bims-ginsta Biomed News
on Genome instability
Issue of 2024–02–04
fiveteen papers selected by
Jinrong Hu, National University of Singapore
  1. An extended wave of global mRNA deadenylation sets up a switch in translation regulation across the mammalian oocyte-to-embryo transition.
  2. Ran-GTP assembles a specialized spindle structure for accurate chromosome segregation in medaka early embryos.
  3. RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis.
  4. Mechanical forces across compartments coordinate cell shape and fate transitions to generate tissue architecture.
  5. Transition of human γ-tubulin ring complex into a closed conformation during microtubule nucleation.
  6. Multiscale biophysical analysis of nucleolus disassembly during mitosis.
  7. An epigenetic barrier sets the timing of human neuronal maturation.
  8. Multiplexed screening reveals how cancer-specific alternative polyadenylation shapes tumor growth in vivo.
  9. In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization.
  10. Lin28a cardiomyocyte-specific modified mRNA translation system induces cardiomyocyte cell division and cardiac repair.
  11. Feedback control of organ size precision is mediated by BMP2-regulated apoptosis in the Drosophila eye.
  12. Hydrolytic endonucleolytic ribozyme (HYER) is programmable for sequence-specific DNA cleavage.
  13. Computational Studies Reveal How Passive Cross-Linkers Regulate Anaphase Spindle Elongation.
  14. Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids.
  15. Stress response silencing by an E3 ligase mutated in neurodegeneration.
  1. Cell Rep. 2024 Jan 31. pii: S2211-1247(24)00038-X. [Epub ahead of print]43(2): 113710
    An extended wave of global mRNA deadenylation sets up a switch in translation regulation across the mammalian oocyte-to-embryo transition.
    Katherine Lee, Kyucheol Cho, Robert Morey, Heidi Cook-Andersen.
      Without new transcription, gene expression across the oocyte-to-embryo transition (OET) relies instead on regulation of mRNA poly(A) tails to control translation. However, how tail dynamics shape translation across the OET in mammals remains unclear. We perform long-read RNA sequencing to uncover poly(A) tail lengths across the mouse OET and, incorporating published ribosome profiling data, provide an integrated, transcriptome-wide analysis of poly(A) tails and translation across the entire transition. We uncover an extended wave of global deadenylation during fertilization in which short-tailed, oocyte-deposited mRNAs are translationally activated without polyadenylation through resistance to deadenylation. Subsequently, in the embryo, mRNAs are readenylated and translated in a surge of global polyadenylation. We further identify regulation of poly(A) tail length at the isoform level and stage-specific enrichment of mRNA sequence motifs among regulated transcripts. These data provide insight into the stage-specific mechanisms of poly(A) tail regulation that orchestrate gene expression from oocyte to embryo in mammals.
    Keywords:  3′ UTR motif; CP: Developmental biology; CP: Molecular biology; deadenylation; development; mRNA stability; oocyte-to-embryo transition; polyadenylation; post-transcriptional regulation; translation
    DOI:  https://doi.org/10.1016/j.celrep.2024.113710
  2. Nat Commun. 2024 Feb 01. 15(1): 981
    Ran-GTP assembles a specialized spindle structure for accurate chromosome segregation in medaka early embryos.
    Ai Kiyomitsu, Toshiya Nishimura, Shiang Jyi Hwang, Satoshi Ansai, Masato T Kanemaki, Minoru Tanaka, Tomomi Kiyomitsu.
      Despite drastic cellular changes during cleavage, a mitotic spindle assembles in each blastomere to accurately segregate duplicated chromosomes. Mechanisms of mitotic spindle assembly have been extensively studied using small somatic cells. However, mechanisms of spindle assembly in large vertebrate embryos remain little understood. Here, we establish functional assay systems in medaka (Oryzias latipes) embryos by combining CRISPR knock-in with auxin-inducible degron technology. Live imaging reveals several unexpected features of microtubule organization and centrosome positioning that achieve rapid, accurate cleavage. Importantly, Ran-GTP assembles a dense microtubule network at the metaphase spindle center that is essential for chromosome segregation in early embryos. This unique spindle structure is remodeled into a typical short, somatic-like spindle after blastula stages, when Ran-GTP becomes dispensable for chromosome segregation. We propose that despite the presence of centrosomes, the chromosome-derived Ran-GTP pathway has essential roles in functional spindle assembly in large, rapidly dividing vertebrate early embryos, similar to acentrosomal spindle assembly in oocytes.
