bims-ginsta Biomed News
on Genome instability
Issue of 2023–10–22
25 papers selected by
Jinrong Hu, National University of Singapore
  1. MRCK ensures cortex-chromatin "social distancing" to enable egg spindle rotation.
  2. Modelling how plant cell-cycle progression leads to cell size regulation.
  3. A DEAD-box helicase drives the partitioning of a pro-differentiation NAB protein into nuclear foci.
  4. FGFR2 is essential for salivary gland duct homeostasis and MAPK-dependent seromucous acinar cell differentiation.
  5. Nrg1 Regulates Cardiomyocyte Migration and Cell Cycle in Ventricular Development.
  6. Abl2 repairs microtubules and phase separates with tubulin to promote microtubule nucleation.
  7. Single-cell transcriptomics illuminates regulatory steps driving anterior-posterior patterning of Drosophila embryonic mesoderm.
  8. Mitochondria-lysosome-related organelles mediate mitochondrial clearance during cellular dedifferentiation.
  9. The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5.
  10. Epigenetic regulation limits competence of pluripotent stem cell-derived oocytes.
  11. Regulation of the dynamic RNA Pol II elongation rate in Drosophila embryos.
  12. Luteinizing hormone stimulates ingression of mural granulosa cells within the mouse preovulatory follicle.
  13. Structure of a human replisome shows the organisation and interactions of a DNA replication machine.
  14. CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors.
  15. TERRA R-loops connect and protect sister telomeres in mitosis.
  16. The cellular states and fates of shed intestinal cells.
  17. A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells.
  18. Adaptive preservation of orphan ribosomal proteins in chaperone-dispersed condensates.
  19. Localized T3 production modifies the transcriptome and promotes the hepatocyte-like lineage in iPSC-derived hepatic organoids.
  20. ZNF692 organizes a hub specialized in 40S ribosomal subunit maturation enhancing translation in rapidly proliferating cells.
  21. Combined inactivation of RB and Hippo converts differentiating Drosophila photoreceptors into eye progenitor cells through derepression of homothorax.
  22. A guide to studying mitochondria transfer.
  23. Evidence for lung barrier regeneration by differentiation prior to binucleated and stem cell division.
  24. Profilin1 is required to prevent mitotic catastrophe in murine and human glomerular diseases.
  25. Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.
  1. J Cell Biol. 2023 Nov 06. pii: e202310009. [Epub ahead of print]222(11):
    MRCK ensures cortex-chromatin "social distancing" to enable egg spindle rotation.
    Takaya Totsuka, Takashi Akera, Michael F Olson.
      During the second meiotic cell division, egg cells discard one set of chromatids to the polar body to produce a large haploid gamete. Meiotic spindle rotation is a critical step to ensure proper polar body extrusion. In this issue, Bourdais et al. (2023. J. Cell Biol.https://doi.org/10.1083/jcb.202211029) have identified MRCKβ as an essential kinase for efficient spindle rotation. MRCK activates cortical myosin II rings overlying the spindle to prevent the notoriously sticky interaction between the cell cortex and chromatin to facilitate spindle rotation. Furthermore, Bourdais et al. found that the same MRCK-myosin II pathway also operates in zygotes to promote parental genome unification.
    DOI:  https://doi.org/10.1083/jcb.202310009
  2. PLoS Comput Biol. 2023 Oct 20. 19(10): e1011503
    Modelling how plant cell-cycle progression leads to cell size regulation.
    Daniel Williamson, William Tasker-Brown, James A H Murray, Angharad R Jones, Leah R Band.
      Populations of cells typically maintain a consistent size, despite cell division rarely being precisely symmetrical. Therefore, cells must possess a mechanism of "size control", whereby the cell volume at birth affects cell-cycle progression. While size control mechanisms have been elucidated in a number of other organisms, it is not yet clear how this mechanism functions in plants. Here, we present a mathematical model of the key interactions in the plant cell cycle. Model simulations reveal that the network of interactions exhibits limit-cycle solutions, with biological switches underpinning both the G1/S and G2/M cell-cycle transitions. Embedding this network model within growing cells, we test hypotheses as to how cell-cycle progression can depend on cell size. We investigate two different mechanisms at both the G1/S and G2/M transitions: (i) differential expression of cell-cycle activator and inhibitor proteins (with synthesis of inhibitor proteins being independent of cell size), and (ii) equal inheritance of inhibitor proteins after cell division. The model demonstrates that both these mechanisms can lead to larger daughter cells progressing through the cell cycle more rapidly, and can thus contribute to cell-size control. To test how these features enable size homeostasis over multiple generations, we then simulated these mechanisms in a cell-population model with multiple rounds of cell division. These simulations suggested that integration of size-control mechanisms at both G1/S and G2/M provides long-term cell-size homeostasis. We concluded that while both size independence and equal inheritance of inhibitor proteins can reduce variations in cell size across individual cell-cycle phases, combining size-control mechanisms at both G1/S and G2/M is essential to maintain size homeostasis over multiple generations. Thus, our study reveals how features of the cell-cycle network enable cell-cycle progression to depend on cell size, and provides a mechanistic understanding of how plant cell populations maintain consistent size over generations.
    DOI:  https://doi.org/10.1371/journal.pcbi.1011503
  3. Nat Commun. 2023 Oct 18. 14(1): 6593
    A DEAD-box helicase drives the partitioning of a pro-differentiation NAB protein into nuclear foci.
    Akiko Doi, Gianmarco D Suarez, Rita Droste, H Robert Horvitz.
      How cells regulate gene expression in a precise spatiotemporal manner during organismal development is a fundamental question in biology. Although the role of transcriptional condensates in gene regulation has been established, little is known about the function and regulation of these molecular assemblies in the context of animal development and physiology. Here we show that the evolutionarily conserved DEAD-box helicase DDX-23 controls cell fate in Caenorhabditis elegans by binding to and facilitating the condensation of MAB-10, the C. elegans homolog of mammalian NGFI-A-binding (NAB) protein. MAB-10 is a transcriptional cofactor that functions with the early growth response (EGR) protein LIN-29 to regulate the transcription of genes required for exiting the cell cycle, terminal differentiation, and the larval-to-adult transition. We suggest that DEAD-box helicase proteins function more generally during animal development to control the condensation of NAB proteins important in cell identity and that this mechanism is evolutionarily conserved. In mammals, such a mechanism might underlie terminal cell differentiation and when dysregulated might promote cancerous growth.
    DOI:  https://doi.org/10.1038/s41467-023-42345-9
  4. Nat Commun. 2023 Oct 14. 14(1): 6485
    FGFR2 is essential for salivary gland duct homeostasis and MAPK-dependent seromucous acinar cell differentiation.
    Marit H Aure, Jennifer M Symonds, Carlos U Villapudua, Joshua T Dodge, Sabine Werner, Wendy M Knosp, Matthew P Hoffman.
      Exocrine acinar cells in salivary glands (SG) are critical for oral health and loss of functional acinar cells is a major clinical challenge. Fibroblast growth factor receptors (FGFR) are essential for early development of multiple organs, including SG. However, the role of FGFR signaling in specific populations later in development and during acinar differentiation are unknown. Here, we use scRNAseq and conditional deletion of murine FGFRs in vivo to identify essential roles for FGFRs in craniofacial, early SG development and progenitor function during duct homeostasis. Importantly, we also discover that FGFR2 via MAPK signaling is critical for seromucous acinar differentiation and secretory gene expression, while FGFR1 is dispensable. We show that FGF7, expressed by myoepithelial cells (MEC), activates the FGFR2-dependent seromucous transcriptional program. Here, we propose a model where MEC-derived FGF7 drives seromucous acinar differentiation, providing a rationale for targeting FGFR2 signaling in regenerative therapies to restore acinar function.
    DOI:  https://doi.org/10.1038/s41467-023-42243-0
  5. Circ Res. 2023 Oct 17.
    Nrg1 Regulates Cardiomyocyte Migration and Cell Cycle in Ventricular Development.
    Joaquim Grego-Bessa, Paula Gómez-Apiñaniz, Belén Prados, Manuel José Gómez, Donal MacGrogan, José Luis de la Pompa.
       BACKGROUND: Cardiac ventricles provide the contractile force of the beating heart throughout life. How the primitive endocardium-layered myocardial projections called trabeculae form and mature into the adult ventricles is of great interest for biology and regenerative medicine. Trabeculation is dependent on the signaling protein Nrg1 (neuregulin-1). However, the mechanism of action of Nrg1 and its role in ventricular wall maturation are poorly understood.
    METHODS: We investigated the functions and downstream mechanisms of Nrg1 signaling during ventricular chamber development using confocal imaging, transcriptomics, and biochemical approaches in mice with cardiac-specific inactivation or overexpression of Nrg1.
    RESULTS: Analysis of cardiac-specific Nrg1 mutant mice showed that the transcriptional program underlying cardiomyocyte-oriented cell division and trabeculae formation depends on endocardial Nrg1 to myocardial ErbB2 (erb-b2 receptor tyrosine kinase 2) signaling and phospho-Erk (extracellular signal-regulated kinase; pErk) activation. Early endothelial loss of Nrg1 and reduced pErk activation diminished cardiomyocyte Pard3 and Crumbs2 protein and altered cytoskeletal gene expression and organization. These alterations are associated with abnormal gene expression related to mitotic spindle organization and a shift in cardiomyocyte division orientation. Nrg1 is crucial for trabecular growth and ventricular wall thickening by regulating an epithelial-to-mesenchymal transition-like process in cardiomyocytes involving migration, adhesion, cytoskeletal actin turnover, and timely progression through the cell cycle G2/M phase. Ectopic cardiac Nrg1 overexpression and high pErk signaling caused S-phase arrest, sustained high epithelial-to-mesenchymal transition-like gene expression, and prolonged trabeculation, blocking compact myocardium maturation. Myocardial trabecular patterning alterations resulting from above- or below-normal Nrg1-dependent pErk activation were concomitant with sarcomere actin cytoskeleton disorganization. The Nrg1 loss- and gain-of-function transcriptomes were enriched for Yap1 (yes-associated protein-1) gene signatures, identifying Yap1 as a potential downstream effector. Furthermore, biochemical and imaging data reveal that Nrg1 influences pErk activation and Yap1 nuclear-cytoplasmic distribution during trabeculation.
