ArticleGenome biology2006
Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics.
Article in Genome biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 63 citations in OpenAlex.
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- Reverse Chromatin Immunoprecipitation (R-ChIP) enables investigation of the upstream regulators of plant genes.Communications biology · 2020Article
- Regulation of Cell Type-Specific Immunity Networks in Arabidopsis Roots.The Plant cell · 2020Article
- Enhanced Maps of Transcription Factor Binding Sites Improve Regulatory Networks Learned from Accessible Chromatin Data.Plant physiology · 2019Article
- TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information.Nucleic acids research · 2018Article
- Article
- A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants.Plant physiology · 2016Article
- Genome-Wide Analysis of the Aquaporin Gene Family in Chickpea (Frontiers in plant science · 2016Article
- A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana.The Plant cell · 2014Article
- Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis.The Plant cell · 2014Article
- Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites.Plant methods · 2013Article
- Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants.The Plant cell · 2012Article
- Systematic prediction of cis-regulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics.Plant physiology · 2012Article
- Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription.BMC plant biology · 2012Article
- Systematic identification of functional plant modules through the integration of complementary data sources.Plant physiology · 2012Article
- Molecular analysis of a sunflower gene encoding an homologous of the B subunit of a CAAT binding factor.Molecular biology reports · 2012Article
- Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar.Plant physiology · 2012Article
- Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen Phytophthora infestans.PloS one · 2012Article
- Distribution of short interstitial telomere motifs in two plant genomes: putative origin and function.BMC plant biology · 2010Article
- Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.Molecular systems biology · 2010Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTranscriptional regulation plays an important role in the control of many biological processes. Transcription factor binding sites (TFBSs) are the functional elements that determine transcriptional activity and are organized into separable cis-regulatory modules, each defining the cooperation of several transcription factors required for a specific spatio-temporal expression pattern. Consequently, the discovery of novel TFBSs in promoter sequences is an important step to improve our understanding of gene regulation.
resultsHere, we applied a detection strategy that combines features of classic motif overrepresentation approaches in co-regulated genes with general comparative footprinting principles for the identification of biologically relevant regulatory elements and modules in Arabidopsis thaliana, a model system for plant biology. In total, we identified 80 TFBSs and 139 regulatory modules, most of which are novel, and primarily consist of two or three regulatory elements that could be linked to different important biological processes, such as protein biosynthesis, cell cycle control, photosynthesis and embryonic development. Moreover, studying the physical properties of some specific regulatory modules revealed that Arabidopsis promoters have a compact nature, with cooperative TFBSs located in close proximity of each other.
conclusionThese results create a starting point to unravel regulatory networks in plants and to study the regulation of biological processes from a systems biology point of view.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.