bims-ginsta 2024-05-26 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2024–05–26
34 papers selected by
Jinrong Hu, National University of Singapore

E-cadherin tunes tissue mechanical behavior before and during morphogenetic tissue flows.
Genome-wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression.
Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization.
Tead4 and Tfap2c generate bipotency and a bistable switch in totipotent embryos to promote robust lineage diversification.
SnapShot: Cell size control.
Dynamic RNA polymerase II occupancy drives differentiation of the intestine under the direction of HNF4.
Histone H1.0 couples cellular mechanical behaviors to chromatin structure.
Patterning and folding of intestinal villi by active mesenchymal dewetting.
Small spaces, big problems: The abnormal nucleoplasm of micronuclei and its consequences.
Circadian regulation of macromolecular complex turnover and proteome renewal.
Cell Competition Eliminates Aneuploid Human Pluripotent Stem Cells.
The Neurog2-Tbr2 axis forms a continuous transition to the neurogenic gene expression state in neural stem cells.
Clonal gametes enable polyploid genome design.
An evolutionarily conserved mechanism controls reversible amyloids of pyruvate kinase via pH-sensing regions.
Conserved physical mechanisms of cell and tissue elongation.
Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues.
TET activity safeguards pluripotency throughout embryonic dormancy.
Adding intrinsically disordered proteins to biological ageing clocks.
Ligand binding initiates single-molecule integrin conformational activation.
Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition.
SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice.
Active nuclear positioning and actomyosin contractility maintain leader cell integrity during gonadogenesis.
Acquisition of epithelial plasticity in human chronic liver disease.
Coordination of actin plus-end dynamics by IQGAP1, formin, and capping protein.
Endothelial deletion of p53 generates transitional endothelial cells and improves lung development during neonatal hyperoxia.
Multiple intersecting pathways are involved in CPEB1 phosphorylation and regulation of translation during mouse oocyte meiosis.
The Rac pathway prevents cell fragmentation in a nonprotrusively migrating leader cell during C. elegans gonad organogenesis.
Iron accumulation in ovarian microenvironment damages the local redox balance and oocyte quality in aging mice.
Adhesive anti-fibrotic interfaces on diverse organs.
Mechanobiology: Shaping the future of cellular form and function.
A communication hub for phosphoregulation of kinetochore-microtubule attachment.
β1 integrins regulate cellular behavior and cardiomyocyte organization during ventricular wall formation.
In vitro reconstitution of epigenetic reprogramming in the human germ line.
Integrative analysis of transcriptome, DNA methylome and chromatin accessibility reveals candidate therapeutic targets in hypertrophic cardiomyopathy.

bioRxiv. 2024 May 08. pii: 2024.05.07.592778. [Epub ahead of print]

E-cadherin tunes tissue mechanical behavior before and during morphogenetic tissue flows.

Xun Wang, Christian M Cupo, Sassan Ostvar, Andrew D Countryman, Karen E Kasza.

Adhesion between epithelial cells enables the remarkable mechanical behavior of epithelial tissues during morphogenesis. However, it remains unclear how cell-cell adhesion influences mechanics in static as well as in dynamically flowing epithelial tissues. Here, we systematically modulate E-cadherin-mediated adhesion in the Drosophila embryo and study the effects on the mechanical behavior of the germband epithelium before and during dramatic tissue remodeling and flow associated with body axis elongation. Before axis elongation, we find that increasing E-cadherin levels produces tissue comprising more elongated cells and predicted to be more fluid-like, providing reduced resistance to tissue flow. During axis elongation, we find that the dominant effect of E-cadherin is tuning the speed at which cells proceed through rearrangement events, revealing potential roles for E-cadherin in generating friction between cells. Before and during axis elongation, E-cadherin levels influence patterns of actomyosin-dependent forces, supporting the notion that E-cadherin tunes tissue mechanics in part through effects on actomyosin. Taken together, these findings reveal dual-and sometimes opposing-roles for E-cadherin-mediated adhesion in controlling tissue structure and dynamics in vivo that result in unexpected relationships between adhesion and flow.

DOI: https://doi.org/10.1101/2024.05.07.592778
Genome Biol. 2024 May 21. 25(1): 126

Genome-wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression.

Patricia Rojas, Jianming Wang, Giovanni Guglielmi, Martina Mustè Sadurnì, Lucas Pavlou, Geoffrey Ho Duen Leung, Vijay Rajagopal, Fabian Spill, Marco Saponaro.

   BACKGROUND: DNA replication progression can be affected by the presence of physical barriers like the RNA polymerases, leading to replication stress and DNA damage. Nonetheless, we do not know how transcription influences overall DNA replication progression.
RESULTS: To characterize sites where DNA replication forks stall and pause, we establish a genome-wide approach to identify them. This approach uses multiple timepoints during S-phase to identify replication fork/stalling hotspots as replication progresses through the genome. These sites are typically associated with increased DNA damage, overlapped with fragile sites and with breakpoints of rearrangements identified in cancers but do not overlap with replication origins. Overlaying these sites with a genome-wide analysis of RNA polymerase II transcription, we find that replication fork stalling/pausing sites inside genes are directly related to transcription progression and activity. Indeed, we find that slowing down transcription elongation slows down directly replication progression through genes. This indicates that transcription and replication can coexist over the same regions. Importantly, rearrangements found in cancers overlapping transcription-replication collision sites are detected in non-transformed cells and increase following treatment with ATM and ATR inhibitors. At the same time, we find instances where transcription activity favors replication progression because it reduces histone density.
CONCLUSIONS: Altogether, our findings highlight how transcription and replication overlap during S-phase, with both positive and negative consequences for replication fork progression and genome stability by the coexistence of these two processes.

Keywords:  DNA damage; DNA replication; RNA Pol II transcription; Replication fork pausing/stalling; Replication fork speed; Replication stress; Transcription elongation

DOI:  https://doi.org/10.1186/s13059-024-03278-8
Nat Commun. 2024 May 21. 15(1): 4338

Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization.

Aayush Kant, Zixian Guo, Vinayak Vinayak, Maria Victoria Neguembor, Wing Shun Li, Vasundhara Agrawal, Emily Pujadas, Luay Almassalha, Vadim Backman, Melike Lakadamyali, Maria Pia Cosma, Vivek B Shenoy.

In interphase nuclei, chromatin forms dense domains of characteristic sizes, but the influence of transcription and histone modifications on domain size is not understood. We present a theoretical model exploring this relationship, considering chromatin-chromatin interactions, histone modifications, and chromatin extrusion. We predict that the size of heterochromatic domains is governed by a balance among the diffusive flux of methylated histones sustaining them and the acetylation reactions in the domains and the process of loop extrusion via supercoiling by RNAPII at their periphery, which contributes to size reduction. Super-resolution and nano-imaging of five distinct cell lines confirm the predictions indicating that the absence of transcription leads to larger heterochromatin domains. Furthermore, the model accurately reproduces the findings regarding how transcription-mediated supercoiling loss can mitigate the impacts of excessive cohesin loading. Our findings shed light on the role of transcription in genome organization, offering insights into chromatin dynamics and potential therapeutic targets.

