{"messages":[{"status":"ok","category":"all"}], "collection":[{"title":"Isotype specific loss of HP1\u03b1 but not of HP1\u03b2 uncovers genomic regions that behave as HP1\u03b1-dependent common fragile sites","authors":"Yaacoub, K.; Nguyen, T. N.; JULIEN, E.; Cammas, F. M.","author_corresponding":"Florence Marie Cammas","author_corresponding_institution":"IGH","doi":"10.64898\/2026.08.14.744815","date":"2026-08-15","version":"1","type":"new results","license":"cc_by","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/08\/15\/2026.08.14.744815.source.xml","abstract":"HP1 proteins are highly evolutionarily conserved chromatin-associated factors known to play essential roles in genome stability and nuclear organization. In mammals, three HP1 isoforms, HP1, HP1{beta} and HP1{gamma}, have been described, but their individual functions remain incompletely characterized. Here, we inactivated HP1 or HP1{beta} in different cell lines and quantified chromosomal breaks on metaphase spreads in the presence or absence of aphidicolin-induced replication stress. Loss of HP1, but not of HP1{beta}, led to a significant increase of chromosomal breaks on chromosome arms and within pericentromeric heterochromatin under these conditions. Mechanistically, loss of HP1 was associated with a reduction in replication fork velocity, suggesting that HP1 deficiency induces a replication stress that sensitizes specific genomic loci to replication perturbation. Consistent with this, HP1 loss was associated with a moderate but consistent increase in {gamma}H2AX and 53BP1 foci, an increased occurrence of DNA synthesis during mitosis, and enhanced recruitment of FANCD2, all recognized as hallmarks of common fragile site (CFS) expression. In addition, rescue experiments using a chromodomain mutant HP1 (V22M) unable to bind H3K9me3 indicated that HP1 protective function over these specific foci did not require its interaction with this histone mark. Altogether, these data indicate that, independently of its binding to H3K9me3, HP1 stabilizes specific genomic regions that behave as HP1-dependent fragile sites, at least in part by regulating replication fork progression, limiting mitotic DNA synthesis possibly by competing with FANCD2 for chromatin access at these regions.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Streamlining large-scale high-resolution electron tomography with VolWeaver","authors":"Bregy, I.; Mesman, R.; Tassan-Lugrezin, S.; Kooij, T. W. A.; van Niftrik, L. W. A.","author_corresponding":"Irina Bregy","author_corresponding_institution":"Radboud University","doi":"10.64898\/2026.08.14.744809","date":"2026-08-15","version":"1","type":"new results","license":"cc_no","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/08\/15\/2026.08.14.744809.source.xml","abstract":"Researchers using electron microscopy must often balance a trade-off between obtaining high-resolution structural information and preserving sufficient cellular context. At one end of this spectrum, single particle cryo-electron microscopy and cryo-electron tomography provide near-molecular detail but are typically limited to relatively small fields of view. At the other, volume electron microscopy approaches, such as scanning electron microscopy of resin-embedded specimens, capture large cellular volumes but generally at lower resolution. Consequently, linking nanoscale structural information to larger cellular architecture remains a significant challenge. To address this gap, we optimised a transmission electron tomography workflow for resin-embedded malaria parasites that allows us to visualise targeted regions of interest at nanometre-scale resolution while retaining several micrometres of surrounding cellular context. Here, we present our current best-practice pipeline for sample preparation, tomogram acquisition, and reconstruction. In addition, we introduce VolWeaver, a data-processing framework, that integrates high-resolution tomographic datasets into 2 serial section volume reconstructions, enabling the visualisation and interpretation of ultrastructural features within their broader cellular environment.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Polarized F-actin establishes cell interactions required for the formation of a stem cell niche","authors":"Rhymer, E.; Johnson, R.; Hughes, R. M.; Anllo, L.","author_corresponding":"Lauren Anllo","author_corresponding_institution":"East Carolina University","doi":"10.64898\/2026.08.13.744741","date":"2026-08-15","version":"1","type":"new results","license":"cc_by_nc_nd","category":"developmental biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/08\/15\/2026.08.13.744741.source.xml","abstract":"Lifelong stem cells are maintained by a cellular microenvironment called the niche, which enables tissue homeostasis. Proper niche construction is essential for persistent function, but studying niche formation is challenged by the inaccessibility of most niches to in vivo visualization during development. Innovations imaging the Drosophila testis are now allowing investigation of niche inception. F-actin polarizes to precise cell interfaces during testis niche assembly. Yet it is unknown whether polarization directs niche cell motility, or reflects adhesive sorting in response to formation of niche cell contacts. By adapting a method to optogenetically manipulate cortical F-actin via disruption of Rho1, we interrogate the role for cytoskeletal polarization during niche formation with tissue and temporal specificity. Rho1-mediated disruption of F-actin polarization caused defects in niche anterior assembly and architecture. Also, fewer cells adopted bona fide niche identity, given diminished Fas3, N-Cadherin, and Islet. These disrupted niches fail in signaling to germ cells to establish stem cell identity. We reveal that polarized F-actin is crucial for establishing cell contacts to form a functional niche, and to maintain cell identity in the developing tissue.