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Loop extrusion mediates physiological Igh locus contraction for RAG scanning.

Hai-Qiang Dai1,2, Hongli Hu3,4, Jiangman Lou3,4

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Investigating RAG scanning in progenitor B cells reveals that locus contraction occurs independently of V(D)J recombination. This process is regulated by cohesin-mediated loop extrusion and CTCF-binding elements, impacting DNA accessibility.

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Area of Science:

  • Immunology
  • Molecular Biology
  • Genetics

Background:

  • RAG endonuclease initiates Igh V(D)J recombination by scanning chromatin for recombination signal sequences (RSSs).
  • Cohesin-mediated loop extrusion facilitates long-range RAG scanning, while CTCF-binding elements (CBEs) can impede this process.
  • The V(H) locus undergoes a poorly understood contraction in progenitor B cells, potentially improving distal V(H) accessibility.

Purpose of the Study:

  • To elucidate the mechanisms underlying V(H) locus contraction and its impact on RAG scanning.
  • To investigate the role of loop extrusion and CBEs in regulating V(D)J recombination in progenitor B cells.

Main Methods:

  • Analysis of a V(H) locus inversion in mouse primary progenitor B cells.
  • Assessment of V(H)-RSS and cryptic RSS rearrangement.
  • Evaluation of RAG scanning beyond the V(H) locus.
  • Investigation of wings apart-like protein homologue (WAPL) expression and depletion.

Main Results:

  • V(H) locus inversion abrogated V(H)-RSS and normally convergent cryptic RSS rearrangement, despite locus contraction.
  • Inversion activated utilization of oppositely oriented cryptic V(H)-RSSs and RAG scanning beyond the V(H) locus.
  • Low WAPL expression in primary progenitor B cells correlated with locus contraction and RAG scanning; WAPL depletion activated these processes.

Conclusions:

  • Deregulation of CBE impediments promotes RAG scanning of the V(H) locus via loop extrusion in progenitor B cells.
  • Loop extrusion is implicated in V(H) locus contraction, with WAPL influencing cohesin dynamics.
  • These findings provide mechanistic insight into V(H) locus accessibility and V(D)J recombination regulation.