    CONCLUSIONS: These data establish the Nrg1-ErbB2/ErbB4 (erb-b2 receptor tyrosine kinase 4)-pErk axis as a crucial regulator of cardiomyocyte cell cycle progression and migration during ventricular development.
    Keywords:  actin cytoskeleton; actins; cell cycle; myocardium; sarcomeres
    DOI:  https://doi.org/10.1161/CIRCRESAHA.123.323321
  6. Curr Biol. 2023 Oct 18. pii: S0960-9822(23)01234-4. [Epub ahead of print]
    Abl2 repairs microtubules and phase separates with tubulin to promote microtubule nucleation.
    Daisy Duan, Wanqing Lyu, Pengxin Chai, Shaojie Ma, Kuanlin Wu, Chunxiang Wu, Yong Xiong, Nenad Sestan, Kai Zhang, Anthony J Koleske.
      Abl family kinases are evolutionarily conserved regulators of cell migration and morphogenesis. Genetic experiments in Drosophila suggest that Abl family kinases interact functionally with microtubules to regulate axon guidance and neuronal morphogenesis. Vertebrate Abl2 binds to microtubules and promotes their plus-end elongation, both in vitro and in cells, but the molecular mechanisms by which Abl2 regulates microtubule (MT) dynamics are unclear. We report here that Abl2 regulates MT assembly via condensation and direct interactions with both the MT lattice and tubulin dimers. We find that Abl2 promotes MT nucleation, which is further facilitated by the ability of the Abl2 C-terminal half to undergo liquid-liquid phase separation (LLPS) and form co-condensates with tubulin. Abl2 binds to regions adjacent to MT damage, facilitates MT repair via fresh tubulin recruitment, and increases MT rescue frequency and lifetime. Cryo-EM analyses strongly support a model in which Abl2 engages tubulin C-terminal tails along an extended MT lattice conformation at damage sites to facilitate repair via fresh tubulin recruitment. Abl2Δ688-790, which closely mimics a naturally occurring splice isoform, retains binding to the MT lattice but does not bind tubulin, promote MT nucleation, or increase rescue frequency. In COS-7 cells, MT reassembly after nocodazole treatment is greatly slowed in Abl2 knockout COS-7 cells compared with wild-type cells, and these defects are rescued by re-expression of Abl2, but not Abl2Δ688-790. We propose that Abl2 locally concentrates tubulin to promote MT nucleation and recruits it to defects in the MT lattice to enable repair and rescue.
    Keywords:  abl; lattice repair; microtubule dynamics; nucleation; phase separation; tubulin
    DOI:  https://doi.org/10.1016/j.cub.2023.09.018
  7. Cell Rep. 2023 Oct 17. pii: S2211-1247(23)01301-3. [Epub ahead of print]42(10): 113289
    Single-cell transcriptomics illuminates regulatory steps driving anterior-posterior patterning of Drosophila embryonic mesoderm.
    Jingjing Sun, Chen Zhang, Fan Gao, Angelike Stathopoulos.
      Single-cell technologies promise to uncover how transcriptional programs orchestrate complex processes during embryogenesis. Here, we apply a combination of single-cell technology and genetic analysis to investigate the dynamic transcriptional changes associated with Drosophila embryo morphogenesis at gastrulation. Our dataset encompassing the blastoderm-to-gastrula transition provides a comprehensive single-cell map of gene expression across cell lineages validated by genetic analysis. Subclustering and trajectory analyses revealed a surprising stepwise progression in patterning to transition zygotic gene expression and specify germ layers as well as uncovered an early role for ecdysone signaling in epithelial-to-mesenchymal transition in the mesoderm. We also show multipotent progenitors arise prior to gastrulation by analyzing the transcription trajectory of caudal mesoderm cells, including a derivative that ultimately incorporates into visceral muscles of the midgut and hindgut. This study provides a rich resource of gastrulation and elucidates spatially regulated temporal transitions of transcription states during the process.
    Keywords:  CP: Cell biology; CP: Developmental biology
    DOI:  https://doi.org/10.1016/j.celrep.2023.113289
  8. Cell Rep. 2023 Oct 19. pii: S2211-1247(23)01303-7. [Epub ahead of print]42(10): 113291
    Mitochondria-lysosome-related organelles mediate mitochondrial clearance during cellular dedifferentiation.
    Xiaowen Ma, Sharon Manley, Hui Qian, Yuan Li, Chen Zhang, Kevin Li, Benjamin Ding, Fengli Guo, Allen Chen, Xing Zhang, Meilian Liu, Meihua Hao, Benjamin Kugler, E Matthew Morris, John Thyfault, Ling Yang, Hiromi Sesaki, Hong-Min Ni, Heidi McBride, Wen-Xing Ding.
