bims-ginsta 2023-10-08 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2023–10–08
fourteen papers selected by
Jinrong Hu, National University of Singapore

Microtubules oppose cortical actomyosin-driven membrane ingression during C. elegans meiosis I polar body extrusion.
Chromosome biorientation requires Aurora B's spatial separation from its outer kinetochore substrates, but not its turnover at kinetochores.
A disordered region controls cBAF activity via condensation and partner recruitment.
ATR promotes clearance of damaged DNA and damaged cells by rupturing micronuclei.
Active cell divisions generate fourfold orientationally ordered phase in living tissue.
Notch1 cortical signaling regulates epithelial architecture and cell-cell adhesion.
Partial spontaneous intersubunit rotations in pretranslocation ribosomes.
The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil.
Differential effects of aneuploidy on growth and differentiation in human intestinal stem cells.
A subpopulation of lipogenic brown adipocytes drives thermogenic memory.
Mitophagy for cardioprotection.
An ESCRT grommet cooperates with a diffusion barrier to maintain nuclear integrity.
Replication-induced DNA secondary structures drive fork uncoupling and breakage.
Spatial-temporal proliferation of hepatocytes during pregnancy revealed by genetic lineage tracing.

PLoS Genet. 2023 Oct 02. 19(10): e1010984

Microtubules oppose cortical actomyosin-driven membrane ingression during C. elegans meiosis I polar body extrusion.

Alyssa R Quiogue, Eisuke Sumiyoshi, Adam Fries, Chien-Hui Chuang, Bruce Bowerman.

During C. elegans oocyte meiosis I cytokinesis and polar body extrusion, cortical actomyosin is locally remodeled to assemble a contractile ring that forms within and remains part of a much larger and actively contractile cortical actomyosin network. This network both mediates contractile ring dynamics and generates shallow ingressions throughout the oocyte cortex during polar body extrusion. Based on our analysis of requirements for CLS-2, a member of the CLASP family of proteins that stabilize microtubules, we recently proposed that a balance of actomyosin-mediated tension and microtubule-mediated stiffness limits membrane ingression throughout the oocyte during meiosis I polar body extrusion. Here, using live cell imaging and fluorescent protein fusions, we show that CLS-2 is part of a group of kinetochore proteins, including the scaffold KNL-1 and the kinase BUB-1, that also co-localize during meiosis I to structures called linear elements, which are present within the assembling oocyte spindle and also are distributed throughout the oocyte in proximity to, but appearing to underlie, the actomyosin cortex. We further show that KNL-1 and BUB-1, like CLS-2, promote the proper organization of sub-cortical microtubules and also limit membrane ingression throughout the oocyte. Moreover, nocodazole or taxol treatment to destabilize or stabilize oocyte microtubules leads to, respectively, excess or decreased membrane ingression throughout the oocyte. Furthermore, taxol treatment, and genetic backgrounds that elevate the levels of cortically associated microtubules, both suppress excess membrane ingression in cls-2 mutant oocytes. We propose that linear elements influence the organization of sub-cortical microtubules to generate a stiffness that limits cortical actomyosin-driven membrane ingression throughout the oocyte during meiosis I polar body extrusion. We discuss the possibility that this regulation of sub-cortical microtubule dynamics facilitates actomyosin contractile ring dynamics during C. elegans oocyte meiosis I cell division.

DOI: https://doi.org/10.1371/journal.pgen.1010984
Curr Biol. 2023 Sep 28. pii: S0960-9822(23)01219-8. [Epub ahead of print]

Chromosome biorientation requires Aurora B's spatial separation from its outer kinetochore substrates, but not its turnover at kinetochores.

Shuyu Li, Luis J Garcia-Rodriguez, Tomoyuki U Tanaka.

