interact functionally and biochemically.8,14,15,16,17,18,19,20 We now report that the desmosome-IF system integrated by desmoplakin (DP) facilitates active tension sensing at AJs for epithelial homeostasis. DP function is necessary for mechanosensitive RhoA signaling at AJs to be activated when tension was applied to epithelial monolayers. This effect required DP to anchor IFs to desmosomes and recruit the dystonin (DST) cytolinker to apical junctions. DP RNAi reduced the mechanical load that was applied to the cadherin complex by increased monolayer tension. Consistent with reduced mechanical signal strength, DP RNAi compromised assembly of the Myosin VI-E-cadherin mechanosensor that activates RhoA. The integrated DP-IF system therefore supports AJ mechanotransduction by enhancing the mechanical load of tissue tension that is transmitted to E-cadherin. This crosstalk was necessary for efficient elimination of apoptotic epithelial cells by apical extrusion, demonstrating its contribution to epithelial homeostasis.
    Keywords:  RhoA signaling; desmoplakin; epithelia; intermediate filaments; mechanotransduction
    DOI:  https://doi.org/10.1016/j.cub.2024.07.074
  10. Cell. 2024 Aug 11. pii: S0092-8674(24)00825-0. [Epub ahead of print]
    Dynamic regulation of tissue fluidity controls skin repair during wound healing.
    Rahul M Sarate, Joel Hochstetter, Manon Valet, Adrien Hallou, Yura Song, Nordin Bansaccal, Melanie Ligare, Mariaceleste Aragona, Dan Engelman, Anaïs Bauduin, Otger Campàs, Benjamin D Simons, Cedric Blanpain.
      During wound healing, different pools of stem cells (SCs) contribute to skin repair. However, how SCs become activated and drive the tissue remodeling essential for skin repair is still poorly understood. Here, by developing a mouse model allowing lineage tracing and basal cell lineage ablation, we monitor SC fate and tissue dynamics during regeneration using confocal and intravital imaging. Analysis of basal cell rearrangements shows dynamic transitions from a solid-like homeostatic state to a fluid-like state allowing tissue remodeling during repair, as predicted by a minimal mathematical modeling of the spatiotemporal dynamics and fate behavior of basal cells. The basal cell layer progressively returns to a solid-like state with re-epithelialization. Bulk, single-cell RNA, and epigenetic profiling of SCs, together with functional experiments, uncover a common regenerative state regulated by the EGFR/AP1 axis activated during tissue fluidization that is essential for skin SC activation and tissue repair.
    Keywords:  AP1 transcription factor; Voronoi model; intravital; lineage ablation; regenerative state; skin; stem cells; tissue fluidity; tissue repair; wound healing
    DOI:  https://doi.org/10.1016/j.cell.2024.07.031
  11. Nature. 2024 Aug 21.
    Stem cells tightly regulate dead cell clearance to maintain tissue fitness.
    Katherine S Stewart, Merve Deniz Abdusselamoglu, Matthew T Tierney, Anita Gola, Yun Ha Hur, Kevin A U Gonzales, Shaopeng Yuan, Alain R Bonny, Yihao Yang, Nicole R Infarinato, Christopher J Cowley, John M Levorse, Hilda Amalia Pasolli, Sourav Ghosh, Carla V Rothlin, Elaine Fuchs.
      Billions of cells are eliminated daily from our bodies1-4. Although macrophages and dendritic cells are dedicated to migrating and engulfing dying cells and debris, many epithelial and mesenchymal tissue cells can digest nearby apoptotic corpses1-4. How these non-motile, non-professional phagocytes sense and eliminate dying cells while maintaining their normal tissue functions is unclear. Here we explore the mechanisms that underlie their multifunctionality by exploiting the cyclical bouts of tissue regeneration and degeneration during hair cycling. We show that hair follicle stem cells transiently unleash phagocytosis at the correct time and place through local molecular triggers that depend on both lipids released by neighbouring apoptotic corpses and retinoids released by healthy counterparts. We trace the heart of this dual ligand requirement to RARγ-RXRα, whose activation enables tight regulation of apoptotic cell clearance genes and provides an effective, tunable mechanism to offset phagocytic duties against the primary stem cell function of preserving tissue integrity during homeostasis. Finally, we provide functional evidence that hair follicle stem cell-mediated phagocytosis is not simply redundant with professional phagocytes but rather has clear benefits to tissue fitness. Our findings have broad implications for other non-motile tissue stem or progenitor cells that encounter cell death in an immune-privileged niche.
