The CUT&RUN suspect list of problematic regions of the genome

The CUT&RUN suspect list of problematic regions of the genome

Blog Article

Abstract Background Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an increasingly popular technique to map genome-wide binding profiles of histone modifications, transcription factors, and co-factors.The ENCODE project and others have compiled blacklists for ChIP-seq which have been widely adopted: markbroyard.com these lists contain regions of high and unstructured signal, regardless of cell type or protein target, indicating that these are false positives.While CUT&RUN obtains similar results to ChIP-seq, its biochemistry and subsequent data analyses are different.

We found that this results in a CUT&RUN-specific set of undesired high-signal regions.Results We compile suspect lists based on CUT&RUN data for the human and mouse genomes, identifying regions consistently called as peaks in negative controls.Using published CUT&RUN data from our and other labs, we show that the CUT&RUN suspect regions can persist even when peak calling is performed with SEACR or MACS2 against a negative control and after ENCODE blacklist removal.

Moreover, we experimentally validate the CUT&RUN suspect lists by performing reiterative negative control experiments in which no specific protein is targeted, showing that they capture more than 80% of the peaks identified.Conclusions We propose that removing these problematic regions can substantially bempresas.com improve peak calling in CUT&RUN experiments, resulting in more reliable datasets.