  For correct chromosome segregation in mitosis, sister kinetochores must interact with microtubules from opposite spindle poles (biorientation). For this, aberrant kinetochore-microtubule interaction must be resolved (error correction) by Aurora B kinase. Once biorientation is formed, tension is applied on kinetochore-microtubule interaction, stabilizing this interaction. The mechanism for this tension-dependent process has been debated. Here, we study how Aurora B localizations at different kinetochore sites affect the biorientation establishment and maintenance in budding yeast. Without the physiological Aurora B-INCENP recruitment mechanisms, engineered recruitment of Aurora B-INCENP to the inner kinetochore, but not to the outer kinetochore, prior to biorientation supports the subsequent biorientation establishment. Moreover, when the physiological Aurora B-INCENP recruitment mechanisms are present, an engineered Aurora B-INCENP recruitment to the outer kinetochore, but not to the inner kinetochore, during metaphase (after biorientation establishment) disrupts biorientation, which is dependent on the Aurora B kinase activity. These results suggest that the spatial separation of Aurora B from its outer kinetochore substrates is required to stabilize kinetochore-microtubule interaction when biorientation is formed and tension is applied on this interaction. Meanwhile, Aurora B exhibits dynamic turnover on the centromere/kinetochore during early mitosis, a process thought to be crucial for error correction and biorientation. However, using the engineered Aurora B-INCENP recruitment to the inner kinetochore, we demonstrate that, even without such a turnover, Aurora B-INCENP can efficiently support biorientation. Our study provides important insights into how Aurora B promotes error correction for biorientation in a tension-dependent manner.

Keywords:  Aurora B; Ipl1; budding yeast; chromosome biorientation; chromosome segregation; error correction; kinetochore; microtubule; mitosis; tension

DOI:  https://doi.org/10.1016/j.cub.2023.09.006
Cell. 2023 Sep 29. pii: S0092-8674(23)00965-0. [Epub ahead of print]

A disordered region controls cBAF activity via condensation and partner recruitment.

Ajinkya Patil, Amy R Strom, Joao A Paulo, Clayton K Collings, Kiersten M Ruff, Min Kyung Shinn, Akshay Sankar, Kasey S Cervantes, Tobias Wauer, Jessica D St Laurent, Grace Xu, Lindsay A Becker, Steven P Gygi, Rohit V Pappu, Clifford P Brangwynne, Cigall Kadoch.

  Intrinsically disordered regions (IDRs) represent a large percentage of overall nuclear protein content. The prevailing dogma is that IDRs engage in non-specific interactions because they are poorly constrained by evolutionary selection. Here, we demonstrate that condensate formation and heterotypic interactions are distinct and separable features of an IDR within the ARID1A/B subunits of the mSWI/SNF chromatin remodeler, cBAF, and establish distinct "sequence grammars" underlying each contribution. Condensation is driven by uniformly distributed tyrosine residues, and partner interactions are mediated by non-random blocks rich in alanine, glycine, and glutamine residues. These features concentrate a specific cBAF protein-protein interaction network and are essential for chromatin localization and activity. Importantly, human disease-associated perturbations in ARID1B IDR sequence grammars disrupt cBAF function in cells. Together, these data identify IDR contributions to chromatin remodeling and explain how phase separation provides a mechanism through which both genomic localization and functional partner recruitment are achieved.

Keywords:  ARID1A; ARID1B; ATP-dependent chromatin remodeling; IDRs; cBAF complexes; condensates; intrinsically disordered regions; mammalian SWI/SNF complexes; phase separation; transcription factors

DOI:  https://doi.org/10.1016/j.cell.2023.08.032
Mol Cell. 2023 Sep 22. pii: S1097-2765(23)00698-6. [Epub ahead of print]

ATR promotes clearance of damaged DNA and damaged cells by rupturing micronuclei.

Yoon Ki Joo, Elizabeth M Black, Isabelle Trier, Wisse Haakma, Lee Zou, Lilian Kabeche.

  The human ataxia telangiectasia mutated and Rad3-related (ATR) kinase functions in the nucleus to protect genomic integrity. Micronuclei (MN) arise from genomic and chromosomal instability and cause aneuploidy and chromothripsis, but how MN are removed is poorly understood. Here, we show that ATR is active in MN and promotes their rupture in S phase by phosphorylating Lamin A/C at Ser395, which primes Ser392 for CDK1 phosphorylation and destabilizes the MN envelope. In cells harboring MN, ATR or CDK1 inhibition reduces MN rupture. Consequently, ATR inhibitor (ATRi) diminishes activation of the cytoplasmic DNA sensor cGAS and compromises cGAS-dependent autophagosome accumulation in MN and clearance of micronuclear DNA. Furthermore, ATRi reduces cGAS-mediated senescence and killing of MN-bearing cancer cells by natural killer cells. Thus, in addition to the canonical ATR signaling pathway, an ATR-CDK1-Lamin A/C axis promotes MN rupture to clear damaged DNA and cells, protecting the genome in cell populations through unexpected cell-autonomous and cell-non-autonomous mechanisms.

Keywords:  ATR; CDK1; DNA damage; STING; TREX1; autophagosome; autophagy; cGAS; cell-autonomous; cell-non-autonomous; clearance; damaged DNA; micronuclear DNA; micronuclei; micronucleus; natural killer cells; nuclear envelope; rupture

DOI:  https://doi.org/10.1016/j.molcel.2023.09.003
Nat Phys. 2023 Aug;19(8): 1201-1210

Active cell divisions generate fourfold orientationally ordered phase in living tissue.

Dillon J Cislo, Fengshuo Yang, Haodong Qin, Anastasios Pavlopoulos, Mark J Bowick, Sebastian J Streichan.

Morphogenesis, the process through which genes generate form, establishes tissue-scale order as a template for constructing the complex shapes of the body plan. The extensive growth required to build these ordered substrates is fuelled by cell proliferation, which, naively, should destroy order. Understanding how active morphogenetic mechanisms couple cellular and mechanical processes to generate order-rather than annihilate it-remains an outstanding question in animal development. We show that cell divisions are the primary drivers of tissue flow, leading to a fourfold orientationally ordered phase. Waves of anisotropic cell proliferation propagate across the embryo with precise patterning. Defects introduced into the nascent lattice by cell divisions are moved out of the tissue bulk towards the boundary by subsequent divisions. Specific cell proliferation rates and orientations enable cell divisions to organize rather than fluidize the tissue. We observe this using live imaging and tissue cartography to analyse the dynamics of fourfold tissue ordering in the trunk segmental ectoderm of the crustacean Parhyale hawaiensis beginning 72 h after egg lay. The result is a robust, active mechanism for generating global orientational order in a non-equilibrium system that sets the stage for the subsequent development of shape and form.

DOI: https://doi.org/10.1038/s41567-023-02025-3
J Cell Biol. 2023 Dec 04. pii: e202303013. [Epub ahead of print]222(12):

Notch1 cortical signaling regulates epithelial architecture and cell-cell adhesion.

Matthew J White, Kyle A Jacobs, Tania Singh, Lakyn N Mayo, Annie Lin, Christopher S Chen, Young-Wook Jun, Matthew L Kutys.

Notch receptors control tissue morphogenic processes that involve coordinated changes in cell architecture and gene expression, but how a single receptor can produce these diverse biological outputs is unclear. Here, we employ a 3D model of a human ductal epithelium to reveal tissue morphogenic defects result from loss of Notch1, but not Notch1 transcriptional signaling. Instead, defects in duct morphogenesis are driven by dysregulated epithelial cell architecture and mitogenic signaling which result from the loss of a transcription-independent, Notch1 cortical signaling mechanism that ultimately functions to stabilize adherens junctions and cortical actin. We identify that Notch1 localization and cortical signaling are tied to apical-basal cell restructuring and discover that a Notch1-FAM83H interaction underlies control of epithelial adherens junctions and cortical actin. Together, these results offer new insights into Notch1 signaling and regulation and advance a paradigm in which transcriptional and cell adhesive programs might be coordinated by a single receptor.

DOI: https://doi.org/10.1083/jcb.202303013
Proc Natl Acad Sci U S A. 2023 Oct 10. 120(41): e2114979120

Partial spontaneous intersubunit rotations in pretranslocation ribosomes.

Tianhan Huang, Junhong Choi, Arjun Prabhakar, Joseph D Puglisi, Alexey Petrov.

  The two main steps of translation, peptidyl transfer, and translocation are accompanied by counterclockwise and clockwise rotations of the large and small ribosomal subunits with respect to each other. Upon peptidyl transfer, the small ribosomal subunit rotates counterclockwise relative to the large subunit, placing the ribosome into the rotated conformation. Simultaneously, tRNAs move into the hybrid conformation, and the L1 stalk moves inward toward the P-site tRNA. The conformational dynamics of pretranslocation ribosomes were extensively studied by ensemble and single-molecule methods. Different experimental modalities tracking ribosomal subunits, tRNAs, and the L1 stalk showed that pretranslocation ribosomes undergo spontaneous conformational transitions. Thus, peptidyl transfer unlocks the ribosome and decreases an energy barrier for the reverse ribosome rotation during translocation. However, the tracking of translation with ribosomes labeled at rRNA helices h44 and H101 showed a lack of spontaneous rotations in pretranslocation complexes. Therefore, reverse intersubunit rotations occur during EF-G catalyzed translocation. To reconcile these views, we used high-speed single-molecule microscopy to follow translation in real time. We showed spontaneous rotations in puromycin-released h44-H101 dye-labeled ribosomes. During elongation, the h44-H101 ribosomes undergo partial spontaneous rotations. Spontaneous rotations in h44-H101-labeled ribosomes are restricted prior to aminoacyl-tRNA binding. The pretranslocation h44-H101 ribosomes spontaneously exchanged between three different rotational states. This demonstrates that peptidyl transfer unlocks spontaneous rotations and pretranslocation ribosomes can adopt several thermally accessible conformations, thus supporting the Brownian model of translocation.

Keywords:  intersubunit rotation; ribosome; single-molecule FRET; translation

DOI:  https://doi.org/10.1073/pnas.2114979120
Proc Natl Acad Sci U S A. 2023 Oct 10. 120(41): e2307289120

The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil.

Mehrshad Ebadi, Quinten Bafort, Eshchar Mizrachi, Pieter Audenaert, Pieter Simoens, Marc Van Montagu, Dries Bonte, Yves Van de Peer.

  The importance of whole-genome duplication (WGD) for evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary dead end, there is growing evidence that polyploidization can help overcome environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete or outlive nonpolyploids at times of environmental upheaval remain elusive, especially for autopolyploids, in which heterosis effects are limited. On the longer term, WGD might increase both mutational and environmental robustness due to redundancy and increased genetic variation, but on the short-or even immediate-term, selective advantages of WGDs are harder to explain. Here, by duplicating artificially generated Gene Regulatory Networks (GRNs), we show that duplicated GRNs-and thus duplicated genomes-show higher signal output variation than nonduplicated GRNs. This increased variation leads to niche expansion and can provide polyploid populations with substantial advantages to survive environmental turmoil. In contrast, under stable environments, GRNs might be maladaptive to changes, a phenomenon that is exacerbated in duplicated GRNs. We believe that these results provide insights into how genome duplication and (auto)polyploidy might help organisms to adapt quickly to novel conditions and to survive ecological uproar or even cataclysmic events.

Keywords:  cataclysmic events; environmental turmoil; gene regulatory networks; polyploidy; whole-genome duplication

DOI:  https://doi.org/10.1073/pnas.2307289120
bioRxiv. 2023 Sep 24. pii: 2023.09.23.559117. [Epub ahead of print]

Differential effects of aneuploidy on growth and differentiation in human intestinal stem cells.

Blake A Johnson, Albert Z Liu, Tianhao Bi, Yi Dong, Taibo Li, Dingjingyu Zhou, Akshay Narkar, Yufei Wu, Sean X Sun, Tatianna C Larman, Jin Zhu, Rong Li.

Aneuploidy, a near ubiquitous genetic feature of tumors, is a context-dependent driver of cancer evolution; however, the mechanistic basis of this role remains unclear. Here, by inducing heterogeneous aneuploidy in non-transformed human colon organoids (colonoids), we investigate how the effects of aneuploidy on cell growth and differentiation may promote malignant transformation. Single-cell RNA sequencing reveals that the gene expression signature across over 100 unique aneuploid karyotypes is enriched with p53 responsive genes. The primary driver of p53 activation is karyotype complexity. Complex aneuploid cells with multiple unbalanced chromosomes activate p53 and undergo G1 cell-cycle arrest, independent of DNA damage and without evidence of senescence. By contrast, simple aneuploid cells with 1-3 chromosomes gained or lost continue to proliferate, demonstrated by single cell tracking in colonoids. Notably, simple aneuploid cells exhibit impaired differentiation when niche factors are withdrawn. These findings suggest that while complex aneuploid cells are eliminated from the normal epithelium due to p53 activation, simple aneuploid cells can escape this checkpoint and may contribute to niche factor-independent growth of cancer-initiating cells.

