bims-ginsta Biomed News
on Genome instability
Issue of 2024‒05‒19
25 papers selected by
Jinrong Hu, National University of Singapore
  1. Vertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin.
  2. Whi5 hypo- and hyper-phosphorylation dynamics control cell-cycle entry and progression.
  3. DNA damage induces p53-independent apoptosis through ribosome stalling.
  4. Transcription stress at telomeres leads to cytosolic DNA release and paracrine senescence.
  5. The first two blastomeres contribute unequally to the human embryo.
  6. Single-cell 3D genome structure reveals distinct human pluripotent states.
  7. RNA polymerase II-mediated rDNA transcription mediates rDNA copy number expansion in Drosophila.
  8. Post-translational modification-dependent oligomerization switch in regulation of global transcription and DNA damage repair during genotoxic stress.
  9. Polyploid sugarcane genome architecture.
  10. The matrisome landscape controlling in vivo germ cell fates.
  11. GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells.
  12. SMAD2/3-SMYD2 and developmental transcription factors cooperate with cell cycle inhibitors to guide tissue formation.
  13. The killifish germline regulates longevity and somatic repair in a sex-specific manner.
  14. Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes.
  15. The PD-1-PD-L1 pathway maintains an immunosuppressive environment essential for neonatal heart regeneration.
  16. Automated profiling of gene function during embryonic development.
  17. Polyglutamine-mediated ribotoxicity disrupts proteostasis and stress responses in Huntington's disease.
  18. Mitochondrial heterogeneity and adaptations to cellular needs.
  19. Chromatin regulates alternative polyadenylation via the RNA polymerase II elongation rate.
  20. A step-by-step guide to fragmenting bundled actin filaments.
  21. FMNL2 regulates actin for endoplasmic reticulum and mitochondria distribution in oocyte meiosis.
  22. Reduced Levels of Lagging Strand Polymerases Shape Stem Cell Chromatin.
  23. Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics.
  24. Human embryos embrace asymmetry to form the body.
  25. Identification of Prominin-2 as a new player of cardiomyocyte senescence in the aging heart.
  1. Cell. 2024 May 08. pii: S0092-8674(24)00409-4. [Epub ahead of print]
    Vertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin.
    Carlos Sacristan, Kumiko Samejima, Lorena Andrade Ruiz, Moonmoon Deb, Maaike L A Lambers, Adam Buckle, Chris A Brackley, Daniel Robertson, Tetsuya Hori, Shaun Webb, Robert Kiewisz, Tristan Bepler, Eloïse van Kwawegen, Patrik Risteski, Kruno Vukušić, Iva M Tolić, Thomas Müller-Reichert, Tatsuo Fukagawa, Nick Gilbert, Davide Marenduzzo, William C Earnshaw, Geert J P L Kops.
      Centromeres are scaffolds for the assembly of kinetochores that ensure chromosome segregation during cell division. How vertebrate centromeres obtain a three-dimensional structure to accomplish their primary function is unclear. Using super-resolution imaging, capture-C, and polymer modeling, we show that vertebrate centromeres are partitioned by condensins into two subdomains during mitosis. The bipartite structure is found in human, mouse, and chicken cells and is therefore a fundamental feature of vertebrate centromeres. Super-resolution imaging and electron tomography reveal that bipartite centromeres assemble bipartite kinetochores, with each subdomain binding a distinct microtubule bundle. Cohesin links the centromere subdomains, limiting their separation in response to spindle forces and avoiding merotelic kinetochore-spindle attachments. Lagging chromosomes during cancer cell divisions frequently have merotelic attachments in which the centromere subdomains are separated and bioriented. Our work reveals a fundamental aspect of vertebrate centromere biology with implications for understanding the mechanisms that guarantee faithful chromosome segregation.
    Keywords:  centromere; chromatin organization; chromosomal instability; cohesin; condensin; kinetochore; mitosis
    DOI:  https://doi.org/10.1016/j.cell.2024.04.014
  2. Curr Biol. 2024 May 08. pii: S0960-9822(24)00526-8. [Epub ahead of print]
    Whi5 hypo- and hyper-phosphorylation dynamics control cell-cycle entry and progression.
    Jordan Xiao, Jonathan J Turner, Mardo Kõivomägi, Jan M Skotheim.