    DOI:  https://doi.org/10.1038/s41467-024-45251-w
  3. Nat Commun. 2024 Jan 29. 15(1): 848
    RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis.
    Emily G Kaye, Kavyashree Basavaraju, Geoffrey M Nelson, Helena D Zomer, Debarun Roy, Irene Infancy Joseph, Reza Rajabi-Toustani, Huanyu Qiao, Karen Adelman, Prabhakara P Reddi.
      Male germ cell development requires precise regulation of gene activity in a cell-type and stage-specific manner, with perturbations in gene expression during spermatogenesis associated with infertility. Here, we use steady-state, nascent and single-cell RNA sequencing strategies to comprehensively characterize gene expression across male germ cell populations, to dissect the mechanisms of gene control and provide new insights towards therapy. We discover a requirement for pausing of RNA Polymerase II (Pol II) at the earliest stages of sperm differentiation to establish the landscape of gene activity across development. Accordingly, genetic knockout of the Pol II pause-inducing factor NELF in immature germ cells blocks differentiation to spermatids. Further, we uncover unanticipated roles for Pol II pausing in the regulation of meiosis during spermatogenesis, with the presence of paused Pol II associated with double-strand break (DSB) formation, and disruption of meiotic gene expression and DSB repair in germ cells lacking NELF.
    DOI:  https://doi.org/10.1038/s41467-024-45177-3
  4. Nat Cell Biol. 2024 Feb 01.
    Mechanical forces across compartments coordinate cell shape and fate transitions to generate tissue architecture.
    Clémentine Villeneuve, Ali Hashmi, Irene Ylivinkka, Elizabeth Lawson-Keister, Yekaterina A Miroshnikova, Carlos Pérez-González, Satu-Marja Myllymäki, Fabien Bertillot, Bhagwan Yadav, Tao Zhang, Danijela Matic Vignjevic, Marja L Mikkola, M Lisa Manning, Sara A Wickström.
      Morphogenesis and cell state transitions must be coordinated in time and space to produce a functional tissue. An excellent paradigm to understand the coupling of these processes is mammalian hair follicle development, which is initiated by the formation of an epithelial invagination-termed placode-that coincides with the emergence of a designated hair follicle stem cell population. The mechanisms directing the deformation of the epithelium, cell state transitions and physical compartmentalization of the placode are unknown. Here we identify a key role for coordinated mechanical forces stemming from contractile, proliferative and proteolytic activities across the epithelial and mesenchymal compartments in generating the placode structure. A ring of fibroblast cells gradually wraps around the placode cells to generate centripetal contractile forces, which, in collaboration with polarized epithelial myosin activity, promote elongation and local tissue thickening. These mechanical stresses further enhance compartmentalization of Sox9 expression to promote stem cell positioning. Subsequently, proteolytic remodelling locally softens the basement membrane to facilitate a release of pressure on the placode, enabling localized cell divisions, tissue fluidification and epithelial invagination into the underlying mesenchyme. Together, our experiments and modelling identify dynamic cell shape transformations and tissue-scale mechanical cooperation as key factors for orchestrating organ formation.
    DOI:  https://doi.org/10.1038/s41556-023-01332-4
  5. Science. 2024 Feb 02. eadk6160
    Transition of human γ-tubulin ring complex into a closed conformation during microtubule nucleation.
    Cláudia Brito, Marina Serna, Pablo Guerra, Oscar Llorca, Thomas Surrey.