      Dysfunctional mitochondria are removed via multiple pathways, such as mitophagy, a selective autophagy process. Here, we identify an intracellular hybrid mitochondria-lysosome organelle (termed the mitochondria-lysosome-related organelle [MLRO]), which regulates mitochondrial homeostasis independent of canonical mitophagy during hepatocyte dedifferentiation. The MLRO is an electron-dense organelle that has either a single or double membrane with both mitochondria and lysosome markers. Mechanistically, the MLRO is likely formed from the fusion of mitochondria-derived vesicles (MDVs) with lysosomes through a PARKIN-, ATG5-, and DRP1-independent process, which is negatively regulated by transcription factor EB (TFEB) and associated with mitochondrial protein degradation and hepatocyte dedifferentiation. The MLRO, which is galectin-3 positive, is reminiscent of damaged lysosome and could be cleared by overexpression of TFEB, resulting in attenuation of hepatocyte dedifferentiation. Together, results from this study suggest that the MLRO may act as an alternative mechanism for mitochondrial quality control independent of canonical autophagy/mitophagy involved in cell dedifferentiation.
    Keywords:  ATG5; CP: Cell biology; DRP1; autophagy; hepatocytes; lysosome; mitophagy
    DOI:  https://doi.org/10.1016/j.celrep.2023.113291
  9. Stem Cell Reports. 2023 Oct 11. pii: S2213-6711(23)00373-9. [Epub ahead of print]
    The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5.
    Bonnie E J Maven, Casey A Gifford, Melanie Weilert, Barbara Gonzalez-Teran, Ruth Hüttenhain, Angelo Pelonero, Kathryn N Ivey, Kaitlen Samse-Knapp, Wesley Kwong, David Gordon, Michael McGregor, Tomohiro Nishino, Eyuche Okorie, Sage Rossman, Mauro W Costa, Nevan J Krogan, Julia Zeitlinger, Deepak Srivastava.
      Congenital heart disease often arises from perturbations of transcription factors (TFs) that guide cardiac development. ISLET1 (ISL1) is a TF that influences early cardiac cell fate, as well as differentiation of other cell types including motor neuron progenitors (MNPs) and pancreatic islet cells. While lineage specificity of ISL1 function is likely achieved through combinatorial interactions, its essential cardiac interacting partners are unknown. By assaying ISL1 genomic occupancy in human induced pluripotent stem cell-derived cardiac progenitors (CPs) or MNPs and leveraging the deep learning approach BPNet, we identified motifs of other TFs that predicted ISL1 occupancy in each lineage, with NKX2.5 and GATA motifs being most closely associated to ISL1 in CPs. Experimentally, nearly two-thirds of ISL1-bound loci were co-occupied by NKX2.5 and/or GATA4. Removal of NKX2.5 from CPs led to widespread ISL1 redistribution, and overexpression of NKX2.5 in MNPs led to ISL1 occupancy of CP-specific loci. These results reveal how ISL1 guides lineage choices through a combinatorial code that dictates genomic occupancy and transcription.
    Keywords:  ISL1; NKX2.5; cardiac development; cardiac progenitor; cell specification; combinatorial code; transcription factor motifs; transcription factors; transcriptional regulation
    DOI:  https://doi.org/10.1016/j.stemcr.2023.09.014
  10. EMBO J. 2023 Oct 18. e113955
    Epigenetic regulation limits competence of pluripotent stem cell-derived oocytes.
    Eishi Aizawa, Evgeniy A Ozonov, Yumiko K Kawamura, Charles-Etienne Dumeau, So Nagaoka, Tomoya S Kitajima, Mitinori Saitou, Antoine Hfm Peters, Anton Wutz.
      Recent studies have reported the differentiation of pluripotent cells into oocytes in vitro. However, the developmental competence of in vitro-generated oocytes remains low. Here, we perform a comprehensive comparison of mouse germ cell development in vitro over all culture steps versus in vivo with the goal to understand mechanisms underlying poor oocyte quality. We show that the in vitro differentiation of primordial germ cells to growing oocytes and subsequent follicle growth is critical for competence for preimplantation development. Systematic transcriptome analysis of single oocytes that were subjected to different culture steps identifies genes that are normally upregulated during oocyte growth to be susceptible for misregulation during in vitro oogenesis. Many misregulated genes are Polycomb targets. Deregulation of Polycomb repression is therefore a key cause and the earliest defect known in in vitro oocyte differentiation. Conversely, structurally normal in vitro-derived oocytes fail at zygotic genome activation and show abnormal acquisition of 5-hydroxymethylcytosine on maternal chromosomes. Our data identify epigenetic regulation at an early stage of oogenesis limiting developmental competence and suggest opportunities for future improvements.
    Keywords:  epigenetics; germline; in vitro culture; oocyte; pluripotent stem cell
    DOI:  https://doi.org/10.15252/embj.2023113955
  11. Cell Rep. 2023 Oct 12. pii: S2211-1247(23)01237-8. [Epub ahead of print]42(10): 113225
    Regulation of the dynamic RNA Pol II elongation rate in Drosophila embryos.
    Samuel H Keller, Hao Deng, Bomyi Lim.