      Progression through the cell cycle depends on the phosphorylation of key substrates by cyclin-dependent kinases. In budding yeast, these substrates include the transcriptional inhibitor Whi5 that regulates G1/S transition. In early G1 phase, Whi5 is hypo-phosphorylated and inhibits the Swi4/Swi6 (SBF) complex that promotes transcription of the cyclins CLN1 and CLN2. In late G1, Whi5 is rapidly hyper-phosphorylated by Cln1 and Cln2 in complex with the cyclin-dependent kinase Cdk1. This hyper-phosphorylation inactivates Whi5 and excludes it from the nucleus. Here, we set out to determine the molecular mechanisms responsible for Whi5's multi-site phosphorylation and how they regulate the cell cycle. To do this, we first identified the 19 Whi5 sites that are appreciably phosphorylated and then determined which of these sites are responsible for G1 hypo-phosphorylation. Mutation of 7 sites removed G1 hypo-phosphorylation, increased cell size, and delayed the G1/S transition. Moreover, the rapidity of Whi5 hyper-phosphorylation in late G1 depends on "priming" sites that dock the Cks1 subunit of Cln1,2-Cdk1 complexes. Hyper-phosphorylation is crucial for Whi5 nuclear export, normal cell size, full expression of SBF target genes, and timely progression through both the G1/S transition and S/G2/M phases. Thus, our work shows how Whi5 phosphorylation regulates the G1/S transition and how it is required for timely progression through S/G2/M phases and not only G1 as previously thought.
    Keywords:  Cdk; Cks1; G1/S; Whi5; cell cycle control; cell size control; multi-site phosphorylation
    DOI:  https://doi.org/10.1016/j.cub.2024.04.052
  3. Science. 2024 May 17. 384(6697): 785-792
    DNA damage induces p53-independent apoptosis through ribosome stalling.
    Nicolaas J Boon, Rafaela A Oliveira, Pierré-René Körner, Adva Kochavi, Sander Mertens, Yuval Malka, Rhianne Voogd, Suzanne E M van der Horst, Maarten A Huismans, Lidwien P Smabers, Jonne M Draper, Lodewyk F A Wessels, Peter Haahr, Jeanine M L Roodhart, Ton N M Schumacher, Hugo J Snippert, Reuven Agami, Thijn R Brummelkamp.
      In response to excessive DNA damage, human cells can activate p53 to induce apoptosis. Cells lacking p53 can still undergo apoptosis upon DNA damage, yet the responsible pathways are unknown. We observed that p53-independent apoptosis in response to DNA damage coincided with translation inhibition, which was characterized by ribosome stalling on rare leucine-encoding UUA codons and globally curtailed translation initiation. A genetic screen identified the transfer RNAse SLFN11 and the kinase GCN2 as factors required for UUA stalling and global translation inhibition, respectively. Stalled ribosomes activated a ribotoxic stress signal conveyed by the ribosome sensor ZAKα to the apoptosis machinery. These results provide an explanation for the frequent inactivation of SLFN11 in chemotherapy-unresponsive tumors and highlight ribosome stalling as a signaling event affecting cell fate in response to DNA damage.
    DOI:  https://doi.org/10.1126/science.adh7950
  4. Nat Commun. 2024 May 14. 15(1): 4061
    Transcription stress at telomeres leads to cytosolic DNA release and paracrine senescence.
    Athanasios Siametis, Kalliopi Stratigi, Despoina Giamaki, Georgia Chatzinikolaou, Alexia Akalestou-Clocher, Evi Goulielmaki, Brian Luke, Björn Schumacher, George A Garinis.
      Transcription stress has been linked to DNA damage -driven aging, yet the underlying mechanism remains unclear. Here, we demonstrate that Tcea1-/- cells, which harbor a TFIIS defect in transcription elongation, exhibit RNAPII stalling at oxidative DNA damage sites, impaired transcription, accumulation of R-loops, telomere uncapping, chromatin bridges, and genome instability, ultimately resulting in cellular senescence. We found that R-loops at telomeres causally contribute to the release of telomeric DNA fragments in the cytoplasm of Tcea1-/- cells and primary cells derived from naturally aged animals triggering a viral-like immune response. TFIIS-defective cells release extracellular vesicles laden with telomeric DNA fragments that target neighboring cells, which consequently undergo cellular senescence. Thus, transcription stress elicits paracrine signals leading to cellular senescence, promoting aging.
    DOI:  https://doi.org/10.1038/s41467-024-48443-6
  5. Cell. 2024 May 09. pii: S0092-8674(24)00455-0. [Epub ahead of print]
    The first two blastomeres contribute unequally to the human embryo.
    Sergi Junyent, Maciej Meglicki, Roman Vetter, Rachel Mandelbaum, Catherine King, Ekta M Patel, Lisa Iwamoto-Stohl, Clare Reynell, Dong-Yuan Chen, Patrizia Rubino, Nabil Arrach, Richard J Paulson, Dagmar Iber, Magdalena Zernicka-Goetz.
