Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice

Gomez-Porras J, Riano-Pachon DM, Dreyer I, Mayer JE, Mueller-Roeber B (2007)
BMC GENOMICS 8(1): 260.

Journal Article | Published | English

No fulltext has been uploaded

Author
; ; ; ;
Abstract
Background: In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid ( ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an insilico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements ( CREs), ABRE and CE3, in thale cress ( Arabidopsis thaliana) and rice ( Oryza sativa). Results: Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element ( CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes ( ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Conclusion: Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be needed to test whether the observed differences are extrapolatable to monocots and dicots in general, and to understand how they contribute to the fine-tuning of the hormonal response. The outcome of our investigation can now be used to direct future experimentation designed to further dissect the ABA-dependent regulatory networks.
Publishing Year
ISSN
PUB-ID

Cite this

Gomez-Porras J, Riano-Pachon DM, Dreyer I, Mayer JE, Mueller-Roeber B. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC GENOMICS. 2007;8(1): 260.
Gomez-Porras, J., Riano-Pachon, D. M., Dreyer, I., Mayer, J. E., & Mueller-Roeber, B. (2007). Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC GENOMICS, 8(1): 260.
Gomez-Porras, J., Riano-Pachon, D. M., Dreyer, I., Mayer, J. E., and Mueller-Roeber, B. (2007). Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC GENOMICS 8:260.
Gomez-Porras, J., et al., 2007. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC GENOMICS, 8(1): 260.
J. Gomez-Porras, et al., “Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice”, BMC GENOMICS, vol. 8, 2007, : 260.
Gomez-Porras, J., Riano-Pachon, D.M., Dreyer, I., Mayer, J.E., Mueller-Roeber, B.: Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC GENOMICS. 8, : 260 (2007).
Gomez-Porras, Judith, Riano-Pachon, Diego Mauricio, Dreyer, Ingo, Mayer, Jorge E., and Mueller-Roeber, Bernd. “Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice”. BMC GENOMICS 8.1 (2007): 260.
This data publication is cited in the following publications:
This publication cites the following data publications:

48 Citations in Europe PMC

Data provided by Europe PubMed Central.