DOI: https://doi.org/10.1038/s41467-024-48698-z
Nat Struct Mol Biol. 2024 May 24.

Tead4 and Tfap2c generate bipotency and a bistable switch in totipotent embryos to promote robust lineage diversification.

Meng Zhu, Maciej Meglicki, Adiyant Lamba, Peizhe Wang, Christophe Royer, Karen Turner, Muhammad Abdullah Jauhar, Celine Jones, Tim Child, Kevin Coward, Jie Na, Magdalena Zernicka-Goetz.

The mouse and human embryo gradually loses totipotency before diversifying into the inner cell mass (ICM, future organism) and trophectoderm (TE, future placenta). The transcription factors TFAP2C and TEAD4 with activated RHOA accelerate embryo polarization. Here we show that these factors also accelerate the loss of totipotency. TFAP2C and TEAD4 paradoxically promote and inhibit Hippo signaling before lineage diversification: they drive expression of multiple Hippo regulators while also promoting apical domain formation, which inactivates Hippo. Each factor activates TE specifiers in bipotent cells, while TFAP2C also activates specifiers of the ICM fate. Asymmetric segregation of the apical domain reconciles the opposing regulation of Hippo signaling into Hippo OFF and the TE fate, or Hippo ON and the ICM fate. We propose that the bistable switch established by TFAP2C and TEAD4 is exploited to trigger robust lineage diversification in the developing embryo.

DOI: https://doi.org/10.1038/s41594-024-01311-9
Cell. 2024 May 23. pii: S0092-8674(24)00456-2. [Epub ahead of print]187(11): 2896-2896.e1

SnapShot: Cell size control.

Bruce Futcher, Douglas R Kellogg.

Cell size exhibits remarkable diversity across and within organisms. Size variation correlates with DNA content and growth rates and is regulated by complex models of cell size control that are yet to be mechanistically defined. To view this SnapShot, open or download the PDF.

DOI: https://doi.org/10.1016/j.cell.2024.04.030
Cell Rep. 2024 May 19. pii: S2211-1247(24)00570-9. [Epub ahead of print]43(6): 114242

Dynamic RNA polymerase II occupancy drives differentiation of the intestine under the direction of HNF4.

Kiranmayi Vemuri, Sneha Kumar, Lei Chen, Michael P Verzi.

  Terminal differentiation requires massive restructuring of the transcriptome. During intestinal differentiation, the expression patterns of nearly 4,000 genes are altered as cells transition from progenitor cells in crypts to differentiated cells in villi. We identify dynamic occupancy of RNA polymerase II (Pol II) to gene promoters as the primary driver of transcriptomic shifts during intestinal differentiation in vivo. Changes in enhancer-promoter looping interactions accompany dynamic Pol II occupancy and are dependent upon HNF4, a pro-differentiation transcription factor. Using genetic loss-of-function, chromatin immunoprecipitation sequencing (ChIP-seq), and immunoprecipitation (IP) mass spectrometry, we demonstrate that HNF4 collaborates with chromatin remodelers and loop-stabilizing proteins and facilitates Pol II occupancy at hundreds of genes pivotal to differentiation. We also explore alternate mechanisms that drive differentiation gene expression and find that pause-release of Pol II and post-transcriptional mRNA stability regulate smaller subsets of differentially expressed genes. These studies provide insights into the mechanisms of differentiation in renewing adult tissue.

Keywords:  CP: Genomics; CP: Molecular biology; HNF4 transcription factors; Pol II ChIP-seq; RNA polymerase II; chromatin looping; crypt-villus axis; dynamic Pol II occupancy; intestinal epithelium; post-transcriptional gene regulation; promoter-proximal pausing; rapid immunoprecipitation mass spectrometry of endogenous proteins

DOI:  https://doi.org/10.1016/j.celrep.2024.114242
Nat Cardiovasc Res. 2024 ;3(4): 441-459

Histone H1.0 couples cellular mechanical behaviors to chromatin structure.

Shuaishuai Hu, Douglas J Chapski, Natalie D Gehred, Todd H Kimball, Tatiana Gromova, Angelina Flores, Amy C Rowat, Junjie Chen, René R Sevag Packard, Emily Olszewski, Jennifer Davis, Christoph D Rau, Timothy A McKinsey, Manuel Rosa-Garrido, Thomas M Vondriska.

  Tuning of genome structure and function is accomplished by chromatin-binding proteins, which determine the transcriptome and phenotype of the cell. Here we investigate how communication between extracellular stress and chromatin structure may regulate cellular mechanical behaviors. We demonstrate that histone H1.0, which compacts nucleosomes into higher-order chromatin fibers, controls genome organization and cellular stress response. We show that histone H1.0 has privileged expression in fibroblasts across tissue types and that its expression is necessary and sufficient to induce myofibroblast activation. Depletion of histone H1.0 prevents cytokine-induced fibroblast contraction, proliferation and migration via inhibition of a transcriptome comprising extracellular matrix, cytoskeletal and contractile genes, through a process that involves locus-specific H3K27 acetylation. Transient depletion of histone H1.0 in vivo prevents fibrosis in cardiac muscle. These findings identify an unexpected role of linker histones to orchestrate cellular mechanical behaviors, directly coupling force generation, nuclear organization and gene transcription.

Keywords:  Cardiovascular diseases; Cell biology; Histone post-translational modifications; Physiology

DOI:  https://doi.org/10.1038/s44161-024-00460-w
Cell. 2024 May 20. pii: S0092-8674(24)00465-3. [Epub ahead of print]

Patterning and folding of intestinal villi by active mesenchymal dewetting.

Tyler R Huycke, Teemu J Häkkinen, Hikaru Miyazaki, Vasudha Srivastava, Emilie Barruet, Christopher S McGinnis, Ali Kalantari, Jake Cornwall-Scoones, Dedeepya Vaka, Qin Zhu, Hyunil Jo, Roger Oria, Valerie M Weaver, William F DeGrado, Matt Thomson, Krishna Garikipati, Dario Boffelli, Ophir D Klein, Zev J Gartner.

