bims-ginsta 2025-01-26 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2025–01–26
37 papers selected by
Jinrong Hu, National University of Singapore

Fascin structural plasticity mediates flexible actin bundle construction.
Mouse totipotent blastomere-like cells model embryogenesis from zygotic genome activation to post implantation.
Temporal and regional X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing.
Aurora B controls microtubule stability to regulate abscission dynamics in stem cells.
Anillin tunes contractility and regulates barrier function during Rho flare-mediated tight junction remodeling.
Mitochondrial protein import stress.
Intercellular mRNA transfer alters the human pluripotent stem cell state.
Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution.
Regionalized regulation of actomyosin organization influences cardiomyocyte cell shape changes during chamber curvature formation.
KDM6B-dependent epigenetic programming of uterine fibroblasts in early pregnancy regulates parturition timing in mice.
mTor limits autophagy to facilitate cell volume expansion and rapid wound repair in Drosophila embryos.
Structural insights into actin filament turnover.
Multiscale footprints reveal the organization of cis-regulatory elements.
N-Cadherin promotes cardiac regeneration by potentiating pro-mitotic β-Catenin signaling in cardiomyocytes.
Molecular Regulation of Cardiomyocyte Maturation.
Real-time visualization of reconstituted transcription reveals RNA polymerase II activation mechanisms at single promoters.
Mapping cells through time and space with moscot.
Rectification of planar orientation angle switches behavior and replenishes contractile junctions.
An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development.
Positively charged specificity site in cyclin B1 is essential for mitotic fidelity.
Mitochondrial NAD+ transporter SLC25A51 linked to human aortic disease.
Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease.
Unidirectional MCM translocation away from ORC drives origin licensing.
Cdkn1c orchestrates a molecular network that regulates the euploidy of the male mouse germline stem cells.
Sequencing technologies to measure translation in single cells.
SMC motor proteins extrude DNA asymmetrically and can switch directions.
Stretch-induced endogenous electric fields drive directed collective cell migration in vivo.
A biophysical basis for the spreading behavior and limited diffusion of Xist.
Continuous cell type diversification throughout the embryonic and postnatal mouse visual cortex development.
Long somatic DNA-repeat expansion drives neurodegeneration in Huntington's disease.
Myosin-based nucleation of actin filaments contributes to stereocilia development critical for hearing.
RNA molecule rejuvenates ageing mice by restoring old cells.
The deubiquitinase USP5 prevents accumulation of protein aggregates in cardiomyocytes.
Lysosomal dysfunction and inflammatory sterol metabolism in pulmonary arterial hypertension.
Restrictor slows early transcription elongation to render RNA polymerase II susceptible to termination at non-coding RNA loci.
Two ligands of Arp2/3 complex, yeast coronin and GMF, interact and synergize in pruning branched actin networks.
At early stages of heart development, the first and second heart fields are a continuum of lateral head mesoderm-derived, cardiogenic cells.

Nat Struct Mol Biol. 2025 Jan 20.

Fascin structural plasticity mediates flexible actin bundle construction.

Rui Gong, Matthew J Reynolds, Keith R Carney, Keith Hamilton, Tamara C Bidone, Gregory M Alushin.

Fascin cross-links actin filaments (F-actin) into bundles that support tubular membrane protrusions including filopodia and stereocilia. Fascin dysregulation drives aberrant cell migration during metastasis, and fascin inhibitors are under development as cancer therapeutics. Here, we use cryo-EM, cryo-electron tomography coupled with custom denoising and computational modeling to probe human fascin-1's F-actin cross-linking mechanisms across spatial scales. Our fascin cross-bridge structure reveals an asymmetric F-actin binding conformation that is allosterically blocked by the inhibitor G2. Reconstructions of seven-filament hexagonal bundle elements, variability analysis and simulations show how structural plasticity enables fascin to bridge varied interfilament orientations, accommodating mismatches between F-actin's helical symmetry and bundle hexagonal packing. Tomography of many-filament bundles and modeling uncover geometric rules underlying emergent fascin binding patterns, as well as the accumulation of unfavorable cross-links that limit bundle size. Collectively, this work shows how fascin harnesses fine-tuned nanoscale structural dynamics to build and regulate micron-scale F-actin bundles.

DOI: https://doi.org/10.1038/s41594-024-01477-2
Cell Stem Cell. 2025 Jan 10. pii: S1934-5909(24)00446-6. [Epub ahead of print]

Mouse totipotent blastomere-like cells model embryogenesis from zygotic genome activation to post implantation.

Bing Peng, Qingyi Wang, Feixiang Zhang, Hui Shen, Peng Du.

  Embryo development begins with zygotic genome activation (ZGA), eventually generating blastocysts for implantation. However, in vitro systems modeling the pre-implantation development are still absent and challenging. Here, we used mouse totipotent blastomere-like cells (TBLCs) to develop spontaneous differentiation and blastoid formation systems, respectively. We found Wnt signaling enabled the rapid expansion of TBLCs and the optimization of their culture medium. We successfully developed a TBLC-spontaneous differentiation system in which mouse TBLCs (mTBLCs) firstly converted into two types of ZGA-like cells (ZLCs) distinguished by Zscan4 expression. Surprisingly, Zscan4-, but not Zscan4+, ZLCs further passed through intermediate 4-cell and then 8-cell/morula stages to produce epiblast, primitive endoderm, and trophectoderm lineages. Significantly, single TBLCs underwent expansion, compaction, and polarization to efficiently generate blastocyst-like structures and even post-implantation egg-cylinder-like structures. Conclusively, we established TBLC-based differentiation and embryo-like structure formation systems to model early embryonic development, offering criteria for evaluating and understanding totipotency.

Keywords:  Wnt signaling; blastoid; preimplantation; splicing inhibition; spontaneous differentiation; totipotent; totipotent blastomere-like cell

DOI:  https://doi.org/10.1016/j.stem.2024.12.006
Nat Struct Mol Biol. 2025 Jan 21.

Temporal and regional X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing.

Clara Roidor, Laurène Syx, Emmanuelle Beyne, Peggy Raynaud, Dina Zielinski, Aurélie Teissandier, Caroline Lee, Marius Walter, Nicolas Servant, Karim Chebli, Deborah Bourc'his, M Azim Surani, Maud Borensztein.

Random X-chromosome inactivation is a hallmark of female mammalian somatic cells. This epigenetic mechanism, mediated by the long noncoding RNA Xist, occurs in the early embryo and is stably maintained throughout life, although inactivation is lost during primordial germ cell (PGC) development. Using a combination of single-cell allele-specific RNA sequencing and low-input chromatin profiling on developing mouse PGCs, we provide a detailed map of X-linked gene reactivation. Despite the absence of Xist expression, PGCs still harbor a fully silent X chromosome at embryonic day 9.5 (E9.5). Subsequently, X-linked genes undergo gradual and distinct regional reactivation. At E12.5, a substantial part of the inactive X chromosome resists reactivation, retaining an epigenetic memory of its silencing. Our findings define the orchestration of reactivation of the inactive X chromosome, a key event in female PGC reprogramming with direct implications for reproduction.

DOI: https://doi.org/10.1038/s41594-024-01469-2
Cell Rep. 2025 Jan 23. pii: S2211-1247(25)00009-9. [Epub ahead of print]44(2): 115238

Aurora B controls microtubule stability to regulate abscission dynamics in stem cells.

Snježana Kodba, Amber Öztop, Eri van Berkum, Eugene A Katrukha, Malina K Iwanski, Wilco Nijenhuis, Lukas C Kapitein, Agathe Chaigne.