      Retrospective lineage reconstruction of humans predicts that dramatic clonal imbalances in the body can be traced to the 2-cell stage embryo. However, whether and how such clonal asymmetries arise in the embryo is unclear. Here, we performed prospective lineage tracing of human embryos using live imaging, non-invasive cell labeling, and computational predictions to determine the contribution of each 2-cell stage blastomere to the epiblast (body), hypoblast (yolk sac), and trophectoderm (placenta). We show that the majority of epiblast cells originate from only one blastomere of the 2-cell stage embryo. We observe that only one to three cells become internalized at the 8-to-16-cell stage transition. Moreover, these internalized cells are more frequently derived from the first cell to divide at the 2-cell stage. We propose that cell division dynamics and a cell internalization bottleneck in the early embryo establish asymmetry in the clonal composition of the future human body.
    Keywords:  2-cell blastomere asymmetries; epiblast; human development; human embryo; hypoblast; lineage tracing; non-invasive live imaging; placenta; preimplantation development
    DOI:  https://doi.org/10.1016/j.cell.2024.04.029
  6. Genome Biol. 2024 May 13. 25(1): 122
    Single-cell 3D genome structure reveals distinct human pluripotent states.
    Niannian Li, Kairang Jin, Bin Liu, Mingzhu Yang, PanPan Shi, Dai Heng, Jichang Wang, Lin Liu.
      BACKGROUND: Pluripotent states of embryonic stem cells (ESCs) with distinct transcriptional profiles affect ESC differentiative capacity and therapeutic potential. Although single-cell RNA sequencing has revealed additional subpopulations and specific features of naive and primed human pluripotent stem cells (hPSCs), the underlying mechanisms that regulate their specific transcription and that control their pluripotent states remain elusive.RESULTS: By single-cell analysis of high-resolution, three-dimensional (3D) genomic structure, we herein demonstrate that remodeling of genomic structure is highly associated with the pluripotent states of human ESCs (hESCs). The naive pluripotent state is featured with specialized 3D genomic structures and clear chromatin compartmentalization that is distinct from the primed state. The naive pluripotent state is achieved by remodeling the active euchromatin compartment and reducing chromatin interactions at the nuclear center. This unique genomic organization is linked to enhanced chromatin accessibility on enhancers and elevated expression levels of naive pluripotent genes localized to this region. In contradistinction, the primed state exhibits intermingled genomic organization. Moreover, active euchromatin and primed pluripotent genes are distributed at the nuclear periphery, while repressive heterochromatin is densely concentrated at the nuclear center, reducing chromatin accessibility and the transcription of naive genes.
    CONCLUSIONS: Our data provide insights into the chromatin structure of ESCs in their naive and primed states, and we identify specific patterns of modifications in transcription and chromatin structure that might explain the genes that are differentially expressed between naive and primed hESCs. Thus, the inversion or relocation of heterochromatin to euchromatin via compartmentalization is related to the regulation of chromatin accessibility, thereby defining pluripotent states and cellular identity.
    Keywords:  Chromatin accessibility; Genome structure; Human embryonic stem cells; Naive; Pluripotency; Primed
    DOI:  https://doi.org/10.1186/s13059-024-03268-w
  7. PLoS Genet. 2024 May 17. 20(5): e1011136
    RNA polymerase II-mediated rDNA transcription mediates rDNA copy number expansion in Drosophila.
    George J Watase, Yukiko M Yamashita.
      Ribosomal DNA (rDNA), which encodes ribosomal RNA, is an essential but unstable genomic element due to its tandemly repeated nature. rDNA's repetitive nature causes spontaneous intrachromatid recombination, leading to copy number (CN) reduction, which must be counteracted by a mechanism that recovers CN to sustain cells' viability. Akin to telomere maintenance, rDNA maintenance is particularly important in cell types that proliferate for an extended time period, most notably in the germline that passes the genome through generations. In Drosophila, the process of rDNA CN recovery, known as 'rDNA magnification', has been studied extensively. rDNA magnification is mediated by unequal sister chromatid exchange (USCE), which generates a sister chromatid that gains the rDNA CN by stealing copies from its sister. However, much remains elusive regarding how germ cells sense rDNA CN to decide when to initiate magnification, and how germ cells balance between the need to generate DNA double-strand breaks (DSBs) to trigger USCE vs. avoiding harmful DSBs. Recently, we identified an rDNA-binding Zinc-finger protein Indra as a factor required for rDNA magnification, however, the underlying mechanism of action remains unknown. Here we show that Indra is a negative regulator of rDNA magnification, balancing the need of rDNA magnification and repression of dangerous DSBs. Mechanistically, we show that Indra is a repressor of RNA polymerase II (Pol II)-dependent transcription of rDNA: Under low rDNA CN conditions, Indra protein amount is downregulated, leading to Pol II-mediated transcription of rDNA. This results in the expression of rDNA-specific retrotransposon, R2, which we have shown to facilitate rDNA magnification via generation of DBSs at rDNA. We propose that differential use of Pol I and Pol II plays a critical role in regulating rDNA CN expansion only when it is necessary.
