ArticleThe Plant cell2007
G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis.
Article in The Plant cell, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 47 citations in OpenAlex.
- Characterization and functional analysis of conserved non-coding sequences among poaceae: insights into gene regulation and phenotypic variation in maize.BMC genomics · 2025Article
- A Study of GUS Expression inPlants (Basel, Switzerland) · 2023Article
- Novel genome characteristics contribute to the invasiveness of Phragmites australis (common reed).Molecular ecology · 2022Article
- Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae.The New phytologist · 2020Article
- An inferred fitness consequence map of the rice genome.Nature plants · 2020Article
- Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize.The Plant cell · 2017Article
- A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants.Plant physiology · 2016Article
- Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana.BMC genomics · 2016Article
- Arabidopsis Motif Scanner.BMC bioinformatics · 2016Article
- Evolution of Cis-Regulatory Elements and Regulatory Networks in Duplicated Genes of Arabidopsis.Plant physiology · 2015Article
- CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses in chickpea.Journal of biosciences · 2015Article
- The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates.The Plant cell · 2014Article
- The histone modification H3K27me3 is retained after gene duplication and correlates with conserved noncoding sequences in Arabidopsis.Genome biology and evolution · 2014Article
- Flower development under drought stress: morphological and transcriptomic analyses reveal acute responses and long-term acclimation in Arabidopsis.The Plant cell · 2013Article
- Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses.Frontiers in plant science · 2013Article
- The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the Paleohexaploid Brassica rapa.Genome biology and evolution · 2013Article
- Conserved Non-Coding Sequences are Associated with Rates of mRNA Decay in Arabidopsis.Frontiers in plant science · 2013Article
- Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis.Genome biology · 2012Article
- Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants.The Plant cell · 2012Article
- Systematic identification of functional plant modules through the integration of complementary data sources.Plant physiology · 2012Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A tetraploidy left Arabidopsis thaliana with 6358 pairs of homoeologs that, when aligned, generated 14,944 intragenomic conserved noncoding sequences (CNSs). Our previous work assembled these phylogenetic footprints into a database. We show that known transcription factor (TF) binding motifs, including the G-box, are overrepresented in these CNSs. A total of 254 genes spanning long lengths of CNS-rich chromosomes (Bigfoot) dominate this database. Therefore, we made subdatabases: one containing Bigfoot genes and the other containing genes with three to five CNSs (Smallfoot). Bigfoot genes are generally TFs that respond to signals, with their modal CNS positioned 3.1 kb 5' from the ATG. Smallfoot genes encode components of signal transduction machinery, the cytoskeleton, or involve transcription. We queried each subdatabase with each possible 7-nucleotide sequence. Among hundreds of hits, most were purified from CNSs, and almost all of those significantly enriched in CNSs had no experimental history. The 7-mers in CNSs are not 5'- to 3'-oriented in Bigfoot genes but are often oriented in Smallfoot genes. CNSs with one G-box tend to have two G-boxes. CNSs were shared with the homoeolog only and with no other gene, suggesting that binding site turnover impedes detection. Bigfoot genes may function in adaptation to environmental change.
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