Next Article in Journal
Down-Regulation of miR-129-5p and the let-7 Family in Neuroendocrine Tumors and Metastases Leads to Up-Regulation of Their Targets Egr1, G3bp1, Hmga2 and Bach1
Previous Article in Journal
Altered Actions of Memantine and NMDA-Induced Currents in a New Grid2-Deleted Mouse Line
 
Search for Articles:
Title / Keyword
Author / Affiliation
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
Journals
Genes
Volume 5
Issue 4
10.3390/genes5041115
genes-logo
Submit to this Journal Review for this Journal Edit a Special Issue
► Article Menu

Article Menu

share announcement question_answer thumb_up
...
textsms
...
Article

Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential

by
Yukio Kurihara
1,
Yuko Makita
1,
Mika Kawashima
1,
Hidefumi Hamasaki
1,
Yoshiharu Y. Yamamoto
2 and
Minami Matsui
1,*
1
Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
2
The United Graduate School of Agricultural Science, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
*
Author to whom correspondence should be addressed.
Genes 2014, 5(4), 1115-1131; https://doi.org/10.3390/genes5041115
Received: 17 November 2014 / Revised: 13 December 2014 / Accepted: 16 December 2014 / Published: 19 December 2014
View Full-Text Download PDF
Browse Figures

Abstract

Several transcription factors (TFs) coordinate to regulate expression of specific genes at the transcriptional level. In Arabidopsis thaliana it is estimated that approximately 10% of all genes encode TFs or TF-like proteins. It is important to identify target genes that are directly regulated by TFs in order to understand the complete picture of a plant’s transcriptome profile. Here, we investigate the role of the LONG HYPOCOTYL5 (HY5) transcription factor that acts as a regulator of photomorphogenesis. We used an in vitro genomic DNA binding assay coupled with immunoprecipitation and next-generation sequencing (gDB-seq) instead of the in vivo chromatin immunoprecipitation (ChIP)-based methods. The results demonstrate that the HY5-binding motif predicted here was similar to the motif reported previously and that in vitro HY5-binding loci largely overlapped with the HY5-targeted candidate genes identified in previous ChIP-chip analysis. By combining these results with microarray analysis, we identified hundreds of HY5-binding genes that were differentially expressed in hy5. We also observed delayed induction of some transcripts of HY5-binding genes in hy5 mutants in response to blue-light exposure after dark treatment. Thus, an in vitro gDNA-binding assay coupled with sequencing is a convenient and powerful method to bridge the gap between identifying TF binding potential and establishing function. View Full-Text
Keywords: plant; transcription factor; HY5; in vitro binding; next-generation sequencing plant; transcription factor; HY5; in vitro binding; next-generation sequencing
►▼ Show Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Supplementary Materials

SciFeed

Share and Cite

MDPI and ACS Style

Kurihara, Y.; Makita, Y.; Kawashima, M.; Hamasaki, H.; Yamamoto, Y.Y.; Matsui, M. Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential. Genes 2014, 5, 1115-1131. https://doi.org/10.3390/genes5041115

AMA Style

Kurihara Y, Makita Y, Kawashima M, Hamasaki H, Yamamoto YY, Matsui M. Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential. Genes. 2014; 5(4):1115-1131. https://doi.org/10.3390/genes5041115

Chicago/Turabian Style

Kurihara, Yukio, Yuko Makita, Mika Kawashima, Hidefumi Hamasaki, Yoshiharu Y. Yamamoto, and Minami Matsui. 2014. "Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential" Genes 5, no. 4: 1115-1131. https://doi.org/10.3390/genes5041115

Find Other Styles

Article Metrics

Article Access Map by Country/Region

1
Only visits after 24 November 2015 are recorded.
Back to TopTop