title: PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond.
abstract: Recently, a number of advances have been implemented into the core ChIP-seq (chromatin immunoprecipitation coupled with next-generation sequencing) methodology to streamline the process, reduce costs or improve data resolution. Several of these emerging ChIP-based methods perform additional chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for artifact removal during bioinformatics analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. This reported method, termed protein attached chromatin capture (PAtCh-Cap), relies on the non-specific capture of chromatin-bound proteins via their carboxylate groups, leaving the DNA accessible for subsequent chemical treatments in parallel with chromatin separately immunoprecipitated for the target protein. Application of this input strategy not only significantly enhanced artifact removal from ChIP-exo data, increasing confidence in peak identification and allowing for de novo motif searching, but also afforded discovery of a novel CTCF binding motif.
authors.affiliation: Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
authors.forename: Tommy W
authors.initials: TW
authors.lastname: Terooatea
authors.affiliation: Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
authors.forename: Amir
authors.initials: A
authors.lastname: Pozner
authors.affiliation: Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA koehntop@chem.utah.edu.
authors.forename: Bethany A
authors.initials: BA
authors.lastname: Buck-Koehntop
mesh_terms: D001671:Biochemistry / Q000379:methods*; D000076246:CCCTC-Binding Factor; D002843:Chromatin / Q000737:chemistry; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology / Q000379:methods; D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D034622:RNA Interference; D012097:Repressor Proteins / Q000378:metabolism
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D002843:Chromatin; D011506:Proteins; D012097:Repressor Proteins