bims-ginsta Biomed News
on Genome instability
Issue of 2024–01–28
24 papers selected by
Jinrong Hu, National University of Singapore
  1. An inappropriate decline in ribosome levels drives a diverse set of neurodevelopmental disorders.
  2. Cytoskeleton crosstalk: Casting stable actin bundles with dynamic microtubule molds.
  3. Degradation and translation of maternal mRNA for embryogenesis.
  4. Type 2 cytokine signaling in macrophages protects from cellular senescence and organismal aging.
  5. Coordination of cohesin and DNA replication observed with purified proteins.
  6. Self-renewing human naïve pluripotent stem cells dedifferentiate in 3D culture and form blastoids spontaneously.
  7. Programmed disassembly of a microtubule-based membrane protrusion network coordinates 3D epithelial morphogenesis in Drosophila.
  8. Weakened APC/C activity at mitotic exit drives cancer vulnerability to KIF18A inhibition.
  9. Brd2 is dispensable for genome compartmentalization and replication timing.
  10. Cooperation between Nodal and FGF signals regulates zebrafish cardiac cell migration and heart morphogenesis.
  11. Fascin structural plasticity mediates flexible actin bundle construction.
  12. A single fluorescent probe to examine the dynamics of mitochondria-lysosome interplay and extracellular vesicle role in ferroptosis.
  13. Sperm induction of somatic cell-cell fusion as a novel functional test.
  14. Measures of genetic diversification in somatic tissues at bulk and single-cell resolution.
  15. DNA-guided transcription factor cooperativity shapes face and limb mesenchyme.
  16. PIGB maintains nuclear lamina organization in skeletal muscle of Drosophila.
  17. Regeneration of actin filament branches from the same Arp2/3 complex.
  18. Time-dependent effects of BRAF-V600E on cell cycling, metabolism, and function in engineered myocardium.
  19. An internally controlled system to study microtubule network diversification links tubulin evolution to the use of distinct microtubule regulators.
  20. A spatiotemporal molecular atlas of the ovulating mouse ovary.
  21. Antioxidant sericin averts the disruption of oocyte-follicular cell communication triggered by oxidative stress.
  22. BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair.
  23. Lamins: The backbone of the nucleocytoskeleton interface.
  24. PARP trapping is governed by the PARP inhibitor dissociation rate constant.
  1. bioRxiv. 2024 Jan 09. pii: 2024.01.09.574708. [Epub ahead of print]
    An inappropriate decline in ribosome levels drives a diverse set of neurodevelopmental disorders.
    Chunyang Ni, Leqian Yu, Barbara Vona, Dayea Park, Yulei Wei, Daniel A Schmitz, Yudong Wei, Yi Ding, Masahiro Sakurai, Emily Ballard, Yan Liu, Ashwani Kumar, Chao Xing, Hyung-Goo Kim, Cumhur Ekmekci, Ehsan Ghayoor Karimiani, Shima Imannezhad, Fatemeh Eghbal, Reza Shervin Badv, Eva Maria Christina Schwaibold, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Zahra Metanat, Hosein Eslamiyeh, Ebtissal Khouj, Saleh Mohammed Nasser Alhajj, Aziza Chedrawi, César Augusto Pinheiro Ferreira Alves, Henry Houlden, Michael Kruer, Fowzan S Alkuraya, Can Cenik, Reza Maroofian, Jun Wu, Michael Buszczak.
      Many neurodevelopmental defects are linked to perturbations in genes involved in housekeeping functions, such as those encoding ribosome biogenesis factors. However, how reductions in ribosome biogenesis can result in tissue and developmental specific defects remains a mystery. Here we describe new allelic variants in the ribosome biogenesis factor AIRIM primarily associated with neurodevelopmental disorders. Using human cerebral organoids in combination with proteomic analysis, single-cell transcriptome analysis across multiple developmental stages, and single organoid translatome analysis, we identify a previously unappreciated mechanism linking changes in ribosome levels and the timing of cell fate specification during early brain development. We find ribosome levels decrease during neuroepithelial differentiation, making differentiating cells particularly vulnerable to perturbations in ribosome biogenesis during this time. Reduced ribosome availability more profoundly impacts the translation of specific transcripts, disrupting both survival and cell fate commitment of transitioning neuroepithelia. Enhancing mTOR activity by both genetic and pharmacologic approaches ameliorates the growth and developmental defects associated with intellectual disability linked variants, identifying potential treatment options for specific brain ribosomopathies. This work reveals the cellular and molecular origins of protein synthesis defect-related disorders of human brain development.
    Highlights: AIRIM variants reduce ribosome levels specifically in neural progenitor cells. Inappropriately low ribosome levels cause a transient delay in radial glia fate commitment.Reduced ribosome levels impair translation of a selected subset of mRNAs.Genetic and pharmacologic activation of mTORC1 suppresses AIRIM-linked phenotypes.