  Tissue folds are structural motifs critical to organ function. In the intestine, bending of a flat epithelium into a periodic pattern of folds gives rise to villi, finger-like protrusions that enable nutrient absorption. However, the molecular and mechanical processes driving villus morphogenesis remain unclear. Here, we identify an active mechanical mechanism that simultaneously patterns and folds the intestinal epithelium to initiate villus formation. At the cellular level, we find that PDGFRA+ subepithelial mesenchymal cells generate myosin II-dependent forces sufficient to produce patterned curvature in neighboring tissue interfaces. This symmetry-breaking process requires altered cell and extracellular matrix interactions that are enabled by matrix metalloproteinase-mediated tissue fluidization. Computational models, together with in vitro and in vivo experiments, revealed that these cellular features manifest at the tissue level as differences in interfacial tensions that promote mesenchymal aggregation and interface bending through a process analogous to the active dewetting of a thin liquid film.

Keywords:  Cahn-Hilliard; active fluids; biophysics; cell adhesion; development; extracellular matrix; morphogenesis; patterning; phase separation; self-organization

DOI:  https://doi.org/10.1016/j.cell.2024.04.039
Curr Opin Struct Biol. 2024 May 18. pii: S0959-440X(24)00066-6. [Epub ahead of print]87 102839

Small spaces, big problems: The abnormal nucleoplasm of micronuclei and its consequences.

Molly G Zych, Emily M Hatch.

Micronuclei (MN) form from missegregated chromatin that recruits its own nuclear envelope during mitotic exit and are a common consequence of chromosomal instability. MN are unstable due to errors in nuclear envelope organization and frequently rupture, leading to loss of compartmentalization, loss of nuclear functions, and major changes in genome stability and gene expression. However, recent work found that, even prior to rupture, nuclear processes can be severely defective in MN, which may contribute to rupture-associated defects and have lasting consequences for chromatin structure and function. In this review we discuss work that highlights nuclear function defects in intact MN, including their mechanisms and consequences, and how biases in chromosome missegregation into MN may affect the penetrance of these defects. Illuminating the nuclear environment of MN demonstrates that MN formation alone has major consequences for both the genome and cell and provides new insight into how nuclear content is regulated.

DOI: https://doi.org/10.1016/j.sbi.2024.102839
EMBO J. 2024 May 22.

Circadian regulation of macromolecular complex turnover and proteome renewal.

Estere Seinkmane, Anna Edmondson, Sew Y Peak-Chew, Aiwei Zeng, Nina M Rzechorzek, Nathan R James, James West, Jack Munns, David Cs Wong, Andrew D Beale, John S O'Neill.

  Although costly to maintain, protein homeostasis is indispensable for normal cellular function and long-term health. In mammalian cells and tissues, daily variation in global protein synthesis has been observed, but its utility and consequences for proteome integrity are not fully understood. Using several different pulse-labelling strategies, here we gain direct insight into the relationship between protein synthesis and abundance proteome-wide. We show that protein degradation varies in-phase with protein synthesis, facilitating rhythms in turnover rather than abundance. This results in daily consolidation of proteome renewal whilst minimising changes in composition. Coupled rhythms in synthesis and turnover are especially salient to the assembly of macromolecular protein complexes, particularly the ribosome, the most abundant species of complex in the cell. Daily turnover and proteasomal degradation rhythms render cells and mice more sensitive to proteotoxic stress at specific times of day, potentially contributing to daily rhythms in the efficacy of proteasomal inhibitors against cancer. Our findings suggest that circadian rhythms function to minimise the bioenergetic cost of protein homeostasis through temporal consolidation of protein turnover.

Keywords:  Circadian; Proteostasis; Ribosome; SILAC

DOI:  https://doi.org/10.1038/s44318-024-00121-5
bioRxiv. 2024 May 10. pii: 2024.05.08.593217. [Epub ahead of print]

Cell Competition Eliminates Aneuploid Human Pluripotent Stem Cells.

Amanda Ya, Chenhui Deng, Kristina M Godek.

Human pluripotent stem cells (hPSCs) maintain diploid populations for generations despite a persistently high rate of mitotic errors that cause aneuploidy, or chromosome imbalances. Consequently, to maintain genome stability, aneuploidy must inhibit hPSC proliferation, but the mechanisms are unknown. Here, we surprisingly find that homogeneous aneuploid populations of hPSCs proliferate unlike aneuploid non-transformed somatic cells. Instead, in mosaic populations, cell non-autonomous competition between neighboring diploid and aneuploid hPSCs eliminates less fit aneuploid cells. Aneuploid hPSCs with lower Myc or higher p53 levels relative to diploid neighbors are outcompeted but conversely gain a selective advantage when Myc and p53 relative abundance switches. Thus, although hPSCs frequently missegregate chromosomes and inherently tolerate aneuploidy, Myc- and p53-driven cell competition preserves their genome integrity. These findings have important implications for the use of hPSCs in regenerative medicine and for how diploid human embryos are established despite the prevalence of aneuploidy during early development.

DOI: https://doi.org/10.1101/2024.05.08.593217
Dev Cell. 2024 May 14. pii: S1534-5807(24)00294-6. [Epub ahead of print]

The Neurog2-Tbr2 axis forms a continuous transition to the neurogenic gene expression state in neural stem cells.

Hiromi Shimojo, Taimu Masaki, Ryoichiro Kageyama.

  Neural stem cells (NSCs) differentiate into neuron-fated intermediate progenitor cells (IPCs) via cell division. Although differentiation from NSCs to IPCs is a discrete process, recent transcriptome analyses identified a continuous transcriptional trajectory during this process, raising the question of how to reconcile these contradictory observations. In mouse NSCs, Hes1 expression oscillates, regulating the oscillatory expression of the proneural gene Neurog2, while Hes1 expression disappears in IPCs. Thus, the transition from Hes1 oscillation to suppression is involved in the differentiation of NSCs to IPCs. Here, we found that Neurog2 oscillations induce the accumulation of Tbr2, which suppresses Hes1 expression, generating an IPC-like gene expression state in NSCs. In the absence of Tbr2, Hes1 expression is up-regulated, decreasing the formation of IPCs. These results indicate that the Neurog2-Tbr2 axis forms a continuous transcriptional trajectory to an IPC-like neurogenic state in NSCs, which then differentiate into IPCs via cell division.

Keywords:  Hes1; Neurog2; Notch signaling; Tbr2; intermediate progenitor cell; live imaging; neural stem cell; optogenetics; oscillation

DOI:  https://doi.org/10.1016/j.devcel.2024.04.019
Nat Genet. 2024 May 21.

Clonal gametes enable polyploid genome design.

DOI: https://doi.org/10.1038/s41588-024-01751-5
Dev Cell. 2024 May 21. pii: S1534-5807(24)00271-5. [Epub ahead of print]

An evolutionarily conserved mechanism controls reversible amyloids of pyruvate kinase via pH-sensing regions.

Gea Cereghetti, Vera M Kissling, Lisa M Koch, Alexandra Arm, Claudia C Schmidt, Yannik Thüringer, Nicola Zamboni, Pavel Afanasyev, Miriam Linsenmeier, Cédric Eichmann, Sonja Kroschwald, Jiangtao Zhou, Yiping Cao, Dorota M Pfizenmaier, Thomas Wiegand, Riccardo Cadalbert, Govind Gupta, Daniel Boehringer, Tuomas P J Knowles, Raffaele Mezzenga, Paolo Arosio, Roland Riek, Matthias Peter.

