Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus

Three-dimensional genome organization orchestrates recombination and transcription of immunoglobulin heavy chain (Igh) genes. The structure of wild-type (WT) alleles includes a prominent architectural stripe that extends from a cluster of CTCF binding elements at the 3′ end of the locus (3′CBE), suggesting interactions of this end with sequences throughout the 2 Mb Igh TAD. Here we elucidate interplay between regulatory elements located in the 3′Igh domain (260 kb) that impact the stripe. The CTCF-lacking intronic enhancer, Eµ, promotes stripe formation and tethers sub-TADs between flanking CTCF-bound 3′CBE and IGCR1. Substituting Eµ with an EF1α promoter in different orientations partially recapitulates epigenetic features of WT Igh alleles, including active histone modifications, sub-TAD formation and interactions with the 3′CBE, but does not restore VDJ recombination. Loss of IGCR1 increases the stripe while inverting the 3′CBE redirects the stripe away from the Igh locus. However, inverted 3′CBE continue to serve as a boundary against aberrant activation of genes outside the Igh domain by Eµ. Our observations provide insights into mechanisms by which regulatory elements modulate chromatin structure and stripe formation.