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

Hyojin Kang; Eunkyoo Oh; Giltsu Choi; Doheon Lee

doi:10.1504/IJDMB.2010.035902

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 journal › Article › peer-review

5 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 language	English
Pages (from-to)	588-599
Number of pages	12
Journal	International Journal of Data Mining and Bioinformatics
Volume	4
Issue number	5
DOIs	https://doi.org/10.1504/IJDMB.2010.035902
Publication status	Published - 2010 Oct
Externally published	Yes

Keywords

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

ASJC Scopus subject areas

Information Systems
General Biochemistry,Genetics and Molecular Biology
Library and Information Sciences

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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.",

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author = "Hyojin Kang and Eunkyoo Oh and Giltsu Choi and Doheon Lee",

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AU - Kang, Hyojin

AU - Oh, Eunkyoo

AU - Choi, Giltsu

AU - Lee, Doheon

PY - 2010/10

Y1 - 2010/10

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 - BHLH

KW - Basic helix-loop-helix

KW - ChIP-chip

KW - DNA-binding specificity

KW - G-box

KW - Phytochrome interacting factor 3-LIKE5 (PIL5)

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JO - International Journal of Data Mining and Bioinformatics

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

Abstract

Keywords

ASJC Scopus subject areas

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