New roles for DNA cytosine modification, eRNA, anchors and super-anchors in developing B cell progenitors. Mus musculus

B cell fate is orchestrated by a series of well-characterized developmental regulators. Here we found that the onset of B cell development was accompanied by large-scale changes in DNA cytosine modifications associated with promoters, enhancers and anchors. These changes were tightly linked to alterations in transcription factor occupancy and eRNA transcription. We found that the pre-pro-B to the pro-B cell transition was associated with a global exchange of DNA cytosine modifications for polycomb-mediated repression at CpG islands. Hypomethylated regions were found exclusively in the active/permissive compartment of the nucleus and were predominantly associated with regulatory elements or anchors that orchestrate the folding patterns of the genome. We identified super-anchors, characterized by clusters of hypomethylated CTCF-bound elements, which were predominantly located at boundaries that define topological domains (TAD). A particularly prominent hypomethylated super-anchor was positioned down-stream of the immunoglobulin heavy chain (Igh) locus. Analysis of global formaldehyde-cross linking studies indicated that the Igh locus super-anchor interacts with the VH region repertoire across vast genomic distances. We propose that the Igh locus super-anchor sequesters the VH and DHJH regions into a spatial confined geometric environment to promote rapid first-passage times. Collectively, these studies demonstrate how DNA cytosine modifications associated with regulatory and architectural elements affects patterns of gene expression, folding patterns of the genome and antigen receptor assembly in developing B-lineage cells. Overall design: DNA cytosine methylation profiling of mouse pre-pro-B (E2A-/-) and pro-B (Rag1-/-) cells by whole genome bisulfite sequencing