    DOI:  https://doi.org/10.1038/s41586-024-07855-6
  12. Stem Cell Reports. 2024 Aug 05. pii: S2213-6711(24)00213-3. [Epub ahead of print]
    Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cells.
    Suel-Kee Kim, Seungmae Seo, Genevieve Stein-O'Brien, Amritha Jaishankar, Kazuya Ogawa, Nicola Micali, Victor Luria, Amir Karger, Yanhong Wang, Hyojin Kim, Thomas M Hyde, Joel E Kleinman, Ty Voss, Elana J Fertig, Joo-Heon Shin, Roland Bürli, Alan J Cross, Nicholas J Brandon, Daniel R Weinberger, Joshua G Chenoweth, Daniel J Hoeppner, Nenad Sestan, Carlo Colantuoni, Ronald D McKay.
      Variability between human pluripotent stem cell (hPSC) lines remains a challenge and opportunity in biomedicine. In this study, hPSC lines from multiple donors were differentiated toward neuroectoderm and mesendoderm lineages. We revealed dynamic transcriptomic patterns that delineate the emergence of these lineages, which were conserved across lines, along with individual line-specific transcriptional signatures that were invariant throughout differentiation. These transcriptomic signatures predicted an antagonism between SOX21-driven forebrain fates and retinoic acid-induced hindbrain fates. Replicate lines and paired adult tissue demonstrated the stability of these line-specific transcriptomic traits. We show that this transcriptomic variation in lineage bias had both genetic and epigenetic origins, aligned with the anterior-to-posterior structure of early mammalian development, and was present across a large collection of hPSC lines. These findings contribute to developing systematic analyses of PSCs to define the origin and consequences of variation in the early events orchestrating individual human development.
    Keywords:  SOX21; acid signaling; anterior or posterior neural fates; cell line variation; early embryo; human population; pluripotent stem cells; retinoic
    DOI:  https://doi.org/10.1016/j.stemcr.2024.07.004
  13. Immunity. 2024 Aug 07. pii: S1074-7613(24)00368-6. [Epub ahead of print]
    Rapid phagosome isolation enables unbiased multiomic analysis of human microglial phagosomes.
    Emile Wogram, Felix Sümpelmann, Wentao Dong, Eshaan Rawat, Inés Fernández Maestre, Dongdong Fu, Brandyn Braswell, Andrew Khalil, Joerg M Buescher, Gerhard Mittler, Georg H H Borner, Andreas Vlachos, Stefan Tholen, Oliver Schilling, George W Bell, Angelika S Rambold, Asifa Akhtar, Oliver Schnell, Jürgen Beck, Monther Abu-Remaileh, Marco Prinz, Rudolf Jaenisch.
      Microglia are the resident macrophages of the central nervous system (CNS). Their phagocytic activity is central during brain development and homeostasis-and in a plethora of brain pathologies. However, little is known about the composition, dynamics, and function of human microglial phagosomes under homeostatic and pathological conditions. Here, we developed a method for rapid isolation of pure and intact phagosomes from human pluripotent stem cell-derived microglia under various in vitro conditions, and from human brain biopsies, for unbiased multiomic analysis. Phagosome profiling revealed that microglial phagosomes were equipped to sense minute changes in their environment and were highly dynamic. We detected proteins involved in synapse homeostasis, or implicated in brain pathologies, and identified the phagosome as the site where quinolinic acid was stored and metabolized for de novo nicotinamide adenine dinucleotide (NAD+) generation in the cytoplasm. Our findings highlight the central role of phagosomes in microglial functioning in the healthy and diseased brain.
