SEQanswers

Go Back   SEQanswers > Literature Watch



Similar Threads
Thread Thread Starter Forum Replies Last Post
ChIP-Seq: ChIP-Seq Data Analysis: Identification of Protein-DNA Binding Sites with SI Newsbot! Literature Watch 0 12-02-2011 05:51 AM
PubMed: An effective approach for identification of in vivo protein-DNA binding sites Newsbot! Literature Watch 0 02-11-2010 03:10 AM
PubMed: Genome-wide identification of human RNA editing sites by parallel DNA capturi Newsbot! Literature Watch 0 05-30-2009 06:07 AM
PubMed: Genome-wide analysis of transcription factor binding sites based on ChIP-Seq Newsbot! Literature Watch 1 01-27-2009 05:26 AM
PubMed: Genome-wide analysis of transcription factor binding sites based on ChIP-Seq Newsbot! Literature Watch 0 08-20-2008 06:00 AM

Reply
 
Thread Tools
Old 08-08-2008, 06:02 AM   #1
Newsbot!
RSS Posting Maniac
 

Join Date: Feb 2008
Posts: 1,443
Default PubMed: Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq

Syndicated from PubMed RSS Feeds

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

Nucleic Acids Res. 2008 Aug 6;

Authors: Jothi R, Cuddapah S, Barski A, Cui K, Zhao K

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 ( approximately 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.

PMID: 18684996 [PubMed - as supplied by publisher]



More...
Newsbot! is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:10 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO