Widespread misinterpretable ChIP-seq bias in yeast

PloS One
Daechan ParkVishwanath R Iyer

Abstract

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to detect genome-wide interactions between a protein of interest and DNA in vivo. Loci showing strong enrichment over adjacent background regions are typically considered to be sites of binding. Insufficient attention has been given to systematic artifacts inherent to the ChIP-seq procedure that might generate a misleading picture of protein binding to certain loci. We show here that unrelated transcription factors appear to consistently bind to the gene bodies of highly transcribed genes in yeast. Strikingly, several types of negative control experiments, including a protein that is not expected to bind chromatin, also showed similar patterns of strong binding within gene bodies. These false positive signals were evident across sequencing platforms and immunoprecipitation protocols, as well as in previously published datasets from other labs. We show that these false positive signals derive from high rates of transcription, and are inherent to the ChIP procedure, although they are exacerbated by sequencing library construction procedures. This expression bias is strong enough that a known transcriptional repressor like Tup1 can erroneously appear to...Continue Reading

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Datasets Mentioned

BETA
GSE13322
GSE51251

Methods Mentioned

BETA
immunoprecipitation
ChIP
ChIP-seq
tandem affinity purification
PCR
pull-down
Genome Sequencing
pull down
ChIPs
RNA-seq

Software Mentioned

NimbleScan
Sono
SOLiD
MACS2
MAnorm
matplotlib
numpy
seq
Bioconductor limma
Excel

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