    Keywords:  glioblastoma; human pluripotent stem cells; metabolomics; microglia; organelle; phagocytosis; phagosome; proteomics; quinolinic acid; synaptic pruning
    DOI:  https://doi.org/10.1016/j.immuni.2024.07.019
  14. Nat Genet. 2024 Aug 22.
    Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules.
    Ignasi Toledano, Fran Supek, Ben Lehner.
      Premature termination codons (PTCs) cause ~10-20% of inherited diseases and are a major mechanism of tumor suppressor gene inactivation in cancer. A general strategy to alleviate the effects of PTCs would be to promote translational readthrough. Nonsense suppression by small molecules has proven effective in diverse disease models, but translation into the clinic is hampered by ineffective readthrough of many PTCs. Here we directly tackle the challenge of defining drug efficacy by quantifying the readthrough of ~5,800 human pathogenic stop codons by eight drugs. We find that different drugs promote the readthrough of complementary subsets of PTCs defined by local sequence context. This allows us to build interpretable models that accurately predict drug-induced readthrough genome-wide, and we validate these models by quantifying endogenous stop codon readthrough. Accurate readthrough quantification and prediction will empower clinical trial design and the development of personalized nonsense suppression therapies.
    DOI:  https://doi.org/10.1038/s41588-024-01878-5
  15. EMBO J. 2024 Aug 19.
    Mouse models to investigate in situ cell fate decisions induced by p53.
    Elizabeth Lieschke, Annabella F Thomas, Andrew Kueh, Georgia K Atkin-Smith, Pedro L Baldoni, John E La Marca, Savannah Young, Allan Shuai Huang, Aisling M Ross, Lauren Whelan, Deeksha Kaloni, Lin Tai, Gordon K Smyth, Marco J Herold, Edwin D Hawkins, Andreas Strasser, Gemma L Kelly.
      Investigating how transcription factors control complex cellular processes requires tools that enable responses to be visualised at the single-cell level and their cell fate to be followed over time. For example, the tumour suppressor p53 (also called TP53 in humans and TRP53 in mice) can initiate diverse cellular responses by transcriptional activation of its target genes: Puma to induce apoptotic cell death and p21 to induce cell cycle arrest/cell senescence. However, it is not known how these processes are regulated and initiated in different cell types. Also, the context-dependent interaction partners and binding loci of p53 remain largely elusive. To be able to examine these questions, we here developed knock-in mice expressing triple-FLAG-tagged p53 to facilitate p53 pull-down and two p53 response reporter mice, knocking tdTomato and GFP into the Puma/Bbc3 and p21 gene loci, respectively. By crossing these reporter mice into a p53-deficient background, we show that the new reporters reliably inform on p53-dependent and p53-independent initiation of both apoptotic or cell cycle arrest/senescence programs, respectively, in vitro and in vivo.
    Keywords:  Apoptosis; Cancer; Cell Cycle Arrest; Reporter Mice; p53/TRP53/TP53
    DOI:  https://doi.org/10.1038/s44318-024-00189-z
  16. Nature. 2024 Aug 21.
    NAC guides a ribosomal multienzyme complex for nascent protein processing.
    Alfred M Lentzsch, Denis Yudin, Martin Gamerdinger, Sowmya Chandrasekar, Laurenz Rabl, Alain Scaiola, Elke Deuerling, Nenad Ban, Shu-Ou Shan.
      Approximately 40% of the mammalian proteome undergoes N-terminal methionine excision and acetylation, mediated sequentially by methionine aminopeptidase (MetAP) and N-acetyltransferase A (NatA), respectively1. Both modifications are strictly cotranslational and essential in higher eukaryotic organisms1. The interaction, activity and regulation of these enzymes on translating ribosomes are poorly understood. Here we perform biochemical, structural and in vivo studies to demonstrate that the nascent polypeptide-associated complex2,3 (NAC) orchestrates the action of these enzymes. NAC assembles a multienzyme complex with MetAP1 and NatA early during translation and pre-positions the active sites of both enzymes for timely sequential processing of the nascent protein. NAC further releases the inhibitory interactions from the NatA regulatory protein huntingtin yeast two-hybrid protein K4,5 (HYPK) to activate NatA on the ribosome, enforcing cotranslational N-terminal acetylation. Our results provide a mechanistic model for the cotranslational processing of proteins in eukaryotic cells.