  Abscission is the last step of cell division. It separates the two sister cells and consists of cutting the cytoplasmic bridge. Abscission is mediated by the ESCRT membrane remodeling machinery, which also triggers the severing of a thick bundle of microtubules. Here, we show that rather than being passive actors in abscission, microtubules control abscission speed. Using mouse embryonic stem cells, which transition from slow to fast abscission during exit from naive pluripotency, we investigate the molecular mechanism for the regulation of abscission dynamics and identify crosstalk between Aurora B activity and microtubule stability. We demonstrate that naive stem cells maintain high Aurora B activity on the bridge after cytokinesis. This high Aurora B activity leads to transient microtubule stabilization that delays abscission by decreasing MCAK recruitment to the midbody. In turn, stable microtubules promote the activity of Aurora B. Overall, our data demonstrate that Aurora B-dependent microtubule stability controls abscission dynamics.

Keywords:  Aurora B; CP: Cell biology; CP: Stem cell research; MCAK; abscission; cytoplasmic bridges; microtubules; stem cells

DOI:  https://doi.org/10.1016/j.celrep.2025.115238
Mol Biol Cell. 2025 Jan 22. mbcE24110513

Anillin tunes contractility and regulates barrier function during Rho flare-mediated tight junction remodeling.

Zie Craig, Torey R Arnold, Kelsey Walworth, Alexander Walkon, Ann L Miller.

To preserve barrier function, cell-cell junctions must dynamically remodel during cell shape changes. We have previously described a rapid tight junction repair pathway characterized by local, transient activation of RhoA, termed "Rho flares", which repair leaks in tight junctions via promoting local actomyosin-mediated junction remodeling. In this pathway, junction elongation is a mechanical trigger that initiates RhoA activation through an influx of intracellular calcium and recruitment of p115RhoGEF. However, mechanisms that tune the level of RhoA activation and Myosin II contractility during the process remain uncharacterized. Here, we show that the scaffolding protein Anillin localizes to Rho flares and regulates RhoA activity and actomyosin contraction at flares. Knocking down Anillin results in Rho flares with increased intensity but shorter duration. These changes in active RhoA dynamics weaken downstream F-actin and Myosin II accumulation at the site of Rho flares, resulting in decreased junction contraction. Consequently, tight junction breaks are not reinforced following Rho flares. We show that Anillin-driven RhoA regulation is necessary for successfully repairing tight junction leaks and protecting junctions from repeated barrier damage. Together, these results uncover a novel regulatory role for Anillin during tight junction repair and barrier function maintenance. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text].

DOI: https://doi.org/10.1091/mbc.E24-11-0513
Nat Cell Biol. 2025 Jan 22.

Mitochondrial protein import stress.

Nikolaus Pfanner, Fabian den Brave, Thomas Becker.

Mitochondria have to import a large number of precursor proteins from the cytosol. Chaperones keep these proteins in a largely unfolded state and guide them to the mitochondrial import sites. Premature folding, mitochondrial stress and import defects can cause clogging of import sites and accumulation of non-imported precursors, representing a critical burden for cellular proteostasis. Here we discuss how cells respond to mitochondrial protein import stress by regenerating clogged import sites and inducing stress responses. The mitochondrial protein import machinery has a dual role by serving as sensor for detecting mitochondrial dysfunction and inducing stress-response pathways. The production of chaperones that fold or sequester precursor proteins in deposits is induced and the proteasomal activity is increased to remove the excess precursor proteins. Together, these pathways reveal how mitochondria are tightly integrated into a cellular proteostasis and stress response network to maintain cell viability.

DOI: https://doi.org/10.1038/s41556-024-01590-w
Proc Natl Acad Sci U S A. 2025 Jan 28. 122(4): e2413351122

Intercellular mRNA transfer alters the human pluripotent stem cell state.

Yosuke Yoneyama, Ran-Ran Zhang, Mari Maezawa, Hideki Masaki, Masaki Kimura, Yuqi Cai, Mike Adam, Sreeja Parameswaran, Naoaki Mizuno, Joydeep Bhadury, So Maezawa, Hiroshi Ochiai, Hiromitsu Nakauchi, S Steven Potter, Matthew T Weirauch, Takanori Takebe.

  Intercellular transmission of messenger RNA (mRNA) is being explored in mammalian species using immortal cell lines. Here, we uncover an intercellular mRNA transfer phenomenon that allows for the adaptation and reprogramming of human primed pluripotent stem cells (hPSCs). This process is induced by the direct cell contact-mediated coculture with mouse embryonic stem cells under the condition impermissible for primed hPSC culture. Mouse-derived mRNA contents are transmitted into adapted hPSCs only in the coculture. Transfer-specific mRNA analysis shows the enrichment for divergent biological pathways involving transcription/translational machinery and stress-coping mechanisms, wherein such transfer is diminished when direct cell contacts are lost. After 5 d of coculture with mouse embryonic stem cells, surface marker analysis and global gene profiling confirmed that mRNA transfer-prone hPSC efficiently gains a naïve-like state. Furthermore, transfer-specific knockdown experiments targeting mouse-specific transcription factor-coding mRNAs in hPSC show that mouse-derived Tfcp2l1, Tfap2c, and Klf4 are indispensable for human naïve-like conversion. Thus, interspecies mRNA transfer triggers cellular reprogramming in mammalian cells. Our results support that episodic mRNA transfer can occur in cell cooperative and competitive processes, which provides a fresh perspective on understanding the roles of mRNA mobility for intra- and interspecies cellular communications.

Keywords:  cell–cell communication; mRNA transfer; pluripotency; reprogramming

DOI:  https://doi.org/10.1073/pnas.2413351122
Cell. 2025 Jan 12. pii: S0092-8674(24)01425-9. [Epub ahead of print]

Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution.

Ke-Ran Li, Pei-Long Yu, Qi-Qi Zheng, Xin Wang, Xuan Fang, Lin-Chen Li, Cheng-Ran Xu.

  During early mammalian development, the endoderm germ layer forms the foundation of the respiratory and digestive systems through complex patterning. This intricate process, guided by a series of cell fate decisions, remains only partially understood. Our study introduces innovative genetic tracing codes for 14 distinct endodermal regions using novel mouse strains. By integrating high-throughput and high-precision single-cell RNA sequencing with sophisticated imaging, we detailed the spatiotemporal and genetic lineage differentiation of the endoderm at single-cell resolution. We discovered an unexpected multipotentiality within early endodermal regions, allowing differentiation into various organ primordia. This research illuminates the complex and underestimated phenomenon where endodermal organs develop from multiple origins, prompting a reevaluation of traditional differentiation models. Our findings advance understanding in developmental biology and have significant implications for regenerative medicine and the development of advanced organoid models, providing insights into the intricate mechanisms that guide organogenesis.

Keywords:  cellular differentiation; five-dimensional cell lineage tracing; genetic lineage tracing; mouse endodermal organogenesis; multi-origin organs; single-cell RNA sequencing; spatiotemporal analysis

DOI:  https://doi.org/10.1016/j.cell.2024.12.012
bioRxiv. 2025 Jan 08. pii: 2025.01.07.631779. [Epub ahead of print]

Regionalized regulation of actomyosin organization influences cardiomyocyte cell shape changes during chamber curvature formation.

Dena M Leerberg, Gabriel B Avillion, Rashmi Priya, Didier Y R Stainier, Deborah Yelon.