  Amyloids are known as irreversible aggregates associated with neurodegenerative diseases. However, recent evidence shows that a subset of amyloids can form reversibly and fulfill essential cellular functions. Yet, the molecular mechanisms regulating functional amyloids and distinguishing them from pathological aggregates remain unclear. Here, we investigate the conserved principles of amyloid reversibility by studying the essential metabolic enzyme pyruvate kinase (PK) in yeast and human cells. We demonstrate that yeast PK (Cdc19) and human PK (PKM2) form reversible amyloids through a pH-sensitive amyloid core. Stress-induced cytosolic acidification promotes aggregation via protonation of specific glutamate (yeast) or histidine (human) residues within the amyloid core. Mutations mimicking protonation cause constitutive PK aggregation, while non-protonatable PK mutants remain soluble even upon stress. Physiological PK aggregation is coupled to metabolic rewiring and glycolysis arrest, causing severe growth defects when misregulated. Our work thus identifies an evolutionarily conserved, potentially widespread mechanism regulating functional amyloids during stress.

Keywords:  aggregate disassembly; aggregate regulation; amyloid regulation; functional amyloids; isoforms; protein aggregation; pyruvate kinase; reversible amyloids; stress response; stress-induced pH changes

DOI:  https://doi.org/10.1016/j.devcel.2024.04.018
Development. 2024 May 15. pii: dev202687. [Epub ahead of print]151(10):

Conserved physical mechanisms of cell and tissue elongation.

Arthur Boutillon, Samhita P Banavar, Otger Campàs.

  Living organisms have the ability to self-shape into complex structures appropriate for their function. The genetic and molecular mechanisms that enable cells to do this have been extensively studied in several model and non-model organisms. In contrast, the physical mechanisms that shape cells and tissues have only recently started to emerge, in part thanks to new quantitative in vivo measurements of the physical quantities guiding morphogenesis. These data, combined with indirect inferences of physical characteristics, are starting to reveal similarities in the physical mechanisms underlying morphogenesis across different organisms. Here, we review how physics contributes to shape cells and tissues in a simple, yet ubiquitous, morphogenetic transformation: elongation. Drawing from observed similarities across species, we propose the existence of conserved physical mechanisms of morphogenesis.

Keywords:  Conserved mechanisms; Elongation; Growth; Mechanics; Mechanobiology; Morphogenesis

DOI:  https://doi.org/10.1242/dev.202687
bioRxiv. 2024 May 07. pii: 2024.05.06.592773. [Epub ahead of print]

Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues.

Elizabeth A Fogarty, Elli M Buchert, Yiqin Ma, Ava B Nicely, Laura A Buttitta.

The mechanisms that maintain a non-cycling status in postmitotic tissues are not well understood. Many cell cycle genes have promoters and enhancers that remain accessible even when cells are terminally differentiated and in a non-cycling state, suggesting their repression must be maintained long term. In contrast, enhancer decommissioning has been observed for rate-limiting cell cycle genes in the Drosophila wing, a tissue where the cells die soon after eclosion, but it has been unclear if this also occurs in other contexts of terminal differentiation. In this study, we show that enhancer decommissioning also occurs at specific, rate-limiting cell cycle genes in the long-lived tissues of the Drosophila eye and brain, and we propose this loss of chromatin accessibility may help maintain a robust postmitotic state. We examined the decommissioned enhancers at specific rate-limiting cell cycle genes and show that they encode dynamic temporal and spatial expression patterns that include shared, as well as tissue-specific elements, resulting in broad gene expression with developmentally controlled temporal regulation. We extend our analysis to cell cycle gene expression and chromatin accessibility in the mammalian retina using a published dataset, and find that the principles of cell cycle gene regulation identified in terminally differentiating Drosophila tissues are conserved in the differentiating mammalian retina. We propose a robust, non-cycling status is maintained in long-lived postmitotic tissues through a combination of stable repression at most cell cycle gens, alongside enhancer decommissioning at specific rate-limiting cell cycle genes.
Highlights: In long-lived postmitotic Drosophila tissues, most cell cycle genes retain accessible chromatin despite persistent transcriptional downregulation. Cell cycle genes with accessible enhancers remain activatable during terminal differentiation, suggesting their repression must be continuously maintained in the postmitotic state.Long-lived postmitotic tissues decommission enhancers at specific, rate-limiting cell cycle genes in a developmentally regulated manner. Genome-wide enhancer identification performed in cell culture misses many developmentally dynamic enhancers in vivo . Decommissioned enhancers at cell cycle genes include shared and tissue-specific elements that in combination, result in broad gene expression with temporal regulation. The principles of cell cycle gene regulation identified in Drosophila are conserved in the mammalian retina.

DOI: https://doi.org/10.1101/2024.05.06.592773
Nat Struct Mol Biol. 2024 May 23.

TET activity safeguards pluripotency throughout embryonic dormancy.

Maximilian Stötzel, Chieh-Yu Cheng, Ibrahim A IIik, Abhishek Sampath Kumar, Persia Akbari Omgba, Vera A van der Weijden, Yufei Zhang, Martin Vingron, Alexander Meissner, Tuğçe Aktaş, Helene Kretzmer, Aydan Bulut-Karslioğlu.

Dormancy is an essential biological process for the propagation of many life forms through generations and stressful conditions. Early embryos of many mammals are preservable for weeks to months within the uterus in a dormant state called diapause, which can be induced in vitro through mTOR inhibition. Cellular strategies that safeguard original cell identity within the silent genomic landscape of dormancy are not known. Here we show that the protection of cis-regulatory elements from silencing is key to maintaining pluripotency in the dormant state. We reveal a TET-transcription factor axis, in which TET-mediated DNA demethylation and recruitment of methylation-sensitive transcription factor TFE3 drive transcriptionally inert chromatin adaptations during dormancy transition. Perturbation of TET activity compromises pluripotency and survival of mouse embryos under dormancy, whereas its enhancement improves survival rates. Our results reveal an essential mechanism for propagating the cellular identity of dormant cells, with implications for regeneration and disease.

DOI: https://doi.org/10.1038/s41594-024-01313-7
Nat Cell Biol. 2024 May 23.

Adding intrinsically disordered proteins to biological ageing clocks.

Dorothee Dormann, Edward Anton Lemke.