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Location-dependent proteomics of the aorta reveal an atherosclerotic disease gradient shaped by hemodynamics","authors":"Jokumsen, K. V.; Christoffersen, C.; Davies, M. J.; Gamon, L. F.","author_corresponding":"Luke F Gamon","author_corresponding_institution":"Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Sciences Malmo, Lund University, Malmo, Sweden","doi":"10.64898\/2026.08.13.744640","date":"2026-08-15","version":"1","type":"new results","license":"cc_by_nd","category":"biochemistry","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/08\/15\/2026.08.13.744640.source.xml","abstract":"Background and aims: Atherosclerotic plaques form preferentially at vascular sites exposed to disturbed blood flow, yet the protein changes underlying this site-specific plaque development remain unclear. Mouse models are widely used to study atherosclerosis but yield only limited amounts of tissue, previously restricting proteomic studies. However, recent advances in mass spectrometry now enable proteomic profiling of very small tissue samples. We aimed to utilise this to uncover site-specific protein changes in aortic regions prone or resistant to plaque formation. Methods: Aortic arches from apolipoprotein E-deficient (ApoE-\/-) mice fed a Western diet (WD) for 16 weeks were dissected into plaques from the major branches and inner curvature and visibly healthy regions. Proteins were extracted, enzymatically digested, and analysed by liquid chromatography-tandem mass spectrometry (LC-MS\/MS). Results: More than 4000 proteins were identified per sample despite their small size (< 1 mg tissue). Principal component analysis showed clustering by both disease status and anatomical location within the aortic arch, indicating distinct proteomes. Proteins known to drive atherosclerosis -- including vascular cell adhesion molecule 1 (Vcam1), apolipoprotein B (Apob), lipoprotein lipase (Lpl), and galectin 3 (Lgals3) -- were most abundant in advanced plaques and decreased progressively across anatomical regions, reaching their lowest levels in healthy regions furthest from the plaques. Enrichment analysis highlighted pathways related to the extracellular matrix, immune system, hemostasis, and lipoprotein transport as central to disease progression. Conclusions: This study demonstrates the feasibility of region-resolved proteomics in individual murine aortas and provide new molecular insights into the site-specific nature of atherosclerotic plaque development.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"NIR-II squeezed light-field microscopy enables high-speed volumetric imaging of deep-tissue dynamics in vivo","authors":"Kim, D. Y.; Zang, Z.; Lin, E. Y.; Zhao, R.; Wang, J.; Hsiai, T.; Sletten, E. M.; Gao, L.","author_corresponding":"Liang Gao","author_corresponding_institution":"University of California, Los Angeles","doi":"10.64898\/2026.08.13.744709","date":"2026-08-15","version":"1","type":"new results","license":"cc_by_nc_nd","category":"bioengineering","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/08\/15\/2026.08.13.744709.source.xml","abstract":"High-speed three-dimensional imaging in scattering tissues remains challenging because volumetric microscopy generally requires scanning, whereas snapshot light-field approaches divide limited detector pixels among multiple views. This constraint is particularly severe in the second near-infrared window (NIR-II), where commonly used InGaAs cameras typically have relatively small sensor formats and high detector noise. Here we introduce NIR-II squeezed light-field microscopy (NIR-II SLIM), which optically rotates and compresses multiple perspective views before detection, allowing efficient use of camera pixels while retaining complementary spatial information for three-dimensional reconstruction. NIR-II SLIM acquires volumes at up to 600 volumes per second with a reconstructed lateral sampling grid of 512 by 512 pixels. We use the method for label-free four-dimensional imaging of cardiac dynamics in pigmented late-larval zebrafish, resolving chamber deformation and millisecond-scale atrioventricular-valve motion, and for NIR-II fluorescence imaging of vascular and lymphatic transport in mice. NIR-II SLIM provides a detector-efficient approach for high-speed volumetric imaging of rapid biological dynamics in scattering tissues.","funder":"NA","published":"NA","server":"bioRxiv"}]}