Cardiac chambers emerge from a heart tube that balloons and bends to create expanded ventricular and atrial structures, each containing a convex outer curvature (OC) and a recessed inner curvature (IC). A comprehensive understanding of the cellular and molecular mechanisms underlying the formation of these characteristic curvatures remains lacking. Here, we demonstrate in zebrafish that the initially similar populations of OC and IC ventricular cardiomyocytes diverge in the organization of their actomyosin cytoskeleton and subsequently acquire distinct OC and IC cell shapes. Altering actomyosin dynamics hinders cell shape changes in the OC, and mosaic analyses indicate that actomyosin regulates cardiomyocyte shape in a cell-autonomous manner. Additionally, both blood flow and the transcription factor Tbx5a influence the basal enrichment of actomyosin and squamous cell morphologies in the OC. Together, our findings demonstrate that intrinsic and extrinsic factors intersect to control actomyosin organization in OC cardiomyocytes, which in turn promotes the cell shape changes that drive curvature morphogenesis.

DOI: https://doi.org/10.1101/2025.01.07.631779
Cell. 2025 Jan 13. pii: S0092-8674(24)01432-6. [Epub ahead of print]

KDM6B-dependent epigenetic programming of uterine fibroblasts in early pregnancy regulates parturition timing in mice.

Tara I McIntyre, Omar Valdez, Nathan P Kochhar, Brittany Davidson, Bushra Samad, Longhui Qiu, Kenneth Hu, Alexis J Combes, Adrian Erlebacher.

  Current efforts investigating parturition timing mechanisms have focused on the proximal triggers of labor onset generated in late pregnancy. By studying the delayed parturition phenotype of mice with uterine fibroblast deficiencies in the histone H3K27me3 demethylase KDM6B, we provide evidence that parturition timing is regulated by events that take place in early pregnancy. Immediately after copulation, uterine fibroblasts engage in a locus-specific epigenetic program that abruptly adjusts H3K27me3 levels across their genome. In the absence of KDM6B, many of the adjusted loci over-accumulate H3K27me3. This over-accumulation leads to nearby genes being misexpressed in mid-to-late gestation, a delayed effect partly attributable to a second locus-specific but KDM6B-independent process initiated within uterine fibroblasts soon after implantation. This second process employs progressive H3K27me3 loss to temporally structure post-midgestational patterns of gene induction. Further dissection of the ways uterine programming controls parturition timing may have relevance to human pregnancy complications such as preterm labor.

Keywords:  H3K27me3; KDM6B; epigenetic programming; fibroblasts; mouse pregnancy; parturition; progesterone; uterus

DOI:  https://doi.org/10.1016/j.cell.2024.12.019
Dev Cell. 2025 Jan 10. pii: S1534-5807(24)00778-0. [Epub ahead of print]

mTor limits autophagy to facilitate cell volume expansion and rapid wound repair in Drosophila embryos.

Gordana Scepanovic, Negar Balaghi, Katheryn E Rothenberg, Rodrigo Fernandez-Gonzalez.

  Embryonic wounds repair rapidly, with no inflammation or scarring. Embryonic wound healing is driven by collective cell movements facilitated by the increase in the volume of the cells adjacent to the wound. The mechanistic target of rapamycin (mTor) complex 1 (TORC1) is associated with cell growth. We found that disrupting TORC1 signaling in Drosophila embryos prevented cell volume increases and slowed down wound repair. Catabolic processes, such as autophagy, can inhibit cell growth. Five-dimensional microscopy demonstrated that the number of autophagosomes decreased during wound repair, suggesting that autophagy must be tightly regulated for rapid wound healing. mTor inhibition increased autophagy, and activating autophagy prevented cell volume expansion and slowed down wound closure. Finally, reducing autophagy in embryos with disrupted TORC1 signaling rescued cell volume changes and rapid wound repair. Together, our results show that TORC1 activation upon wounding negatively regulates autophagy, allowing cells to increase their volumes to facilitate rapid wound healing.

Keywords:  Drosophila embryo; cell volume; collective cell movement; epithelial morphogenesis; image analysis; quantitative microscopy; wound healing

DOI:  https://doi.org/10.1016/j.devcel.2024.12.039
Trends Cell Biol. 2025 Jan 22. pii: S0962-8924(24)00277-0. [Epub ahead of print]

Structural insights into actin filament turnover.

Wout Oosterheert, Micaela Boiero Sanders, Peter Bieling, Stefan Raunser.

  The dynamic turnover of actin filaments drives the morphogenesis and migration of all eukaryotic cells. This review summarizes recent insights into the molecular mechanisms of actin polymerization and disassembly obtained through high-resolution structures of actin filament assemblies. We first describe how, upon polymerization, actin subunits age within the filament through changes in their associated adenine nucleotide. We then focus on the molecular basis of actin filament growth at the barbed end and how this process is modulated by core regulators such as profilin, formin, and capping protein (CP). Finally, the mechanisms underlying actin filament pointed-end depolymerization through disassembly factors cofilin/cyclase-associated protein (CAP) or DNase I are discussed. These findings contribute to a structural understanding of how actin filament dynamics are regulated in a complex cellular environment.

Keywords:  actin; barbed end; cytoskeleton; filament turnover; pointed end; structural biology

DOI:  https://doi.org/10.1016/j.tcb.2024.12.009
Nature. 2025 Jan 22.

Multiscale footprints reveal the organization of cis-regulatory elements.

Yan Hu, Max A Horlbeck, Ruochi Zhang, Sai Ma, Rojesh Shrestha, Vinay K Kartha, Fabiana M Duarte, Conrad Hock, Rachel E Savage, Ajay Labade, Heidi Kletzien, Alia Meliki, Andrew Castillo, Neva C Durand, Eugenio Mattei, Lauren J Anderson, Tristan Tay, Andrew S Earl, Noam Shoresh, Charles B Epstein, Amy J Wagers, Jason D Buenrostro.

Cis-regulatory elements (CREs) control gene expression and are dynamic in their structure and function, reflecting changes in the composition of diverse effector proteins over time1. However, methods for measuring the organization of effector proteins at CREs across the genome are limited, hampering efforts to connect CRE structure to their function in cell fate and disease. Here we developed PRINT, a computational method that identifies footprints of DNA-protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size. Using these multiscale footprints, we created the seq2PRINT framework, which uses deep learning to allow precise inference of transcription factor and nucleosome binding and interprets regulatory logic at CREs. Applying seq2PRINT to single-cell chromatin accessibility data from human bone marrow, we observe sequential establishment and widening of CREs centred on pioneer factors across haematopoiesis. We further discover age-associated alterations in the structure of CREs in murine haematopoietic stem cells, including widespread reduction of nucleosome footprints and gain of de novo identified Ets composite motifs. Collectively, we establish a method for obtaining rich insights into DNA-binding protein dynamics from chromatin accessibility data, and reveal the architecture of regulatory elements across differentiation and ageing.

DOI: https://doi.org/10.1038/s41586-024-08443-4
Nat Commun. 2025 Jan 21. 16(1): 896

N-Cadherin promotes cardiac regeneration by potentiating pro-mitotic β-Catenin signaling in cardiomyocytes.

Yi-Wei Tsai, Yi-Shuan Tseng, Yu-Shuo Wu, Wei-Lun Song, Min-Yi You, Yun-Chia Hsu, Wen-Pin Chen, Wei-Han Huang, Jia-Ci Chng, Chai-Ling Lim, Ke-Hsuan Wei, Shih-Lei Ben Lai, Wen-Chih Lee, Kai-Chien Yang.

