Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting.

ABSTRACT: Precise control of gene expression requires the coordinated action of multiple factors at cis-regulatory elements. We recently developed single-molecule footprinting to simultaneously resolve the occupancy of multiple proteins including transcription factors, RNA polymerase II and nucleosomes on single DNA molecules genome-wide. The technique combines the use of cytosine methyltransferases to footprint the genome with bisulfite sequencing to resolve transcription factor binding patterns at cis-regulatory elements. DNA footprinting is performed by incubating permeabilized nuclei with recombinant methyltransferases. Upon DNA extraction, whole-genome or targeted bisulfite libraries are prepared and loaded on Illumina sequencers. The protocol can be completed in 4-5 d in any laboratory with ac

SUBMITTER: Kleinendorst RWD 

PROVIDER: S-EPMC7613001 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature