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High-intensity UV laser ChIP-seq for the study of protein-DNA interactions in living cells

ABSTRACT: Genome-wide mapping of transcription factor binding is generally performed by chemical protein-DNA crosslinking, followed by chromatin immunoprecipitation and deep sequencing (ChIP-seq). Here we present the ChIP-seq technique based on photochemical crosslinking of protein-DNA interactions by high-intensity ultraviolet (UV) laser irradiation in living mammalian cells (UV-ChIP-seq). UV laser irradiation induces efficient and instant formation of covalent “zero-length” crosslinks exclusively between nucleic acids and proteins that are in immediate contact, thus resulting in a “snapshot” of direct protein-DNA interactions in their natural environment. We applied UV-ChIP-seq for genome-wide profiling of the sequence-specific transcriptional repressor B-cell lymphoma 6 (BCL6) in human diffuse large B-cell lymphoma (DLBCL) cells. Our approach resulted in sensitive and precise protein-DNA binding profiles, highly enriched in canonical BCL6 DNA sequence motifs. UV-ChIP-seq also revealed numerous previously undetectable BCL6 binding sites, particularly in more condensed, inaccessible areas of chromatin.

ORGANISM(S): Homo sapiens

PROVIDER: GSE103125 | GEO | 2017/11/06

SECONDARY ACCESSION(S): PRJNA400227

REPOSITORIES: GEO

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