Adult human hearts exhibit limited regenerative capacity. Post-injury cardiomyocyte (CM) loss can lead to myocardial dysfunction and failure. Although neonatal mammalian hearts can regenerate, the underlying molecular mechanisms remain elusive. Herein, comparative transcriptome analyses identify adherens junction protein N-Cadherin as a crucial regulator of CM proliferation/renewal. Its expression correlates positively with mitotic genes and shows an age-dependent reduction. N-Cadherin is upregulated in the neonatal mouse heart following injury, coinciding with increased CM mitotic activities. N-Cadherin knockdown reduces, whereas overexpression increases, the proliferation activity of neonatal mouse CMs and human induced pluripotent stem cell-derived CMs. Mechanistically, N-Cadherin binds and stabilizes pro-mitotic transcription regulator β-Catenin, driving CM self-renewal. Targeted N-Cadherin deletion in CMs impedes cardiac regeneration in neonatal mice, leading to excessive scarring. N-Cadherin overexpression, by contrast, promotes regeneration in adult mouse hearts following ischemic injury. N-Cadherin targeting presents a promising avenue for promoting cardiac regeneration and restoring function in injured adult human hearts.

DOI: https://doi.org/10.1038/s41467-025-56216-y
Curr Cardiol Rep. 2025 Jan 21. 27(1): 32

Molecular Regulation of Cardiomyocyte Maturation.

Bhavana Shewale, Tasneem Ebrahim, Arushi Samal, Nicole Dubois.

   PURPOSE OF THE REVIEW: This review aims to discuss the process of cardiomyocyte maturation, with a focus on the underlying molecular mechanisms required to form a fully functional heart. We examine both long-standing concepts associated with cardiac maturation and recent developments, and the overall complexity of molecularly integrating all the processes that lead to a mature heart.
RECENT FINDINGS: Cardiac maturation, defined here as the sequential changes that occurring before the heart reaches full maturity, has been a subject of investigation for decades. Recently, there has been a renewed, highly focused interest in this process, driven by clinically motivated research areas where enhancing maturation may lead to improved therapeutic opportunities. These include using pluripotent stem cell models for cell therapy and disease modeling, as well as recent advancements in adult cardiac regeneration approaches. We highlight key processes underlying maturation of the heart, including cellular and organ growth, and electrophysiological, metabolic, and contractile maturation. We further discuss how these processes integrate and interact to contribute to the overall complexity of the developing heart. Finally, we emphasize the transformative potential for translating relevant maturation concepts to emerging models of heart disease and regeneration.

Keywords:  Cardiac regeneration; Electrophysiological maturation; Extracellular matrix; Mechanotransduction; Metabolic maturation; Sarcomere maturation

DOI:  https://doi.org/10.1007/s11886-024-02189-1
bioRxiv. 2025 Jan 06. pii: 2025.01.06.631569. [Epub ahead of print]

Real-time visualization of reconstituted transcription reveals RNA polymerase II activation mechanisms at single promoters.

Megan Palacio, Dylan J Taatjes.

RNA polymerase II (RNAPII) is regulated by sequence-specific transcription factors (TFs) and the pre-initiation complex (PIC): TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, Mediator. TFs and Mediator contain intrinsically-disordered regions (IDRs) and form phase-separated condensates, but how IDRs control RNAPII function remains poorly understood. Using purified PIC factors, we developed a Real-time In-vitro Fluorescence Transcription assay (RIFT) for second-by-second visualization of RNAPII transcription at hundreds of promoters simultaneously. We show rapid RNAPII activation is IDR-dependent, without condensate formation. For example, the MED1-IDR can functionally replace a native TF, activating RNAPII with similar (not identical) kinetics; however, MED1-IDR squelches transcription as a condensate, but activates as a single-protein. TFs and Mediator cooperatively activate RNAPII bursting and re-initiation and surprisingly, Mediator can drive TF-promoter recruitment, without TF-DNA binding. Collectively, RIFT addressed questions largely intractable with cell-based methods, yielding mechanistic insights about IDRs, condensates, enhancer-promoter communication, and RNAPII bursting that complement live-cell imaging data.

DOI: https://doi.org/10.1101/2025.01.06.631569
Nature. 2025 Jan 22.

Mapping cells through time and space with moscot.

Dominik Klein, Giovanni Palla, Marius Lange, Michal Klein, Zoe Piran, Manuel Gander, Laetitia Meng-Papaxanthos, Michael Sterr, Lama Saber, Changying Jing, Aimée Bastidas-Ponce, Perla Cota, Marta Tarquis-Medina, Shrey Parikh, Ilan Gold, Heiko Lickert, Mostafa Bakhti, Mor Nitzan, Marco Cuturi, Fabian J Theis.

Single-cell genomic technologies enable the multimodal profiling of millions of cells across temporal and spatial dimensions. However, experimental limitations hinder the comprehensive measurement of cells under native temporal dynamics and in their native spatial tissue niche. Optimal transport has emerged as a powerful tool to address these constraints and has facilitated the recovery of the original cellular context1-4. Yet, most optimal transport applications are unable to incorporate multimodal information or scale to single-cell atlases. Here we introduce multi-omics single-cell optimal transport (moscot), a scalable framework for optimal transport in single-cell genomics that supports multimodality across all applications. We demonstrate the capability of moscot to efficiently reconstruct developmental trajectories of 1.7 million cells from mouse embryos across 20 time points. To illustrate the capability of moscot in space, we enrich spatial transcriptomic datasets by mapping multimodal information from single-cell profiles in a mouse liver sample and align multiple coronal sections of the mouse brain. We present moscot.spatiotemporal, an approach that leverages gene-expression data across both spatial and temporal dimensions to uncover the spatiotemporal dynamics of mouse embryogenesis. We also resolve endocrine-lineage relationships of delta and epsilon cells in a previously unpublished mouse, time-resolved pancreas development dataset using paired measurements of gene expression and chromatin accessibility. Our findings are confirmed through experimental validation of NEUROD2 as a regulator of epsilon progenitor cells in a model of human induced pluripotent stem cell islet cell differentiation. Moscot is available as open-source software, accompanied by extensive documentation.

DOI: https://doi.org/10.1038/s41586-024-08453-2
J Cell Biol. 2025 Apr 03. pii: e202309069. [Epub ahead of print]224(4):

Rectification of planar orientation angle switches behavior and replenishes contractile junctions.

Katie Linvill, Liam J Russell, Timothy E Vanderleest, Hui Miao, Yi Xie, J Todd Blankenship, Dinah Loerke.

In the early Drosophila embryo, germband elongation is driven by oriented cell intercalation through t1 transitions, where vertical (dorsal-ventral aligned) interfaces contract and then resolve into new horizontal (anterior-posterior aligned) interfaces. Here, we show that contractile events produce a continuous "rectification" of cell interfaces, in which interfaces systematically rotate toward more vertical orientations. As interfaces rotate, their behavior transitions from elongating to contractile regimes, indicating that the planar polarized identities of cell-cell interfaces are continuously re-interpreted in time depending on their orientation angle. Rotating interfaces acquire higher levels of Myosin II motor proteins as they become more vertical, while disruptions to the contractile molecular machinery reduce the rates of rotation. Through this angle rectification, the available pool of contractile interfaces is continuously replenished, as new interfaces acquire a contractile identity through rotation. Thus, individual cells acquire additional interfaces that are capable of undergoing t1 transitions, allowing cells to participate in multiple staggered rounds of intercalation events.

DOI: https://doi.org/10.1083/jcb.202309069
Cell. 2025 Jan 16. pii: S0092-8674(24)01426-0. [Epub ahead of print]

An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development.

