Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding

• Main Authors: Tomasz Szczesnik, Joshua W. K. Ho, Richard Sherwood
• Format: Article
• Language: English
• Published: BMC 2019-06-01
• Series: Epigenetics & Chromatin
• Subjects: Dam; DamID; Tcf7l2; Transcription factor
• Online Access: http://link.springer.com/article/10.1186/s13072-019-0273-x

Abstract DamID, in which a protein of interest is fused to Dam methylase, enables mapping of protein-DNA binding through readout of adenine methylation in genomic DNA. DamID offers a compelling alternative to chromatin immunoprecipitation sequencing (ChIP-Seq), particularly in cases where cell number or antibody availability is limiting. This comes at a cost, however, of high non-specific signal and a lowered spatial resolution of several kb, limiting its application to transcription factor-DNA binding. Here we show that mutations in Dam, when fused to the transcription factor Tcf7l2, greatly reduce non-specific methylation. Combined with a simplified DamID sequencing protocol, we find that these Dam mutants allow for accurate detection of transcription factor binding at a sensitivity and spatial resolution closely matching that seen in ChIP-seq.