GEM, a member of the GRAM domain family of proteins, is part of the ABA signaling pathway.
Mauri N, Fernandez-Marcos M, Costas C, Desvoyes B, Pichel A, Caro E, Gutierrez C., Sci Rep 6(), 2016
PMID: 26939893
Functional analysis of the Arabidopsis thaliana MUTE promoter reveals a regulatory region sufficient for stomatal-lineage expression.
Mahoney AK, Anderson EM, Bakker RA, Williams AF, Flood JJ, Sullivan KC, Pillitteri LJ., Planta 243(4), 2016
PMID: 26748914
Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL.
Barrero JM, Cavanagh C, Verbyla KL, Tibbits JF, Verbyla AP, Huang BE, Rosewarne GM, Stephen S, Wang P, Whan A, Rigault P, Hayden MJ, Gubler F., Genome Biol. 16(), 2015
PMID: 25962727
Abscisic acid (ABA) regulation of Arabidopsis SR protein gene expression.
Cruz TM, Carvalho RF, Richardson DN, Duque P., Int J Mol Sci 15(10), 2014
PMID: 25268622
Abscisic acid perception and signaling: structural mechanisms and applications.
Ng LM, Melcher K, Teh BT, Xu HE., Acta Pharmacol. Sin. 35(5), 2014
PMID: 24786231
BnNAC485 is involved in abiotic stress responses and flowering time in Brassica napus.
Ying L, Chen H, Cai W., Plant Physiol. Biochem. 79(), 2014
PMID: 24690671
Identification, occurrence, and validation of DRE and ABRE Cis-regulatory motifs in the promoter regions of genes of Arabidopsis thaliana.
Mishra S, Shukla A, Upadhyay S, Sanchita , Sharma P, Singh S, Phukan UJ, Meena A, Khan F, Tripathi V, Shukla RK, Shrama A., J Integr Plant Biol 56(4), 2014
PMID: 24581225
Bidirectional promoters in seed development and related hormone/stress responses.
Kourmpetli S, Lee K, Hemsley R, Rossignol P, Papageorgiou T, Drea S., BMC Plant Biol. 13(), 2013
PMID: 24261334
Genome-wide analysis of endosperm-specific genes in rice.
Nie DM, Ouyang YD, Wang X, Zhou W, Hu CG, Yao J., Gene 530(2), 2013
PMID: 23948082
Patterns and evolution of ACGT repeat cis-element landscape across four plant genomes.
Mehrotra R, Sethi S, Zutshi I, Bhalothia P, Mehrotra S., BMC Genomics 14(), 2013
PMID: 23530833
microRNAs responsive to ozone-induced oxidative stress in Arabidopsis thaliana.
Iyer NJ, Jia X, Sunkar R, Tang G, Mahalingam R., Plant Signal Behav 7(4), 2012
PMID: 22499183
Molecular analysis of a sunflower gene encoding an homologous of the B subunit of a CAAT binding factor.
Salvini M, Sani E, Fambrini M, Pistelli L, Pucciariello C, Pugliesi C., Mol. Biol. Rep. 39(6), 2012
PMID: 22359114
Gene expression profile changes in germinating rice.
He D, Han C, Yang P., J Integr Plant Biol 53(10), 2011
PMID: 21910826
Prediction of new abiotic stress genes in Arabidopsis thaliana and Oryza sativa according to enumeration-based statistical analysis.
Cserhati M, Turoczy Z, Zombori Z, Cserzo M, Dudits D, Pongor S, Gyorgyey J., Mol. Genet. Genomics 285(5), 2011
PMID: 21437642
Prediction and validation of promoters involved in the abscisic acid response in Physcomitrella patens.
Timmerhaus G, Hanke ST, Buchta K, Rensing SA., Mol Plant 4(4), 2011
PMID: 21398384
OsLEA1a, a new Em-like protein of cereal plants.
Shih MD, Huang LT, Wei FJ, Wu MT, Hoekstra FA, Hsing YI., Plant Cell Physiol. 51(12), 2010
PMID: 21097897
Two ABREs, two redundant root-specific and one W-box cis-acting elements are functional in the sunflower HAHB4 promoter.
Manavella PA, Dezar CA, Ariel FD, Chan RL., Plant Physiol. Biochem. 46(10), 2008
PMID: 18586510

48 References

Data provided by Europe PubMed Central.

The Institute for Genomic Research
AUTHOR UNKNOWN, 0
Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems.
Maruyama K, Sakuma Y, Kasuga M, Ito Y, Seki M, Goda H, Shimada Y, Yoshida S, Shinozaki K, Yamaguchi-Shinozaki K., Plant J. 38(6), 2004
PMID: 15165189
Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray.
Seki M, Ishida J, Narusaka M, Fujita M, Nanjo T, Umezawa T, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K., Funct. Integr. Genomics 2(6), 2002
PMID: 12444421
Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress.
Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF., Plant Physiol. 130(4), 2002
PMID: 12481097
Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.
Yazaki J, Shimatani Z, Hashimoto A, Nagata Y, Fujii F, Kojima K, Suzuki K, Taya T, Tonouchi M, Nelson C, Nakagawa A, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S., Physiol. Genomics 17(2), 2004
PMID: 14982972
Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses.
Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Shinozaki K., Plant Physiol. 133(4), 2003
PMID: 14645724
PlnTFDB: an integrative plant transcription factor database.
Riano-Pachon DM, Ruzicic S, Dreyer I, Mueller-Roeber B., BMC Bioinformatics 8(), 2007
PMID: 17286856
Role of arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression.
Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K., Plant Cell 9(10), 1997
PMID: 9368419
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
Arabidopsis Genome Initiative., Nature 408(6814), 2000
PMID: 11130711
The map-based sequence of the rice genome.
International Rice Genome Sequencing Project., Nature 436(7052), 2005
PMID: 16100779

Gómez-Porras JL., 2005
Deciphering principles of transcription regulation in eukaryotic genomes.
Nguyen DH, D'haeseleer P., Mol. Syst. Biol. 2(), 2006
PMID: 16738557
EMBOSS: the European Molecular Biology Open Software Suite.
Rice P, Longden I, Bleasby A., Trends Genet. 16(6), 2000
PMID: 10827456
Weblogo
AUTHOR UNKNOWN, 0

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 17672917
PubMed | Europe PMC

Search this title in

Google Scholar