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RNAPII transit through nucleosomes in vivo produces hexasomal intermediates

ABSTRACT: All histone-DNA contacts in a nucleosome must be disrupted for RNA polymerase II (RNAPII) to transcribe through chromatin. However, the structural transitions of the nucleosome during transcription in vivo are unknown. To identify nucleosomal intermediates formed during transcription in vivo, we mapped subnucleosomal protections in Drosophila cells using Micrococcal Nuclease followed by deep sequencing. At the first nucleosome position downstream of the transcription start site, we identified hexasomes lacking an H2A/H2B dimer. Inhibiting topoisomerases or depleting histone chaperones increased dimer loss, whereas inhibiting release of paused RNAPII or reducing RNAPII elongation decreased dimer loss. Our results suggest that positive torsion generated by elongating RNAPII evicts the distal H2A/H2B dimer in vivo. We also identified diagnostic subnucleosomal particle remnants in cell-free human DNA data as a relic of transcribed genes from the tissue-of-origin. Thus the identification of subnucleosomal particle fragments from nuclease protection data represents a general strategy for structural epigenomics.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE98351 | GEO | 2017/12/22

SECONDARY ACCESSION(S): PRJNA384800

REPOSITORIES: GEO

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