Nucleic Acids Research Advance Access originally published online on August 6, 2008
Nucleic Acids Research 2008 36(16):5221-5231; doi:10.1093/nar/gkn488
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2008, Vol. 36, No. 16 5221-5231
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Computational Biology |
Genome-wide identification of in vivo protein–DNA binding sites from ChIP-Seq data
Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20894, USA
*To whom correspondence should be addressed. Tel: +1 301 496 2098; Fax: +1 301 480 0961; Email: zhaok{at}nhlbi.nih.gov
Received May 15, 2008. Revised July 3, 2008. Accepted July 16, 2008.
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 (
25–50 nt) 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 26 814, 5813 and 73 956 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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  P. Navratilova and T. S. Becker Genomic regulatory blocks in vertebrates and implications in human disease Brief Funct Genomic Proteomic, June 26, 2009; (2009) elp019v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Tuteja, P. White, J. Schug, and K. H. Kaestner Extracting transcription factor targets from ChIP-Seq data Nucleic Acids Res., June 24, 2009; (2009) gkp536v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Narlikar and I. Ovcharenko Identifying regulatory elements in eukaryotic genomes Brief Funct Genomic Proteomic, June 4, 2009; (2009) elp014v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. G Hoffman and S. J M Jones Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing J. Endocrinol., April 1, 2009; 201(1): 1 - 13. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Ho, R. Jothi, J. L. Ronan, K. Cui, K. Zhao, and G. R. Crabtree An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network PNAS, March 31, 2009; 106(13): 5187 - 5191. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Cuddapah, R. Jothi, D. E. Schones, T.-Y. Roh, K. Cui, and K. Zhao Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains Genome Res., January 1, 2009; 19(1): 24 - 32. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. N. Packer, Y. Xing, S. Q. Harper, L. Jones, and B. L. Davidson The Bifunctional microRNA miR-9/miR-9* Regulates REST and CoREST and Is Downregulated in Huntington's Disease J. Neurosci., December 31, 2008; 28(53): 14341 - 14346. [Abstract] [Full Text] [PDF]
|
|