ArticleFrontiers in plant science2013
Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses.
Article in Frontiers in plant science, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 39 citations in OpenAlex.
- The landscape of regulatory element evolution in a C4 perennial grass.BMC genomics · 2026Article
- Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development.Plant communications · 2025Article
- Decoding plant responses to waterlogging: from stress signals to molecular mechanisms and their future implications.Plant molecular biology · 2025Review
- Exploiting light energy utilization strategies in Populus simonii through multitrait-GWAS: insights from stochastic differential models.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Conserved noncoding sequences and de novo Mutator insertion alleles are imprinted in maize.Plant physiology · 2023Article
- Mapping responsive genomic elements to heat stress in a maize diversity panel.Genome biology · 2022Article
- Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses.The Plant cell · 2020Article
- The prevalence, evolution and chromatin signatures of plant regulatory elements.Nature plants · 2019Article
- pDHS-ELM: computational predictor for plant DNase I hypersensitive sites based on extreme learning machines.Molecular genetics and genomics : MGG · 2018Article
- Coexpression network revealing the plasticity and robustness of population transcriptome during the initial stage of domesticating energy crop Miscanthus lutarioriparius.Plant molecular biology · 2018Article
- Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome.Plant physiology · 2018Article
- Single-Base Resolution Map of Evolutionary Constraints and Annotation of Conserved Elements across Major Grass Genomes.Genome biology and evolution · 2018Article
- Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize.The Plant cell · 2017Article
- Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize.Genome biology · 2017Article
- Widespread natural variation of DNA methylation within angiosperms.Genome biology · 2016Article
- A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants.Plant physiology · 2016Article
- Subfunctionalization of peroxisome proliferator response elements accounts for retention of duplicated fabp1 genes in zebrafish.BMC evolutionary biology · 2016Article
- RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize.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
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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
Conserved non-coding sequences (CNS) are islands of non-coding sequence that, like protein coding exons, show less divergence in sequence between related species than functionless DNA. Several CNSs have been demonstrated experimentally to function as cis-regulatory regions. However, the specific functions of most CNSs remain unknown. Previous searches for CNS in plants have either anchored on exons and only identified nearby sequences or required years of painstaking manual annotation. Here we present an open source tool that can accurately identify CNSs between any two related species with sequenced genomes, including both those immediately adjacent to exons and distal sequences separated by >12 kb of non-coding sequence. We have used this tool to characterize new motifs, associate CNSs with additional functions, and identify previously undetected genes encoding RNA and protein in the genomes of five grass species. We provide a list of 15,363 orthologous CNSs conserved across all grasses tested. We were also able to identify regulatory sequences present in the common ancestor of grasses that have been lost in one or more extant grass lineages. Lists of orthologous gene pairs and associated CNSs are provided for reference inbred lines of arabidopsis, Japonica rice, foxtail millet, sorghum, brachypodium, and maize.
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