      Microtubules are essential for intracellular organization and chromosome segregation. They are nucleated by the γ-tubulin ring complex (γTuRC). However, isolated vertebrate γTuRC adopts an open conformation that deviates from the microtubule structure, raising the question of the nucleation mechanism. Here we determine cryo-electron microscopy structures of human γTuRC bound to a nascent microtubule. Structural changes of the complex into a closed conformation ensure that γTuRC templates the 13-protofilament microtubules that exist in human cells. Closure is mediated by a latch that interacts with incorporating tubulin, making it part of the closing mechanism. Further rearrangements involve all γ-tubulin ring complex subunits and the removal of the actin-containing luminal bridge. Our proposed mechanism of microtubule nucleation by human γTuRC relies on large-scale structural changes that are likely the target of regulation in cells.
    DOI:  https://doi.org/10.1126/science.adk6160
  6. Proc Natl Acad Sci U S A. 2024 Feb 06. 121(6): e2312250121
    Multiscale biophysical analysis of nucleolus disassembly during mitosis.
    An T Pham, Madhav Mani, Xiaozhong Wang, Reza Vafabakhsh.
      During cell division, precise and regulated distribution of cellular material between daughter cells is a critical step and is governed by complex biochemical and biophysical mechanisms. To achieve this, membraneless organelles and condensates often require complete disassembly during mitosis. The biophysical principles governing the disassembly of condensates remain poorly understood. Here, we used a physical biology approach to study how physical and material properties of the nucleolus, a prominent nuclear membraneless organelle in eukaryotic cells, change during mitosis and across different scales. We found that nucleolus disassembly proceeds continuously through two distinct phases with a slow and reversible preparatory phase followed by a rapid irreversible phase that was concurrent with the nuclear envelope breakdown. We measured microscopic properties of nucleolar material including effective diffusion rates and binding affinities as well as key macroscopic properties of surface tension and bending rigidity. By incorporating these measurements into the framework of critical phenomena, we found evidence that near mitosis surface tension displays a power-law behavior as a function of biochemically modulated interaction strength. This two-step disassembly mechanism maintains structural and functional stability of nucleolus while enabling its rapid and efficient disassembly in response to cell cycle cues.
    Keywords:  critical phenomena; membraneless organelles; nucleolus disassembly
    DOI:  https://doi.org/10.1073/pnas.2312250121
  7. Nature. 2024 Jan 31.
    An epigenetic barrier sets the timing of human neuronal maturation.
    Gabriele Ciceri, Arianna Baggiolini, Hyein S Cho, Meghana Kshirsagar, Silvia Benito-Kwiecinski, Ryan M Walsh, Kelly A Aromolaran, Alberto J Gonzalez-Hernandez, Hermany Munguba, So Yeon Koo, Nan Xu, Kaylin J Sevilla, Peter A Goldstein, Joshua Levitz, Christina S Leslie, Richard P Koche, Lorenz Studer.
      The pace of human brain development is highly protracted compared with most other species1-7. The maturation of cortical neurons is particularly slow, taking months to years to develop adult functions3-5. Remarkably, such protracted timing is retained in cortical neurons derived from human pluripotent stem cells (hPSCs) during in vitro differentiation or upon transplantation into the mouse brain4,8,9. Those findings suggest the presence of a cell-intrinsic clock setting the pace of neuronal maturation, although the molecular nature of this clock remains unknown. Here we identify an epigenetic developmental programme that sets the timing of human neuronal maturation. First, we developed a hPSC-based approach to synchronize the birth of cortical neurons in vitro which enabled us to define an atlas of morphological, functional and molecular maturation. We observed a slow unfolding of maturation programmes, limited by the retention of specific epigenetic factors. Loss of function of several of those factors in cortical neurons enables precocious maturation. Transient inhibition of EZH2, EHMT1 and EHMT2 or DOT1L, at progenitor stage primes newly born neurons to rapidly acquire mature properties upon differentiation. Thus our findings reveal that the rate at which human neurons mature is set well before neurogenesis through the establishment of an epigenetic barrier in progenitor cells. Mechanistically, this barrier holds transcriptional maturation programmes in a poised state that is gradually released to ensure the prolonged timeline of human cortical neuron maturation.