Research into how the young and old differ, and which biomarkers reflect the diverse biological processes underlying ageing, is a current and fast-growing field. Biological clocks provide a means to evaluate whether a molecule, cell, tissue or even an entire organism is old or young. Here we summarize established and emerging molecular clocks as timepieces. We emphasize that intrinsically disordered proteins (IDPs) tend to transform into a β-sheet-rich aggregated state and accumulate in non-dividing or slowly dividing cells as they age. We hypothesize that understanding these protein-based molecular ageing mechanisms might provide a conceptual pathway to determining a cell's health age by probing the aggregation state of IDPs, which we term the IDP clock.

DOI: https://doi.org/10.1038/s41556-024-01423-w
Cell. 2024 May 14. pii: S0092-8674(24)00475-6. [Epub ahead of print]

Ligand binding initiates single-molecule integrin conformational activation.

Jing Li, Myung Hyun Jo, Jiabin Yan, Taylor Hall, Joon Lee, Uriel López-Sánchez, Sophia Yan, Taekjip Ha, Timothy A Springer.

  Integrins link the extracellular environment to the actin cytoskeleton in cell migration and adhesiveness. Rapid coordination between events outside and inside the cell is essential. Single-molecule fluorescence dynamics show that ligand binding to the bent-closed integrin conformation, which predominates on cell surfaces, is followed within milliseconds by two concerted changes, leg extension and headpiece opening, to give the high-affinity integrin conformation. The extended-closed integrin conformation is not an intermediate but can be directly accessed from the extended-open conformation and provides a pathway for ligand dissociation. In contrast to ligand, talin, which links the integrin β-subunit cytoplasmic domain to the actin cytoskeleton, modestly stabilizes but does not induce extension or opening. Integrin activation is thus initiated by outside-in signaling and followed by inside-out signaling. Our results further imply that talin binding is insufficient for inside-out integrin activation and that tensile force transmission through the ligand-integrin-talin-actin cytoskeleton complex is required.

Keywords:  FRET; inside-out signaling; integrin activation pathway; integrin conformational changes; integrin conformational dynamics; ligand; outside-in signaling; single molecule; talin

DOI:  https://doi.org/10.1016/j.cell.2024.04.049
Dev Cell. 2024 May 17. pii: S1534-5807(24)00297-1. [Epub ahead of print]

Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition.

Teresa Krammer, Hannah T Stuart, Elena Gromberg, Keisuke Ishihara, Dillon Cislo, Manuela Melchionda, Fernando Becerril Perez, Jingkui Wang, Elena Costantini, Stefanie Lehr, Laura Arbanas, Alexandra Hörmann, Ralph A Neumüller, Nicola Elvassore, Eric Siggia, James Briscoe, Anna Kicheva, Elly M Tanaka.

  During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable "winning" floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering.

Keywords:  developmental biology; floorplate; neural tube; organoids; pattern formation; self-organization; stem cell differentiation; stem cells

DOI:  https://doi.org/10.1016/j.devcel.2024.04.021
Development. 2022 Aug 01. pii: dev200864. [Epub ahead of print]149(15):

SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice.

Saya Ichihara, Koji Nagao, Takehisa Sakaguchi, Chikashi Obuse, Takashi Sado.

  Stable silencing of the inactive X chromosome (Xi) in female mammals is crucial for the development of embryos and their postnatal health. SmcHD1 is essential for stable silencing of the Xi, and its functional deficiency results in derepression of many X-inactivated genes. Although SmcHD1 has been suggested to play an important role in the formation of higher-order chromatin structure of the Xi, the underlying mechanism is largely unknown. Here, we explore the epigenetic state of the Xi in SmcHD1-deficient epiblast stem cells and mouse embryonic fibroblasts in comparison with their wild-type counterparts. The results suggest that SmcHD1 underlies the formation of H3K9me3-enriched blocks on the Xi, which, although the importance of H3K9me3 has been largely overlooked in mice, play a crucial role in the establishment of the stably silenced state. We propose that the H3K9me3 blocks formed on the Xi facilitate robust heterochromatin formation in combination with H3K27me3, and that the substantial loss of H3K9me3 caused by SmcHD1 deficiency leads to aberrant distribution of H3K27me3 on the Xi and derepression of X-inactivated genes.

Keywords:  Heterochromatin; Histone modifications; X chromosome inactivation

DOI:  https://doi.org/10.1242/dev.200864
Curr Biol. 2024 May 17. pii: S0960-9822(24)00389-0. [Epub ahead of print]

Active nuclear positioning and actomyosin contractility maintain leader cell integrity during gonadogenesis.

Priti Agarwal, Simon Berger, Tom Shemesh, Ronen Zaidel-Bar.

  Proper distribution of organelles can play an important role in a moving cell's performance. During C. elegans gonad morphogenesis, the nucleus of the leading distal tip cell (DTC) is always found at the front, yet the significance of this localization is unknown. Here, we identified the molecular mechanism that keeps the nucleus at the front, despite a frictional force that pushes it backward. The Klarsicht/ANC-1/Syne homology (KASH) domain protein UNC-83 links the nucleus to the motor protein kinesin-1 that moves along a polarized acentrosomal microtubule network. Interestingly, disrupting nuclear positioning on its own did not affect gonad morphogenesis. However, reducing actomyosin contractility on top of nuclear mispositioning led to a dramatic phenotype: DTC splitting and gonad bifurcation. Long-term live imaging of the double knockdown revealed that, while the gonad attempted to perform a planned U-turn, the DTC was stretched due to the lagging nucleus until it fragmented into a nucleated cell and an enucleated cytoplast, each leading an independent gonadal arm. Remarkably, the enucleated cytoplast had polarity and invaded, but it could only temporarily support germ cell proliferation. Based on a qualitative biophysical model, we conclude that the leader cell employs two complementary mechanical approaches to preserve its integrity and ensure proper organ morphogenesis while navigating through a complex 3D environment: active nuclear positioning by microtubule motors and actomyosin-driven cortical contractility.

Keywords:  C. elegans; LINC complex; cell migration; cytoskeleton; development; gonad; mechanobiology; microtubules; morphogenesis; nucleus

DOI:  https://doi.org/10.1016/j.cub.2024.03.049
Nature. 2024 May 22.

Acquisition of epithelial plasticity in human chronic liver disease.

Christopher Gribben, Vasileios Galanakis, Alexander Calderwood, Eleanor C Williams, Ruben Chazarra-Gil, Miguel Larraz, Carla Frau, Tobias Puengel, Adrien Guillot, Foad J Rouhani, Krishnaa Mahbubani, Edmund Godfrey, Susan E Davies, Emmanouil Athanasiadis, Kourosh Saeb-Parsy, Frank Tacke, Michael Allison, Irina Mohorianu, Ludovic Vallier.