      An increasing number of studies have shown the key role that RNA polymerase II (RNA Pol II) elongation plays in gene regulation. We systematically examine how various enhancers, promoters, and gene body composition influence the RNA Pol II elongation rate through a single-cell-resolution live imaging assay. By using reporter constructs containing 5' MS2 and 3' PP7 repeating stem loops, we quantify the rate of RNA Pol II elongation in live Drosophila embryos. We find that promoters and exonic gene lengths have no effect on elongation rate, while enhancers and the presence of long introns may significantly change how quickly RNA Pol II moves across a gene. Furthermore, we observe in multiple constructs that the RNA Pol II elongation rate accelerates after the transcriptional onset of nuclear cycle 14 in Drosophila embryos. Our study provides a single-cell view of various mechanisms that affect the dynamic RNA Pol II elongation rate, ultimately affecting the rate of mRNA production.
    Keywords:  CP: Molecular biology; Drosophila; MS2; PP7; elongation rate; enhancers; live imaging; transcription
    DOI:  https://doi.org/10.1016/j.celrep.2023.113225
  12. Biol Reprod. 2023 Oct 17. pii: ioad142. [Epub ahead of print]
    Luteinizing hormone stimulates ingression of mural granulosa cells within the mouse preovulatory follicle.
    Corie M Owen, Laurinda A Jaffe.
      Luteinizing hormone (LH) induces ovulation by acting on its receptors in the mural granulosa cells that surround a mammalian oocyte in an ovarian follicle. However, much remains unknown about how activation of the LH receptor modifies the structure of the follicle such that the oocyte is released and the follicle remnants are transformed into the corpus luteum. The present study shows that the preovulatory surge of LH stimulates LH receptor-expressing granulosa cells, initially located almost entirely in the outer layers of the mural granulosa, to rapidly extend inwards, intercalating between other cells. The cellular ingression begins within 30 minutes of the peak of the LH surge, and the proportion of LH receptor-expressing cell bodies in the inner half of the mural granulosa layer increases until the time of ovulation, which occurs at about 10 hours after the LH peak. During this time, many of the initially flask-shaped cells appear to detach from the basal lamina, acquiring a rounder shape with multiple filipodia. Starting at about 4 hours after the LH peak, the mural granulosa layer at the apical surface of the follicle where ovulation will occur begins to thin, and the basolateral surface develops invaginations and constrictions. Our findings raise the question of whether LH stimulation of granulosa cell ingression may contribute to these changes in the follicular structure that enable ovulation.
    Keywords:  Ovarian follicle; granulosa cell; ingression; luteinizing hormone receptor; migration; ovulation
    DOI:  https://doi.org/10.1093/biolre/ioad142
  13. EMBO J. 2023 Oct 16. e115685
    Structure of a human replisome shows the organisation and interactions of a DNA replication machine.
    Morgan L Jones, Yasemin Baris, Martin Rg Taylor, Joseph Tp Yeeles.
      
    DOI:  https://doi.org/10.15252/embj.2023115685
  14. Cell Rep. 2023 Oct 17. pii: S2211-1247(23)01271-8. [Epub ahead of print]42(10): 113259
    CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors.
    Yuting Liu, Xin Wan, Hu Li, Yingxi Chen, Xiaodi Hu, Hebing Chen, Dahai Zhu, Cheng Li, Yong Zhang.
      CCCTC-binding factor (CTCF), a ubiquitously expressed architectural protein, has emerged as a key regulator of cell identity gene transcription. However, the precise molecular mechanism underlying specialized functions of CTCF remains elusive. Here, we investigate the mechanism through integrative analyses of primary hepatocytes, myocytes, and B cells from mouse and human. We demonstrate that CTCF cooperates with lineage-specific pioneer transcription factors (TFs), including MyoD, FOXA, and PU.1, to control cell identity at 1D and 3D levels. At the 1D level, pioneer TFs facilitate lineage-specific CTCF occupancy via opening chromatin. At the 3D level, CTCF and pioneer TFs form regulatory hubs to govern the expression of cell identity genes. This mechanism is validated using MyoD-null mice, CTCF knockout mice, and CRISPR editing during myogenic differentiation. Collectively, these findings uncover a general mechanism whereby CTCF acts as a cell identity cofactor to control cell identity genes via orchestrating regulatory hubs with pioneer TFs.
    Keywords:  3D genome; CP: Molecular biology; CP: Stem cell research; CRISPR editing; CTCF; MyoD; cell identity; pioneer transcription factor; regulatory hub
    DOI:  https://doi.org/10.1016/j.celrep.2023.113259
  15. Cell Rep. 2023 Oct 14. pii: S2211-1247(23)01247-0. [Epub ahead of print]42(10): 113235
    TERRA R-loops connect and protect sister telomeres in mitosis.
    Samantha Sze, Amit Bhardwaj, Priyanka Fnu, Kameron Azarm, Rachel Mund, Katherine Ring, Susan Smith.