    DOI:  https://doi.org/10.1101/2024.01.09.574708
  2. Curr Biol. 2024 Jan 22. pii: S0960-9822(23)01684-6. [Epub ahead of print]34(2): R72-R74
    Cytoskeleton crosstalk: Casting stable actin bundles with dynamic microtubule molds.
    Farah Haque, Radhika Subramanian.
      Actin-microtubule crosstalk diversifies cytoskeletal networks. A new study provides insight into how the microtubule polymerase CKAP5 mediates actin-microtubule crosstalk. CKAP5 directs the assembly of stable actin bundles on dynamic microtubules; in turn, the actin bundles align growing microtubules along their length.
    DOI:  https://doi.org/10.1016/j.cub.2023.12.028
  3. Trends Genet. 2024 Jan 22. pii: S0168-9525(23)00283-4. [Epub ahead of print]
    Degradation and translation of maternal mRNA for embryogenesis.
    Guanghui Yang, Qiliang Xin, Jurrien Dean.
      Maternal mRNAs accumulate during egg growth and must be judiciously degraded or translated to ensure successful development of mammalian embryos. In this review we integrate recent investigations into pathways controlling rapid degradation of maternal mRNAs during the maternal-to-zygotic transition. Degradation is not indiscriminate, and some mRNAs are selectively protected and rapidly translated after fertilization for reprogramming the zygotic genome during early embryogenesis. Oocyte specific cofactors and pathways have been illustrated to control different futures of maternal mRNAs. We discuss mechanisms that control the fate of maternal mRNAs during late oogenesis and after fertilization. Issues to be resolved in current maternal mRNA research are described, and future research directions are proposed.
    Keywords:  mammalian embryogenesis; maternal mRNA degradation; maternal mRNA translation; zygotic genome activation
    DOI:  https://doi.org/10.1016/j.tig.2023.12.008
  4. Immunity. 2024 Jan 17. pii: S1074-7613(24)00026-8. [Epub ahead of print]
    Type 2 cytokine signaling in macrophages protects from cellular senescence and organismal aging.
    Zhao Zhou, Jingfei Yao, Dongmei Wu, Xun Huang, Yushuang Wang, Xinmeng Li, Qiang Lu, Yifu Qiu.
      Accumulation of senescent cells in organs and tissues is a hallmark of aging and known to contribute to age-related diseases. Although aging-associated immune dysfunction, or immunosenescence, is known to contribute to this process, the underlying mechanism remains elusive. Here, we report that type 2 cytokine signaling deficiency accelerated aging and, conversely, that the interleukin-4 (IL-4)-STAT6 pathway protected macrophages from senescence. Mechanistically, activated STAT6 promoted the expression of genes involved in DNA repair both via homologous recombination and Fanconi anemia pathways. Conversely, STAT6 deficiency induced release of nuclear DNA into the cytoplasm to promote tissue inflammation and organismal aging. Importantly, we demonstrate that IL-4 treatment prevented macrophage senescence and improved the health span of aged mice to an extent comparable to senolytic treatment, with further additive effects when combined. Together, our findings support that type 2 cytokine signaling protects macrophages from immunosenescence and thus hold therapeutic potential for improving healthy aging.
    Keywords:  DNA repair; IL-4; STAT6; aging; immunosenescence; inflammaging; macrophage; type 2 cytokine
    DOI:  https://doi.org/10.1016/j.immuni.2024.01.001
  5. Nature. 2024 Jan 24.
    Coordination of cohesin and DNA replication observed with purified proteins.
    Yasuto Murayama, Shizuko Endo, Yumiko Kurokawa, Ayako Kurita, Sanae Iwasaki, Hiroyuki Araki.
      Two newly duplicated copies of genomic DNA are held together by the ring-shaped cohesin complex to ensure faithful inheritance of the genome during cell division1-3. Cohesin mediates sister chromatid cohesion by topologically entrapping two sister DNAs during DNA replication4,5, but how cohesion is established at the replication fork is poorly understood. Here, we studied the interplay between cohesin and replication by reconstituting a functional replisome using purified proteins. Once DNA is encircled before replication, the cohesin ring accommodates replication in its entirety, from initiation to termination, leading to topological capture of newly synthesized DNA. This suggests that topological cohesin loading is a critical molecular prerequisite to cope with replication. Paradoxically, topological loading per se is highly rate limiting and hardly occurs under the replication-competent physiological salt concentration. This inconsistency is resolved by the replisome-associated cohesion establishment factors Chl1 helicase and Ctf4 (refs. 6,7), which promote cohesin loading specifically during continuing replication. Accordingly, we found that bubble DNA, which mimics the state of DNA unwinding, induces topological cohesin loading and this is further promoted by Chl1. Thus, we propose that cohesin converts the initial electrostatic DNA-binding mode to a topological embrace when it encounters unwound DNA structures driven by enzymatic activities including replication. Together, our results show how cohesin initially responds to replication, and provide a molecular model for the establishment of sister chromatid cohesion.
