ArticlePlant physiology2012
Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar.
Article in Plant physiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 28 citations in OpenAlex.
- Secondary Wall Regulating NACs Differentially Bind at the Promoter at aFrontiers in plant science · 2018Article
- Article
- Genome-wide analysis of cis-regulatory element structure and discovery of motif-driven gene co-expression networks in grapevine.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- PETModule: a motif module based approach for enhancer target gene prediction.Scientific reports · 2016Article
- PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples.Database : the journal of biological databases and curation · 2015Article
- SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data.Nucleic acids research · 2014Article
- 'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences.Database : the journal of biological databases and curation · 2014Article
- Conserved cis-regulatory modules in promoters of genes encoding wheat high-molecular-weight glutenin subunits.Frontiers in plant science · 2014Article
- Functional evolution of cis-regulatory modules of STMADS11 superclade MADS-box genes.Plant molecular biology · 2013Article
- Navigating the transcriptional roadmap regulating plant secondary cell wall deposition.Frontiers in plant science · 2013Review
- Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes.Genome research · 2012Article
- Systematic prediction of cis-regulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics.Plant physiology · 2012Article
- Uncovering transcription factor modules using one- and three-dimensional analyses.The Journal of biological chemistry · 2012Review
- Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis.The Plant cell · 2012Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The identification of cis-regulatory modules (CRMs) can greatly advance our understanding of gene regulatory mechanisms. Despite the existence of binding sites of more than three transcription factors (TFs) in a CRM, studies in plants often consider only the cooccurrence of binding sites of one or two TFs. In addition, CRM studies in plants are limited to combinations of only a few families of TFs. It is thus not clear how widespread plant TFs work together, which TFs work together to regulate plant genes, and how the combinations of these TFs are shared by different plants. To fill these gaps, we applied a frequent pattern-mining-based approach to identify frequently used cis-regulatory sequence combinations in the promoter sequences of two plant species, Arabidopsis (Arabidopsis thaliana) and poplar (Populus trichocarpa). A cis-regulatory sequence here corresponds to a DNA motif bound by a TF. We identified 18,638 combinations composed of two to six cis-regulatory sequences that are shared by the two plant species. In addition, with known cis-regulatory sequence combinations, gene function annotation, gene expression data, and known functional gene sets, we showed that the functionality of at least 96.8% and 65.2% of these shared combinations in Arabidopsis are partially supported, under a false discovery rate of 0.1 and 0.05, respectively. Finally, we discovered that 796 of the 18,638 combinations might relate to functions that are important in bioenergy research. Our work will facilitate the study of gene transcriptional regulation in plants.
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