      Resolution of cohesion between sister telomeres in human cells depends on TRF1-mediated recruitment of the polyADP-ribosyltransferase tankyrase to telomeres. In human aged cells, due to insufficient recruitment of TRF1/tankyrase to shortened telomeres, sisters remain cohered in mitosis. This persistent cohesion plays a protective role, but the mechanism by which sisters remain cohered is not well understood. Here we show that telomere repeat-containing RNA (TERRA) holds sister telomeres together through RNA-DNA hybrid (R-loop) structures. We show that a tankyrase-interacting partner, the RNA-binding protein C19orf43, is required for repression of TERRA R-loops. Persistent telomere cohesion in C19orf43-depleted cells is counteracted by RNaseH1, confirming that RNA-DNA hybrids hold sisters together. Consistent with a protective role for persistent telomere cohesion, depletion of C19orf43 in aged cells reduces DNA damage and delays replicative senescence. We propose that the inherent inability of shortened telomeres to recruit R-loop-repressing machinery permits a controlled onset of senescence.
    Keywords:  C19orf43; CP: Molecular biology; R-Loops; RNA-DNA hybrids; RNaseH; TERRA; TRF1; cohesion; senescence; tankyrase; telomeres
    DOI:  https://doi.org/10.1016/j.celrep.2023.113235
  16. Nat Metab. 2023 Oct 19.
    The cellular states and fates of shed intestinal cells.
    Keren Bahar Halpern, Yael Korem Kohanim, Adi Biram, Yotam Harnik, Adi Egozi, Oran Yakubovsky, Ziv Shulman, Shalev Itzkovitz.
      The intestinal epithelium is replaced every few days1. Enterocytes are shed into the gut lumen predominantly from the tips of villi2,3 and have been believed to rapidly die upon their dissociation from the tissue4,5. However, technical limitations prohibited studying the cellular states and fates of shed intestinal cells. Here we show that shed epithelial cells remain viable and upregulate distinct anti-microbial programmes upon shedding, using bulk and single-cell RNA sequencing of male mouse intestinal faecal washes. We further identify abundant shedding of immune cells, which is elevated in mice with dextran sulfate sodium-induced colitis. We find that faecal host transcriptomics reflect changes in the intestinal tissue following perturbations. Our study suggests potential functions of shed cells in the intestinal lumen and demonstrates that host cell transcriptomes in intestinal washes can be used to probe tissue states.
    DOI:  https://doi.org/10.1038/s42255-023-00905-9
  17. Cell. 2023 Oct 12. pii: S0092-8674(23)01040-1. [Epub ahead of print]
    A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells.
    Li Li, Sarah Bowling, Sean E McGeary, Qi Yu, Bianca Lemke, Karel Alcedo, Yuemeng Jia, Xugeng Liu, Mark Ferreira, Allon M Klein, Shou-Wen Wang, Fernando D Camargo.
      Cellular lineage histories and their molecular states encode fundamental principles of tissue development and homeostasis. Current lineage-recording mouse models have insufficient barcode diversity and single-cell lineage coverage for profiling tissues composed of millions of cells. Here, we developed DARLIN, an inducible Cas9 barcoding mouse line that utilizes terminal deoxynucleotidyl transferase (TdT) and 30 CRISPR target sites. DARLIN is inducible, generates massive lineage barcodes across tissues, and enables the detection of edited barcodes in ∼70% of profiled single cells. Using DARLIN, we examined fate bias within developing hematopoietic stem cells (HSCs) and revealed unique features of HSC migration. Additionally, we established a protocol for joint transcriptomic and epigenomic single-cell measurements with DARLIN and found that cellular clonal memory is associated with genome-wide DNA methylation rather than gene expression or chromatin accessibility. DARLIN will enable the high-resolution study of lineage relationships and their molecular signatures in diverse tissues and physiological contexts.
    Keywords:  DNA methylation; hematopoiesis; lineage tracing; multiomics; single cell
    DOI:  https://doi.org/10.1016/j.cell.2023.09.019
  18. Nat Cell Biol. 2023 Oct 16.
    Adaptive preservation of orphan ribosomal proteins in chaperone-dispersed condensates.
    Asif Ali, Rania Garde, Olivia C Schaffer, Jared A M Bard, Kabir Husain, Samantha Keyport Kik, Kathleen A Davis, Sofia Luengo-Woods, Maya G Igarashi, D Allan Drummond, Allison H Squires, David Pincus.
      Ribosome biogenesis is among the most resource-intensive cellular processes, with ribosomal proteins accounting for up to half of all newly synthesized proteins in eukaryotic cells. During stress, cells shut down ribosome biogenesis in part by halting rRNA synthesis, potentially leading to massive accumulation of aggregation-prone 'orphan' ribosomal proteins (oRPs). Here we show that, during heat shock in yeast and human cells, oRPs accumulate as reversible peri-nucleolar condensates recognized by the Hsp70 co-chaperone Sis1/DnaJB6. oRP condensates are liquid-like in cell-free lysate but solidify upon depletion of Sis1 or inhibition of Hsp70. When cells recover from heat shock, oRP condensates disperse in a Sis1- and Hsp70-dependent manner, and the oRP constituents are incorporated into functional ribosomes in the cytosol, enabling cells to efficiently resume growth. Preserving biomolecules in reversible condensates-like mRNAs in cytosolic stress granules and oRPs at the nucleolar periphery-may be a primary function of the Hsp70 chaperone system.
