Genome-wide DNA-binding specificity of PIL5, an Arabidopsis basic Helix-Loop-Helix (bHLH) transcription factor

Hyojin Kang, Eunkyoo Oh, Giltsu Choi, Doheon Lee

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

PIL5 is a member of the basic Helix-Loop-Helix (bHLH) transcription factor superfamily. We previously showed that PIL5 binds to the G-box (CACGTG) motif with high affinity. However, since there are many randomly matched G-box motifs throughout the genome, other factors must account for the in-vivo PIL5 binding specificity. In this study, we investigated if in-vivo PIL5 binding sites can be explained by any other attributes extracted from various sources. Our results showed that PIL5 binding sites can be explained by attributes such as neighbouring motif composition, nucleosome density, DNA methylation and distance from transcription start site in addition to G-box.

Original languageEnglish
Pages (from-to)588-599
Number of pages12
JournalInternational Journal of Data Mining and Bioinformatics
Volume4
Issue number5
DOIs
Publication statusPublished - 2010 Oct 1
Externally publishedYes

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Keywords

  • Arabidopsis
  • Basic helix-loop-helix
  • BHLH
  • ChIP-chip
  • DNA-binding specificity
  • G-box
  • Phytochrome interacting factor 3-LIKE5 (PIL5)

ASJC Scopus subject areas

  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)
  • Library and Information Sciences

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