Computer analysis of colocalization of the TFs’ binding sites in the genome according to the ChIP-seq data

Computer analysis of colocalization of the TFs’ binding sites in the genome according to the... A computer program for calculating clusters of binding sites of various transcription factors (TFs) according to the genomic coordinates of the ChIP-seq (Chromatin ImmunoPrecipitation-sequencing) profile peaks is developed. The statistical features of the distribution of the transcription factors’ binding sites (TFBSs) in the mouse genome, obtained with the help of ChIP-seq experiments in embryonic stem cells, are considered. Clusters of sites containing at least four binding sites of various TFs in the mouse genome are determined and their localization relative to the regulatory regions of the genes is described. Two types of colocalization of the sites are confirmed: clusters containing binding sites of factors Oct4, Nanog, and Sox2 located in the distal regions and clusters with n-Myc and c-Myc binding sites located mainly in the promoter regions of mouse genes. Analysis of the new ChIP-seq data on the binding of TFs Nr5a2, Tbx3, Cep, SRF, and USF1 in the same cell type confirmed the differentiation of clusters of the TFBSs into two types: those containing pluripotency regulator binding sites (Oct4, Nanog, and Sox2) and those not containing them. A computer program for the statistical processing of the data on the location of the sites in the genes is developed; it uses the experimental data on site localization obtained by ChIP-seq methods in mouse and human genomes. With the help of this program, the localization patterns of the binding sites of various TFs are detected. The distances between the closest binding sites of the TF groups Oct4, Nanog, and Sox2 and the binding sites of other factors in site clusters that serve as a basis for the analysis of the joint binding of protein complexes to DNA are calculated. The fraction of the presence of the known nucleotide motifs of TFBSs in the genomic regions of ChIP-seq is calculated. The weight matrices for such nucleotide motifs are recalculated. The correlation between the presence of motifs and the ChIP-seq binding intensity is shown. The programs implementing the computerized methods for assessing the clustering of binding sites of various TFs for new ChIP-seq data are available upon request from the authors. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Russian Journal of Genetics: Applied Research Springer Journals

Computer analysis of colocalization of the TFs’ binding sites in the genome according to the ChIP-seq data

Loading next page...
 
/lp/springer_journal/computer-analysis-of-colocalization-of-the-tfs-binding-sites-in-the-WwZacDjp4o
Publisher
Pleiades Publishing
Copyright
Copyright © 2017 by Pleiades Publishing, Ltd.
Subject
Biomedicine; Human Genetics
ISSN
2079-0597
eISSN
2079-0600
D.O.I.
10.1134/S2079059717050057
Publisher site
See Article on Publisher Site

References

You’re reading a free preview. Subscribe to read the entire article.


DeepDyve is your
personal research library

It’s your single place to instantly
discover and read the research
that matters to you.

Enjoy affordable access to
over 12 million articles from more than
10,000 peer-reviewed journals.

All for just $49/month

Explore the DeepDyve Library

Unlimited reading

Read as many articles as you need. Full articles with original layout, charts and figures. Read online, from anywhere.

Stay up to date

Keep up with your field with Personalized Recommendations and Follow Journals to get automatic updates.

Organize your research

It’s easy to organize your research with our built-in tools.

Your journals are on DeepDyve

Read from thousands of the leading scholarly journals from SpringerNature, Elsevier, Wiley-Blackwell, Oxford University Press and more.

All the latest content is available, no embargo periods.

See the journals in your area

Monthly Plan

  • Read unlimited articles
  • Personalized recommendations
  • No expiration
  • Print 20 pages per month
  • 20% off on PDF purchases
  • Organize your research
  • Get updates on your journals and topic searches

$49/month

Start Free Trial

14-day Free Trial

Best Deal — 39% off

Annual Plan

  • All the features of the Professional Plan, but for 39% off!
  • Billed annually
  • No expiration
  • For the normal price of 10 articles elsewhere, you get one full year of unlimited access to articles.

$588

$360/year

billed annually
Start Free Trial

14-day Free Trial