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Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination.

Daniel J Bolland1, Hashem Koohy1, Andrew L Wood1

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Variable (V), diversity (D), and joining (J) (V(D)J) recombination shapes immune receptor diversity. New VDJ sequencing reveals epigenetic features downstream of V genes that regulate recombination efficiency, distinct from gene expression.

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Area of Science:

  • Immunology
  • Genetics
  • Molecular Biology

Background:

  • Variable (V), diversity (D), and joining (J) (V(D)J) recombination is crucial for generating diverse antigen receptors.
  • Understanding the regulation of V(D)J recombination is essential for deciphering immune system development and function.

Purpose of the Study:

  • To develop and apply a DNA-based sequencing technique for quantitative profiling of V(D)J recombination products.
  • To identify epigenetic features associated with V gene recombination efficiency and regulation.

Main Methods:

  • Developed VDJ sequencing (VDJ-seq), a next-generation sequencing method for profiling recombination.
  • Utilized machine learning to integrate VDJ-seq data with local chromatin profiles.
  • Analyzed epigenetic signatures at cis-regulatory elements downstream of V genes.

Main Results:

  • Identified a 200-fold range in recombination efficiency across mouse Igh V genes.
  • Discovered cis-regulatory elements downstream of V genes, distinct from expression regulators, that govern recombination.
  • Found two mutually exclusive chromatin signatures (CTCF/RAD21 and PAX5/IRF4) at these elements, correlating with V gene evolutionary history.

Conclusions:

  • Local chromatin signatures downstream of V genes are critical regulators of V(D)J recombination efficiency.
  • These findings reveal a novel layer of epigenetic control over immune receptor gene assembly.
  • VDJ-seq provides an unbiased method for studying V gene usage and recombination regulation.