    DOI:  https://doi.org/10.1038/s41586-023-06984-8
  8. Nat Commun. 2024 Feb 01. 15(1): 959
    Multiplexed screening reveals how cancer-specific alternative polyadenylation shapes tumor growth in vivo.
    Austin M Gabel, Andrea E Belleville, James D Thomas, Siegen A McKellar, Taylor R Nicholas, Toshihiro Banjo, Edie I Crosse, Robert K Bradley.
      Alternative polyadenylation (APA) is strikingly dysregulated in many cancers. Although global APA dysregulation is frequently associated with poor prognosis, the importance of most individual APA events is controversial simply because few have been functionally studied. Here, we address this gap by developing a CRISPR-Cas9-based screen to manipulate endogenous polyadenylation and systematically quantify how APA events contribute to tumor growth in vivo. Our screen reveals individual APA events that control mouse melanoma growth in an immunocompetent host, with concordant associations in clinical human cancer. For example, forced Atg7 3' UTR lengthening in mouse melanoma suppresses ATG7 protein levels, slows tumor growth, and improves host survival; similarly, in clinical human melanoma, a long ATG7 3' UTR is associated with significantly prolonged patient survival. Overall, our study provides an easily adaptable means to functionally dissect APA in physiological systems and directly quantifies the contributions of recurrent APA events to tumorigenic phenotypes.
    DOI:  https://doi.org/10.1038/s41467-024-44931-x
  9. Nat Genet. 2024 Jan 30.
    In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization.
    Elisa Oberbeckmann, Kimberly Quililan, Patrick Cramer, A Marieke Oudelaar.
      Eukaryotic genomes are organized into chromatin domains. The molecular mechanisms driving the formation of these domains are difficult to dissect in vivo and remain poorly understood. Here we reconstitute Saccharomyces cerevisiae chromatin in vitro and determine its 3D organization at subnucleosome resolution by micrococcal nuclease-based chromosome conformation capture and molecular dynamics simulations. We show that regularly spaced and phased nucleosome arrays form chromatin domains in vitro that resemble domains in vivo. This demonstrates that neither loop extrusion nor transcription is required for basic domain formation in yeast. In addition, we find that the boundaries of reconstituted domains correspond to nucleosome-free regions and that insulation strength scales with their width. Finally, we show that domain compaction depends on nucleosome linker length, with longer linkers forming more compact structures. Together, our results demonstrate that regular nucleosome positioning is important for the formation of chromatin domains and provide a proof-of-principle for bottom-up 3D genome studies.
    DOI:  https://doi.org/10.1038/s41588-023-01649-8
  10. J Mol Cell Cardiol. 2024 Jan 30. pii: S0022-2828(24)00017-8. [Epub ahead of print]
    Lin28a cardiomyocyte-specific modified mRNA translation system induces cardiomyocyte cell division and cardiac repair.
    Ajit Magadum, Jiacheng Sun, Neha Singh, Ann Anu Kurian, Elena Chepurko, Anthony Fargnoli, Roger Hajjar, Jianyi Zhang, Lior Zangi.
      The mammalian heart has a limited regenerative capacity. Previous work suggested the heart can regenerate during development and immediately after birth by inducing cardiomyocyte (CM) proliferation; however, this capacity is lost seven days after birth. modRNA gene delivery, the same technology used successfully in the two mRNA vaccines against SARS-CoV-2, can prompt cardiac regeneration, cardiovascular regeneration and cardiac protection. We recently established a novel CM-specific modRNA translational system (SMRTs) that allows modRNA translation only in CMs. We demonstrated that this system delivers potent intracellular genes (e.g., cell cyclepromoting Pkm2), which are beneficial when expressed in one cell type (i.e., CMs) but not others (non-CMs). Here, we identify Lin28a as an important regulator of the CM cell cycle. We show that Lin28a is expressed in CMs during development and immediately after birth, but not during adulthood. We describe that specific delivery of Lin28a into CM, using CM SMRTs, enables CM cell division and proliferation. Further, we determine that this proliferation leads to cardiac repair and better outcome post MI. Moreover, we identify the molecular pathway of Lin28a in CMs. We also demonstrate that Lin28a suppress Let-7 which is vital for CM proliferation, partially due to its suppressive role on cMYC, HMGA2 and K-RAS.