For many adult human organs, tissue regeneration during chronic disease remains a controversial subject. Regenerative processes are easily observed in animal models, and their underlying mechanisms are becoming well characterized1-4, but technical challenges and ethical aspects are limiting the validation of these results in humans. We decided to address this difficulty with respect to the liver. This organ displays the remarkable ability to regenerate after acute injury, although liver regeneration in the context of recurring injury remains to be fully demonstrated. Here we performed single-nucleus RNA sequencing (snRNA-seq) on 47 liver biopsies from patients with different stages of metabolic dysfunction-associated steatotic liver disease to establish a cellular map of the liver during disease progression. We then combined these single-cell-level data with advanced 3D imaging to reveal profound changes in the liver architecture. Hepatocytes lose their zonation and considerable reorganization of the biliary tree takes place. More importantly, our study uncovers transdifferentiation events that occur between hepatocytes and cholangiocytes without the presence of adult stem cells or developmental progenitor activation. Detailed analyses and functional validations using cholangiocyte organoids confirm the importance of the PI3K-AKT-mTOR pathway in this process, thereby connecting this acquisition of plasticity to insulin signalling. Together, our data indicate that chronic injury creates an environment that induces cellular plasticity in human organs, and understanding the underlying mechanisms of this process could open new therapeutic avenues in the management of chronic diseases.

DOI: https://doi.org/10.1038/s41586-024-07465-2
J Cell Biol. 2024 Sep 02. pii: e202305065. [Epub ahead of print]223(9):

Coordination of actin plus-end dynamics by IQGAP1, formin, and capping protein.

Morgan L Pimm, Brian K Haarer, Alexander D Nobles, Laura M Haney, Alexandra G Marcin, Marcela Alcaide Eligio, Jessica L Henty-Ridilla.

Cell processes require precise regulation of actin polymerization that is mediated by plus-end regulatory proteins. Detailed mechanisms that explain plus-end dynamics involve regulators with opposing roles, including factors that enhance assembly, e.g., the formin mDia1, and others that stop growth (capping protein, CP). We explore IQGAP1's roles in regulating actin filament plus-ends and the consequences of perturbing its activity in cells. We confirm that IQGAP1 pauses elongation and interacts with plus ends through two residues (C756 and C781). We directly visualize the dynamic interplay between IQGAP1 and mDia1, revealing that IQGAP1 displaces the formin to influence actin assembly. Using four-color TIRF, we show that IQGAP1's displacement activity extends to formin-CP "decision complexes," promoting end-binding protein turnover at plus-ends. Loss of IQGAP1 or its plus-end activities disrupts morphology and migration, emphasizing its essential role. These results reveal a new role for IQGAP1 in promoting protein turnover on filament ends and provide new insights into how plus-end actin assembly is regulated in cells.

DOI: https://doi.org/10.1083/jcb.202305065
bioRxiv. 2024 May 08. pii: 2024.05.07.593014. [Epub ahead of print]

Endothelial deletion of p53 generates transitional endothelial cells and improves lung development during neonatal hyperoxia.

Lisandra Vila Ellis, Jonathan D Bywaters, Jichao Chen.

Bronchopulmonary dysplasia (BPD), a prevalent and chronic lung disease affecting premature newborns, results in vascular rarefaction and alveolar simplification. Although the vasculature has been recognized as a main player in this disease, the recently found capillary heterogeneity and cellular dynamics of endothelial subpopulations in BPD remain unclear. Here, we show Cap2 cells are damaged during neonatal hyperoxic injury, leading to their replacement by Cap1 cells which, in turn, significantly decline. Single-cell RNA-seq identifies the activation of numerous p53 target genes in endothelial cells, including Cdkn1a (p21) . While global deletion of p53 results in worsened vasculature, endothelial-specific deletion of p53 reverses the vascular phenotype and improves alveolar simplification during hyperoxia. This recovery is associated with the emergence of a transitional EC state, enriched for oxidative stress response genes and growth factors. These findings implicate the p53 pathway in EC type transition during injury-repair and highlights the endothelial contributions to BPD.

DOI: https://doi.org/10.1101/2024.05.07.593014
Development. 2024 May 24. pii: dev.202712. [Epub ahead of print]

Multiple intersecting pathways are involved in CPEB1 phosphorylation and regulation of translation during mouse oocyte meiosis.

Chisato Kunitomi, Mayra Romero, Enrico Maria Daldello, Karen Schindler, Marco Conti.

  The RNA-binding protein cytoplasmic polyadenylation element binding 1 (CPEB1) plays a fundamental role in regulating mRNA translation in oocytes. However, the specifics of how and which protein kinase cascades modulate CPEB1 activity is still controversial. Using genetic and pharmacological tools and detailed time courses, we reevaluated the relationship between CPEB1 phosphorylation and translation activation during mouse oocyte maturation. We show that both the CDK1/MAPK and AURKA/PLK1 pathways converge on CPEB1 phosphorylation during prometaphase of meiosis I. Only inactivation of the CDK1/MAPK pathway disrupts translation, while inactivation of either pathway leads to CPEB1 stabilization. However, CPEB1stabilization induced by inactivation of the AURKA/PLK1 pathway does not affect translation, indicating that destabilization/degradation is not linked with translational activation. The accumulation of endogenous CCNB1 protein closely recapitulates the translation data that uses an exogenous template. These findings support the overarching hypothesis that the activation of translation during prometaphase in mouse oocytes relies on a CDK1/MAPK-dependent CPEB1 phosphorylation, and translational activation precedes CPEB1 destabilization.

Keywords:  CPEB1; Meiosis; Translation; mRNA; oocyte

DOI:  https://doi.org/10.1242/dev.202712
Curr Biol. 2024 May 17. pii: S0960-9822(24)00586-4. [Epub ahead of print]

The Rac pathway prevents cell fragmentation in a nonprotrusively migrating leader cell during C. elegans gonad organogenesis.

Noor Singh, Pu Zhang, Karen Jian Li, Kacy Lynn Gordon.

  The C. elegans hermaphrodite distal tip cell (DTC) leads gonadogenesis. Loss-of-function mutations in a C. elegans ortholog of the Rac1 GTPase (ced-10) and its GEF complex (ced-5/DOCK180, ced-2/CrkII, ced-12/ELMO) cause gonad migration defects related to directional sensing; we discovered an additional defect class of gonad bifurcation in these mutants. Using genetic approaches, tissue-specific and whole-body RNAi, and in vivo imaging of endogenously tagged proteins and marked cells, we find that loss of Rac1 or its regulators causes the DTC to fragment as it migrates. Both products of fragmentation-the now-smaller DTC and the membranous patch of cellular material-localize important stem cell niche signaling (LAG-2 ligand) and migration (INA-1/integrin subunit alpha) factors to their membranes, but only one retains the DTC nucleus and therefore the ability to maintain gene expression over time. The enucleate patch can lead a bifurcating branch off the gonad arm that grows through germ cell proliferation. Germ cells in this branch differentiate as the patch loses LAG-2 expression. While the nucleus is surprisingly dispensable for aspects of leader cell function, it is required for stem cell niche activity long term. Prior work found that Rac1-/-;Rac2-/- mouse erythrocytes fragment; in this context, our new findings support the conclusion that maintaining a cohesive but deformable cell is a conserved function of this important cytoskeletal regulator.

