RT Journal Article
SR Electronic
T1 High similarity among ChEC-seq datasets
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.02.04.429774
DO 10.1101/2021.02.04.429774
A1 Chitvan Mittal
A1 Matthew J. Rossi
A1 B. Franklin Pugh
YR 2021
UL http://biorxiv.org/content/early/2021/02/05/2021.02.04.429774.abstract
AB ChEC-seq is a method used to identify protein-DNA interactions across a genome. It involves fusing micrococcal nuclease (MNase) to a protein of interest. In principle, specific genome-wide interactions of the fusion protein with chromatin result in local DNA cleavages that can be mapped by DNA sequencing. ChEC-seq has been used to draw conclusions about broad gene-specificities of certain protein-DNA interactions. In particular, the transcriptional regulators SAGA, TFIID, and Mediator are reported to generally occupy the promoter/UAS of genes transcribed by RNA polymerase II in yeast. Here we compare published yeast ChEC-seq data performed with a variety of protein fusions across essentially all genes, and find high similarities with negative controls. We conclude that ChEC-seq patterning for SAGA, TFIID, and Mediator differ little from background at most promoter regions, and thus cannot be used to draw conclusions about broad gene specificity of these factors.Competing Interest StatementThe authors have declared no competing interest.