Biology subjects

Andrau, J.-C.

Publications and source records attributed to Andrau, J.-C..

4 recordsLinked to original sources

bioRxiv2025

Extracellular matrix stiffness modulates nuclear lamina organisation and sets nuclear conditions for PRC2 repression.

Capability of cells to respond to tissue-level elasticity has important physiological and pathological implications. Stiffening of the extracellular matrix (ECM) promotes invasive behaviour of cancer cells, supports the transformation of fibroblasts into cancer-associated fibroblasts and primes stem cell differentiation programs. Here, we investigated how ECM stiffness modulates the Nuclear Lamina (NL) and its impact on gene expression programs, epigenetic marking and 3D genome organisation. By combining hydrogel cell culturing of primary fibroblasts, genomics and super-resolution microscopy, we found that ECM stiffness modifies composition of the NL, modulates long range chromatin interactions, induces changes in chromatin motion and regulates thousands of genes. We identified a specific set of genes coding proteins involved in pathways related to mechanical adaptation such as adhesion and signalling. These genes harbour an apparent bivalent chromatin signature and are expressed under soft condition while repressed in stiff condition through Polycomb Repressive Complex 2 (PRC2). We found that this stiffness-specific repression is tempered by mechano-transduction and the NL. This work uncovers mechano-dependent NL composition, changes in 3D genome organisation and in chromatin motion which underlie adaptative gene expression programs controlled through PRC2.

genomics↗

bioRxiv2023

G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausing

Despite their central role in transcription, it has been difficult to define universal sequences associated to eukaryotic promoters. Within chromatin context, recruitment of the transcriptional machinery requires opening of the promoter but how DNA elements could contribute to this process has remained elusive. Here, we show that G-quadruplex (G4) secondary structures are highly enriched mammalian core promoter elements. G4s are located at the deepest point of nucleosome exclusion at promoters and correlate with maximum promoter activity. We found that experimental G4s exclude nucleosomes both in vivo and in vitro and display a strong positioning potential. At model promoters, impairing G4s affected both transcriptional activity and chromatin opening. G4 destabilization also resulted in an inactive promoter state and affected transition to effective RNA production in live imaging experiments. Finally, G4 stabilization resulted in global reduction of proximal promoter pausing. Altogether, our data introduce G4s as bona fide promoter elements allowing nucleosome exclusion and facilitating pause release by the RNA Polymerase II.

genomics↗

bioRxiv2021

The control of transcriptional memory by stable mitotic bookmarking

To maintain cellular identities during development, gene expression profiles must be faithfully propagated through cell generations. The reestablishment of gene expression patterns upon mitotic exit is thought to be mediated, in part, by mitotic bookmarking by transcription factors (TF). However, the mechanisms and functions of TF mitotic bookmarking during early embryogenesis remain poorly understood. In this study, taking advantage of the naturally synchronized mitoses of Drosophila early embryos, we provide evidence that the pioneer-like transcription factor GAF acts as stable mitotic bookmarker during zygotic genome activation. We report that GAF remains associated to a large fraction of its interphase targets including at cis-regulatory sequences of key developmental genes, with both active and repressive chromatin signatures. GAF mitotic targets are globally accessible during mitosis and are bookmarked via histone acetylation (H4K8ac). By monitoring the kinetics of transcriptional activation in living embryos, we provide evidence that GAF binding establishes competence for rapid activation upon mitotic exit.

developmental biology↗

bioRxiv2020

Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting

Promoter-proximal polymerase pausing is a key process regulating gene expression. In latent HIV-1 cells, it prevents viral transcription and is essential for latency maintenance, while in acutely infected cells the viral factor Tat releases paused polymerase to induce viral expression. Pausing is fundamental for HIV-1, but how it contributes to bursting and stochastic viral reactivation is unclear. Here, we performed single molecule imaging of HIV-1 transcription, and we developed a quantitative analysis method that manages multiple time scales from seconds to days, and that rapidly fits many models of promoter dynamics. We found that RNA polymerases enter a long-lived pause at latent HIV-1 promoters (>20 minutes), thereby effectively limiting viral transcription. Surprisingly and in contrast to current models, pausing appears stochastic and not obligatory, with only a small fraction of the polymerases undergoing long-lived pausing in absence of Tat. One consequence of stochastic pausing is that HIV-1 transcription occurs in bursts in latent cells, thereby facilitating latency exit and providing a rationale for the stochasticity of viral rebounds.

systems biology↗