ArticlePlant physiology2016
A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants.
Article in Plant physiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 52 citations in OpenAlex.
- Comparative genomic characterization and germination-associated expression of DET2 and CER10 related reductases in Chenopodium quinoa.Protoplasma · 2026Article
- Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.Plant biotechnology journal · 2026Article
- Design and Testing of Root-Specific Synthetic Promoters by Machine Learning.International journal of molecular sciences · 2026Article
- Lineage-specific evolution of regulatory landscapes in a polyploid plant and its diploid progenitors.bioRxiv : the preprint server for biology · 2026Article
- Big data approaches to understanding gene regulatory networks in the shoot apical meristem andFrontiers in plant science · 2026Review
- Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development.Plant communications · 2025Article
- Review
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits.Nature communications · 2024Article
- Functional investigation of five R2R3-MYB transcription factors associated with wood development in Eucalyptus using DAP-seq-ML.Plant molecular biology · 2023Article
- Review
- Conserved noncoding sequences and de novo Mutator insertion alleles are imprinted in maize.Plant physiology · 2023Article
- Cis-regulatory sequences in plants: Their importance, discovery, and future challenges.The Plant cell · 2022Review
- The evolutionary landscape and expression pattern of plant lincRNAs.RNA biology · 2022Article
- Primer Design for the Analysis of Closely Related Species: Application of Noncoding mtDNA and cpDNA Sequences.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The native cistrome and sequence motif families of the maize ear.PLoS genetics · 2021Article
- Genomic editing of intronic enhancers unveils their role in fine-tuning tissue-specific gene expression in Arabidopsis thaliana.The Plant cell · 2021Article
- Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize.Genome research · 2021Article
- Evolution of Conserved Noncoding Sequences in Arabidopsis thaliana.Molecular biology and evolution · 2021Article
- Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators.Nature plants · 2021Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors (TFs) regulate gene expression by binding cis-regulatory elements, of which the identification remains an ongoing challenge owing to the prevalence of large numbers of nonfunctional TF binding sites. Powerful comparative genomics methods, such as phylogenetic footprinting, can be used for the detection of conserved noncoding sequences (CNSs), which are functionally constrained and can greatly help in reducing the number of false-positive elements. In this study, we applied a phylogenetic footprinting approach for the identification of CNSs in 10 dicot plants, yielding 1,032,291 CNSs associated with 243,187 genes. To annotate CNSs with TF binding sites, we made use of binding site information for 642 TFs originating from 35 TF families in Arabidopsis (Arabidopsis thaliana). In three species, the identified CNSs were evaluated using TF chromatin immunoprecipitation sequencing data, resulting in significant overlap for the majority of data sets. To identify ultraconserved CNSs, we included genomes of additional plant families and identified 715 binding sites for 501 genes conserved in dicots, monocots, mosses, and green algae. Additionally, we found that genes that are part of conserved mini-regulons have a higher coherence in their expression profile than other divergent gene pairs. All identified CNSs were integrated in the PLAZA 3.0 Dicots comparative genomics platform (http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/) together with new functionalities facilitating the exploration of conserved cis-regulatory elements and their associated genes. The availability of this data set in a user-friendly platform enables the exploration of functional noncoding DNA to study gene regulation in a variety of plant species, including crops.
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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.