Literature Selections for ChIP-seq¶
ChIP-Seq¶
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We used this method to map the binding sites for Cse4, Ste12 and Pol II throughout the yeast genome and we found 148 binding targets for Cse4, 823 targets for Ste12 and 2508 targets for PolII. Cse4 was strongly bound to all yeast centromeres as expected and the remaining non-centromeric t
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Emphasizes adjusting for gene locus length and that two commonly used gene set enrichment methods, Fisher’s exact test and the binomial test implemented in Genomic Regions Enrichment of Annotations Tool (GREAT), can have highly inflated type I error rates and biases in ranking.
Bias issues¶
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We analyzed ChIP-Seq peaks of the Sir2, Sir3, and Sir4 silencing proteins and discovered 238 unexpected euchromatic loci that exhibited enrichment of all three. Surprisingly, published ChIP-Seq datasets for the Ste12 transcription factor and the centromeric Cse4 protein indicated that these proteins were also enriched in the same euchromatic regions with the high Sir protein levels. The 238 loci, termed ”hyper-ChIPable“, were in highly expressed regions with strong polymerase II and polymerase III enrichment signals, and the correlation between transcription level and ChIP enrichment was not limited to these 238 loci but extended genome-wide. ... Whereas ChIP is a broadly valuable technique, some published conclusions based upon ChIP procedures may merit reevaluation in light of these findings.
Insightful post on PubPeer related to this
Oh, also, if you are not aware of it, Vishy Iyer’s recent PLOS One paper finds the exact same artifact as we do. http://www.plosone.org/article/authors/info%3Adoi%2F10.1371%2Fjournal.pone.0083506;jsessionid=F590D75E9C265BA38D012211B9B97E33 And related to this discussion: http://www.biomedcentral.com/1471-2164/11/414 http://www.biomedcentral.com/1471-2164/14/254/abstrac http://www.biomedcentral.com/1471-2164/14/638 And this paper from Kevin Struhl: http://www.plosone.org/article/related/info%3Adoi%2F10.1371%2Fjournal.pone.0005029;jsessionid=93B6A4A5F2062E6B1F15E8997133060D
Below are other publications reporting the expression-associated ChIP artifact. Fan X, 2009 “Where Does Mediator Bind In Vivo?” (Work in S. cerevisiae questioning reports of pervasive genome-wide binding of the Mediator complex.) Waldminghaus T, 2010 “ChIP on Chip: surprising results are often artifacts” (Work in E. coli; also see arising correspondence Schindler D, 2013.) Park D, 2013 “Widespread Misinterpretable ChIP-seq Bias in Yeast” (Analysis very similar to ours.) Kasinathan S, 2014 “High-resolution mapping of transcription factor binding sites on native chromatin” (Questions specificity of standard ChIP in S. cerevisiae and at HOT regions of Drosophila. This work possibly provides a solution to the artifact with a modification of the ChIP technique.) http://www.ncbi.nlm.nih.gov/pubmed/24173036#cm24173036_3919
Non-canonical protein-DNA interactions identified by ChIP are not artifacts. Bonocora RP, Fitzgerald DM, Stringer AM, Wade JT. BMC Genomics. 2013 Apr 15;14:254. doi: 10.1186/1471-2164-14-254. (Concerns the E. coli data.)
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The resulting occupied regions of genomes from affinity-purified naturally isolated chromatin (ORGANIC) profiles of Saccharomyces cerevisiae Abf1 and Reb1 provide high-resolution maps that are accurate, as defined by the presence of known TF consensus motifs in identified binding sites, that are not biased toward accessible chromatin and that do not require input normalization.
Motif identification¶
Cis-regulatory Element Annotation System by Hyunjin Shin and Tao Liu from Xiaole Shirley Liu’s Lab
A tool designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad binding factors. As a stand-alone extension of our web application CEAS (Cis-regulatory Element Annotation System), it provides statistics on ChIP enrichment at important genome features such as specific chromosome, promoters, gene bodies, or exons, and infers genes most likely to be regulated by a binding factor. CEAS also enables biologists to visualize the average ChIP enrichment signals over specific genomic features, allowing continuous and broad ChIP enrichment to be perceived which might be too subtle to detect from ChIP peaks alone.
ab initio motif finder MEME and the related MEME suite
MEME-LaB wraps the popular ab initio motif finder in a web tool
Motif-based analysis of large nucleotide data sets using MEME-ChIP