DOI: https://doi.org/10.1101/2023.09.23.559117
Nat Metab. 2023 Oct 02.

A subpopulation of lipogenic brown adipocytes drives thermogenic memory.

Patrick Lundgren, Prateek V Sharma, Lenka Dohnalová, Kyle Coleman, Giulia T Uhr, Susanna Kircher, Lev Litichevskiy, Klaas Bahnsen, Hélène C Descamps, Christina Demetriadou, Jacqueline Chan, Karthikeyani Chellappa, Timothy O Cox, Yael Heyman, Sarshan R Pather, Clarissa Shoffler, Christopher Petucci, Ophir Shalem, Arjun Raj, Joseph A Baur, Nathaniel W Snyder, Kathryn E Wellen, Maayan Levy, Patrick Seale, Mingyao Li, Christoph A Thaiss.

Sustained responses to transient environmental stimuli are important for survival. The mechanisms underlying long-term adaptations to temporary shifts in abiotic factors remain incompletely understood. Here, we find that transient cold exposure leads to sustained transcriptional and metabolic adaptations in brown adipose tissue, which improve thermogenic responses to secondary cold encounter. Primary thermogenic challenge triggers the delayed induction of a lipid biosynthesis programme even after cessation of the original stimulus, which protects from subsequent exposures. Single-nucleus RNA sequencing and spatial transcriptomics reveal that this response is driven by a lipogenic subpopulation of brown adipocytes localized along the perimeter of Ucp1hi adipocytes. This lipogenic programme is associated with the production of acylcarnitines, and supplementation of acylcarnitines is sufficient to recapitulate improved secondary cold responses. Overall, our data highlight the importance of heterogenous brown adipocyte populations for 'thermogenic memory', which may have therapeutic implications for leveraging short-term thermogenesis to counteract obesity.

DOI: https://doi.org/10.1038/s42255-023-00893-w
Basic Res Cardiol. 2023 Oct 05. 118(1): 42

Mitophagy for cardioprotection.

Allen Sam Titus, Eun-Ah Sung, Daniela Zablocki, Junichi Sadoshima.

  Mitochondrial function is maintained by several strictly coordinated mechanisms, collectively termed mitochondrial quality control mechanisms, including fusion and fission, degradation, and biogenesis. As the primary source of energy in cardiomyocytes, mitochondria are the central organelle for maintaining cardiac function. Since adult cardiomyocytes in humans rarely divide, the number of dysfunctional mitochondria cannot easily be diluted through cell division. Thus, efficient degradation of dysfunctional mitochondria is crucial to maintaining cellular function. Mitophagy, a mitochondria specific form of autophagy, is a major mechanism by which damaged or unnecessary mitochondria are targeted and eliminated. Mitophagy is active in cardiomyocytes at baseline and in response to stress, and plays an essential role in maintaining the quality of mitochondria in cardiomyocytes. Mitophagy is mediated through multiple mechanisms in the heart, and each of these mechanisms can partially compensate for the loss of another mechanism. However, insufficient levels of mitophagy eventually lead to mitochondrial dysfunction and the development of heart failure. In this review, we discuss the molecular mechanisms of mitophagy in the heart and the role of mitophagy in cardiac pathophysiology, with the focus on recent findings in the field.

Keywords:  Alternative mitophagy; Drp1; Mitochondrial quality control; Mitophagy

DOI:  https://doi.org/10.1007/s00395-023-01009-x
Nat Cell Biol. 2023 Oct 02.

An ESCRT grommet cooperates with a diffusion barrier to maintain nuclear integrity.

Nicholas R Ader, Linda Chen, Ivan V Surovtsev, William L Chadwick, Elisa C Rodriguez, Megan C King, C Patrick Lusk.

The molecular mechanisms by which the endosomal sorting complexes required for transport (ESCRT) proteins contribute to the integrity of the nuclear envelope (NE) barrier are not fully defined. We leveraged the single NE hole generated by mitotic extrusion of the Schizosaccharomyces pombe spindle pole body to reveal two modes of ESCRT function executed by distinct complements of ESCRT-III proteins, both dependent on CHMP7/Cmp7. A grommet-like function is required to restrict the NE hole in anaphase B, whereas replacement of Cmp7 by a sealing module ultimately closes the NE in interphase. Without Cmp7, nucleocytoplasmic compartmentalization remains intact despite NE discontinuities of up to 540 nm, suggesting mechanisms to limit diffusion through these holes. We implicate spindle pole body proteins as key components of a diffusion barrier acting with Cmp7 in anaphase B. Thus, NE remodelling mechanisms cooperate with proteinaceous diffusion barriers beyond nuclear pore complexes to maintain the nuclear compartment.

DOI: https://doi.org/10.1038/s41556-023-01235-4
EMBO J. 2023 Oct 02. e114334

Replication-induced DNA secondary structures drive fork uncoupling and breakage.

Sophie L Williams, Corella S Casas-Delucchi, Federica Raguseo, Dilek Guneri, Yunxuan Li, Masashi Minamino, Emma E Fletcher, Joseph Tp Yeeles, Ulrich F Keyser, Zoë Ae Waller, Marco Di Antonio, Gideon Coster.

  Sequences that form DNA secondary structures, such as G-quadruplexes (G4s) and intercalated-Motifs (iMs), are abundant in the human genome and play various physiological roles. However, they can also interfere with replication and threaten genome stability. Multiple lines of evidence suggest G4s inhibit replication, but the underlying mechanism remains unclear. Moreover, evidence of how iMs affect the replisome is lacking. Here, we reconstitute replication of physiologically derived structure-forming sequences to find that a single G4 or iM arrest DNA replication. Direct single-molecule structure detection within solid-state nanopores reveals structures form as a consequence of replication. Combined genetic and biophysical characterisation establishes that structure stability and probability of structure formation are key determinants of replisome arrest. Mechanistically, replication arrest is caused by impaired synthesis, resulting in helicase-polymerase uncoupling. Significantly, iMs also induce breakage of nascent DNA. Finally, stalled forks are only rescued by a specialised helicase, Pif1, but not Rrm3, Sgs1, Chl1 or Hrq1. Altogether, we provide a mechanism for quadruplex structure formation and resolution during replication and highlight G4s and iMs as endogenous sources of replication stress.

Keywords:  DNA replication; DNA secondary structures; G-quadruplex and i-Motif; genome stability; replication stress

DOI:  https://doi.org/10.15252/embj.2023114334
Cell Stem Cell. 2023 Sep 27. pii: S1934-5909(23)00323-5. [Epub ahead of print]

Spatial-temporal proliferation of hepatocytes during pregnancy revealed by genetic lineage tracing.

Shun He, Zhihou Guo, Mingshan Zhou, Haichang Wang, Zhuonan Zhang, Mengyang Shi, Xufeng Li, Xueying Yang, Lingjuan He.

  The maternal liver undergoes dramatic enlargement to adapt to the increased metabolic demands during pregnancy. However, the cellular sources for liver growth during pregnancy remain largely elusive. Here, we employed a proliferation recording system, ProTracer, to examine the spatial-temporal proliferation of hepatocytes during pregnancy. We discovered that during early to late pregnancy, hepatocyte proliferation initiated from zone 1, to zone 2, and lastly to zone 3, with the majority of new hepatocytes being generated in zone 2. Additionally, using single-cell RNA sequencing, we observed that Ccnd1 was highly enriched in zone 2 hepatocytes. We further applied dual-recombinase-mediated genetic lineage tracing to reveal that Ccnd1+ hepatocytes expanded preferentially during pregnancy. Moreover, we demonstrated that estrogen induces liver enlargement during pregnancy, which was abolished in Ccnd1 knockout mice. Our work revealed a unique spatial-temporal hepatocyte proliferation pattern during pregnancy, with Ccnd1+ hepatocytes in zone 2 serving as the major cellular source for hepatic enlargement.

Keywords:  Ccnd1; estrogen; genetic lineage tracing; hepatocyte proliferation; pregnancy

DOI:  https://doi.org/10.1016/j.stem.2023.09.002