Biology subjects

Bourc'his, D.

Publications and source records attributed to Bourc'his, D..

10 recordsLinked to original sources

bioRxiv2026

Transposable Element insertions Repurpose Immune Endonucleases as Drivers of Reproductive Isolation in Mice

The emergence of reproductive barriers between closely related populations is a fundamental step in speciation, yet the underlying genetic mechanisms remain poorly understood in mammals. Here we resolve the DDK syndrome, a long-standing model of hybrid incompatibility in mice, by showing that two independent retrotransposon insertions rewire immune Schlafen endoribonuclease genes expression, causing hybrid embryo death. A DDK-private MERVL element drives ectopic oocyte expression of Slfn1, while an intragenic ETn/MusD insertion in incompatible strains is associated with zygotic Slfn15 expression. SLFN1-SLFN15 heterodimerization constitutively activates tRNA ribonuclease activity, leading to global translation inhibition, and integrated stress response activation. Abolishing SLFN1 catalytic activity or SLFN15 expression rescues syndromic embryo development. Our findings uncover a previously unrecognized speciation mechanism in which transposable elements repurpose immune effectors as drivers of postzygotic reproductive isolation.

developmental biology↗

bioRxiv2026

Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland

Single-cell multi-omics methods enable simultaneous mapping of chromatin states and transcriptomes, offering deep insights into gene regulation. Yet, the full potential of these approaches remains untapped for rare cell populations, as most methods require thousands of cells and are limited in their ability to capture multiple molecular layers comprehensively within the same cell. Here, we introduce OneCell CUT&Tag a user-friendly method that provides matched high-resolution epigenome, full-transcriptome, and surface marker quantification from every cell, with input as low as one cell. Using this approach, we uncovered epigenomic priming of basal cells in the mammary gland and captured the dynamics of basal-to-luminal transdifferentiation. We identified a transitional cell population with intermediate epigenomic profiles--absent in reference populations--and demonstrated a continuous epigenomic progression from basal to luminal states, while transcriptomes exhibited a binary switch. Adaptable to diverse samples and tissues, this method also revealed the role of H3K27me3 in shaping zygotic expression programs. By matching multiple layers of molecular information at single-cell resolution, OneCell CUT&Tag dissects the complementary roles of each omics layer in shaping cellular identity and function, opening new avenues to study rare and complex biological systems.

genomics↗

bioRxiv2023

Spatio-temporal X-linked gene reactivation and site-specific retention of epigenetic silencing in the in vivo germline.

Random X-chromosome inactivation (XCI) is a hallmark of female mammalian somatic cells. This epigenetic mechanism, mediated by the long non-coding RNA Xist, occurs in the epiblast and is stably maintained to ensure proper dosage compensation of X-linked genes during life. However, this silencing is lost during primordial germ cell (PGC) development. Using a combination of single-cell allele-specific RNA sequencing and low-input chromatin profiling in developing in vivo PGC, we provide unprecedented detailed maps of gene reactivation. We demonstrated that PGC still carry a fully silent X chromosome on embryonic day (E) 9.5, despite the loss of Xist expression. X-linked genes are then gradually reactivated outside the Xist first-bound regions. At E12.5, a significant part of the inactive X chromosome (Xi) still resists reactivation, carrying an epigenetic memory of its silencing. Late-reactivated genes are enriched in repressive chromatin marks, including DNA methylation and H3K27me3 marks. Our results define the timing of reactivation of the silent X chromosome a key event in female PGC reprogramming with direct implications for reproduction.

developmental biology↗

bioRxiv2022

DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation

Somatic DNA methylation is established early during mammalian development, as embryonic cells transition from naive to primed pluripotency. This precedes the emergence of the three somatic germ layers, but also the segregation of the germline that undergoes genome-wide DNA demethylation after specification. While DNA methylation is essential for embryogenesis, the point at which it becomes critical during differentiation and whether all lineages equally depend on it is unclear. Using culture modeling of cellular transitions, we found that DNA methylation-free embryonic stem cells (ESCs) with a triple DNA methyltransferase knockout (TKO) normally progressed through the continuum of pluripotency states, but demonstrated skewed differentiation abilities towards neural versus other somatic lineages. More saliently, TKO ESCs were fully competent for establishing primordial germ cell-like cells (PGCLCs), even showing temporally extended and self-sustained capacity for the germline fate. By mapping chromatin states, we found that the neural and germline lineages are linked by a similar enhancer dynamics during priming, defined by common sets of methyl-sensitive transcription factors that fail to be decommissioned in absence of DNA methylation. We propose that DNA methylation controls the temporality of a coordinated neural-germline axis of preferred differentiation route during early development.

developmental biology↗

bioRxiv2022

Assessing the influence of distinct IVF culture media on human pre-implantation development using single-embryo transcriptomics

The use of Assisted Reproductive Technologies (ART) is consistently rising across the world. However, making an informed choice on which embryo culture medium should be preferred to ensure satisfactory pregnancy rates and the health of future children critically lacks scientific background. Particularly, embryos within their first days of development are highly sensitive to their micro-environment. Here, we aimed to determine the impact of culture media composition on gene expression of human preimplantation embryos. By employing single-embryo RNA-sequencing after 2 or 5 days of post-fertilization culture in different commercially available media, we revealed medium-specific differences in gene expression changes. In particular, we found that culture medium composition can affect the dynamics of expression of developmentally relevant genes at day-2 but the differences were mitigated at the blastocyst stage. This study highlights the ability of embryos conceived in suboptimal in vitro culture media to recover proper transcriptome competency.

developmental biology↗

bioRxiv2022

Multi-omics comparison of malignant and normal uveal melanocytes reveals novel molecular features of uveal melanoma.