Marlies E Oomen, Diego Rodriguez-Terrones, Mayuko Kurome, Valeri Zakhartchenko, Lorenza Mottes, Kilian Simmet, Camille Noll, Tsunetoshi Nakatani, Carlos Michel Mourra-Diaz, Irene Aksoy, Pierre Savatier, Jonathan Göke, Eckhard Wolf, Henrik Kaessmann, Maria-Elena Torres-Padilla.

  Transcriptional activation of the embryonic genome (EGA) is a major developmental landmark enabling the embryo to become independent from maternal control. The magnitude and control of transcriptional reprogramming during this event across mammals remains poorly understood. Here, we developed Smart-seq+5' for high sensitivity, full-length transcript coverage and simultaneous capture of 5' transcript information from single cells and single embryos. Using Smart-seq+5', we profiled 34 developmental stages in 5 mammalian species and provide an extensive characterization of the transcriptional repertoire of early development before, during, and after EGA. We demonstrate widespread transposable element (TE)-driven transcription across species, including, remarkably, of DNA transposons. We identify 19,657 TE-driven genic transcripts, suggesting extensive TE co-option in early development over evolutionary timescales. TEs display similar expression dynamics across species and species-specific patterns, suggesting shared and divergent regulation. Our work provides a powerful resource for understanding transcriptional regulation of mammalian development.

Keywords:  TSS; ZGA; evolutionary conservation; evolutionary genomics; mammalian preimplantation development; transcriptomics; transposable elements

DOI:  https://doi.org/10.1016/j.cell.2024.12.013
Nat Commun. 2025 Jan 20. 16(1): 853

Positively charged specificity site in cyclin B1 is essential for mitotic fidelity.

Christian Heinzle, Anna Höfler, Jun Yu, Peter Heid, Nora Kremer, Rebecca Schunk, Florian Stengel, Tanja Bange, Andreas Boland, Thomas U Mayer.

Phosphorylation of substrates by cyclin-dependent kinases (CDKs) is the driving force of cell cycle progression. Several CDK-activating cyclins are involved, yet how they contribute to substrate specificity is still poorly understood. Here, we discover that a positively charged pocket in cyclin B1, which is exclusively conserved within B-type cyclins and binds phosphorylated serine- or threonine-residues, is essential for correct execution of mitosis. HeLa cells expressing pocket mutant cyclin B1 are strongly delayed in anaphase onset due to multiple defects in mitotic spindle function and timely activation of the E3 ligase APC/C. Pocket integrity is essential for APC/C phosphorylation particularly at non-consensus CDK1 sites and full in vitro ubiquitylation activity. Our results support a model in which cyclin B1's pocket facilitates sequential substrate phosphorylations involving initial priming events that assist subsequent pocket-dependent phosphorylations even at non-consensus CDK1 motifs.

DOI: https://doi.org/10.1038/s41467-024-55669-x
Nat Cardiovasc Res. 2025 Jan 22.

Mitochondrial NAD+ transporter SLC25A51 linked to human aortic disease.

Gabriel K Adzika, Ricardo A Velázquez Aponte, Joseph A Baur.

DOI: https://doi.org/10.1038/s44161-024-00599-6
Cell. 2025 Jan 15. pii: S0092-8674(24)01429-6. [Epub ahead of print]

Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease.

Rafael Valdés-Mas, Avner Leshem, Danping Zheng, Yotam Cohen, Lara Kern, Niv Zmora, Yiming He, Corine Katina, Shimrit Eliyahu-Miller, Tal Yosef-Hevroni, Liron Richman, Barbara Raykhel, Shira Allswang, Reut Better, Merav Shmueli, Aurelia Saftien, Nyssa Cullin, Fernando Slamovitz, Dragos Ciocan, Kyanna S Ouyang, Uria Mor, Mally Dori-Bachash, Shahar Molina, Yishai Levin, Koji Atarashi, Ghil Jona, Jens Puschhof, Alon Harmelin, Noa Stettner, Minhu Chen, Jotham Suez, Kenya Honda, Wolfgang Lieb, Corinna Bang, Michal Kori, Nitsan Maharshak, Yifat Merbl, Oren Shibolet, Zamir Halpern, Dror S Shouval, Raanan Shamir, Andre Franke, Suhaib K Abdeen, Hagit Shapiro, Alon Savidor, Eran Elinav.

  Host-microbiome-dietary interactions play crucial roles in regulating human health, yet their direct functional assessment remains challenging. We adopted metagenome-informed metaproteomics (MIM), in mice and humans, to non-invasively explore species-level microbiome-host interactions during commensal and pathogen colonization, nutritional modification, and antibiotic-induced perturbation. Simultaneously, fecal MIM accurately characterized the nutritional exposure landscape in multiple clinical and dietary contexts. Implementation of MIM in murine auto-inflammation and in human inflammatory bowel disease (IBD) characterized a "compositional dysbiosis" and a concomitant species-specific "functional dysbiosis" driven by suppressed commensal responses to inflammatory host signals. Microbiome transfers unraveled early-onset kinetics of these host-commensal cross-responsive patterns, while predictive analyses identified candidate fecal host-microbiome IBD biomarker protein pairs outperforming S100A8/S100A9 (calprotectin). Importantly, a simultaneous fecal nutritional MIM assessment enabled the determination of IBD-related consumption patterns, dietary treatment compliance, and small intestinal digestive aberrations. Collectively, a parallelized dietary-bacterial-host MIM assessment functionally uncovers trans-kingdom interactomes shaping gastrointestinal ecology while offering personalized diagnostic and therapeutic insights into microbiome-associated disease.

Keywords:  biomarker; diet; inflammatory bowel disease; metagenome-informed metaproteomics; microbiome

DOI:  https://doi.org/10.1016/j.cell.2024.12.016
Nat Commun. 2025 Jan 17. 16(1): 782

Unidirectional MCM translocation away from ORC drives origin licensing.

Agata Butryn, Julia F Greiwe, Alessandro Costa.

The MCM motor of the eukaryotic replicative helicase is loaded as a double hexamer onto DNA by the Origin Recognition Complex (ORC), Cdc6, and Cdt1. ATP binding supports formation of the ORC-Cdc6-Cdt1-MCM (OCCM) helicase-recruitment complex where ORC-Cdc6 and one MCM hexamer form two juxtaposed rings around duplex DNA. ATP hydrolysis by MCM completes MCM loading but the mechanism is unknown. Here, we used cryo-EM to characterise helicase loading with ATPase-dead Arginine Finger variants of the six MCM subunits. We report the structure of two MCM complexes with different DNA grips, stalled as they mature to loaded MCM. The Mcm2 Arginine Finger-variant stabilises DNA binding by Mcm2 away from ORC/Cdc6. The Arginine Finger-variant of the neighbouring Mcm5 subunit stabilises DNA engagement by Mcm5 downstream of the Mcm2 binding site. Cdc6 and Orc1 progressively disengage from ORC as MCM translocates along DNA. We observe that duplex DNA translocation by MCM involves a set of leading-strand contacts by the pre-sensor 1 ATPase hairpins and lagging-strand contacts by the helix-2-insert hairpins. Mutating any of the MCM residues involved impairs high-salt resistant DNA binding in vitro and double-hexamer formation assessed by electron microscopy. Thus, ATPase-powered duplex DNA translocation away from ORC underlies MCM loading.

DOI: https://doi.org/10.1038/s41467-025-56143-y
Development. 2025 Jan 24. pii: dev.204286. [Epub ahead of print]

Cdkn1c orchestrates a molecular network that regulates the euploidy of the male mouse germline stem cells.

Mito Kanatsu-Shinohara, Takuya Yamamoto, Tianjiao Liu, Keiichi I Nakayama, Takashi Shinohara.

  Karyotype instability in the germline leads to infertility. Unlike the female germline, the male germline continuously produces fertile sperm throughout life. Here we present a molecular network responsible for maintaining karyotype stability in the male mouse germline. Loss of the cyclin-dependent kinase inhibitor Cdkn1c in undifferentiated spermatogonia induced degeneration of spermatogenesis prior to entry into the differentiating spermatogonia. In vitro analysis of spermatogonial stem cells (SSCs) revealed that CDKN1C localized to spindle microtubules during metaphase, and that disupted microtubule dynamics increased its phosphorylation. Cdkn1c deficiency activated the spindle assembly checkpoint and led to centrosome amplification, premature chromosome segregation, and loss of AURKB, and ultimately TRP53-dependent apoptosis. Trp53-deficient SSCs exhibited karyotype defects, but proliferated normally despite reduced CDKN1C and AURKB expression. In contrast, Aurkb depletion upregulated TRP53 and CDKN1C, suggesting a negative feedback loop to maintain euploidy. Thus, Cdkn1c regulates the male germline karyotype.

Keywords:   Cdkn1c ; Trp53 ; Aneuploidy; Male germ cells

DOI:  https://doi.org/10.1242/dev.204286
Nat Rev Mol Cell Biol. 2025 Jan 20.

Sequencing technologies to measure translation in single cells.

Michael VanInsberghe, Alexander van Oudenaarden.

Translation is one of the most energy-intensive processes in a cell and, accordingly, is tightly regulated. Genome-wide methods to measure translation and the translatome and to study the complex regulation of protein synthesis have enabled unprecedented characterization of this crucial step of gene expression. However, technological limitations have hampered our understanding of translation control in multicellular tissues, rare cell types and dynamic cellular processes. Recent optimizations, adaptations and new techniques have enabled these measurements to be made at single-cell resolution. In this Progress, we discuss single-cell sequencing technologies to measure translation, including ribosome profiling, ribosome affinity purification and spatial translatome methods.

DOI: https://doi.org/10.1038/s41580-024-00822-z
Cell. 2025 Jan 10. pii: S0092-8674(24)01433-8. [Epub ahead of print]

SMC motor proteins extrude DNA asymmetrically and can switch directions.

Roman Barth, Iain F Davidson, Jaco van der Torre, Michael Taschner, Stephan Gruber, Jan-Michael Peters, Cees Dekker.

  Structural maintenance of chromosomes (SMC) complexes organize the genome via DNA loop extrusion. Although some SMCs were reported to do so symmetrically, reeling DNA from both sides into the extruded DNA loop simultaneously, others perform loop extrusion asymmetrically toward one direction only. The mechanism underlying this variability remains unclear. Here, we examine the directionality of DNA loop extrusion by SMCs using in vitro single-molecule experiments. We find that cohesin and SMC5/6 do not reel in DNA from both sides, as reported before, but instead extrude DNA asymmetrically, although the direction can switch over time. Asymmetric DNA loop extrusion thus is the shared mechanism across all eukaryotic SMC complexes. For cohesin, direction switches strongly correlate with the turnover of the subunit NIPBL, during which DNA strand switching may occur. Apart from expanding by extrusion, loops frequently diffuse and shrink. The findings reveal that SMCs, surprisingly, can switch directions.

Keywords:  DNA loop extrusion; NIPBL; SMC complexes; SMC5/6; cohesin; condensin; single molecule visualization

DOI:  https://doi.org/10.1016/j.cell.2024.12.020
Nat Mater. 2025 Jan 17.

Stretch-induced endogenous electric fields drive directed collective cell migration in vivo.

Fernando Ferreira, Sofia Moreira, Min Zhao, Elias H Barriga.

Directed collective cell migration is essential for morphogenesis, and chemical, electrical, mechanical and topological features have been shown to guide cell migration in vitro. Here we provide in vivo evidence showing that endogenous electric fields drive the directed collective cell migration of an embryonic stem cell population-the cephalic neural crest of Xenopus laevis. We demonstrate that the voltage-sensitive phosphatase 1 is a key component of the molecular mechanism, enabling neural crest cells to specifically transduce electric fields into a directional cue in vivo. Finally, we propose that endogenous electric fields are mechanically established by the convergent extension movements of the ectoderm, which generate a membrane tension gradient that opens stretch-activated ion channels. Overall, these findings establish a role for electrotaxis in tissue morphogenesis, highlighting the functions of endogenous bioelectrical stimuli in non-neural contexts.

DOI: https://doi.org/10.1038/s41563-024-02060-2
Cell. 2025 Jan 15. pii: S0092-8674(24)01417-X. [Epub ahead of print]

A biophysical basis for the spreading behavior and limited diffusion of Xist.

Mingrui Ding, Danni Wang, Hui Chen, Barry Kesner, Niklas-Benedikt Grimm, Uri Weissbein, Anna Lappala, Jiying Jiang, Carlos Rivera, Jizhong Lou, Pilong Li, Jeannie T Lee.

  Xist RNA initiates X inactivation as it spreads in cis across the chromosome. Here, we reveal a biophysical basis for its cis-limited diffusion. Xist RNA and HNRNPK together drive a liquid-liquid phase separation (LLPS) that encapsulates the chromosome. HNRNPK droplets pull on Xist and internalize the RNA. Once internalized, Xist induces a further phase transition and "softens" the HNRNPK droplet. Xist alters the condensate's deformability, adhesiveness, and wetting properties in vitro. Other Xist-interacting proteins are internalized and entrapped within the droplet, resulting in a concentration of Xist and protein partners within the condensate. We attribute LLPS to HNRNPK's RGG and Xist's repeat B (RepB) motifs. Mutating these motifs causes Xist diffusion, disrupts polycomb recruitment, and precludes the required mixing of chromosomal compartments for Xist's migration. Thus, we hypothesize that phase transitions in HNRNPK condensates allow Xist to locally concentrate silencing factors and to spread through internal channels of the HNRNPK-encapsulated chromosome.

Keywords:  HNRNPK; RGG domain; RepB; Xist RNA; cis-limited spreading; condensates; deformability; droplets; liquid-liquid phase separation; repeat B

DOI:  https://doi.org/10.1016/j.cell.2024.12.004
bioRxiv. 2024 Oct 03. pii: 2024.10.02.616246. [Epub ahead of print]

Continuous cell type diversification throughout the embryonic and postnatal mouse visual cortex development.

Yuan Gao, Cindy T J van Velthoven, Changkyu Lee, Emma D Thomas, Darren Bertagnolli, Daniel Carey, Tamara Casper, Anish Bhaswanth Chakka, Rushil Chakrabarty, Michael Clark, Marie J Desierto, Rebecca Ferrer, Jessica Gloe, Jeff Goldy, Nathan Guilford, Junitta Guzman, Carliana R Halterman, Daniel Hirschstein, Windy Ho, Katelyn James, Rachel McCue, Emma Meyerdierks, Beagan Nguy, Nick Pena, Trangthanh Pham, Nadiya V Shapovalova, Josef Sulc, Amy Torkelson, Alex Tran, Herman Tung, Justin Wang, Kara Ronellenfitch, Boaz Levi, Michael J Hawrylycz, Chelsea Pagan, Nick Dee, Kimberly A Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng.