    DOI:  https://doi.org/10.1371/journal.pgen.1011136
  8. Nat Commun. 2024 May 15. 15(1): 4128
    Post-translational modification-dependent oligomerization switch in regulation of global transcription and DNA damage repair during genotoxic stress.
    Prathama Talukdar, Sujay Pal, Debabrata Biswas.
      Mechanisms of functional cross-talk between global transcriptional repression and efficient DNA damage repair during genotoxic stress are poorly known. In this study, using human AF9 as representative of Super Elongation Complex (SEC) components, we delineate detailed mechanisms of these processes. Mechanistically, we describe that Poly-Serine domain-mediated oligomerization is pre-requisite for AF9 YEATS domain-mediated TFIID interaction-dependent SEC recruitment at the promoter-proximal region for release of paused RNA polymerase II. Interestingly, during genotoxic stress, CaMKII-mediated phosphorylation-dependent nuclear export of AF9-specific deacetylase HDAC5 enhances concomitant PCAF-mediated acetylation of K339 residue. This causes monomerization of AF9 and reduces TFIID interaction for transcriptional downregulation. Furthermore, the K339 acetylation-dependent enhanced AF9-DNA-PKc interaction leads to phosphorylation at S395 residue which reduces AF9-SEC interaction resulting in transcriptional downregulation and efficient repair of DNA damage. After repair, nuclear re-entry of HDAC5 reduces AF9 acetylation and restores its TFIID and SEC interaction to restart transcription.
    DOI:  https://doi.org/10.1038/s41467-024-48530-8
  9. Nat Genet. 2024 May;56(5): 737
    Polyploid sugarcane genome architecture.
    Wei Li.
      
    DOI:  https://doi.org/10.1038/s41588-024-01774-y
  10. Nat Commun. 2024 May 17. 15(1): 4200
    The matrisome landscape controlling in vivo germ cell fates.
    Aqilah Amran, Lara Pigatto, Johanna Farley, Rasoul Godini, Roger Pocock, Sandeep Gopal.
      The developmental fate of cells is regulated by intrinsic factors and the extracellular environment. The extracellular matrix (matrisome) delivers chemical and mechanical cues that can modify cellular development. However, comprehensive understanding of how matrisome factors control cells in vivo is lacking. Here we show that specific matrisome factors act individually and collectively to control germ cell development. Surveying development of undifferentiated germline stem cells through to mature oocytes in the Caenorhabditis elegans germ line enabled holistic functional analysis of 443 conserved matrisome-coding genes. Using high-content imaging, 3D reconstruction, and cell behavior analysis, we identify 321 matrisome genes that impact germ cell development, the majority of which (>80%) are undescribed. Our analysis identifies key matrisome networks acting autonomously and non-autonomously to coordinate germ cell behavior. Further, our results demonstrate that germ cell development requires continual remodeling of the matrisome landscape. Together, this study provides a comprehensive platform for deciphering how extracellular signaling controls cellular development and anticipate this will establish new opportunities for manipulating cell fates.
    DOI:  https://doi.org/10.1038/s41467-024-48283-4
  11. Nat Genet. 2024 May 14.
    GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells.
    Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T Doty, Adam D Munday, Daniel Gao, Li Xin, Janis L Abkowitz, Zhijun Duan, Jian Ma.
      The organization of mammalian genomes features a complex, multiscale three-dimensional (3D) architecture, whose functional significance remains elusive because of limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we introduce genome architecture and gene expression by sequencing (GAGE-seq), a scalable, robust single-cell co-assay measuring 3D genome structure and transcriptome simultaneously within the same cell. Applied to mouse brain cortex and human bone marrow CD34+ cells, GAGE-seq characterized the intricate relationships between 3D genome and gene expression, showing that multiscale 3D genome features inform cell-type-specific gene expression and link regulatory elements to target genes. Integration with spatial transcriptomic data revealed in situ 3D genome variations in mouse cortex. Observations in human hematopoiesis unveiled discordant changes between 3D genome organization and gene expression, underscoring a complex, temporal interplay at the single-cell level. GAGE-seq provides a powerful, cost-effective approach for exploring genome structure and gene expression relationships at the single-cell level across diverse biological contexts.
    DOI:  https://doi.org/10.1038/s41588-024-01745-3
  12. Protein Cell. 2024 May 17. pii: pwae031. [Epub ahead of print]
    SMAD2/3-SMYD2 and developmental transcription factors cooperate with cell cycle inhibitors to guide tissue formation.
    Stefania Militi, Reshma Nibhani, Martin Pook, Siim Pauklin.
