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

Fingerprint

Basic Helix-Loop-Helix Transcription Factors
Transcription factors
Binding sites
Arabidopsis
DNA
Genes
Binding Sites
Genome
Nucleosomes
Transcription Initiation Site
DNA Methylation
Transcription
Chemical analysis

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

Cite this

Genome-wide DNA-binding specificity of PIL5, an Arabidopsis basic Helix-Loop-Helix (bHLH) transcription factor. / Kang, Hyojin; Oh, Eunkyoo; Choi, Giltsu; Lee, Doheon.

In: International Journal of Data Mining and Bioinformatics, Vol. 4, No. 5, 01.10.2010, p. 588-599.

Research output: Contribution to journalArticle

@article{b1f8c0158b5e41cda14a1af58742d440,
title = "Genome-wide DNA-binding specificity of PIL5, an Arabidopsis basic Helix-Loop-Helix (bHLH) transcription factor",
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.",
keywords = "Arabidopsis, Basic helix-loop-helix, BHLH, ChIP-chip, DNA-binding specificity, G-box, Phytochrome interacting factor 3-LIKE5 (PIL5)",
author = "Hyojin Kang and Eunkyoo Oh and Giltsu Choi and Doheon Lee",
year = "2010",
month = "10",
day = "1",
doi = "10.1504/IJDMB.2010.035902",
language = "English",
volume = "4",
pages = "588--599",
journal = "International Journal of Data Mining and Bioinformatics",
issn = "1748-5673",
publisher = "Inderscience Enterprises Ltd",
number = "5",

}

TY - JOUR

T1 - Genome-wide DNA-binding specificity of PIL5, an Arabidopsis basic Helix-Loop-Helix (bHLH) transcription factor

AU - Kang, Hyojin

AU - Oh, Eunkyoo

AU - Choi, Giltsu

AU - Lee, Doheon

PY - 2010/10/1

Y1 - 2010/10/1

N2 - 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.

AB - 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.

KW - Arabidopsis

KW - Basic helix-loop-helix

KW - BHLH

KW - ChIP-chip

KW - DNA-binding specificity

KW - G-box

KW - Phytochrome interacting factor 3-LIKE5 (PIL5)

UR - http://www.scopus.com/inward/record.url?scp=77957996612&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77957996612&partnerID=8YFLogxK

U2 - 10.1504/IJDMB.2010.035902

DO - 10.1504/IJDMB.2010.035902

M3 - Article

VL - 4

SP - 588

EP - 599

JO - International Journal of Data Mining and Bioinformatics

JF - International Journal of Data Mining and Bioinformatics

SN - 1748-5673

IS - 5

ER -