    DOI:  https://doi.org/10.1038/s41556-023-01253-2
  19. JCI Insight. 2023 Oct 19. pii: e173780. [Epub ahead of print]
    Localized T3 production modifies the transcriptome and promotes the hepatocyte-like lineage in iPSC-derived hepatic organoids.
    Jorge Hidalgo-Álvarez, Federico Salas-Lucia, Diana Vera Cruz, Tatiana L Fonseca, Antonio C Bianco.
      Thyroid hormone (TH) levels are low during development, and the deiodinases control TH signaling through tissue-specific activation or inactivation of TH. Here we studied human iPSC-derived hepatic organoids and identified a robust induction in DIO2 expression (the deiodinase that activates T4 to T3) that occurs in hepatoblasts. The surge in D2-T3 per-sists until the hepatoblasts differentiate into hepatocytes- or cholangiocytes-like cells, nei-ther of which express DIO2. Preventing the induction of the D2-T3 signaling modified the expression of key transcription factors, decreased the number of hepatocyte-like cells by 60%, and increased the number of cholangiocyte-like cells by 55% without affecting the growth or the size of the mature liver organoid. Physiological levels of T3 could not ful-ly restore the transition from hepatoblasts to mature cells. This indicates that the timed surge in D2-T3 signaling critically determines the fate of developing human hepatoblasts and the transcriptome of the maturing hepatocytes, with physiological and clinical implica-tions for how the liver handles energy substrates.
    Keywords:  Embryonic development; Endocrinology; Metabolism; Thyroid disease; iPS cells
    DOI:  https://doi.org/10.1172/jci.insight.173780
  20. Cell Rep. 2023 Oct 16. pii: S2211-1247(23)01292-5. [Epub ahead of print]42(10): 113280
    ZNF692 organizes a hub specialized in 40S ribosomal subunit maturation enhancing translation in rapidly proliferating cells.
    M Carmen Lafita-Navarro, Yi-Heng Hao, Chunhui Jiang, Seoyeon Jang, Tsung-Cheng Chang, Isabella N Brown, Niranjan Venkateswaran, Elizabeth Maurais, Weronika Stachera, Yanfeng Zhang, Dorothy Mundy, Jungsoo Han, Vanna M Tran, Marcel Mettlen, Lin Xu, Jeffrey B Woodruff, Nick V Grishin, Lisa Kinch, Joshua T Mendell, Michael Buszczak, Maralice Conacci-Sorrell.
      Increased nucleolar size and activity correlate with aberrant ribosome biogenesis and enhanced translation in cancer cells. One of the first and rate-limiting steps in translation is the interaction of the 40S small ribosome subunit with mRNAs. Here, we report the identification of the zinc finger protein 692 (ZNF692), a MYC-induced nucleolar scaffold that coordinates the final steps in the biogenesis of the small ribosome subunit. ZNF692 forms a hub containing the exosome complex and ribosome biogenesis factors specialized in the final steps of 18S rRNA processing and 40S ribosome maturation in the granular component of the nucleolus. Highly proliferative cells are more reliant on ZNF692 than normal cells; thus, we conclude that effective production of small ribosome subunits is critical for translation efficiency in cancer cells.
    Keywords:  40S; CP: Molecular biology; EXOSC7; EXOSC8; KRR1; MYC; ZNF692; exosome; nucleolus; rRNA; ribosome biogenesis
    DOI:  https://doi.org/10.1016/j.celrep.2023.113280
  21. Dev Cell. 2023 Oct 11. pii: S1534-5807(23)00490-2. [Epub ahead of print]
    Combined inactivation of RB and Hippo converts differentiating Drosophila photoreceptors into eye progenitor cells through derepression of homothorax.
    Alexandra E Rader, Battuya Bayarmagnai, Maxim V Frolov.
      The retinoblastoma (RB) and Hippo pathways interact to regulate cell proliferation and differentiation. However, the mechanism of interaction is not fully understood. Drosophila photoreceptors with inactivated RB and Hippo pathways specify normally but fail to maintain their neuronal identity and dedifferentiate. We performed single-cell RNA sequencing to elucidate the cause of dedifferentiation and to determine the fate of these cells. We find that dedifferentiated cells adopt a progenitor-like fate due to inappropriate activation of the retinal differentiation suppressor homothorax (hth) by Yki/Sd. This results in the activation of a distinct Yki/Hth transcriptional program, driving photoreceptor dedifferentiation. We show that Rbf physically interacts with Yki and, together with the GAGA factor, inhibits the hth expression. Thus, RB and Hippo pathways cooperate to maintain photoreceptor differentiation by preventing inappropriate expression of hth in differentiating photoreceptors. Our work highlights the importance of both RB and Hippo pathway activities for maintaining the state of terminal differentiation.
    Keywords:  Drosophila; Hippo pathway; RB pathway; eye development; single-cell RNA sequencing
    DOI:  https://doi.org/10.1016/j.devcel.2023.09.003
  22. Nat Cell Biol. 2023 Oct 18.
    A guide to studying mitochondria transfer.
    Snigdha Tiash, Jonathan Robert Brestoff, Clair Crewe.