      Tissue formation and organ homeostasis is achieved by precise coordination of proliferation and differentiation of stem cells and progenitors. While deregulation of these processes can result in degenerative disease or cancer, their molecular interplays remain unclear. Here we show that the switch of human pluripotent stem cell (hPSC) self-renewal to differentiation is associated with the induction of distinct cyclin dependent kinase inhibitors (CDKIs). In hPSCs, Activin/Nodal/TGFβ signalling maintains CDKIs in a poised state via SMAD2/3-NANOG-OCT4-EZH2-SNON transcriptional complex. Upon gradual differentiation, CDKIs are induced by successive transcriptional complexes between SMAD2/3-SMYD2 and developmental regulators such as EOMES, thereby lengthening the G1 phase. This, in turn, induces SMAD2/3 transcriptional activity by blocking its linker phosphorylation. Such SMAD2/3-CDKI positive feedback loops drive the exit from pluripotency and stepwise cell fate specification that could be harnessed for producing cells for therapeutic applications. Our study uncovers fundamental mechanisms how cell fate specification is interconnected to cell cycle dynamics and provides insight to autonomous circuitries governing tissue self-formation.
    Keywords:  EZH2; SMYD2; TGFβ/ACTIVIN-SMAD2/3; cell cycle; differentiation; epigenetics; human pluripotent stem cells
    DOI:  https://doi.org/10.1093/procel/pwae031
  13. Nat Aging. 2024 May 15.
    The killifish germline regulates longevity and somatic repair in a sex-specific manner.
    Eitan Moses, Tehila Atlan, Xue Sun, Roman Franěk, Atif Siddiqui, Georgi K Marinov, Sagiv Shifman, David M Zucker, Adi Oron-Gottesman, William J Greenleaf, Ehud Cohen, Oren Ram, Itamar Harel.
      Classical evolutionary theories propose tradeoffs among reproduction, damage repair and lifespan. However, the specific role of the germline in shaping vertebrate aging remains largely unknown. In this study, we used the turquoise killifish (Nothobranchius furzeri) to genetically arrest germline development at discrete stages and examine how different modes of infertility impact life history. We first constructed a comprehensive single-cell gonadal atlas, providing cell-type-specific markers for downstream phenotypic analysis. We show here that germline depletion-but not arresting germline differentiation-enhances damage repair in female killifish. Conversely, germline-depleted males instead showed an extension in lifespan and rejuvenated metabolic functions. Through further transcriptomic analysis, we highlight enrichment of pro-longevity pathways and genes in germline-depleted male killifish and demonstrate functional conservation of how these factors may regulate longevity in germline-depleted Caenorhabditis elegans. Our results, therefore, demonstrate that different germline manipulation paradigms can yield pronounced sexually dimorphic phenotypes, implying alternative responses to classical evolutionary tradeoffs.
    DOI:  https://doi.org/10.1038/s43587-024-00632-0
  14. Nat Genet. 2024 May;56(5): 889-899
    Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes.
    Minsoo Kim, Alexander N Gorelick, Ignacio Vàzquez-García, Marc J Williams, Sohrab Salehi, Hongyu Shi, Adam C Weiner, Nick Ceglia, Tyler Funnell, Tricia Park, Sonia Boscenco, Ciara H O'Flanagan, Hui Jiang, Diljot Grewal, Cerise Tang, Nicole Rusk, Payam A Gammage, Andrew McPherson, Sam Aparicio, Sohrab P Shah, Ed Reznik.
      The extent of cell-to-cell variation in tumor mitochondrial DNA (mtDNA) copy number and genotype, and the phenotypic and evolutionary consequences of such variation, are poorly characterized. Here we use amplification-free single-cell whole-genome sequencing (Direct Library Prep (DLP+)) to simultaneously assay mtDNA copy number and nuclear DNA (nuDNA) in 72,275 single cells derived from immortalized cell lines, patient-derived xenografts and primary human tumors. Cells typically contained thousands of mtDNA copies, but variation in mtDNA copy number was extensive and strongly associated with cell size. Pervasive whole-genome doubling events in nuDNA associated with stoichiometrically balanced adaptations in mtDNA copy number, implying that mtDNA-to-nuDNA ratio, rather than mtDNA copy number itself, mediated downstream phenotypes. Finally, multimodal analysis of DLP+ and single-cell RNA sequencing identified both somatic loss-of-function and germline noncoding variants in mtDNA linked to heteroplasmy-dependent changes in mtDNA copy number and mitochondrial transcription, revealing phenotypic adaptations to disrupted nuclear/mitochondrial balance.
    DOI:  https://doi.org/10.1038/s41588-024-01724-8
  15. Nat Cardiovasc Res. 2024 Mar;3(3): 389-402
    The PD-1-PD-L1 pathway maintains an immunosuppressive environment essential for neonatal heart regeneration.
    Stephanie Vargas Aguilar, Miao Cui, Wei Tan, Efrain Sanchez-Ortiz, Rhonda Bassel-Duby, Ning Liu, Eric N Olson.
