Prediction of bipartite transcriptional regulatory elements using transcriptome data of Arabidopsis.
In our previous study, a methodology was established to predict transcriptional regulatory elements in promoter sequences using transcriptome data based on a frequency comparison of octamers. Some transcription factors, including the NAC family, cannot be covered by this method because their binding sequences have non-specific spacers in the middle of the two binding sites. In order to remove this blind spot in promoter prediction, we have extended our analysis by including bipartite octamers that are composed of '4 bases-a spacer with a flexible length-4 bases'. 8,044 pre-selected bipartite octamers, which had an overrepresentation of specific spacer lengths in promoter sequences and sequences related to core elements removed, were subjected to frequency comparison analysis. Prediction of ER stress-responsive elements in the BiP/BiPL promoter and an ANAC017 target sequence resulted in precise detection of true positives, judged by functional analyses of a reported article and our own in vitro protein-DNA binding assays. These results demonstrate that incorporation of bipartite octamers with continuous ones improves promoter prediction significantly.
Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu City, Gifu 501-1193, Japan.|United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu 501-1193, Japan.|RIKEN CSRS, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.|JST ALCA.
Yoshiharu Y
YY
Yamamoto
RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
Hiroyuki
H
Ichida
United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu 501-1193, Japan.
Ayaka
A
Hieno
Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu City, Gifu 501-1193, Japan.
Daichi
D
Obata
United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu 501-1193, Japan.
Mutsutomo
M
Tokizawa
Center for Gene Research, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan.
Mika
M
Nomoto
Center for Gene Research, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan.
Yasuomi
Y
Tada
United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu 501-1193, Japan.
Kazutaka
K
Kusunoki
Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu City, Gifu 501-1193, Japan.|United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu 501-1193, Japan.
Hiroyuki
H
Koyama
United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu 501-1193, Japan.
Natsuki
N
Hayami
D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D023281:Genomics; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000378:metabolism*; D059467:Transcriptome
D029681:Arabidopsis Proteins; D014157:Transcription Factors
plant genome; promoter prediction; transcriptome