Keywords:  GTPase; Rac; fragmentation; germline; gonad; leader cell; migration; stem cell niche

DOI:  https://doi.org/10.1016/j.cub.2024.04.073
Redox Biol. 2024 May 17. pii: S2213-2317(24)00173-3. [Epub ahead of print]73 103195

Iron accumulation in ovarian microenvironment damages the local redox balance and oocyte quality in aging mice.

Ye Chen, Jiaqi Zhang, Ying Tian, Xiangning Xu, Bicheng Wang, Ziqi Huang, Shuo Lou, Jingyi Kang, Ningning Zhang, Jing Weng, Yuanjing Liang, Wei Ma.

Accumulating oxidative damage is a primary driver of ovarian reserve decline along with aging. However, the mechanism behind the imbalance in reactive oxygen species (ROS) is not yet fully understood. Here we investigated changes in iron metabolism and its relationship with ROS disorder in aging ovaries of mice. We found increased iron content in aging ovaries and oocytes, along with abnormal expression of iron metabolic proteins, including heme oxygenase 1 (HO-1), ferritin heavy chain (FTH), ferritin light chain (FTL), mitochondrial ferritin (FTMT), divalent metal transporter 1 (DMT1), ferroportin1(FPN1), iron regulatory proteins (IRP1 and IRP2) and transferrin receptor 1 (TFR1). Notably, aging oocytes exhibited enhanced ferritinophagy and mitophagy, and consistently, there was an increase in cytosolic Fe2+, elevated lipid peroxidation, mitochondrial dysfunction, and augmented lysosome activity. Additionally, the ovarian expression of p53, p21, p16 and microtubule-associated protein tau (Tau) were also found to be upregulated. These alterations could be phenocopied with in vitro Fe2+ administration in oocytes from 2-month-old mice but were alleviated by deferoxamine (DFO). In vivo application of DFO improved ovarian iron metabolism and redox status in 12-month-old mice, and corrected the alterations in cytosolic Fe2+, ferritinophagy and mitophagy, as well as related degenerative changes in oocytes. Thereby in the whole, DFO delayed the decline in ovarian reserve and significantly increased the number of superovulated oocytes with reduced fragmentation and aneuploidy. Together, our findings suggest that aging-related disturbance in ovarian iron homeostasis contributes to excessive ROS production and that iron chelation may improve ovarian redox status, and efficiently delay the decline in ovarian reserve and oocyte quality in aging mice. These data propose a novel intervention strategy for preserving the ovarian reserve function in elderly women.

DOI: https://doi.org/10.1016/j.redox.2024.103195
Nature. 2024 May 22.

Adhesive anti-fibrotic interfaces on diverse organs.

Jingjing Wu, Jue Deng, Georgios Theocharidis, Tiffany L Sarrafian, Leigh G Griffiths, Roderick T Bronson, Aristidis Veves, Jianzhu Chen, Hyunwoo Yuk, Xuanhe Zhao.

Implanted biomaterials and devices face compromised functionality and efficacy in the long term owing to foreign body reactions and subsequent formation of fibrous capsules at the implant-tissue interfaces1-4. Here we demonstrate that an adhesive implant-tissue interface can mitigate fibrous capsule formation in diverse animal models, including rats, mice, humanized mice and pigs, by reducing the level of infiltration of inflammatory cells into the adhesive implant-tissue interface compared to the non-adhesive implant-tissue interface. Histological analysis shows that the adhesive implant-tissue interface does not form observable fibrous capsules on diverse organs, including the abdominal wall, colon, stomach, lung and heart, over 12 weeks in vivo. In vitro protein adsorption, multiplex Luminex assays, quantitative PCR, immunofluorescence analysis and RNA sequencing are additionally carried out to validate the hypothesis. We further demonstrate long-term bidirectional electrical communication enabled by implantable electrodes with an adhesive interface over 12 weeks in a rat model in vivo. These findings may offer a promising strategy for long-term anti-fibrotic implant-tissue interfaces.

DOI: https://doi.org/10.1038/s41586-024-07426-9
Cell. 2024 May 23. pii: S0092-8674(24)00401-X. [Epub ahead of print]187(11): 2652-2656

Mechanobiology: Shaping the future of cellular form and function.

Celeste M Nelson, Bailong Xiao, Sara A Wickström, Yves F Dufrêne, Daniel J Cosgrove, Carl-Philipp Heisenberg, Sirio Dupont, Amy E Shyer, Alan R Rodrigues, Xavier Trepat, Alba Diz-Muñoz.

Mechanobiology-the field studying how cells produce, sense, and respond to mechanical forces-is pivotal in the analysis of how cells and tissues take shape in development and disease. As we venture into the future of this field, pioneers share their insights, shaping the trajectory of future research and applications.

DOI: https://doi.org/10.1016/j.cell.2024.04.006
Curr Biol. 2024 May 16. pii: S0960-9822(24)00580-3. [Epub ahead of print]

A communication hub for phosphoregulation of kinetochore-microtubule attachment.

Jacob A Zahm, Stephen C Harrison.

  The Mps1 and Aurora B kinases regulate and monitor kinetochore attachment to spindle microtubules during cell division, ultimately ensuring accurate chromosome segregation. In yeast, the critical spindle attachment components are the Ndc80 and Dam1 complexes (Ndc80c and DASH/Dam1c, respectively). Ndc80c is a 600-Å-long heterotetramer that binds microtubules through a globular "head" at one end and centromere-proximal kinetochore components through a globular knob at the other end. Dam1c is a heterodecamer that forms a ring of 16-17 protomers around the shaft of the single kinetochore microtubule in point-centromere yeast. The ring coordinates the approximately eight Ndc80c rods per kinetochore. In published work, we showed that a site on the globular "head" of Ndc80c, including residues from both Ndc80 and Nuf2, binds a bipartite segment in the long C-terminal extension of Dam1. Results reported here show, both by in vitro binding experiments and by crystal structure determination, that the same site binds a conserved segment in the long N-terminal extension of Mps1. It also binds, less tightly, a conserved segment in the N-terminal extension of Ipl1 (yeast Aurora B). Together with results from experiments in yeast cells and from biochemical assays reported in two accompanying papers, the structures and graded affinities identify a communication hub for ensuring uniform bipolar attachment and for signaling anaphase onset.

Keywords:  Aurora B; Mps1; X-ray crystallography; error correction; kinetochore; mitosis; point-centromere yeast; spindle-assembly checkpoint

DOI:  https://doi.org/10.1016/j.cub.2024.04.067
Cardiovasc Res. 2024 May 24. pii: cvae111. [Epub ahead of print]

β1 integrins regulate cellular behavior and cardiomyocyte organization during ventricular wall formation.