      The adult mouse heart responds to injury by scarring with consequent loss of contractile function, whereas the neonatal heart possesses the ability to regenerate. Activation of the immune system is among the first events upon tissue injury. It has been shown that immune response kinetics differ between regeneration and pathological remodeling, yet the underlying mechanisms of the distinct immune reactions during tissue healing remain unclear. Here we show that the immunomodulatory PD-1-PD-L1 pathway is highly active in regenerative neonatal hearts but rapidly silenced later in life. Deletion of the PD-1 receptor or inactivation of its ligand PD-L1 prevented regeneration of neonatal hearts after injury. Disruption of the pathway during neonatal cardiac injury led to increased inflammation and aberrant T cell activation, which ultimately impaired cardiac regeneration. Our findings reveal an immunomodulatory and cardioprotective role for the PD-1-PD-L1 pathway in heart regeneration and offer potential avenues for the control of adult tissue regeneration.
    DOI:  https://doi.org/10.1038/s44161-024-00447-7
  16. Cell. 2024 May 08. pii: S0092-8674(24)00407-0. [Epub ahead of print]
    Automated profiling of gene function during embryonic development.
    Rebecca A Green, Renat N Khaliullin, Zhiling Zhao, Stacy D Ochoa, Jeffrey M Hendel, Tiffany-Lynn Chow, HongKee Moon, Ronald J Biggs, Arshad Desai, Karen Oegema.
      Systematic functional profiling of the gene set that directs embryonic development is an important challenge. To tackle this challenge, we used 4D imaging of C. elegans embryogenesis to capture the effects of 500 gene knockdowns and developed an automated approach to compare developmental phenotypes. The automated approach quantifies features-including germ layer cell numbers, tissue position, and tissue shape-to generate temporal curves whose parameterization yields numerical phenotypic signatures. In conjunction with a new similarity metric that operates across phenotypic space, these signatures enabled the generation of ranked lists of genes predicted to have similar functions, accessible in the PhenoBank web portal, for ∼25% of essential development genes. The approach identified new gene and pathway relationships in cell fate specification and morphogenesis and highlighted the utilization of specialized energy generation pathways during embryogenesis. Collectively, the effort establishes the foundation for comprehensive analysis of the gene set that builds a multicellular organism.
    Keywords:  FACT complex; Integrator complex; automated analysis; cell fate specification; computer vision; de novo serine synthesis; embryonic development; energy generation; phenotypic profiling; tissue morphogenesis
    DOI:  https://doi.org/10.1016/j.cell.2024.04.012
  17. Nat Cell Biol. 2024 May 13.
    Polyglutamine-mediated ribotoxicity disrupts proteostasis and stress responses in Huntington's disease.
    Ranen Aviner, Ting-Ting Lee, Vincent B Masto, Kathy H Li, Raul Andino, Judith Frydman.
      Huntington's disease (HD) is a neurodegenerative disorder caused by expansion of a CAG trinucleotide repeat in the Huntingtin (HTT) gene, encoding a homopolymeric polyglutamine (polyQ) tract. Although mutant HTT (mHTT) protein is known to aggregate, the links between aggregation and neurotoxicity remain unclear. Here we show that both translation and aggregation of wild-type HTT and mHTT are regulated by a stress-responsive upstream open reading frame and that polyQ expansions cause abortive translation termination and release of truncated, aggregation-prone mHTT fragments. Notably, we find that mHTT depletes translation elongation factor eIF5A in brains of symptomatic HD mice and cultured HD cells, leading to pervasive ribosome pausing and collisions. Loss of eIF5A disrupts homeostatic controls and impairs recovery from acute stress. Importantly, drugs that inhibit translation initiation reduce premature termination and mitigate this escalating cascade of ribotoxic stress and dysfunction in HD.
    DOI:  https://doi.org/10.1038/s41556-024-01414-x
  18. Nat Cell Biol. 2024 May;26(5): 674-686
    Mitochondrial heterogeneity and adaptations to cellular needs.
    Melia Granath-Panelo, Shingo Kajimura.
      Although it is well described that mitochondria are at the epicentre of the energy demands of a cell, it is becoming important to consider how each cell tailors its mitochondrial composition and functions to suit its particular needs beyond ATP production. Here we provide insight into mitochondrial heterogeneity throughout development as well as in tissues with specific energy demands and discuss how mitochondrial malleability contributes to cell fate determination and tissue remodelling.
    DOI:  https://doi.org/10.1038/s41556-024-01410-1
  19. Proc Natl Acad Sci U S A. 2024 May 21. 121(21): e2405827121
    Chromatin regulates alternative polyadenylation via the RNA polymerase II elongation rate.
    Joseph V Geisberg, Zarmik Moqtaderi, Kevin Struhl.
