Work

Correspondence: Reply to ‘DNA shape is insufficient to explain binding’

Year: 2017

Type: letter

Abstract: Transcription factors (TFs) are DNA-binding proteins that regulate gene expression. Sequence-specific TFs recognize DNA via specific amino acid-base hydrogen bonds and contacts that read local DNA shape 1 . Studying base and shape readout modes of TFs in vivo has been challenging due to technical issues associated with current approaches for mapping TF-binding sites (TFBSs). We recently introduced Chromatin Endogenous Cleavage with sequencing (ChEC-seq), an in vivo mapping method based on fusing Micrococcal Nuclease (MNase) to a TF (ref. 2 ). Upon addition of calcium to permeabilized cells, tethered MNase cuts DNA adjacent to the bound TF and the released fragments are sequenced to provide a high-resolution genome-wide TFBS map. We used ChEC-seq to map the budding yeast TFs Abf1, Reb1 and Rap1 and obtained data similar to high-resolution ChIP-seq without the need for cross-linking, chromatin solubilization or antibodies.

Source: Nature Communications

DOI: 10.1038/ncomms15644

Authors: Sivakanthan Kasinathan, Gabriel E. Zentner, Beibei Xin, Remo Rohs, Steven Henikoff