The mammalian cortex is composed of a highly diverse set of cell types and develops through a series of temporally regulated events that build out the cell type and circuit foundation for cortical function. The mechanisms underlying the development of different cell types remain elusive. Single-cell transcriptomics provides the capacity to systematically study cell types across the entire temporal range of cortical development. Here, we present a comprehensive and high-resolution transcriptomic and epigenomic cell type atlas of the developing mouse visual cortex. The atlas was built from a single-cell RNA-sequencing dataset of 568,674 high-quality single-cell transcriptomes and a single-nucleus Multiome dataset of 194,545 high-quality nuclei providing both transcriptomic and chromatin accessibility profiles, densely sampled throughout the embryonic and postnatal developmental stages from E11.5 to P56. We computationally reconstructed a transcriptomic developmental trajectory map of all excitatory, inhibitory, and non-neuronal cell types in the visual cortex, identifying branching points marking the emergence of new cell types at specific developmental ages and defining molecular signatures of cellular diversification. In addition to neurogenesis, gliogenesis and early postmitotic maturation in the embryonic stage which gives rise to all the cell classes and nearly all subclasses, we find that increasingly refined cell types emerge throughout the postnatal differentiation process, including the late emergence of many cell types during the eye-opening stage (P11-P14) and the onset of critical period (P21), suggesting continuous cell type diversification at different stages of cortical development. Throughout development, we find cooperative dynamic changes in gene expression and chromatin accessibility in specific cell types, identifying both chromatin peaks potentially regulating the expression of specific genes and transcription factors potentially regulating specific peaks. Furthermore, a single gene can be regulated by multiple peaks associated with different cell types and/or different developmental stages. Collectively, our study provides the most detailed dynamic molecular map directly associated with individual cell types and specific developmental events that reveals the molecular logic underlying the continuous refinement of cell type identities in the developing visual cortex.

DOI: https://doi.org/10.1101/2024.10.02.616246
Cell. 2025 Jan 14. pii: S0092-8674(24)01379-5. [Epub ahead of print]

Long somatic DNA-repeat expansion drives neurodegeneration in Huntington's disease.

Robert E Handsaker, Seva Kashin, Nora M Reed, Steven Tan, Won-Seok Lee, Tara M McDonald, Kiely Morris, Nolan Kamitaki, Christopher D Mullally, Neda R Morakabati, Melissa Goldman, Gabriel Lind, Rhea Kohli, Elisabeth Lawton, Marina Hogan, Kiku Ichihara, Sabina Berretta, Steven A McCarroll.

  In Huntington's disease (HD), striatal projection neurons (SPNs) degenerate during midlife; the core biological question involves how the disease-causing DNA repeat (CAG)n in the huntingtin (HTT) gene leads to neurodegeneration after decades of biological latency. We developed a single-cell method for measuring this repeat's length alongside genome-wide RNA expression. We found that the HTT CAG repeat expands somatically from 40-45 to 100-500+ CAGs in SPNs. Somatic expansion from 40 to 150 CAGs had no apparent cell-autonomous effect, but SPNs with 150-500+ CAGs lost positive and then negative features of neuronal identity, de-repressed senescence/apoptosis genes, and were lost. Our results suggest that somatic repeat expansion beyond 150 CAGs causes SPNs to degenerate quickly and asynchronously. We conclude that in HD, at any one time, most neurons have an innocuous but unstable HTT gene and that HD pathogenesis is a DNA process for almost all of a neuron's life.

Keywords:  CAG; DNA repeats; Huntington’s disease; neurodegeneration; repeat instability; single-nucleus RNA-seq; somatic expansion; striatal projection neurons; triplet repeat disorders

DOI:  https://doi.org/10.1016/j.cell.2024.11.038
Nat Commun. 2025 Jan 22. 16(1): 947

Myosin-based nucleation of actin filaments contributes to stereocilia development critical for hearing.

Zane G Moreland, Fangfang Jiang, Carlos Aguilar, Melanie Barzik, Rui Gong, Ghazaleh Behnammanesh, Jinho Park, Arik Shams, Christian Faaborg-Andersen, Jesse C Werth, Randall Harley, Daniel C Sutton, James B Heidings, Stacey M Cole, Andrew Parker, Susan Morse, Elizabeth Wilson, Yasuharu Takagi, James R Sellers, Steve D M Brown, Thomas B Friedman, Gregory M Alushin, Michael R Bowl, Jonathan E Bird.

Assembly of actin-based stereocilia is critical for cochlear hair cells to detect sound. To tune their mechanosensivity, stereocilia form bundles composed of graded rows of ascending height, necessitating the precise control of actin polymerization. Myosin 15 (MYO15A) drives hair bundle development by delivering critical proteins to growing stereocilia that regulate actin polymerization via an unknown mechanism. Here, we show that MYO15A is itself an actin nucleation-promoting factor. Moreover, a deafness-causing mutation in the MYO15A actin-binding interface inhibits nucleation activity but still preserves some movement on filaments in vitro and partial trafficking on stereocilia in vivo. Stereocilia fail to elongate correctly in this mutant mouse, providing evidence that MYO15A-driven actin nucleation contributes to hair bundle biogenesis. Our work shows that in addition to generating force and motility, the ATPase domain of MYO15A can directly regulate actin polymerization and that disrupting this activity can promote cytoskeletal disease, such as hearing loss.

DOI: https://doi.org/10.1038/s41467-025-55898-8
Nature. 2025 Jan 17.

RNA molecule rejuvenates ageing mice by restoring old cells.

Chris Simms.



Keywords:  Ageing

DOI:  https://doi.org/10.1038/d41586-025-00032-3
Sci Adv. 2025 Jan 24. 11(4): eado3852

The deubiquitinase USP5 prevents accumulation of protein aggregates in cardiomyocytes.

Yvonne Eibach, Silke Kreher, Mareike S Poetsch, Ay Lin Kho, Ulrich Gaertner, Christoph S Clemen, Rolf Schröder, Kai Guo, Hendrik Milting, Benjamin Meder, Michael Potente, Manfred Richter, Andre Schneider, Silke Meiners, Mathias Gaute, Thomas Braun.

Protein homeostasis is crucial for maintaining cardiomyocyte (CM) function. Disruption of proteostasis results in accumulation of protein aggregates causing cardiac pathologies such as hypertrophy, dilated cardiomyopathy (DCM), and heart failure. Here, we identify ubiquitin-specific peptidase 5 (USP5) as a critical determinant of protein quality control (PQC) in CM. CM-specific loss of mUsp5 leads to the accumulation of polyubiquitin chains and protein aggregates, cardiac remodeling, and eventually DCM. USP5 interacts with key components of the proteostasis machinery, including PSMD14, and the absence of USP5 increases activity of the ubiquitin-proteasome system and autophagic flux in CMs. Cardiac-specific hUSP5 overexpression reduces pathological remodeling in pressure-overloaded mouse hearts and attenuates protein aggregate formation in titinopathy and desminopathy models. Since CMs from humans with end-stage DCM show lower USP5 levels and display accumulation of ubiquitinated protein aggregates, we hypothesize that therapeutically increased USP5 activity may reduce protein aggregates during DCM. Our findings demonstrate that USP5 is essential for ubiquitin turnover and proteostasis in mature CMs.

DOI: https://doi.org/10.1126/sciadv.ado3852
Science. 2025 Jan 24. 387(6732): eadn7277

Lysosomal dysfunction and inflammatory sterol metabolism in pulmonary arterial hypertension.

