ArticleThe Plant cell2014
Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis.
Article in The Plant cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 66 citations in OpenAlex.
- Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development.Plant communications · 2025Article
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- Characterization and functional analysis of conserved non-coding sequences among poaceae: insights into gene regulation and phenotypic variation in maize.BMC genomics · 2025Article
- Altered interactions between cis-regulatory elements partially resolve BLADE-ON-PETIOLE genetic redundancy in Capsella rubella.The Plant cell · 2024Article
- Dynamic enhancer transcription associates with reprogramming of immune genes during pattern triggered immunity in Arabidopsis.BMC biology · 2022Article
- Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen-fixing clade.The New phytologist · 2022Article
- The evolutionary landscape and expression pattern of plant lincRNAs.RNA biology · 2022Article
- A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences,Frontiers in plant science · 2022Article
- Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience.Plant, cell & environment · 2021Review
- Evolution of Conserved Noncoding Sequences in Arabidopsis thaliana.Molecular biology and evolution · 2021Article
- Photoperiod-responsive changes in chromatin accessibility in phloem companion and epidermis cells of Arabidopsis leaves.The Plant cell · 2021Article
- Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators.Nature plants · 2021Article
- Regulation of Cell Type-Specific Immunity Networks in Arabidopsis Roots.The Plant cell · 2020Article
- PlantRegMap: charting functional regulatory maps in plants.Nucleic acids research · 2020Article
- Perspectives of CRISPR/Cas-mediatedHorticulture research · 2020Review
- QTG-Finder: A Machine-Learning Based Algorithm To Prioritize Causal Genes of Quantitative Trait Loci in Arabidopsis and Rice.G3 (Bethesda, Md.) · 2019Article
- Enhanced Maps of Transcription Factor Binding Sites Improve Regulatory Networks Learned from Accessible Chromatin Data.Plant physiology · 2019Article
- BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus.BMC bioinformatics · 2019Article
- Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis.Nature communications · 2019Article
- Conserved noncoding sequences conserve biological networks and influence genome evolution.Heredity · 2018Article
Corrections and comments
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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
Transcriptional regulation plays an important role in establishing gene expression profiles during development or in response to (a)biotic stimuli. Transcription factor binding sites (TFBSs) are the functional elements that determine transcriptional activity, and the identification of individual TFBS in genome sequences is a major goal to inferring regulatory networks. We have developed a phylogenetic footprinting approach for the identification of conserved noncoding sequences (CNSs) across 12 dicot plants. Whereas both alignment and non-alignment-based techniques were applied to identify functional motifs in a multispecies context, our method accounts for incomplete motif conservation as well as high sequence divergence between related species. We identified 69,361 footprints associated with 17,895 genes. Through the integration of known TFBS obtained from the literature and experimental studies, we used the CNSs to compile a gene regulatory network in Arabidopsis thaliana containing 40,758 interactions, of which two-thirds act through binding events located in DNase I hypersensitive sites. This network shows significant enrichment toward in vivo targets of known regulators, and its overall quality was confirmed using five different biological validation metrics. Finally, through the integration of detailed expression and function information, we demonstrate how static CNSs can be converted into condition-dependent regulatory networks, offering opportunities for regulatory gene annotation.
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Registered trials
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.