    DOI:  https://doi.org/10.1038/s41586-024-07846-7
  17. Cell Stem Cell. 2024 Aug 13. pii: S1934-5909(24)00257-1. [Epub ahead of print]
    Hallmarks of regeneration.
    Kenneth D Poss, Elly M Tanaka.
      Regeneration is a heroic biological process that restores tissue architecture and function in the face of day-to-day cell loss or the aftershock of injury. Capacities and mechanisms for regeneration can vary widely among species, organs, and injury contexts. Here, we describe "hallmarks" of regeneration found in diverse settings of the animal kingdom, including activation of a cell source, initiation of regenerative programs in the source, interplay with supporting cell types, and control of tissue size and function. We discuss these hallmarks with an eye toward major challenges and applications of regenerative biology.
    Keywords:  regeneration
    DOI:  https://doi.org/10.1016/j.stem.2024.07.007
  18. Nature. 2024 Aug 21.
    Lysosomes drive the piecemeal removal of mitochondrial inner membrane.
    Akriti Prashar, Claudio Bussi, Antony Fearns, Mariana I Capurro, Xiaodong Gao, Hiromi Sesaki, Maximiliano G Gutierrez, Nicola L Jones.
      Mitochondrial membranes define distinct structural and functional compartments. Cristae of the inner mitochondrial membrane (IMM) function as independent bioenergetic units that undergo rapid and transient remodelling, but the significance of this compartmentalized organization is unknown1. Using super-resolution microscopy, here we show that cytosolic IMM vesicles, devoid of outer mitochondrial membrane or mitochondrial matrix, are formed during resting state. These vesicles derived from the IMM (VDIMs) are formed by IMM herniation through pores formed by voltage-dependent anion channel 1 in the outer mitochondrial membrane. Live-cell imaging showed that lysosomes in proximity to mitochondria engulfed the herniating IMM and, aided by the endosomal sorting complex required for transport machinery, led to the formation of VDIMs in a microautophagy-like process, sparing the remainder of the organelle. VDIM formation was enhanced in mitochondria undergoing oxidative stress, suggesting their potential role in maintenance of mitochondrial function. Furthermore, the formation of VDIMs required calcium release by the reactive oxygen species-activated, lysosomal calcium channel, transient receptor potential mucolipin 1, showing an interorganelle communication pathway for maintenance of mitochondrial homeostasis. Thus, IMM compartmentalization could allow for the selective removal of damaged IMM sections via VDIMs, which should protect mitochondria from localized injury. Our findings show a new pathway of intramitochondrial quality control.
    DOI:  https://doi.org/10.1038/s41586-024-07835-w
  19. Nat Struct Mol Biol. 2024 Aug 16.
    Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression.
    Qian Yao, Linying Zhu, Zhen Shi, Subhadra Banerjee, Chongyi Chen.
      DNA supercoiling is a biophysical feature of the double helix with a pivotal role in biological processes. However, understanding of DNA supercoiling in the chromatin remains limited. Here, we developed azide-trimethylpsoralen sequencing (ATMP-seq), a DNA supercoiling assay offering quantitative accuracy while minimizing genomic bias and background noise. Using ATMP-seq, we directly visualized transcription-dependent negative and positive twin-supercoiled domains around genes and mapped kilobase-resolution DNA supercoiling throughout the human genome. Remarkably, we discovered megabase-scale supercoiling domains (SDs) across all chromosomes that are modulated mainly by topoisomerases I and IIβ. Transcription activities, but not the consequent supercoiling accumulation in the local region, contribute to SD formation, indicating the long-range propagation of transcription-generated supercoiling. Genome-wide SDs colocalize with A/B compartments in both human and Drosophila cells but are distinct from topologically associating domains (TADs), with negative supercoiling accumulation at TAD boundaries. Furthermore, genome-wide DNA supercoiling varies between cell states and types and regulates human gene expression, underscoring the importance of supercoiling dynamics in chromatin regulation and function.