      The RNA polymerase II (Pol II) elongation rate influences poly(A) site selection, with slow and fast Pol II derivatives causing upstream and downstream shifts, respectively, in poly(A) site utilization. In yeast, depletion of either of the histone chaperones FACT or Spt6 causes an upstream shift of poly(A) site use that strongly resembles the poly(A) profiles of slow Pol II mutant strains. Like slow Pol II mutant strains, FACT- and Spt6-depleted cells exhibit Pol II processivity defects, indicating that both Spt6 and FACT stimulate the Pol II elongation rate. Poly(A) profiles of some genes show atypical downstream shifts; this subset of genes overlaps well for FACT- or Spt6-depleted strains but is different from the atypical genes in Pol II speed mutant strains. In contrast, depletion of histone H3 or H4 causes a downstream shift of poly(A) sites for most genes, indicating that nucleosomes inhibit the Pol II elongation rate in vivo. Thus, chromatin-based control of the Pol II elongation rate is a potential mechanism, distinct from direct effects on the cleavage/polyadenylation machinery, to regulate alternative polyadenylation in response to genetic or environmental changes.
    Keywords:  RNA polymerase II; alternative polyadenylation; chromatin; histone chaperones; transcription elongation
    DOI:  https://doi.org/10.1073/pnas.2405827121
  20. J Cell Biol. 2024 Jun 03. pii: e202403191. [Epub ahead of print]223(6):
    A step-by-step guide to fragmenting bundled actin filaments.
    Rachel S Kadzik, David R Kovar.
      There has long been conflicting evidence as to how bundled actin filaments, found in cellular structures such as filopodia, are disassembled. In this issue, Chikireddy et al. (https://doi.org/10.1083/jcb.202312106) provide a detailed in vitro analysis of the steps involved in fragmentation of fascin-bundled actin filaments and propose a novel mechanism for severing two-filament bundles.
    DOI:  https://doi.org/10.1083/jcb.202403191
  21. Elife. 2024 May 15. pii: RP92732. [Epub ahead of print]12
    FMNL2 regulates actin for endoplasmic reticulum and mitochondria distribution in oocyte meiosis.
    Meng-Hao Pan, Kun-Huan Zhang, Si-Le Wu, Zhen-Nan Pan, Ming-Hong Sun, Xiao-Han Li, Jia-Qian Ju, Shi-Ming Luo, Xiang-Hong Ou, Shao-Chen Sun.
      During mammalian oocyte meiosis, spindle migration and asymmetric cytokinesis are unique steps for the successful polar body extrusion. The asymmetry defects of oocytes will lead to the failure of fertilization and embryo implantation. In present study, we reported that an actin nucleating factor Formin-like 2 (FMNL2) played critical roles in the regulation of spindle migration and organelle distribution in mouse and porcine oocytes. Our results showed that FMNL2 mainly localized at the oocyte cortex and periphery of spindle. Depletion of FMNL2 led to the failure of polar body extrusion and large polar bodies in oocytes. Live-cell imaging revealed that the spindle failed to migrate to the oocyte cortex, which caused polar body formation defects, and this might be due to the decreased polymerization of cytoplasmic actin by FMNL2 depletion in the oocytes of both mice and pigs. Furthermore, mass spectrometry analysis indicated that FMNL2 was associated with mitochondria and endoplasmic reticulum (ER)-related proteins, and FMNL2 depletion disrupted the function and distribution of mitochondria and ER, showing with decreased mitochondrial membrane potential and the occurrence of ER stress. Microinjecting Fmnl2-EGFP mRNA into FMNL2-depleted oocytes significantly rescued these defects. Thus, our results indicate that FMNL2 is essential for the actin assembly, which further involves into meiotic spindle migration and ER/mitochondria functions in mammalian oocytes.
    Keywords:  actin; developmental biology; endoplasmic reticulum; formin; meiosis; mitochondria; mouse; oocyte; pig
    DOI:  https://doi.org/10.7554/eLife.92732
  22. bioRxiv. 2024 Apr 29. pii: 2024.04.26.591383. [Epub ahead of print]
    Reduced Levels of Lagging Strand Polymerases Shape Stem Cell Chromatin.
    Jonathan Snedeker, Brendon E M Davis, Rajesh Ranjan, Matthew Wooten, Joshua Blundon, Xin Chen.
