A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package

Victor Levitsky, Elena Zemlyanskaya, Dmitry Oshchepkov, Olga Podkolodnaya, Elena Ignatieva, Ivo Grosse, Victoria Mironova, Tatyana Merkulova

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)

Abstract

Recognition of composite elements consisting of two transcription factor binding sites gets behind the studies of tissue-, stage- and condition-specific transcription. Genome-wide data on transcription factor binding generated with ChIP-seq method facilitate an identification of composite elements, but the existing bioinformatics tools either require ChIP-seq datasets for both partner transcription factors, or omit composite elements with motifs overlapping. Here we present an universal Motifs Co-Occurrence Tool (MCOT) that retrieves maximum information about overrepresented composite elements from a single ChIP-seq dataset. This includes homo- and heterotypic composite elements of four mutual orientations of motifs, separated with a spacer or overlapping, even if recognition of motifs within composite element requires various stringencies. Analysis of 52 ChIP-seq datasets for 18 human transcription factors confirmed that for over 60% of analyzed datasets and transcription factors predicted co-occurrence of motifs implied experimentally proven protein-protein interaction of respecting transcription factors. Analysis of 164 ChIP-seq datasets for 57 mammalian transcription factors showed that abundance of predicted composite elements with an overlap of motifs compared to those with a spacer more than doubled; and they had 1.5-fold increase of asymmetrical pairs of motifs with one more conservative 'leading' motif and another one 'guided'.

Original languageEnglish
Pages (from-to)e139
Number of pages14
JournalNucleic Acids Research
Volume47
Issue number21
DOIs
Publication statusPublished - 2 Dec 2019

Keywords

  • Algorithms
  • Animals
  • Binding Sites
  • Chromatin Immunoprecipitation Sequencing/methods
  • Computational Biology/methods
  • Datasets as Topic
  • Humans
  • Mice
  • Nucleotide Motifs/genetics
  • Regulatory Elements, Transcriptional/genetics
  • Sequence Analysis, DNA/methods
  • Transcription Factors/genetics
  • TRANSCRIPTION FACTORS
  • ACTIVATION
  • DNA-BINDING
  • CHROMATIN
  • COMPLEXES
  • COMPOSITE REGULATORY ELEMENTS
  • ENHANCERS
  • DISCOVERY
  • REGIONS
  • NF-KAPPA-B

Fingerprint Dive into the research topics of 'A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package'. Together they form a unique fingerprint.

Cite this