Genome-wide DNA-binding specificity of PIL5, a Arabidopsis basic helix-loop-helix (bHLH) transcription factor

Hyojin Kang, Eunkyoo Oh, Giltsu Choi, Doheon Lee

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

PIL5 is a member of the bHLH transcription factor superfamily and plays crucial roles in phytochrome mediated seed germination process in Arabidopsis. While our previous study shows that PIL5 binds to the G-box (CACGTG) motif with high affinity, other attributes must be involved in determining regulatory specificity. In this study we performed a ChIP-chip assay to obtain genome-wide PIL5 binding sites and investigated other attributes which would affect to PIL5 DNA-binding specificity. Our results confirmed that the existence of G-box in promoter region was the most significant binding attribute. Additionally we also found that other attributes such as neighboring motif composition, distance from transcription start site, nucleosome density, DNA methylation and average gene expression were also contributing to PIL5 DNA-binding specificity. The Random Forest classifier using these attributes can classify PIL5 binding sites from non-binding sites with accuracy of 93.05%.

Original languageEnglish
Title of host publicationProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
Pages353-356
Number of pages4
DOIs
Publication statusPublished - 2008 Dec 1
Externally publishedYes
Event2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 - Philadelphia, PA, United States
Duration: 2008 Nov 32008 Nov 5

Publication series

NameProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008

Conference

Conference2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
CountryUnited States
CityPhiladelphia, PA
Period08/11/308/11/5

Fingerprint

Basic Helix-Loop-Helix Transcription Factors
Transcription factors
Binding sites
Arabidopsis
DNA
Genes
Binding Sites
Genome
Phytochrome
Nucleosomes
Transcription Initiation Site
DNA Methylation
Transcription
Germination
Genetic Promoter Regions
Gene expression
Seed
Assays
Seeds
Classifiers

ASJC Scopus subject areas

  • Molecular Biology
  • Information Systems
  • Biomedical Engineering

Cite this

Kang, H., Oh, E., Choi, G., & Lee, D. (2008). Genome-wide DNA-binding specificity of PIL5, a Arabidopsis basic helix-loop-helix (bHLH) transcription factor. In Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 (pp. 353-356). [4684918] (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008). https://doi.org/10.1109/BIBM.2008.23

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

Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008. p. 353-356 4684918 (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Kang, H, Oh, E, Choi, G & Lee, D 2008, Genome-wide DNA-binding specificity of PIL5, a Arabidopsis basic helix-loop-helix (bHLH) transcription factor. in Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008., 4684918, Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008, pp. 353-356, 2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008, Philadelphia, PA, United States, 08/11/3. https://doi.org/10.1109/BIBM.2008.23
Kang H, Oh E, Choi G, Lee D. Genome-wide DNA-binding specificity of PIL5, a Arabidopsis basic helix-loop-helix (bHLH) transcription factor. In Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008. p. 353-356. 4684918. (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008). https://doi.org/10.1109/BIBM.2008.23
Kang, Hyojin ; Oh, Eunkyoo ; Choi, Giltsu ; Lee, Doheon. / Genome-wide DNA-binding specificity of PIL5, a Arabidopsis basic helix-loop-helix (bHLH) transcription factor. Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008. pp. 353-356 (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008).
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