      Stem cells display asymmetric histone inheritance while non-stem progenitor cells exhibit symmetric patterns in the Drosophila male germline lineage. Here, we report that components involved in lagging strand synthesis, such as DNA polymerase α and δ (Polα and Polδ), have significantly reduced levels in stem cells compared to progenitor cells. Compromising Polα genetically induces the replication-coupled histone incorporation pattern in progenitor cells to be indistinguishable from that in stem cells, which can be recapitulated using a Polα inhibitor in a concentration-dependent manner. Furthermore, stem cell-derived chromatin fibers display a higher degree of old histone recycling by the leading strand compared to progenitor cell-derived chromatin fibers. However, upon reducing Polα levels in progenitor cells, the chromatin fibers now display asymmetric old histone recycling just like GSC-derived fibers. The old versus new histone asymmetry is comparable between stem cells and progenitor cells at both S-phase and M-phase. Together, these results indicate that developmentally programmed expression of key DNA replication components is important to shape stem cell chromatin. Furthermore, manipulating one crucial DNA replication component can induce replication-coupled histone dynamics in non-stem cells in a manner similar to that in stem cells.One Sentence Summary: Delayed lagging strand synthesis regulates asymmetric histone incorporation.
    DOI:  https://doi.org/10.1101/2024.04.26.591383
  23. Cell Stem Cell. 2024 May 10. pii: S1934-5909(24)00144-9. [Epub ahead of print]
    Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics.
    Suzan Stelloo, Maria Teresa Alejo-Vinogradova, Charlotte A G H van Gelder, Dick W Zijlmans, Marek J van Oostrom, Juan Manuel Valverde, Lieke A Lamers, Teja Rus, Paula Sobrevals Alcaraz, Tilman Schäfers, Cristina Furlan, Pascal W T C Jansen, Marijke P A Baltissen, Katharina F Sonnen, Boudewijn Burgering, Maarten A F M Altelaar, Harmjan R Vos, Michiel Vermeulen.
      Gastrulation is a critical stage in embryonic development during which the germ layers are established. Advances in sequencing technologies led to the identification of gene regulatory programs that control the emergence of the germ layers and their derivatives. However, proteome-based studies of early mammalian development are scarce. To overcome this, we utilized gastruloids and a multilayered mass spectrometry-based proteomics approach to investigate the global dynamics of (phospho) protein expression during gastruloid differentiation. Our findings revealed many proteins with temporal expression and unique expression profiles for each germ layer, which we also validated using single-cell proteomics technology. Additionally, we profiled enhancer interaction landscapes using P300 proximity labeling, which revealed numerous gastruloid-specific transcription factors and chromatin remodelers. Subsequent degron-based perturbations combined with single-cell RNA sequencing (scRNA-seq) identified a critical role for ZEB2 in mouse and human somitogenesis. Overall, this study provides a rich resource for developmental and synthetic biology communities endeavoring to understand mammalian embryogenesis.
    Keywords:  ZEB2; dTAG system; developmental biology; enhancers; gastruloids; germ layers; interaction proteomics; proteomics; somitoids; transcription factors
    DOI:  https://doi.org/10.1016/j.stem.2024.04.017
  24. Nature. 2024 May 13.
    Human embryos embrace asymmetry to form the body.
    Sara Reardon.
      
    Keywords:  Cell biology; Developmental biology; Medical research
    DOI:  https://doi.org/10.1038/d41586-024-01403-y
  25. Aging Cell. 2024 May 17. e14204
    Identification of Prominin-2 as a new player of cardiomyocyte senescence in the aging heart.
    D Maggiorani, Y Santin, K Formoso, E Drapé, H Martini, S Brun, G Cousin, O Lairez, F Lezoualc'h, A Parini, V Douin-Echinard, J Mialet-Perez.
      The aging heart is characterized by a number of structural changes leading to ventricular stiffness, impaired resistance to stress and increased risk of developing heart failure (HF). Genetic or pharmacological removal of senescent cells has recently demonstrated the possibility to relieve some cardiac aging features such as hypertrophy and fibrosis. However, the contribution of the different cell types in cardiac aging remains fragmentary due to a lack of cell-specific markers. Cardiomyocytes undergo post-mitotic senescence in response to telomere damage, characterized by persistent DNA damage response and expression of the classical senescence markers p21 and p16, which are shared by many other cell types. In the present study, we used transcriptomic approaches to discover new markers specific for cardiomyocyte senescence. We identified Prominin2 (Prom2), encoding a transmembrane glycoprotein, as the most upregulated gene in cardiomyocytes of aged mice compared to young mice. We showed that Prom2 was upregulated by a p53-dependent pathway in stress-induced premature senescence. Prom2 expression correlated with cardiomyocyte hypertrophy in the hearts of aged mice and was increased in atrial samples of patients with HF with preserved ejection fraction. Consistently, Prom2 overexpression was sufficient to drive senescence, hypertrophy and resistance to cytotoxic stress while Prom2 shRNA silencing inhibited these features in doxorubicin-treated cardiac cells. In conclusion, we identified Prom2 as a new player of cardiac aging, linking cardiomyocyte hypertrophy to senescence. These results could provide a better understanding and targeting of cell-type specific senescence in age-associated cardiac diseases.
    Keywords:  aging; cardiomyocyte; heart; senescence
    DOI:  https://doi.org/10.1111/acel.14204
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