    DOI:  https://doi.org/10.1038/s41586-023-07003-6
  6. Nat Commun. 2024 Jan 22. 15(1): 668
    Self-renewing human naïve pluripotent stem cells dedifferentiate in 3D culture and form blastoids spontaneously.
    Mingyue Guo, Jinyi Wu, Chuanxin Chen, Xinggu Wang, An Gong, Wei Guan, Rowan M Karvas, Kexin Wang, Mingwei Min, Yixuan Wang, Thorold W Theunissen, Shaorong Gao, José C R Silva.
      Human naïve pluripotent stem cells (hnPSCs) can generate integrated models of blastocysts termed blastoids upon switch to inductive medium. However, the underlying mechanisms remain obscure. Here we report that self-renewing hnPSCs spontaneously and efficiently give rise to blastoids upon three dimensional (3D) suspension culture. The spontaneous blastoids mimic early stage human blastocysts in terms of structure, size, and transcriptome characteristics and are capable of progressing to post-implantation stages. This property is conferred by the glycogen synthase kinase-3 (GSK3) signalling inhibitor IM-12 present in 5iLAF self-renewing medium. IM-12 upregulates oxidative phosphorylation-associated genes that underly the capacity of hnPSCs to generate blastoids spontaneously. Starting from day one of self-organization, hnPSCs at the boundary of all 3D aggregates dedifferentiate into E5 embryo-like intermediates. Intermediates co-express SOX2/OCT4 and GATA6 and by day 3 specify trophoblast fate, which coincides with cavity and blastoid formation. In summary, spontaneous blastoid formation results from 3D culture triggering dedifferentiation of hnPSCs into earlier embryo-like intermediates which are then competent to segregate blastocyst fates.
    DOI:  https://doi.org/10.1038/s41467-024-44969-x
  7. EMBO J. 2024 Jan 23.
    Programmed disassembly of a microtubule-based membrane protrusion network coordinates 3D epithelial morphogenesis in Drosophila.
    Ngan Vi Tran, Martti P Montanari, Jinghua Gui, Dmitri Lubenets, Léa Louise Fischbach, Hanna Antson, Yunxian Huang, Erich Brutus, Yasushi Okada, Yukitaka Ishimoto, Tambet Tõnissoo, Osamu Shimmi.
      Comprehensive analysis of cellular dynamics during the process of morphogenesis is fundamental to understanding the principles of animal development. Despite recent advancements in light microscopy, how successive cell shape changes lead to complex three-dimensional tissue morphogenesis is still largely unresolved. Using in vivo live imaging of Drosophila wing development, we have studied unique cellular structures comprising a microtubule-based membrane protrusion network. This network, which we name here the Interplanar Amida Network (IPAN), links the two wing epithelium leaflets. Initially, the IPAN sustains cell-cell contacts between the two layers of the wing epithelium through basal protrusions. Subsequent disassembly of the IPAN involves loss of these contacts, with concomitant degeneration of aligned microtubules. These processes are both autonomously and non-autonomously required for mitosis, leading to coordinated tissue proliferation between two wing epithelia. Our findings further reveal that a microtubule organization switch from non-centrosomal to centrosomal microtubule-organizing centers (MTOCs) at the G2/M transition leads to disassembly of non-centrosomal microtubule-derived IPAN protrusions. These findings exemplify how cell shape change-mediated loss of inter-tissue contacts results in 3D tissue morphogenesis.
    Keywords:  Cellular Protrusion; Epithelial Morphogenesis; Microtubule Dynamics; Non-Centrosomal Microtubule Organizing Center; Three-Dimensional Morphogenesis
    DOI:  https://doi.org/10.1038/s44318-023-00025-w
  8. EMBO J. 2024 Jan 26.
    Weakened APC/C activity at mitotic exit drives cancer vulnerability to KIF18A inhibition.
    Colin R Gliech, Zhong Y Yeow, Daniel Tapias-Gomez, Yuchen Yang, Zhaoyu Huang, Andréa E Tijhuis, Diana Cj Spierings, Floris Foijer, Grace Chung, Nuria Tamayo, Zahra Bahrami-Nejad, Patrick Collins, Thong T Nguyen, Andres Plata Stapper, Paul E Hughes, Marc Payton, Andrew J Holland.
      The efficacy of current antimitotic cancer drugs is limited by toxicity in highly proliferative healthy tissues. A cancer-specific dependency on the microtubule motor protein KIF18A therefore makes it an attractive therapeutic target. Not all cancers require KIF18A, however, and the determinants underlying this distinction remain unclear. Here, we show that KIF18A inhibition drives a modest and widespread increase in spindle assembly checkpoint (SAC) signaling from kinetochores which can result in lethal mitotic delays. Whether cells arrest in mitosis depends on the robustness of the metaphase-to-anaphase transition, and cells predisposed with weak basal anaphase-promoting complex/cyclosome (APC/C) activity and/or persistent SAC signaling through metaphase are uniquely sensitive to KIF18A inhibition. KIF18A-dependent cancer cells exhibit hallmarks of this SAC:APC/C imbalance, including a long metaphase-to-anaphase transition, and slow mitosis overall. Together, our data reveal vulnerabilities in the cell division apparatus of cancer cells that can be exploited for therapeutic benefit.
    Keywords:  Anaphase Promoting Complex (APC/C); Cancer; KIF18A; Mitosis; Spindle Assembly Checkpoint (SAC)
    DOI:  https://doi.org/10.1038/s44318-024-00031-6
  9. bioRxiv. 2023 Nov 19. pii: 2023.11.17.567572. [Epub ahead of print]
    Brd2 is dispensable for genome compartmentalization and replication timing.
    Laura Hinojosa-Gonzalez, Jesse L Turner, Takayo Sasaki, Ferhat Ay, David M Gilbert.
      Replication Timing (RT) refers to the temporal order in which the genome is replicated during S phase. Early replicating regions correlate with the transcriptionally active, accessible euchromatin (A) compartment, while late replicating regions correlate with the heterochromatin (B) compartment and repressive histone marks. Previously, widespread A/B genome compartmentalization changes were reported following Brd2 depletion. Since RT and A/B compartmentalization are two of the most highly correlated chromosome properties, we evaluated the effects of Brd2 depletion on RT. We performed E/L Repli-Seq following Brd2 depletion in the previously described Brd2 conditional degron cell line and found no significant alterations in RT after Brd2 KD. This finding prompted us to re-analyze the Micro-C data from the previous publication. We report that we were unable to detect any compartmentalization changes in Brd2 depleted cells compared to DMSO control using the same data. Taken together, our findings demonstrate that Brd2 depletion alone does not affect A/B compartmentalization or RT in mouse embryonic stem cells.
    DOI:  https://doi.org/10.1101/2023.11.17.567572
  10. bioRxiv. 2024 Jan 06. pii: 2024.01.05.574380. [Epub ahead of print]
    Cooperation between Nodal and FGF signals regulates zebrafish cardiac cell migration and heart morphogenesis.
    Vanessa Gonzalez, Meagan G Grant, Makoto Suzuki, Briana Christophers, Jessica Rowland Williams, Rebecca D Burdine.
      Asymmetric vertebrate heart development is driven by an intricate sequence of morphogenetic cell movements, the coordination of which requires precise interpretation of signaling cues by heart primordia. Here we show that Nodal functions cooperatively with FGF during heart tube formation and asymmetric placement. Both pathways act as migratory stimuli for cardiac progenitor cells (CPCs), but FGF is dispensable for directing heart tube asymmetry, which is governed by Nodal. We further find that Nodal controls CPC migration by inducing left-right asymmetries in the formation of actin-based protrusions in CPCs. Additionally, we define a developmental window in which FGF signals are required for proper heart looping and show cooperativity between FGF and Nodal in this process. We present evidence FGF may promote heart looping through addition of the secondary heart field. Finally, we demonstrate that loss of FGF signaling affects proper development of the atrioventricular canal (AVC), which likely contributes to abnormal chamber morphologies in FGF-deficient hearts. Together, our data shed insight into how the spatiotemporal dynamics of signaling cues regulate the cellular behaviors underlying organ morphogenesis.
    Summary statement: This study explores the cooperative and independent roles of Nodal and FGF signaling in generating heart asymmetry.
    DOI:  https://doi.org/10.1101/2024.01.05.574380
  11. bioRxiv. 2024 Jan 04. pii: 2024.01.03.574123. [Epub ahead of print]
    Fascin structural plasticity mediates flexible actin bundle construction.
    Rui Gong, Matthew J Reynolds, Keith Hamilton, Gregory M Alushin.
      Fascin crosslinks actin filaments (F-actin) into bundles that support tubular membrane protrusions including filopodia, stereocilia, and microvilli. Fascin dysregulation drives aberrant cell migration during metastasis, and fascin inhibitors are under development as cancer therapeutics. Here, we use cryo-electron microscopy and cryo-electron tomography coupled with custom denoising to probe fascin's F-actin crosslinking mechanisms across spatial scales. Our fascin crossbridge structure reveals an asymmetric F-actin binding conformation that is allosterically blocked by the inhibitor G2. Reconstructions of seven-filament hexagonal bundle elements and variability analysis show how structural plasticity enables fascin to bridge varied inter-filament orientations, accommodating mismatches between F-actin's helical symmetry and bundle hexagonal packing. Tomography of many-filament bundles uncovers geometric rules underlying emergent fascin binding patterns, as well as the accumulation of unfavorable crosslinks 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/10.1101/2024.01.03.574123
  12. Dev Cell. 2024 Jan 19. pii: S1534-5807(24)00003-0. [Epub ahead of print]
    A single fluorescent probe to examine the dynamics of mitochondria-lysosome interplay and extracellular vesicle role in ferroptosis.
    Ling-Li Wang, Yu-Zhuo Mai, Ming-Hua Zheng, Guang-Hai Yan, Jing-Yi Jin.
      Ferroptosis is a non-apoptotic form of cell death characterized by iron-dependent lipid peroxidation and glutathione (GSH) depletion. Despite recent advances, challenges remain in understanding the bidirectional interactions or interplay between organelles during ferroptosis. In this study, we aimed to understand the interplay between mitochondria (Mito) and lysosomes (Lyso) in cell homeostasis and ferroptosis. For this purpose, we designed a single fluorescent probe that marks GSH in Mito and hypochlorous acid (HOCl) in Lyso with two distinct emissions. Using this dual-targeted single fluorescent probe (9-morphorino pyronine), we detected Mito-Lyso interplay in ferroptosis. We disclosed differences in Mito-Lyso interplay depending on the induction of ferroptosis. Although erastin treatment decreased GSH, RSL3 triggered a HOCl burst, and FIN56- and FINO2-induced ferroptosis increased GSH and HOCl. Additionally, we showed that only extracellular vesicles generated during erastin-induced ferroptosis could spontaneously move and dock to neighboring cells, resulting in accelerated cell death.
    Keywords:  cell imaging; extracellular vesicles; ferroptosis; fluorescent probe; mitochondria-lysosome interplay
    DOI:  https://doi.org/10.1016/j.devcel.2024.01.003
  13. Elife. 2024 Jan 24. pii: e94228. [Epub ahead of print]13
    Sperm induction of somatic cell-cell fusion as a novel functional test.
    Nicolas G Brukman, Clari Valansi, Benjamin Podbilewicz.
      The fusion of mammalian gametes requires the interaction between IZUMO1 on the sperm and JUNO on the oocyte. We have recently shown that ectopic expression of mouse IZUMO1 induces cell-cell fusion and that sperm can fuse to fibroblasts expressing JUNO. Here, we found that the incubation of mouse sperm with hamster fibroblasts or human epithelial cells in culture induces the fusion between these somatic cells and formation of syncytia, a pattern previously observed with some animal viruses. This sperm-induced cell-cell fusion requires a species-matching JUNO on both fusing cells, can be blocked by an antibody against IZUMO1, and does not rely on the synthesis of new proteins. The fusion is dependent on the sperm's fusogenic capacity, making this a reliable, fast and simple method for predicting sperm function during the diagnosis of male infertility.
    Keywords:  developmental biology; mouse
    DOI:  https://doi.org/10.7554/eLife.94228
  14. Elife. 2024 Jan 24. pii: RP89780. [Epub ahead of print]12
    Measures of genetic diversification in somatic tissues at bulk and single-cell resolution.
    Marius E Moeller, Nathaniel V Mon Père, Benjamin Werner, Weini Huang.
      Intra-tissue genetic heterogeneity is universal to both healthy and cancerous tissues. It emerges from the stochastic accumulation of somatic mutations throughout development and homeostasis. By combining population genetics theory and genomic information, genetic heterogeneity can be exploited to infer tissue organization and dynamics in vivo. However, many basic quantities, for example the dynamics of tissue-specific stem cells remain difficult to quantify precisely. Here, we show that single-cell and bulk sequencing data inform on different aspects of the underlying stochastic processes. Bulk-derived variant allele frequency spectra (VAF) show transitions from growing to constant stem cell populations with age in samples of healthy esophagus epithelium. Single-cell mutational burden distributions allow a sample size independent measure of mutation and proliferation rates. Mutation rates in adult hematopietic stem cells are higher compared to inferences during development, suggesting additional proliferation-independent effects. Furthermore, single-cell derived VAF spectra contain information on the number of tissue-specific stem cells. In hematopiesis, we find approximately 2 × 105 HSCs, if all stem cells divide symmetrically. However, the single-cell mutational burden distribution is over-dispersed compared to a model of Poisson distributed random mutations. A time-associated model of mutation accumulation with a constant rate alone cannot generate such a pattern. At least one additional source of stochasticity would be needed. Possible candidates for these processes may be occasional bursts of stem cell divisions, potentially in response to injury, or non-constant mutation rates either through environmental exposures or cell-intrinsic variation.
    Keywords:  evolutionary biology; evolutionary inferences; healthy human tissues; human; sampling; single-cell mutation burden; stem cell dynamics; varient allele frequency
    DOI:  https://doi.org/10.7554/eLife.89780
  15. Cell. 2024 Jan 17. pii: S0092-8674(23)01438-1. [Epub ahead of print]
    DNA-guided transcription factor cooperativity shapes face and limb mesenchyme.
    Seungsoo Kim, Ekaterina Morgunova, Sahin Naqvi, Seppe Goovaerts, Maram Bader, Mervenaz Koska, Alexander Popov, Christy Luong, Angela Pogson, Tomek Swigut, Peter Claes, Jussi Taipale, Joanna Wysocka.
      Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest that it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how "Coordinator," a long DNA motif composed of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines the regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, whereas HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in the shared regulation of genes involved in cell-type and positional identities and ultimately shapes facial morphology and evolution.
    Keywords:  ALX factors; Coordinator; TWIST1; bHLH; cooperativity; face; homeodomain; limb; mesenchyme; neural crest; transcription factor
    DOI:  https://doi.org/10.1016/j.cell.2023.12.032
  16. J Cell Biol. 2024 Feb 05. pii: e202301062. [Epub ahead of print]223(2):
    PIGB maintains nuclear lamina organization in skeletal muscle of Drosophila.
    Miki Yamamoto-Hino, Masaru Ariura, Masahito Tanaka, Yuka W Iwasaki, Kohei Kawaguchi, Yuta Shimamoto, Satoshi Goto.
      The nuclear lamina (NL) plays various roles and participates in nuclear integrity, chromatin organization, and transcriptional regulation. Lamin proteins, the main components of the NL, form a homogeneous meshwork structure under the nuclear envelope. Lamins are essential, but it is unknown whether their homogeneous distribution is important for nuclear function. Here, we found that PIGB, an enzyme involved in glycosylphosphatidylinositol (GPI) synthesis, is responsible for the homogeneous lamin meshwork in Drosophila. Loss of PIGB resulted in heterogeneous distributions of B-type lamin and lamin-binding proteins in larval muscles. These phenotypes were rescued by expression of PIGB lacking GPI synthesis activity. The PIGB mutant exhibited changes in lamina-associated domains that are large heterochromatic genomic regions in the NL, reduction of nuclear stiffness, and deformation of muscle fibers. These results suggest that PIGB maintains the homogeneous meshwork of the NL, which may be essential for chromatin distribution and nuclear mechanical properties.
    DOI:  https://doi.org/10.1083/jcb.202301062
  17. Sci Adv. 2024 Jan 26. 10(4): eadj7681
    Regeneration of actin filament branches from the same Arp2/3 complex.
    Foad Ghasemi, LuYan Cao, Miroslav Mladenov, Bérengère Guichard, Michael Way, Antoine Jégou, Guillaume Romet-Lemonne.
      Branched actin filaments are found in many key cellular structures. Branches are nucleated by the Arp2/3 complex activated by nucleation-promoting factor (NPF) proteins and bound to the side of preexisting "mother" filaments. Over time, branches dissociate from their mother filament, leading to network reorganization and turnover, but this mechanism is less understood. Here, using microfluidics and purified proteins, we examined the dissociation of individual branches under controlled biochemical and mechanical conditions. We observe that the Arp2/3 complex remains bound to the mother filament after most debranching events, even when accelerated by force. Strikingly, this surviving Arp2/3 complex readily nucleates a new actin filament branch, without being activated anew by an NPF: It simply needs to exchange its nucleotide and bind an actin monomer. The protein glia maturation factor (GMF), which accelerates debranching, prevents branch renucleation. Our results suggest that actin filament renucleation can provide a self-repair mechanism, helping branched networks to sustain mechanical stress in cells over extended periods of time.
    DOI:  https://doi.org/10.1126/sciadv.adj7681
  18. Sci Adv. 2024 Jan 26. 10(4): eadh2598
    Time-dependent effects of BRAF-V600E on cell cycling, metabolism, and function in engineered myocardium.
    Nicholas Strash, Sophia DeLuca, Geovanni L Janer Carattini, Yifan Chen, Tianyu Wu, Abbigail Helfer, Jacob Scherba, Isabella Wang, Mehul Jain, Ramona Naseri, Nenad Bursac.
      Candidate cardiomyocyte (CM) mitogens such as those affecting the extracellular signal-regulated kinase (ERK) signaling pathway represent potential targets for functional heart regeneration. We explored whether activating ERK via a constitutively active mutant of B-raf proto-oncogene (BRAF), BRAF-V600E (caBRAF), can induce proproliferative effects in neonatal rat engineered cardiac tissues (ECTs). Sustained CM-specific caBRAF expression induced chronic ERK activation, substantial tissue growth, deficit in sarcomeres and contractile function, and tissue stiffening, all of which persisted for at least 4 weeks of culture. caBRAF-expressing CMs in ECTs exhibited broad transcriptomic changes, shift to glycolytic metabolism, loss of connexin-43, and a promigratory phenotype. Transient, doxycycline-controlled caBRAF expression revealed that the induction of CM cycling is rapid and precedes functional decline, and the effects are reversible only with short-lived ERK activation. Together, direct activation of the BRAF kinase is sufficient to modulate CM cycling and functional phenotype, offering mechanistic insights into roles of ERK signaling in the context of cardiac development and regeneration.
    DOI:  https://doi.org/10.1126/sciadv.adh2598
  19. bioRxiv. 2024 Jan 09. pii: 2024.01.08.573270. [Epub ahead of print]
    An internally controlled system to study microtubule network diversification links tubulin evolution to the use of distinct microtubule regulators.
    Andrew S Kennard, Katrina B Velle, Ravi Ranjan, Danae Schulz, Lillian K Fritz-Laylin.
      Diverse eukaryotic cells assemble microtubule networks that vary in structure and composition. While we understand how cells build microtubule networks with specialized functions, we do not know how microtubule networks diversify across deep evolutionary timescales. This problem has remained unresolved because most organisms use shared pools of tubulins for multiple networks, making it impossible to trace the evolution of any single network. In contrast, the amoeboflagellate Naegleria uses distinct tubulin genes to build distinct microtubule networks: while Naegleria builds flagella from conserved tubulins during differentiation, it uses divergent tubulins to build its mitotic spindle. This genetic separation makes for an internally controlled system to study independent microtubule networks in a single organismal and genomic context. To explore the evolution of these microtubule networks, we identified conserved microtubule binding proteins and used transcriptional profiling of mitosis and differentiation to determine which are upregulated during the assembly of each network. Surprisingly, most microtubule binding proteins are upregulated during only one process, suggesting that Naegleria uses distinct component pools to specialize its microtubule networks. Furthermore, the divergent residues of mitotic tubulins tend to fall within the binding sites of differentiation-specific microtubule regulators, suggesting that interactions between microtubules and their binding proteins constrain tubulin sequence diversification. We therefore propose a model for cytoskeletal evolution in which pools of microtubule network components constrain and guide the diversification of the entire network, so that the evolution of tubulin is inextricably linked to that of its binding partners.
    DOI:  https://doi.org/10.1101/2024.01.08.573270
  20. Proc Natl Acad Sci U S A. 2024 Jan 30. 121(5): e2317418121
    A spatiotemporal molecular atlas of the ovulating mouse ovary.
    Madhav Mantri, Hanxue Hannah Zhang, Emmanuel Spanos, Yi A Ren, Iwijn De Vlaminck.
      Ovulation is essential for reproductive success, yet the underlying cellular and molecular mechanisms are far from clear. Here, we applied high-resolution spatiotemporal transcriptomics to map out cell type- and ovulation stage-specific molecular programs as function of time during follicle maturation and ovulation in mice. Our analysis revealed dynamic molecular transitions within granulosa cell types that occur in tight coordination with mesenchymal cell proliferation. We identified molecular markers for the emerging cumulus cell fate during the preantral-to-antral transition. We describe transcriptional programs that respond rapidly to ovulation stimulation and those associated with follicle rupture, highlighting the prominent roles of apoptotic and metabolic pathways during the final stages of follicle maturation. We further report stage-specific oocyte-cumulus cell interactions and diverging molecular differentiation in follicles approaching ovulation. Collectively, this study provides insights into the cellular and molecular processes that regulate mouse ovarian follicle maturation and ovulation with important implications for advancing therapeutic strategies in reproductive medicine.
    Keywords:  fertility; folliculogenesis; ovulation; reproductive biology; spatial transcriptomics
    DOI:  https://doi.org/10.1073/pnas.2317418121
  21. Mol Hum Reprod. 2024 Jan 19. pii: gaae001. [Epub ahead of print]
    Antioxidant sericin averts the disruption of oocyte-follicular cell communication triggered by oxidative stress.
    Hafiza Khatun, Ken-Ichi Yamanaka, Satoshi Sugimura.
      Antioxidants are free radical scavengers that increase oocyte quality and improve female fertility by suppressing oxidative stress. However, the related mechanisms remain unclear. The present study was designed to examine whether a reduction of oxidative stress from using the antioxidant sericin led to expanded cumulus cell (CC)-oocyte communication and oocyte developmental acquisition in a bovine model. We found that cumulus-oocyte complexes (COCs) matured in the presence of sericin showed a significantly increased oocyte meiotic maturation rate (P < 0.01) and accelerated subsequent blastocyst formation, as more blastocysts were found at the hatched stage (P < 0.05) compared to that in the control group. In contrast to the control group, sericin suppressed H2O2 levels in COCs, resulting in a markedly enhanced CC-oocyte gap junction communication index and number of transzonal projections, which were preserved until 18 h of oocyte maturation. These findings indicate that sericin reduces disruption of oocyte-follicular cell communication induced by oxidative stress. Sericin consistently increased intra-oocyte GSH levels and reduced oocyte H2O2 levels (P < 0.05), both of which were ablated when GSH synthesis was inhibited by buthionine sulfoximide (an inhibitor of GSH synthesis). Furthermore, the inhibition of GSH synthesis counteracted the positive effects of sericin on subsequent embryo developmental competence (P < 0.01). Intra-oocyte GSH levels were positively associated with blastocyst development and quality. These outcomes demonstrate new perspectives for the improvement of oocyte quality in assisted reproductive technology and may contribute to developing treatment strategies for infertility and cancer.