    Keywords:  Cardiac regeneration; Genetic medicine; Modified mRNA
    DOI:  https://doi.org/10.1016/j.yjmcc.2024.01.007
  11. PLoS Biol. 2024 Jan;22(1): e3002450
    Feedback control of organ size precision is mediated by BMP2-regulated apoptosis in the Drosophila eye.
    Tomas Navarro, Antonella Iannini, Marta Neto, Alejandro Campoy-Lopez, Javier Muñoz-García, Paulo S Pereira, Saúl Ares, Fernando Casares.
      Biological processes are intrinsically noisy, and yet, the result of development-like the species-specific size and shape of organs-is usually remarkably precise. This precision suggests the existence of mechanisms of feedback control that ensure that deviations from a target size are minimized. Still, we have very limited understanding of how these mechanisms operate. Here, we investigate the problem of organ size precision using the Drosophila eye. The size of the adult eye depends on the rates at which eye progenitor cells grow and differentiate. We first find that the progenitor net growth rate results from the balance between their proliferation and apoptosis, with this latter contributing to determining both final eye size and its variability. In turn, apoptosis of progenitor cells is hampered by Dpp, a BMP2/4 signaling molecule transiently produced by early differentiating retinal cells. Our genetic and computational experiments show how the status of retinal differentiation is communicated to progenitors through the differentiation-dependent production of Dpp, which, by adjusting the rate of apoptosis, exerts a feedback control over the net growth of progenitors to reduce final eye size variability.
    DOI:  https://doi.org/10.1371/journal.pbio.3002450
  12. Science. 2024 Feb 02. 383(6682): eadh4859
    Hydrolytic endonucleolytic ribozyme (HYER) is programmable for sequence-specific DNA cleavage.
    Zi-Xian Liu, Shouyue Zhang, Han-Zhou Zhu, Zhi-Hang Chen, Yun Yang, Long-Qi Li, Yuan Lei, Yun Liu, Dan-Yuan Li, Ao Sun, Cheng-Ping Li, Shun-Qing Tan, Gao-Li Wang, Jie-Yi Shen, Shuai Jin, Caixia Gao, Jun-Jie Gogo Liu.
      Ribozymes are catalytic RNAs with diverse functions including self-splicing and polymerization. This work aims to discover natural ribozymes that behave as hydrolytic and sequence-specific DNA endonucleases, which could be repurposed as DNA manipulation tools. Focused on bacterial group II-C introns, we found that many systems without intron-encoded protein propagate multiple copies in their resident genomes. These introns, named HYdrolytic Endonucleolytic Ribozymes (HYERs), cleaved RNA, single-stranded DNA, bubbled double-stranded DNA (dsDNA), and plasmids in vitro. HYER1 generated dsDNA breaks in the mammalian genome. Cryo-electron microscopy analysis revealed a homodimer structure for HYER1, where each monomer contains a Mg2+-dependent hydrolysis pocket and captures DNA complementary to the target recognition site (TRS). Rational designs including TRS extension, recruiting sequence insertion, and heterodimerization yielded engineered HYERs showing improved specificity and flexibility for DNA manipulation.
    DOI:  https://doi.org/10.1126/science.adh4859
  13. J Phys Chem B. 2024 Jan 30.
    Computational Studies Reveal How Passive Cross-Linkers Regulate Anaphase Spindle Elongation.
    Yao Wang, Yu-Ru Liu, Peng-Ye Wang, Ping Xie.