Uveal Melanoma (UM) is a rare cancer resulting from transformation of melanocytes residing in the uveal tract. Integrative analysis has identified four molecular and clinical subsets in UM. To improve our molecular understanding of UM we performed extensive multi-omics characterization comparing two aggressive UM patient-derived xenograft models with normal choroidal melanocytes, including DNA optical mapping, specific histone modifications, and DNA topology analysis by Hi-C. Our gene expression and cytogenetic analyses suggest that genomic instability is a hallmark of UM. We also identified a recurrent deletion in the BAP1 promoter resulting in loss of expression and associated with high risk of metastases in UM patients. Hi-C revealed chromatin topology changes associated with up-regulation of PRAME, an independent prognostic biomarker in UM and potential therapeutic target. Our findings illustrate how multi-omics approaches can improve the understanding of tumorigenesis and reveals two novel mechanisms of gene expression dysregulation in UM.

genomics↗

bioRxiv2021

DNMT3A-dependent DNA methylation is required for spermatogonial stem cells to commit to spermatogenesis

DNA methylation plays a critical role in spermatogenesis, as evidenced by the male sterility of DNA methyltransferase (DNMT) mutant mice. Here, we report a striking division of labor in the establishment of the methylation landscape of male germ cells and its functions in spermatogenesis: while DNMT3C is essential for preventing retrotransposons from interfering with meiosis, DNMT3A broadly methylates the genome--at the exception of DNMT3C-dependent retrotransposons--and controls spermatogonial stem cell (SSC) plasticity. By reconstructing developmental trajectories through single-cell RNA-seq and by profiling chromatin states, we found that Dnmt3A mutant SSCs can only self-renew and no longer differentiate due to spurious enhancer activation that enforces an irreversible stem cell gene program. We therefore provide a novel function for DNA methylation in male fertility: the epigenetic programming of SSC commitment to differentiation and to life-long spermatogenesis supply.

developmental biology↗

bioRxiv2021

The imprinted Zdbf2 gene finely tunes control of feeding and growth in neonates

Genomic imprinting refers to the mono-allelic and parent-specific expression of a subset of genes. While long recognized for their role in embryonic development, imprinted genes have recently emerged as important modulators of postnatal physiology, notably through hypothalamus-driven functions. Here, using mouse models of loss, gain and parental inversion of expression, we report that the paternally expressed Zdbf2 gene controls neonatal growth in mice, in a dose-sensitive but parent-of-origin-independent manner. We further found that Zdbf2-KO neonates failed to fully activate hypothalamic circuits that stimulate appetite, and suffered milk deprivation and diminished circulating Insulin Growth Factor 1 (IGF-1). Consequently, only half of Zdbf2-KO pups survived the first days after birth and those surviving were smaller. This study demonstrates that precise imprinted gene dosage is essential for vital physiological functions at the transition from intra- to extra-uterine life, here the adaptation to oral feeding and optimized body weight gain.

molecular biology↗

bioRxiv2020

m6A RNA methylation regulates the fate of endogenous retroviruses

Endogenous retroviruses (ERVs) are abundant and heterogenous groups of integrated retroviral sequences that impact genome regulation and cell physiology throughout their RNA-centered life cycle1. Failure to repress ERVs is associated with cancer, infertility, senescence and neurodegenerative diseases2-4. Here, using an unbiased genome-scale CRISPR knockout screen in mouse embryonic stem cells, we identify m6A RNA methylation as a novel means of ERV restriction. Methylation of ERV mRNAs is catalyzed by the complex of methyltransferase-like METTL3/METTL145 proteins whose depletion, along with their accessory subunits, WTAP and ZC3H13, led to increased mRNA abundance of Intracisternal A-particles (IAPs) and related ERVK elements specifically, by targeting their 5UTR region. Using controlled auxin-dependent degradation of the METTL3/METTL14 enzymatic complex, we showed that IAP mRNA and protein abundance is dynamically and inversely correlated with m6A catalysis. By monitoring mRNA degradation rates upon METTL3/14 double degron, we further proved that m6A methylation destabilizes IAP transcripts. Finally, similarly to m6A writers, triple knockout of the m6A readers YTHDF1, DF2 and DF36 increased IAP mRNA abundance. This study sheds light onto a novel function of RNA methylation in protecting cellular integrity by clearing reactive ERV-derived RNA species, which may be especially important when transcriptional silencing is less stringent.

cell biology↗

bioRxiv2018

Dynamic enhancer partitioning instructs activation of a growth regulator during exit from naïve pluripotency

During early mammalian development, the genome undergoes profound transitions in chromatin states, topological organization and recruitment of cis regulatory factors involved in transcriptional control. How these three layers of gene regulation interact is the matter of intense research. The Zdbf2 gene--which is involved in growth control--provides a valuable model to study this question: upon exit from naive pluripotency and prior to tissue differentiation, it undergoes a switch in usage from a distal to a proximal promoter, along with a switch in chromatin states, from polycomb to DNA methylation occupancy. Using an embryonic stem cell (ESC) culture system to mimic this period, we show here that four enhancers contribute to the Zdbf2 promoter switch, concomitantly with dynamic changes in chromosome architecture. Indeed, CTCF plays a key role in partitioning the locus in ESCs, to facilitate enhancer contact with the distal Zdbf2 promoter only. Partition relieving enhances proximal Zdbf2 promoter activity, as observed during differentiation or with mutants that lack local CTCF-based partition. Importantly, we show that CTCF-based regulation occurs independently of the polycomb and DNA methylation pathways. Our study reveals the importance of multi-layered regulatory frameworks to ensure proper spatio-temporal activation of developmentally important genes.

molecular biology↗