TY - JOUR
T1 - Patterns of cis-element enrichment reveal potential regulatory modules involved in the transcriptional regulation of anoxia response of japonica rice
AU - Mohanty, Bijayalaxmi
AU - Herath, Venura
AU - Wijaya, Edward
AU - Yeo, Hock Chuan
AU - de los Reyes, Benildo G.
AU - Lee, Dong Yup
N1 - Funding Information:
This work was supported by the National University of Singapore , Biomedical Research Council of A*STAR (Agency for Science, Technology and Research), Singapore and a grant from the Next-Generation BioGreen 21 Program (SSAC, No. PJ008184 ), Rural Development Administration, Republic of Korea. Contributions from BGDR and VH were supported by the Maine Agricultural and Forest Experiment Station. We thank Prof. Vladimir B. Bajic for the Dragon Motif Builder Program.
PY - 2012/12/15
Y1 - 2012/12/15
N2 - Unlike other cereal species, rice is able to germinate and elongate under anoxia. The regulatory mechanism that configures the transcriptome of rice during anaerobic germination is yet to be established. In this study, the major regulatory modules among anoxia-responsive genes in rice identified from published microarray data were predicted by ab initio analysis of cis-regulatory information content. Statistically overrepresented sequence motifs were detected from bona fide promoter sequences [-. 1000 to +. 200], revealing various patterns of cis-element enrichment that are highly correlated with bZIP, ERF and MYB types of transcription factors. As implied by the cis-element enrichment patterns, combinatorial mechanisms configure the overall changes in gene expression during anoxic germination and coleoptile elongation. High enrichment of cis-elements associated with ARF, bZIP, ERF, MYB and WRKY (SUSIBA2) transcription factors was also detected among the glycolytic and fermentative associated genes that were upregulated during anoxia. The patterns established from the global analysis of cis-element distribution for upregulated and downregulated genes and their associations with potential cognate regulatory transcription factors indicate the significant roles of ethylene and abscisic acid mediated signaling during coleoptile elongation under anoxia. In addition, the regulation of genes encoding enzymes in the glycolytic and fermentative metabolism could be associated with abscisic acid and auxin in rice coleoptiles to maintain sugar and ATP levels for longer survival.
AB - Unlike other cereal species, rice is able to germinate and elongate under anoxia. The regulatory mechanism that configures the transcriptome of rice during anaerobic germination is yet to be established. In this study, the major regulatory modules among anoxia-responsive genes in rice identified from published microarray data were predicted by ab initio analysis of cis-regulatory information content. Statistically overrepresented sequence motifs were detected from bona fide promoter sequences [-. 1000 to +. 200], revealing various patterns of cis-element enrichment that are highly correlated with bZIP, ERF and MYB types of transcription factors. As implied by the cis-element enrichment patterns, combinatorial mechanisms configure the overall changes in gene expression during anoxic germination and coleoptile elongation. High enrichment of cis-elements associated with ARF, bZIP, ERF, MYB and WRKY (SUSIBA2) transcription factors was also detected among the glycolytic and fermentative associated genes that were upregulated during anoxia. The patterns established from the global analysis of cis-element distribution for upregulated and downregulated genes and their associations with potential cognate regulatory transcription factors indicate the significant roles of ethylene and abscisic acid mediated signaling during coleoptile elongation under anoxia. In addition, the regulation of genes encoding enzymes in the glycolytic and fermentative metabolism could be associated with abscisic acid and auxin in rice coleoptiles to maintain sugar and ATP levels for longer survival.
KW - Anaerobic stress
KW - Gene regulation
KW - Motifs
KW - Oryza sativa
KW - Promoters
KW - Transcription factors
UR - http://www.scopus.com/inward/record.url?scp=84868195004&partnerID=8YFLogxK
U2 - 10.1016/j.gene.2012.09.048
DO - 10.1016/j.gene.2012.09.048
M3 - Article
C2 - 23010196
AN - SCOPUS:84868195004
VL - 511
SP - 235
EP - 242
JO - Gene
JF - Gene
SN - 0378-1119
IS - 2
ER -