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Cited by 539Genomics and Chromatin DynamicsGenomics and Phylogenetic StudiesBioinformatics and Genomic Networks

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

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Jothi, Raja, Cuddapah, Suresh, Barski, Artem, Cui, Kairong, Zhao, Keji·2008·Nucleic Acids Research
DOI 10.1093/nar/gkn488PMC PMC2532738
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Abstract

ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with ultra high-throughput massively parallel sequencing, is increasingly being used for mapping protein–DNA interactions in-vivo on a genome scale. Typically, short sequence reads from ChIP-Seq are mapped to a reference genome for further analysis. Although genomic regions enriched with mapped reads could be inferred as approximate binding regions, short read lengths (∼25-50nt) pose challenges for determining the exact binding sites within these regions. Here, we present SISSRs (Site Identification from Short Sequence Reads), a novel algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments. The sensitivity and specificity of SISSRs are demonstrated by applying it on ChIP-Seq data for three widely studied and well-characterized human transcription factors: CTCF (CCCTC-binding factor), NRSF (neuron-restrictive silencer factor) and STAT1 (signal transducer and activator of transcription protein 1). We identified 26814, 5813 and 73956 binding sites for CTCF, NRSF and STAT1 proteins, respectively, which is 32, 299 and 78% more than that inferred previously for the respective proteins. Motif analysis revealed that an overwhelming majority of the identified binding sites contained the previously established consensus binding sequence for the respective proteins, thus attesting for SISSRs’ accuracy. SISSRs’ sensitivity and precision facilitated further analyses of ChIP-Seq data revealing interesting insights, which we believe will serve as guidance for designing ChIP-Seq experiments to map in vivo protein–DNA interactions. We also show that tag densities at the binding sites are a good indicator of protein–DNA binding affinity, which could be used to distinguish and characterize strong and weak binding sites. Using tag density as an indicator of DNA-binding affinity, we have identified core residues within the NRSF and CTCF binding sites that are critical for a stronger DNA binding.

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  • Canonical and non-canonical REST binding motifs have been mapped in close proximity to 22 miRNA sites in the human genome, including several near neuron-enriched miRNAs.

    “Indeed, canonical and non-canonical REST binding motifs have recently been mapped in close proximity to 22 miRNA sites in the human genome, including several of which are located within close proximity to neuron enriched miRNAs (Bruce et al., 2004; Jothi et al., 2008).”

    From The Bifunctional microRNA miR-9/miR-9* Regulates REST and CoREST and Is Downregulated in Huntington's Disease (2008) · cites this paper as Jothi et al., 2008

  • Resolution ranges from tens to hundreds of base pairs depending on the quality of the peak.

    “Resolution ranges from tens to hundreds of base pairs depending on the quality of the peak (136, 190).”

    From Genomic and biochemical insights into the specificity of ETS transcription factors (2011) · cites this paper as [190]

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Cited by

Sorted by citations

Authors
Jothi, R., Cuddapah, S., Barski, A., Cui, K., & Zhao, K.
Affiliations
National Institutes of Health (US)
Corresponding author
Zhao, Keji
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2008-08-06
Volume
36
Issue
16
Pages
5221-5231
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkn488
PMC
PMC2532738
OpenAlex
W2104865962
Cited by
539
References
1
Citations by year
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FWCI
28.97
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
  • Intramural Research Program of the National Heart Lung and Blood Institute
  • National Institutes of Health
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
ChIP-seq, protein-DNA binding sites, short read mapping, CTCF, NRSF, STAT1, transcription factors, binding site identification, binding affinity
MeSH terms
CCCTC-Binding Factor, RE1-Silencing Transcription Factor, Algorithms, Base Sequence, Binding Sites, DNA-Binding Proteins, HeLa Cells, Humans, Molecular Sequence Data, Repressor Proteins, Transcription Factors, Jurkat Cells, Genomics, Chromatin Immunoprecipitation, Regulatory Elements, Transcriptional, STAT1 Transcription Factor

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