Carnevali, D. | bioRxiv Science

bioRxiv2025

PARP1 Regulates 3D Structure and Function of Super-Enhancers and Hormone-Control Regions in Breast Cancer Cells

Poly (ADP-ribose) polymerase 1 (PARP1) has been linked to various genomic pathways and in the maintenance of genomic stability. PARP1 has also been postulated to regulate cis-regulatory elements, but the mechanisms remain largely unknown. Here, we employed genomic approaches to show how PARP1 occupies Super-Enhancers (SEs) of luminal A T47D breast cancer cells and how some PARP1 is dynamically relodged by progesterone at hormone-control regions (HCRs). Disruption of PARP1 causes transcriptome reprogramming, altering the expression of both SE-associated and HCRs-regulated genes. This is achieved through a dual coordinated action in the establishment of long-range and intra-TADs chromatin loops, which are lost upon PARP1 ablation, but enforced by its catalytic inhibition. We show that PARP1 also plays a role in regulation of chromatin compartments. Our results reveal PARP1, as a new chromatin looper and compartments organizer controlling SEs and HCRs genes linked to cell identity and hormonal response in breast cancer cells via 3D genome organization. Highlights (Separate document)O_LIPARP1 occupies cell specific super-enhancers and hormone-control regions. C_LIO_LILoss of PARP1 alters the cell identity and progestin-induced gene expression signature. C_LIO_LIGene expression changes upon PARP1 loss relay on altered 3D chromatin looping and compartments. C_LI eTOC blurbWe have discovered that the nuclear repair protein and cancer drug target; PARP1 is preferentially bound at super-enhancers. The binding of PARP1 is essential for the underlying, cell specific gene expression program and the 3D structure of the chromatin surrounding the super-enhancer regions. Graphical abstractSeparate document O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/668155v1_ufig1.gif" ALT="Figure 1"> View larger version (81K): org.highwire.dtl.DTLVardef@1da9027org.highwire.dtl.DTLVardef@2e1966org.highwire.dtl.DTLVardef@8582eaorg.highwire.dtl.DTLVardef@155e77b_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2023

SMARCAD1 and TOPBP1 contribute to heterochromatin maintenance at the transition from the 2C-like to the pluripotent state

Chromocenters are established after the 2-cell (2C) stage during mouse embryonic development, but the factors that mediate chromocenter formation remain largely unknown. To identify regulators of 2C heterochromatin establishment, we generated an inducible system to convert embryonic stem cells (ESCs) to 2C-like cells. This conversion is marked by a global reorganization and dispersion of H3K9me3-heterochromatin foci, which are then reversibly formed upon re-entry into pluripotency. By profiling the chromatin-bound proteome (chromatome) through genome capture of ESCs transitioning to 2C-like cells, we uncover chromatin regulators involved in de novo heterochromatin formation. We identified TOPBP1 and investigated its binding partner SMARCAD1. SMARCAD1 and TOPBP1 associate with H3K9me3-heterochromatin in ESCs. Interestingly, the nuclear localization of SMARCAD1 is lost in 2C-like cells. SMARCAD1 or TOPBP1 depletion in mouse embryos leads to developmental arrest, reduction of H3K9me3, and remodeling of heterochromatin foci. Collectively, our findings contribute to comprehending the maintenance of chromocenters during early development.

developmental biology↗