    Keywords:  antioxidant sericin; oocyte competence; oocyte maturation; oocyte–follicular cell communication; oxidative stress; transzonal projections
    DOI:  https://doi.org/10.1093/molehr/gaae001
  22. Mol Cell. 2024 Jan 15. pii: S1097-2765(23)01071-7. [Epub ahead of print]
    BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair.
    Pei Xin Lim, Mahdia Zaman, Weiran Feng, Maria Jasin.
      Tumor suppressor BRCA2 functions in homology-directed repair (HDR), the protection of stalled replication forks, and the suppression of replicative gaps, but their relative contributions to genome integrity and chemotherapy response are under scrutiny. Here, we report that mouse and human cells require a RAD51 filament stabilization motif in BRCA2 for fork protection and gap suppression but not HDR. In mice, the loss of fork protection/gap suppression does not compromise genome stability or shorten tumor latency. By contrast, HDR deficiency increases spontaneous and replication stress-induced chromosome aberrations and tumor predisposition. Unlike with HDR, fork protection/gap suppression defects are also observed in Brca2 heterozygous cells, likely due to reduced RAD51 stabilization at stalled forks/gaps. Gaps arise from PRIMPOL activity, which is associated with 5-hydroxymethyl-2'-deoxyuridine sensitivity due to the formation of SMUG1-generated abasic sites and is exacerbated by poly(ADP-ribose) polymerase (PARP) inhibition. However, HDR proficiency has the major role in mitigating sensitivity to chemotherapeutics, including PARP inhibitors.
    Keywords:  BRCA2; PARP inhibitors; PRIMPOL; RAD51; gap suppression; hmdU; homologous recombination; homology-directed repair; stalled fork protection
    DOI:  https://doi.org/10.1016/j.molcel.2023.12.025
  23. Curr Opin Cell Biol. 2024 Jan 22. pii: S0955-0674(23)00162-X. [Epub ahead of print]86 102313
    Lamins: The backbone of the nucleocytoskeleton interface.
    Joan M Sobo, Nicholas S Alagna, Sean X Sun, Katherine L Wilson, Karen L Reddy.
      The nuclear lamina (NL) is a crucial component of the inner nuclear membrane (INM) and consists of lamin filaments and associated proteins. Lamins are type V intermediate filament proteins essential for maintaining the integrity and mechanical properties of the nucleus. In human cells, 'B-type' lamins (lamin B1 and lamin B2) are ubiquitously expressed, while 'A-type' lamins (lamin A, lamin C, and minor isoforms) are expressed in a tissue- and development-specific manner. Lamins homopolymerize to form filaments that localize primarily near the INM, but A-type lamins also localize to and function in the nucleoplasm. Lamins play central roles in the assembly, structure, positioning, and mechanics of the nucleus, modulating cell signaling and influencing development, differentiation, and other activities. This review highlights recent findings on the structure and regulation of lamin filaments, providing insights into their multifaceted functions, including their role as "mechanosensors", delving into the emerging significance of lamin filaments as vital links between cytoskeletal and nuclear structures, chromatin organization, and the genome.
    DOI:  https://doi.org/10.1016/j.ceb.2023.102313
  24. Cell Chem Biol. 2024 Jan 20. pii: S2451-9456(23)00476-2. [Epub ahead of print]
    PARP trapping is governed by the PARP inhibitor dissociation rate constant.
    Angelica A Gopal, Bianca Fernandez, Justin Delano, Ralph Weissleder, J Matthew Dubach.
      Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are a class of cancer drugs that enzymatically inhibit PARP activity at sites of DNA damage. Yet, PARPi function mainly by trapping PARP1 onto DNA with a wide range of potency among the clinically relevant inhibitors. How PARPi trap and why some are better trappers remain unknown. Here, we show trapping occurs primarily through a kinetic phenomenon at sites of DNA damage that correlates with PARPi koff. Our results suggest PARP trapping is not the physical stalling of PARP1 on DNA, rather the high probability of PARP re-binding damaged DNA in the absence of other DNA-binding protein recruitment. These results clarify how PARPi trap, shed new light on how PARPi function, and describe how PARPi properties correlate to trapping potency.
    Keywords:  DNA damage repair; PARP; PARP inhibitor; PARP trapping; PARP1; dissociation rate; protein recruitment
    DOI:  https://doi.org/10.1016/j.chembiol.2023.12.019
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