H2A.B facilitates transcription elongation at methylated CpG loci.

H2A. B is a unique histone H2A variant that only exists in mammals. Here we found that H2A. B is ubiquitously expressed in major organs. Genome-wide analysis of H2A. B in mouse ES cells shows that H2A. B is associated with methylated DNA in gene body regions. Moreover, H2A. B-enriched gene loci are actively transcribed. One typical example is that H2A. B is enriched in a set of differentially methylated regions at imprinted loci and facilitates transcription elongation. These results suggest that H2A. B positively regulates transcription elongation by overcoming DNA methylation in the transcribed region. It provides a novel mechanism by which transcription is regulated at DNA hypermethylated regions.