      
    DOI:  https://doi.org/10.1038/s41556-023-01246-1
  23. J Cell Biol. 2023 Dec 04. pii: e202212088. [Epub ahead of print]222(12):
    Evidence for lung barrier regeneration by differentiation prior to binucleated and stem cell division.
    Joshua Guild, Nicholas H Juul, Andres Andalon, Hiroki Taenaka, Robert J Coffey, Michael A Matthay, Tushar J Desai.
      With each breath, oxygen diffuses across remarkably thin alveolar type I (AT1) cells into underlying capillaries. Interspersed cuboidal AT2 cells produce surfactant and act as stem cells. Even transient disruption of this delicate barrier can promote capillary leak. Here, we selectively ablated AT1 cells, which uncovered rapid AT2 cell flattening with near-continuous barrier preservation, culminating in AT1 differentiation. Proliferation subsequently restored depleted AT2 cells in two phases, mitosis of binucleated AT2 cells followed by replication of mononucleated AT2 cells. M phase entry of binucleated and S phase entry of mononucleated cells were both triggered by AT1-produced hbEGF signaling via EGFR to Wnt-active AT2 cells. Repeated AT1 cell killing elicited exuberant AT2 proliferation, generating aberrant daughter cells that ceased surfactant function yet failed to achieve AT1 differentiation. This hyperplasia eventually resolved, yielding normal-appearing alveoli. Overall, this specialized regenerative program confers a delicate simple epithelium with functional resiliency on par with the physical durability of thicker, pseudostratified, or stratified epithelia.
    DOI:  https://doi.org/10.1083/jcb.202212088
  24. J Clin Invest. 2023 Oct 17. pii: e171237. [Epub ahead of print]
    Profilin1 is required to prevent mitotic catastrophe in murine and human glomerular diseases.
    Xuefei Tian, Christopher E Pedigo, Ke Li, Xiaotao Ma, Patricia Bunda, John Pell, Angela Lek, Jianlei Gu, Yan Zhang, Paulina X Medina Rangel, Wei Li, Eike Schwartze, Soichiro Nagata, Gabriel Lerner, Sudhir Perincheri, Anupama Priyadarshini, Hongyu Zhao, Monkol Lek, Madhav C Menon, Rongguo Fu, Shuta Ishibe.
      The progression of proteinuric kidney diseases is associated with podocyte loss but the mechanisms underlying this process remain unclear. Podocytes re-enter the cell cycle to repair double-stranded DNA (dsDNA) breaks. However, the unsuccessful repair can result in podocytes crossing the G1/S checkpoint and undergoing abortive cytokinesis. In this study, we identified Pfn1 as indispensable in maintaining glomerular integrity - its tissue-specific loss in mouse podocytes results in severe proteinuria and kidney failure. Our results suggest that this phenotype is due to podocyte mitotic catastrophe (MC), characterized histologically and ultrastructurally by abundant multinucleated cells, irregular nuclei, and mitotic spindles. Podocyte cell cycle re-entry was identified using FUCCI2aR mice and observed altered expression of cell-cycle associated proteins such as p21, p53, Cyclin B1, and Cyclin D1. Podocyte-specific translating ribosome affinity purification (TRAP) and RNAseq revealed the downregulation of Ribosomal RNA-processing protein 8 (Rrp8). Over-expression of Rrp8 in Pfn1 KO podocytes partially rescued the phenotype in vitro. Clinical and ultrastructural tomographic analysis of patients with diverse proteinuric kidney diseases further validated the presence of MC podocytes and reduction in podocyte PFN1 expression within kidney tissues. These results suggest that profilin1 is essential in regulating the podocyte cell cycle and its disruption leads to MC and subsequent podocyte loss.
    Keywords:  Cell Biology; Cell cycle; Nephrology
    DOI:  https://doi.org/10.1172/JCI171237
  25. Nat Commun. 2023 Oct 16. 14(1): 6519
    Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.
    Riccardo Calandrelli, Xingzhao Wen, John Lalith Charles Richard, Zhifei Luo, Tri C Nguyen, Chien-Ju Chen, Zhijie Qi, Shuanghong Xue, Weizhong Chen, Zhangming Yan, Weixin Wu, Kathia Zaleta-Rivera, Rong Hu, Miao Yu, Yuchuan Wang, Wenbo Li, Jian Ma, Bing Ren, Sheng Zhong.
      The interphase genome is dynamically organized in the nucleus and decorated with chromatin-associated RNA (caRNA). It remains unclear whether the genome architecture modulates the spatial distribution of caRNA and vice versa. Here, we generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human cells. These maps reveal the chromosomal domains demarcated by locally transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the spreading of caRNA is constrained by the boundaries of topologically associating domains (TADs), demonstrating the role of the 3D genome structure in modulating the spatial distribution of RNA. Conversely, stopping transcription or acute depletion of RNA induces thousands of chromatin loops genome-wide. Activation or suppression of the transcription of specific genes suppresses or creates chromatin loops straddling these genes. Deletion of a specific caRNA-producing genomic sequence promotes chromatin loops that straddle the interchromosomal target sequences of this caRNA. These data suggest a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization.
    DOI:  https://doi.org/10.1038/s41467-023-42274-7
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