Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning [ChIP-Seq]

ABSTRACT: RAG endonuclease initiates V(D)J recombination in progenitor (pro)-B cells. Upon binding a recombination center (RC)-based JH, RAG scans upstream chromatin via loop extrusion, potentially mediated by cohesin, to locate Ds and assemble a DJH-based RC. CTCF looping factor-bound elements (CBEs) within the IGCR1 element upstream of the Ds impede RAG-scanning; but their inactivation allows scanning to proximal VHs where additional CBEs activate rearrangement and impede scanning any further upstream. Distal VH utilization is thought to involve diffusional RC access following large-scale Igh locus contraction. Here, we test the potential of linear RAG-scanning to mediate distal VH usage in G1-arrested, v-Abl-pro-B cell lines, which undergo robust D-to-JH rearrangement, but little VH-to-DJH rearrangement, presumably due to lack of locus contraction. Through an auxin-induced approach, we degrade cohesin-component Rad21 or CTCF in these G1-arrested lines, which maintain substantial viability throughout four-day experiments. Rad21 degradation eliminated all V(D)J recombination and RAG-scanning-associated interactions, except RC-located DQ52-to-JH joining in which synapsis occurs by diffusion11. Remarkably, while CTCF degradation suppressed most CBE-based chromatin interactions, it promoted robust RC interactions with, and VH-to-DJH joining of, distal VHs, with patterns similar to those of "locus-contracted" primary pro-B cells. Thus, down-modulation of CTCF-bound scanning-impediment activity promotes cohesin-driven RAG-scanning across the 2.7Mb Igh locus.

ORGANISM(S): Mus musculus

PROVIDER: GSE142779 | GEO | 2020/05/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning [GRO-Seq]

Project description:RAG endonuclease initiates V(D)J recombination in progenitor (pro)-B cells. Upon binding a recombination center (RC)-based JH, RAG scans upstream chromatin via loop extrusion, potentially mediated by cohesin, to locate Ds and assemble a DJH-based RC. CTCF looping factor-bound elements (CBEs) within the IGCR1 element upstream of the Ds impede RAG-scanning; but their inactivation allows scanning to proximal VHs where additional CBEs activate rearrangement and impede scanning any further upstream. Distal VH utilization is thought to involve diffusional RC access following large-scale Igh locus contraction. Here, we test the potential of linear RAG-scanning to mediate distal VH usage in G1-arrested, v-Abl-pro-B cell lines, which undergo robust D-to-JH rearrangement, but little VH-to-DJH rearrangement, presumably due to lack of locus contraction. Through an auxin-induced approach, we degrade cohesin-component Rad21 or CTCF in these G1-arrested lines, which maintain substantial viability throughout four-day experiments. Rad21 degradation eliminated all V(D)J recombination and RAG-scanning-associated interactions, except RC-located DQ52-to-JH joining in which synapsis occurs by diffusion11. Remarkably, while CTCF degradation suppressed most CBE-based chromatin interactions, it promoted robust RC interactions with, and VH-to-DJH joining of, distal VHs, with patterns similar to those of "locus-contracted" primary pro-B cells. Thus, down-modulation of CTCF-bound scanning-impediment activity promotes cohesin-driven RAG-scanning across the 2.7Mb Igh locus.

2020-05-11 | GSE142780 | GEO

CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning [3C-HTGTS]

2020-05-11 | GSE142778 | GEO

CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning [LAM-HTGTS]

2020-05-11 | GSE142777 | GEO

CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning [dataset 3]

Project description:RAG endonuclease initiates antibody heavy chain variable region exon assembly from V, D, and J segments within a chromosomal V(D)J recombination center (RC) by cleaving between paired gene segments and flanking recombination signal sequences (RSSs). The IGCR1 control region promotes DJH intermediate formation by isolating Ds, JHs, and RC from upstream VHs in a chromatin loop anchored by CTCF-binding elements ("CBEs"). How VHs access the DJHRC for VH to DJH rearrangement was unknown. We report that CBEs immediately downstream of frequently rearranged VH-RSSs increase recombination potential of their associated VH far beyond that provided by RSSs alone. This CBE activity becomes particularly striking upon IGCR1 inactivation, which allows RAG, likely via loop extrusion, to linearly scan chromatin far upstream. VH-associated CBEs stabilize interactions of D-proximal VHs first encountered by the DJHRC during linear RAG scanning and, thereby, promote dominant rearrangement of these VHs by an unanticipated chromatin accessibility-enhancing CBE function.

2018-07-03 | GSE113022 | GEO

CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning [dataset 2]

2018-07-03 | GSE112822 | GEO

CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning [dataset 1]

2018-07-03 | GSE112781 | GEO

Loop Extrusion Mediates Physiological Locus Contraction for V(D)J Recombination (LAM-HTGTS)

Project description:Immunoglobulin heavy chain locus (Igh) VH, D, and JH gene segments are developmentally assembled into V(D)J exons. RAG endonuclease initiates V(D)J recombination by binding a JH-recombination signal sequence (RSS) within a chromatin-based recombination center (RC) and then, in an orientation-dependent process, scans upstream D-containing chromatin presented by cohesin-mediated loop extrusion for convergent D-RSSs to initiate DJH-RC formation. In primary pro-B cells, 100s of upstream VH-associated RSSs, embedded in convergent orientation to the DJH-RC-RSS, gain proximity to the DJH-RC for VH-to-DJH joining via a mechanistically-undefined VH-locus contraction process. Here, we report that a 2.4 mega-base VH locus inversion in primary pro-B cells nearly abrogates rearrangements of normally convergent VH-RSSs and cryptic RSSs, even though locus contraction per se is maintained. Moreover, this inversion activated rearrangement of both cryptic VH-locus RSSs normally in the opposite orientation and, unexpectedly, of normally-oriented cryptic RSSs within multiple, sequential upstream convergent-CBE domains. Primary pro-B cells had significantly reduced transcription of Wapl, a cohesin-unloading factor, versus levels in v-Abl pro-B lines that lack marked locus contraction or distal VH rearrangements. Correspondingly, Wapl depletion in v-Abl lines activated VH-locus contraction and orientation-specific RAG-scanning across the VH-locus. Our findings indicate that locus contraction and physiological VH-to-DJH joining both are regulated via circumvention of CBE scanning impediments.

2020-11-08 | GSE151906 | GEO

Loop Extrusion Mediates Physiological Locus Contraction for V(D)J Recombination (3C-HTGTS)

2020-11-08 | GSE151909 | GEO

Loop Extrusion Mediates Physiological Locus Contraction for V(D)J Recombination (ChIP-Seq)

2020-11-08 | GSE151908 | GEO

Loop Extrusion Mediates Physiological Locus Contraction for V(D)J Recombination (GRO-Seq)

2020-11-08 | GSE151907 | GEO