ArticleProceedings of the National Academy of Sciences of the United States of America2007
Arabidopsis intragenomic conserved noncoding sequence.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development.Plant communications · 2025Article
- Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research.The Plant journal : for cell and molecular biology · 2021Article
- Article
- Single-Base Resolution Map of Evolutionary Constraints and Annotation of Conserved Elements across Major Grass Genomes.Genome biology and evolution · 2018Article
- Evolution of Cis-Regulatory Elements and Regulatory Networks in Duplicated Genes of Arabidopsis.Plant physiology · 2015Article
- Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis.The Plant cell · 2014Article
- 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
- pENCODE: a plant encyclopedia of DNA elements.Annual review of genetics · 2014Review
- An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.Nature genetics · 2013Article
- The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the Paleohexaploid Brassica rapa.Genome biology and evolution · 2013Article
- Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses.Frontiers in plant science · 2013Article
- Conserved Non-Coding Sequences are Associated with Rates of mRNA Decay in Arabidopsis.Frontiers in plant science · 2013Article
- Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants.The Plant cell · 2012Article
- New cis-regulatory elements in the Rht-D1b locus region of wheat.Functional & integrative genomics · 2012Article
- Article
- Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids.The Plant cell · 2011Article
- Expressed sequence tag analysis of khat (Catha edulis) provides a putative molecular biochemical basis for the biosynthesis of phenylpropylamino alkaloids.Genetics and molecular biology · 2011Article
- Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure.Heredity · 2011Article
- Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
After the most recent tetraploidy in the Arabidopsis lineage, most gene pairs lost one, but not both, of their duplicates. We manually inspected the 3,179 retained gene pairs and their surrounding gene space still present in the genome using a custom-made viewer application. The display of these pairs allowed us to define intragenic conserved noncoding sequences (CNSs), identify exon annotation errors, and discover potentially new genes. Using a strict algorithm to sort high-scoring pair sequences from the bl2seq data, we created a database of 14,944 intragenomic Arabidopsis CNSs. The mean CNS length is 31 bp, ranging from 15 to 285 bp. There are approximately 1.7 CNSs associated with a typical gene, and Arabidopsis CNSs are found in all areas around exons, most frequently in the 5' upstream region. Gene ontology classifications related to transcription, regulation, or "response to ..." external or endogenous stimuli, especially hormones, tend to be significantly overrepresented among genes containing a large number of CNSs, whereas protein localization, transport, and metabolism are common among genes with no CNSs. There is a 1.5% overlap between these CNSs and the 218,982 putative RNAs in the Arabidopsis Small RNA Project database, allowing for two mismatches. These CNSs provide a unique set of noncoding sequences enriched for function. CNS function is implied by evolutionary conservation and independently supported because CNS-richness predicts regulatory gene ontology categories.
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