Lloyd D Harvey, Mona Alotaibi, Yi-Yin Tai, Ying Tang, Hee-Jung J Kim, Neil J Kelly, Wei Sun, Chen-Shan C Woodcock, Sanya Arshad, Miranda K Culley, Wadih El Khoury, Rong Xie, Yassmin Al Aaraj, Jingsi Zhao, Neha Hafeez, Rashmi J Rao, Siyi Jiang, Vinny Negi, Anna Kirillova, Dror Perk, Annie M Watson, Claudette M St Croix, Donna B Stolz, Ji Young Lee, Mary Hongying Cheng, Manling Zhang, Samuel Detmer, Edward Guzman, Rajith S Manan, Rajan Saggar, Kathleen J Haley, Aaron B Waxman, Satoshi Okawa, Tae-Hwi Schwantes-An, Michael W Pauciulo, Bing Wang, Amy Webb, Caroline Chauvet, Daniel G Anderson, William C Nichols, Ankit A Desai, Robert Lafyatis, S Mehdi Nouraie, Haodi Wu, Jeffrey G McDonald, Susan Cheng, Ivet Bahar, Thomas Bertero, Raymond L Benza, Mohit Jain, Stephen Y Chan.

Vascular inflammation regulates endothelial pathophenotypes, particularly in pulmonary arterial hypertension (PAH). Dysregulated lysosomal activity and cholesterol metabolism activate pathogenic inflammation, but their relevance to PAH is unclear. Nuclear receptor coactivator 7 (NCOA7) deficiency in endothelium produced an oxysterol and bile acid signature through lysosomal dysregulation, promoting endothelial pathophenotypes. This oxysterol signature overlapped with a plasma metabolite signature associated with human PAH mortality. Mice deficient for endothelial Ncoa7 or exposed to an inflammatory bile acid developed worsened PAH. Genetic predisposition to NCOA7 deficiency was driven by single-nucleotide polymorphism rs11154337, which alters endothelial immunoactivation and is associated with human PAH mortality. An NCOA7-activating agent reversed endothelial immunoactivation and rodent PAH. Thus, we established a genetic and metabolic paradigm that links lysosomal biology and oxysterol processes to endothelial inflammation and PAH.

DOI: https://doi.org/10.1126/science.adn7277
bioRxiv. 2025 Jan 10. pii: 2025.01.08.631787. [Epub ahead of print]

Restrictor slows early transcription elongation to render RNA polymerase II susceptible to termination at non-coding RNA loci.

Claudia A Mimoso, Hanneke Vlaming, Nathalie P de Wagenaar, Karen Adelman.

The eukaryotic genome is broadly transcribed by RNA polymerase II (RNAPII) to produce protein-coding messenger RNAs (mRNAs) and a repertoire of non-coding RNAs (ncRNAs). Whereas RNAPII is very processive during mRNA transcription, it terminates rapidly during synthesis of many ncRNAs, particularly those that arise opportunistically from accessible chromatin at gene promoters or enhancers. The divergent fates of mRNA versus ncRNA species raise many questions about how RNAPII and associated machineries discriminate functional from spurious transcription. The Restrictor complex, comprised of the RNA binding protein ZC3H4 and RNAPII-interacting protein WDR82, has been implicated in restraining the expression of ncRNAs. However, the determinants of Restrictor targeting and the mechanism of transcription suppression remain unclear. Here, we investigate Restrictor using unbiased sequence screens, and rapid protein degradation followed by nascent RNA sequencing. We find that Restrictor promiscuously suppresses early elongation by RNAPII, but this activity is blocked at most mRNAs by the presence of a 5' splice site. Consequently, Restrictor is a critical determinant of transcription directionality at divergent promoters and prevents transcriptional interference. Finally, our data indicate that rather than directly terminating RNAPII, Restrictor acts by reducing the rate of transcription elongation, rendering RNAPII susceptible to early termination by other machineries.

DOI: https://doi.org/10.1101/2025.01.08.631787
J Biol Chem. 2025 Jan 16. pii: S0021-9258(25)00038-9. [Epub ahead of print] 108191

Two ligands of Arp2/3 complex, yeast coronin and GMF, interact and synergize in pruning branched actin networks.

Neha Koundinya, Rey M Aguilar, Kathryn Wetzel, Meagan R Tomasso, Priyashree Nagarajan, Emma R McGuirk, Shae B Padrick, Bruce L Goode.

  The rapid turnover of branched actin networks underlies key in vivo processes such as lamellipodial extension, endocytosis, phagocytosis, and intracellular transport. However, our understanding of the mechanisms used to dissociate, or 'prune', branched filaments has remained limited. Glia maturation factor (GMF) is a cofilin family protein that binds to Arp2/3 complex and catalyzes branch dissociation. Here, we show that another ligand of Arp2/3 complex, S. cerevisiae coronin (Crn1), enhances Gmf1-mediated debranching by 8-10 fold, and that these effects depend on Arp2/3-binding 'C' and 'A' motifs in Crn1. Further, we show that Crn1 directly binds with high affinity (KD = 1.4 nM) to S. cerevisiae GMF (Gmf1), and together they form a stable ternary Crn1-Gmf1-Arp2/3 complex in solution. Using single molecule analysis, we show that Gmf1 binds transiently and multiple times to F-actin branch junctions prior to debranching. These and other results suggest a mechanism of mutual recruitment, in which Crn1 increases the on-rate of Gmf1 for branch junctions and Gmf1 blocks Crn1 binding to actin filament sides, increasing its availability to bind branch junctions. Taken together, these observations reveal an unanticipated mechanism in which two distinct ligands of Arp2/3 complex bind to each other and synergize to prune actin branches.

Keywords:  Arp2/3 complex; GMF; actin; coronin; yeast

DOI:  https://doi.org/10.1016/j.jbc.2025.108191
Dev Biol. 2025 Jan 21. pii: S0012-1606(25)00021-1. [Epub ahead of print]

At early stages of heart development, the first and second heart fields are a continuum of lateral head mesoderm-derived, cardiogenic cells.

Matthew Wolton, Megan G Davey, Susanne Dietrich.

  Pioneering work in the chicken established that the initial development of the heart consists of two stages: the quick assembly of a beating heart, followed by the recruitment of cells from adjacent tissues to deliver the mature in-and outflow tract. Cells to build the primitive heart were dubbed the first heart field (FHF) cells, cells to be recruited later the second heart field (SHF) cells. The current view is that these cells represent distinct, maybe even pre-determined lineages. However, it is still unclear where exactly FHF and SHF are located at different stages of development, and whether there is a sharp boundary or rather an overlap between the two. It is also unclear whether both FHF cells and SHF cells originate from the lateral head mesoderm (LHM), whether the paraxial head mesoderm (PHM) contributes to the SHF, and where the LHM-PHM boundary might be. To investigate this problem, we exploited the size, ease of access and exquisite anatomy of the chicken embryo and used traditional strategies as well as newly developed transgenic lines to trace the location of cardiogenic fields and boundaries from the time the first heart-markers are expressed to the time SHF cell recruitment ceases. Our work shows that both FHF and SHF stem from the LHM. We also found that FHF and SHF lack a distinct anatomical boundary. Rather, FHF and SHF are a continuum, and the recruitment of cells into the heart is a chance event depending on morphogenetic movements, the position of cells within the moving tissues, the separation of the somatic and splanchnic LHM, and the separation of the heart from the splanchnic subpharyngeal mesoderm during heart-looping. Reconciling our and previous studies we propose that first and second heart field precursors are specified but not determined, thus relying on morphogenetic processes and local environments to realise their cardiogenic potential.

Keywords:  Heart development; chicken embryo; fate mapping; first heart field; head mesoderm; second heart field; transgenic chicken

DOI:  https://doi.org/10.1016/j.ydbio.2025.01.009