Characterization of Loop Extrusion and Regulatory Elements in IgH Locus Structure and Function

V(D)J recombination is a highly ordered and stepwise process that enables antigen receptors to detect a wide variety of antigens. The Igh locus undergoes large-scale locus contraction prior rearranging in pro B cells. A series of nested chromatin loops anchored by a series of distal VH enhancers, EVH1-4 and the Pax5-activated intergenic repeat 4 and 6 (PAIR4/PAIR6) have been identified in the Igh locus by HiC. EVH1 has been demonstrated to modulate Igh locus structure and VH gene usage during Igh rearrangement, linking Igh locus architecture with function (Nat Comm. 14:1225). Furthermore, this raises the possibility that the remaining loop anchors, EVH2-4, PAIR4, and PAIR6 might similarly affect Igh locus structure and function. Additionally, loop extrusion is a process that forms chromatin loops by extruding chromatin through cohesin’s ring structure and is a critical regulator of distal V(D)J recombination. However, the relationship between chromatin looping and loop extrusion remains incompletely understood. To this end, these studies demonstrate that EVH2, EVH4, and PAIR4 modulate Igh locus structure in pro-B cells. We also show that cohesin mediated loop extrusion alone is insufficient to generate full Igh locus contraction, rather it is augmented by EVH2 and EVH4. In contrast, PAIR4 is an important component of cohesin-mediated loop extrusion in the Igh locus. Furthermore, we demonstrate that cis regulatory elements regulate accessibility in the Igh locus, which is correlated with rates of V-DJH joining. Collectively, this demonstrates the importance of cis regulatory elements in Igh locus organization and function.

Author dc:creator

• Ellen Brandenburg Drake (24400643)

• Health Sciences
• Immunology

Statement dc:rights

• In Copyright
• Open Access after 2031-05-01

DOI dc:identifier

https://doi.org/10.25417/uic.32995736.v1

OAI identifier oai:identifier

oai:figshare.com:article/32995736