      In eukaryotic cell division, a series of events are organized to produce two daughter cells. The spindle elongation in anaphase B is essential for providing enough space to maintain cell size and distribute sister chromatids properly, which is associated with microtubules and microtubule-associated proteins such as kinesin-5 Eg5 and the Ase1-related protein, PRC1. The available experimental data indicated that after the start of anaphase B more PRC1 proteins can bind to the antiparallel microtubule pairs in the spindle but the excess amount of PRC1 proteins can lead to the failure of cell division, indicating that PRC1 proteins can regulate the spindle elongation in a concentration-dependent manner. However, the underlying mechanism of the PRC1 proteins regulating the spindle elongation has not been explained up to now. Here, we use a simplified model, where only the two important participants (kinesin-5 Eg5 motors and PRC1 proteins) are considered, to study the spindle elongation during anaphase B. We first show that only in the appropriate range of the PRC1 concentration can the spindle elongation complete properly. Furthermore, we explore the underlying mechanism of PRC1 as a regulator for spindle elongation.
    DOI:  https://doi.org/10.1021/acs.jpcb.3c07655
  14. Nat Protoc. 2024 Feb 01.
    Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids.
    João Pedro Alves-Lopes, Frederick C K Wong, M Azim Surani.
      Human primordial germ cells (hPGCs), the precursors of eggs and sperm, start their complex development shortly after specification and during their migration to the primitive gonads. Here, we describe protocols for specifying hPGC-like cells (hPGCLCs) from resetting precursors and progressing them with the support of human hindgut organoids. Resetting hPGCLCs (rhPGCLCs) are specified from human embryonic stem cells (hESCs) transitioning from the primed into the naive state of pluripotency. Hindgut organoids are also derived from hESCs after a sequential differentiation into a posterior endoderm/hindgut fate. Both rhPGCLCs and hindgut organoids are combined and co-cultured for 25 d. The entire procedure takes ~1.5 months and can be successfully implemented by a doctoral or graduate student with basic skills and experience in hESC cultures. The co-culture system supports the progression of rhPGCLCs at a developmental timing analogous to that observed in vivo. Compared with previously developed hPGCLC progression protocols, which depend on co-cultures with mouse embryonic gonadal tissue, our co-culture system represents a developmentally relevant model closer to the environment that hPGCs first encounter after specification. Together with the potential for investigations of events during hPGC specification and early development, these protocols provide a practical approach to designing efficient models for in vitro gametogenesis. Notably, the rhPGCLC-hindgut co-culture system can also be adapted to study failings in hPGC migration, which are associated with the etiology of some forms of infertility and germ cell tumors.
    DOI:  https://doi.org/10.1038/s41596-023-00945-1
  15. Nature. 2024 Jan 31.
    Stress response silencing by an E3 ligase mutated in neurodegeneration.
    Diane L Haakonsen, Michael Heider, Andrew J Ingersoll, Kayla Vodehnal, Samuel R Witus, Takeshi Uenaka, Marius Wernig, Michael Rapé.
      Stress response pathways detect and alleviate adverse conditions to safeguard cell and tissue homeostasis, yet their prolonged activation induces apoptosis and disrupts organismal health1-3. How stress responses are turned off at the right time and place remains poorly understood. Here we report a ubiquitin-dependent mechanism that silences the cellular response to mitochondrial protein import stress. Crucial to this process is the silencing factor of the integrated stress response (SIFI), a large E3 ligase complex mutated in ataxia and in early-onset dementia that degrades both unimported mitochondrial precursors and stress response components. By recognizing bifunctional substrate motifs that equally encode protein localization and stability, the SIFI complex turns off a general stress response after a specific stress event has been resolved. Pharmacological stress response silencing sustains cell survival even if stress resolution failed, which underscores the importance of signal termination and provides a roadmap for treating neurodegenerative diseases caused by mitochondrial import defects.
    DOI:  https://doi.org/10.1038/s41586-023-06985-7
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