    DOI:  https://doi.org/10.1038/s41594-024-01377-5
  20. Nat Cell Biol. 2024 Aug 21.
    RNA sequestration in P-bodies sustains myeloid leukaemia.
    Srikanth Kodali, Ludovica Proietti, Gemma Valcarcel, Anna V López-Rubio, Patrizia Pessina, Thomas Eder, Junchao Shi, Annie Jen, Núria Lupión-Garcia, Anne C Starner, Mason D Bartels, Yingzhi Cui, Caroline M Sands, Ainoa Planas-Riverola, Alba Martínez, Talia Velasco-Hernandez, Laureano Tomás-Daza, Bernhard Alber, Gabriele Manhart, Isabella Maria Mayer, Karoline Kollmann, Alessandro Fatica, Pablo Menendez, Evgenia Shishkova, Rachel E Rau, Biola M Javierre, Joshua Coon, Qi Chen, Eric L Van Nostrand, Jose L Sardina, Florian Grebien, Bruno Di Stefano.
      Post-transcriptional mechanisms are fundamental safeguards of progenitor cell identity and are often dysregulated in cancer. Here, we identified regulators of P-bodies as crucial vulnerabilities in acute myeloid leukaemia (AML) through genome-wide CRISPR screens in normal and malignant haematopoietic progenitors. We found that leukaemia cells harbour aberrantly elevated numbers of P-bodies and show that P-body assembly is crucial for initiation and maintenance of AML. Notably, P-body loss had little effect upon homoeostatic haematopoiesis but impacted regenerative haematopoiesis. Molecular characterization of P-bodies purified from human AML cells unveiled their critical role in sequestering messenger RNAs encoding potent tumour suppressors from the translational machinery. P-body dissolution promoted translation of these mRNAs, which in turn rewired gene expression and chromatin architecture in leukaemia cells. Collectively, our findings highlight the contrasting and unique roles of RNA sequestration in P-bodies during tissue homoeostasis and oncogenesis. These insights open potential avenues for understanding myeloid leukaemia and future therapeutic interventions.
    DOI:  https://doi.org/10.1038/s41556-024-01489-6
  21. Nat Commun. 2024 Aug 21. 15(1): 6989
    In-depth analysis of transcriptomes in ovarian cortical follicles from children and adults reveals interfollicular heterogeneity.
    Ilmatar Rooda, Jasmin Hassan, Jie Hao, Magdalena Wagner, Elisabeth Moussaud-Lamodière, Kersti Jääger, Marjut Otala, Katri Knuus, Cecilia Lindskog, Kiriaki Papaikonomou, Sebastian Gidlöf, Cecilia Langenskiöld, Hartmut Vogt, Per Frisk, Johan Malmros, Timo Tuuri, Andres Salumets, Kirsi Jahnukainen, Agne Velthut-Meikas, Pauliina Damdimopoulou.
      The ovarian cortical reserve of follicles is vital for fertility. Some medical treatments are toxic to follicles, leading to premature ovarian insufficiency. Ovarian tissue cryopreservation is an established method to preserve fertility in adults and even applied in prepuberty despite unproven efficacy. Here, we analyze transcriptomes of 120 cortical follicles from children and adults for detailed comparison. We discover heterogeneity with two main types of follicles in both age groups: one with expected oocyte-granulosa profiles and another with predicted role in signaling. Transcriptional changes during growth to the secondary stage are similar overall in children and adults, but variations related to extracellular matrix, theca cells, and miRNA profiles are found. Notably, cyclophosphamide dose correlates with interferon signaling in child follicles. Additionally, morphology alone is insufficient for follicle categorization suggesting a need for additional markers. Marker genes for early follicle activation are determined. These findings will help refine follicular classification and fertility preservation techniques across critical ages.
    DOI:  https://doi.org/10.1038/s41467-024-51185-0
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