A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination

Abstract

SUMMARYDuring class switch recombination (CSR), B cells replace the Igh Cμ or δ exons with another down-stream constant region exon (CH), altering the anti-body isotype. CSR occurs through the introduction of AID-mediated double-strand breaks (DSBs) in switch regions and subsequent ligation of broken ends. Here, we developed an assay to investigate the dynamics of DSB formation in individual cells. We demonstrate that the upstream switch region Sμ is first targeted during recombination and that the mechanism underlying this control relies on 53BP1. Surprisingly, regulation of break order occurs through residual binding of 53BP1 to chromatin before the introduction of damage and independent of its established role in DNA repair. Using chromosome conformation capture, we show that 53BP1 mediates changes in chromatin architecture that affect break order. Finally, our results explain how changes in Igh architecture in the absence of 53BP1 could promote inversional rearrangements that compromise CSR.

Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2

“…Data were visualized with R software suite (www.r-project.org). To generate a 4C library for sequencing, we adapted our recently described protocol (Raviram et al, 2016; Rocha et al, 2016) to capture interactions from the SOX2 promoter.…”

Dynamic 3D chromosomal landscapes in acute leukemia

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“…19 20 In light of these reports, our understanding of how changes in chromatin organization contribute 21 to cancer pathogenesis remains largely unexplored barring a few examples 2,17,18 . In this study, 22 using T cell acute lymphoblastic leukemia (T-ALL) as a model disease 19,20 , we investigated 23 potential reorganization of the global chromatin architecture between primary T cell leukemia 24 samples, leukemia cell lines and healthy T cell controls. Our analysis identified recurrent 25 structural TAD boundary changes and significant alterations in intra-TAD chromatin interactions 26 (TAD activity) that mirrored changes in gene expression.…”

The impact of endogenous retroviruses on nuclear organization and gene expression

“…To address this question we used Hi-C and ChIP-seq data from a splenic murine lymphoma IgM+ B cell line, CH12 that is used as a model for B cells in the same developmental stage as those we use here [58]. We performed a principal component analysis on 200 Kb-binned Hi-C data and classified each bin as compartment A and B depending on a positive or negative principal component score, respectively [59] (Fig.…”

“…Resting mature splenic B cells were isolated as previously described [78] using magnetic beads for CD43 depletion from either C57/Bl6 Taconic mice (C57BL/6NTac) or from 129S6 mice also from Taconic (129S6/SvEvTac). Processing of 4C material was performed as described previously [58] using Dpn2 and Csp6I as enzymes for DNA digestion. Briefly, cells were fixed with formaldehyde and digested in situ with Dpn2.…”