Azria, B. | bioRxiv Science

bioRxiv2026

CTCF-mediated cis-regulatory chromatin insulation enforces a central B-cell tolerance checkpoint

The generation of a diverse and self-tolerant B cell repertoire is essential for adaptive immunity and is achieved through V(D)J recombination. In mice, Ig{kappa} is the dominant light chain, whereas Ig{lambda} rearrangement typically occurs in response to nonproductive or autoreactive Ig{kappa} recombination, a process termed receptor editing. Recombination at the RS element deletes the Ig{kappa} constant exon, silencing the locus and enabling Ig{lambda} expression. However, the epigenetic regulatory framework that orchestrates and governs receptor editing remains poorly defined. Here, we identify a CTCF-binding insulator element (CBE) within the 3' Ig{kappa} super-enhancer (3'-SE{kappa}) that regulates receptor editing and directs the {kappa}-to-{lambda} switch required for Ig{lambda} B-cell development. Mechanistically, loss of this CBE activates an insulated enhancer within the 3'-SE{kappa}, causing aberrant V{kappa} rearrangements and altered chromatin interactions through disrupted loop extrusion dynamics. Notably, loss of this CBE in mice leads to increased autoantibody production by ten weeks of age, demonstrating that CBE-mediated chromatin architecture shapes B cell fate by constraining autoreactive potential. Collectively, our findings define a novel CTCF-dependent cis-regulatory insulation checkpoint that connects chromatin loop extrusion to antigen-driven receptor editing, thereby enforcing B-cell tolerance.

immunology↗

bioRxiv2024

ChIP-seq of Urinary Cell-Free Chromatin Infers Tissue Origin and Detects Tumor-Derived Cell-Free DNA in Bladder Cancer

Urine contains fragments of cell-free DNA, which hold valuable molecular insights into the processes occurring within the urinary system and the whole body. It is unknown whether these fragments are in the form of chromatin, as in the cell of origin, and whether they maintain the cell of origin chromatin modifications. Here, we examine these questions using cell-free chromatin immunoprecipitation followed by sequencing (cfChIP-seq) on human urine. We demonstrate that we can capture cell-free nucleosomes (cf-nucleosomes) from urine and that these preserve multiple histone post-translational modifications indicative of activation and repression. By analyzing these modifications, we identified the primary tissues contributing to cf-nucleosomes in a cohort of healthy individuals. Notably, we observe distinct populations of circulating cf-nucleosomes in urine samples from healthy donors with a contribution from the kidney, which are not detected in matched urine exfoliated cells or matching plasma samples. We further show that, at most, a negligible amount of urine cf-nucleosomes originates from plasma, suggesting that kidney filtration excludes plasma-circulating nucleosomes from urine. Additionally, we show that urine cf nucleosomes can report pathologically driven changes in the urine of bladder cancer patients, reflecting tumor-associated transcriptional programs and immune responses. Our findings highlight the potential of urine cf nucleosomes as accessible, noninvasive biomarkers for both basic research in renal physiology and monitoring urinary pathologies. Key FindingsO_LIUrine cell-free nucleosomes exist and retain multiple histone marks that are informative of gene promoters and enhancers. C_LIO_LIUrine cfChIP-seq identifies bladder, kidney, and immune cells as the major contributing organs to the pool of urine cell-free nucleosomes. C_LIO_LIThe populations of cell-free nucleosomes in urine and blood are distinct and primarily disjoint, suggesting that few, if any, nucleosomes cross the blood-urine interface. C_LIO_LIUrine cell-free nucleosomes reflect pathologically driven changes in tumors and immune cells responding to the tumor. C_LI

genomics↗