Lianjie Miao, Yangyang Lu, Anika Nusrat, Luqi Zhao, Micah Castillo, Yongqi Xiao, Hongyang Guo, Yu Liu, Preethi Gunaratne, Robert J Schwartz, Alan R Burns, Ashok Kumar, C Michael DiPersio, Mingfu Wu.

AIMS: The mechanisms regulating the cellular behavior and cardiomyocyte organization during ventricular wall morphogenesis are poorly understood. Cardiomyocytes are surrounded by extracellular matrix (ECM) and interact with ECM via integrins. This study aims to determine whether and how β1 integrins regulate cardiomyocyte behavior and organization during ventricular wall morphogenesis in the mouse.
METHODS AND RESULTS: We applied mRNA deep sequencing and immunostaining to determine the expression repertoires of α/β integrins and their ligands in the embryonic heart. Integrin β1 subunit (β1) and some of its ECM ligands are asymmetrically distributed and enriched in the luminal side of cardiomyocytes, and fibronectin surrounds cardiomyocytes, creating a network for them. Itgb1, which encodes the β1, was deleted via Nkx2.5Cre/+ to generate myocardial-specific Itgb1 knockout (B1KO) mice. B1KO hearts display an absence of a trabecular zone but a thicker compact zone. The levels of hyaluronic acid and versican, essential for trabecular initiation, were not significantly different between control and B1KO. Instead, fibronectin, a ligand of β1, was absent in the myocardium of B1KO hearts. Furthermore, B1KO cardiomyocytes display a random cellular orientation and fail to undergo perpendicular cell division, be organized properly, and establish the proper tissue architecture to form trabeculae. Mosaic clonal lineage tracing showed that Itgb1 regulates cardiomyocyte transmural migration and proliferation autonomously.
CONCLUSIONS: β1 is asymmetrically localized in the cardiomyocytes, and some of its ECM ligands are enriched along the luminal side of the myocardium, and fibronectin surrounds cardiomyocytes. β1 integrins are required for cardiomyocytes to attach to the ECM network. This engagement provides structural support for cardiomyocytes to maintain shape, undergo perpendicular division, and establish cellular organization. Deletion of Itgb1 leads to loss of β1 and fibronectin and prevents cardiomyocytes from engaging the ECM network, resulting in failure to establish tissue architecture to form trabeculae.

DOI: https://doi.org/10.1093/cvr/cvae111
Nature. 2024 May 20.

In vitro reconstitution of epigenetic reprogramming in the human germ line.

Yusuke Murase, Ryuta Yokogawa, Yukihiro Yabuta, Masahiro Nagano, Yoshitaka Katou, Manami Mizuyama, Ayaka Kitamura, Pimpitcha Puangsricharoen, Chika Yamashiro, Bo Hu, Ken Mizuta, Kosuke Ogata, Yasushi Ishihama, Mitinori Saitou.

Epigenetic reprogramming resets parental epigenetic memories and differentiates primordial germ cells (PGCs) into mitotic pro-spermatogonia or oogonia, ensuring sexually dimorphic germ-cell development for totipotency 1. In vitro reconstitution of epigenetic reprogramming in humans remains a fundamental challenge. Here, we establish a robust strategy for inducing epigenetic reprogramming and differentiation of pluripotent stem cell (PSC)-derived human PGC-like cells (hPGCLCs) into mitotic pro-spermatogonia or oogonia, coupled with their extensive amplification (~>1010-fold). Strikingly, bone morphogenetic protein (BMP) signalling is a key driver of these processes: BMP-driven hPGCLC differentiation involves an attenuation of the mitogen-activated protein kinase/extracellular-regulated kinase (MAPK/ERK) pathway and both de novo and maintenance DNA methyltransferase (DNMT) activities, likely promoting replication-coupled, passive DNA demethylation. On the other hand, hPGCLCs deficient in tens-eleven translocation (TET) 1, an active DNA demethylase abundant in human germ cells 2,3, differentiate into extraembryonic cells, including amnion, with de-repression of key genes bearing bivalent promoters; these cells fail to fully activate genes vital for spermatogenesis and oogenesis, with their promoters remaining methylated. Our study elucidates the framework of epigenetic reprogramming in humans, making a fundamental advance in human biology, and through the generation of abundant mitotic pro-spermatogonia and oogonia-like cells, represents a milestone for human in vitro gametogenesis (IVG) research and its potential translation into reproductive medicine.

DOI: https://doi.org/10.1038/s41586-024-07526-6
Protein Cell. 2024 May 23. pii: pwae032. [Epub ahead of print]

Integrative analysis of transcriptome, DNA methylome and chromatin accessibility reveals candidate therapeutic targets in hypertrophic cardiomyopathy.

Junpeng Gao, Mengya Liu, Minjie Lu, Yuxuan Zheng, Yan Wang, Jingwei Yang, Xiaohui Xue, Yun Liu, Fuchou Tang, Shuiyun Wang, Lei Song, Lu Wen, Jizheng Wang.

  Hypertrophic cardiomyopathy (HCM) is the most common inherited heart disease and is characterized by primary left ventricular hypertrophy usually caused by mutations in sarcomere genes. The mechanism underlying cardiac remodeling in HCM remains incompletely understood. An investigation of HCM through integrative analysis at multi-omics levels will be helpful for treating HCM. DNA methylation and chromatin accessibility, as well as gene expression, were assessed by nucleosome occupancy and methylome sequencing (NOMe-seq) and RNA-seq, respectively, using the cardiac tissues of HCM patients. Compared with those of the controls, the transcriptome, DNA methylome and chromatin accessibility of the HCM myocardium showed multifaceted differences. At the transcriptome level, HCM hearts returned to the fetal gene program through decreased sarcomeric and metabolic gene expression and increased extracellular matrix gene expression. In the DNA methylome, hypermethylated and hypomethylated differentially methylated regions (DMRs) were identified in HCM. At the chromatin accessibility level, HCM hearts showed changes in different genome elements. Several transcription factors (TFs), including SP1 and EGR1, exhibited a fetal-like pattern of binding motifs in nucleosome-depleted regions (NDRs) in HCM. In particular, the inhibition of SP1 or EGR1 in an HCM mouse model harboring sarcomere mutations markedly alleviated the HCM phenotype of the mutant mice and reversed fetal gene reprogramming. Overall, this study not only provides a high precision multi-omics map of HCM heart tissue but also sheds light on the therapeutic strategy by intervening the fetal gene reprogramming in HCM.

Keywords:  DNA methylation; chromatin accessibility; fetal gene reprogramming; hypertrophic cardiomyopathy; multi-omics; therapy

DOI:  https://doi.org/10.1093/procel/pwae032