ArticlePLoS computational biology2019
CNEr: A toolkit for exploring extreme noncoding conservation.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis.Journal of integrative plant biology · 2026Article
- A new super-pangenome pipeline reveals domestication signatures of conserved noncoding sequences in the orange subfamily.Molecular biology and evolution · 2026Article
- Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes.Nature ecology & evolution · 2026Article
- Loss of Conserved Noncoding Elements Likely Shaped the Evolution of Regressed Phenotypes in Cavefish.Genome biology and evolution · 2025Article
- Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.Nature genetics · 2025Article
- Cost-effective solutions for high-throughput enzymatic DNA methylation sequencing.PLoS genetics · 2025Article
- Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach.Nature protocols · 2024Review
- A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons.bioRxiv : the preprint server for biology · 2024Article
- Extreme genome scrambling in marine planktonicGenome research · 2024Article
- Conserved Noncoding Elements Evolve Around the Same Genes Throughout Metazoan Evolution.Genome biology and evolution · 2024Article
- Extensive Loss and Gain of Conserved Noncoding Elements During Early Teleost Evolution.Genome biology and evolution · 2024Article
- PlantFUNCO: Integrative Functional Genomics Database Reveals Clues into Duplicates Divergence Evolution.Molecular biology and evolution · 2024Article
- DNA Conserved in Diverse Animals Since the Precambrian Controls Genes for Embryonic Development.Molecular biology and evolution · 2023Article
- Article
- Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation.Nature ecology & evolution · 2022Article
- Genome-wide identification, phylogeny, and gene duplication of the epigenetic regulators in Fagaceae.Physiologia plantarum · 2022Article
- Article
- Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.Molecular biology and evolution · 2022Article
- dbCNS: A New Database for Conserved Noncoding Sequences.Molecular biology and evolution · 2021Article
- Draft Genome Sequence of Saccharomyces cerevisiae LW2591Y, a Laboratory Strain forMicrobiology resource announcements · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Conserved Noncoding Elements (CNEs) are elements exhibiting extreme noncoding conservation in Metazoan genomes. They cluster around developmental genes and act as long-range enhancers, yet nothing that we know about their function explains the observed conservation levels. Clusters of CNEs coincide with topologically associating domains (TADs), indicating ancient origins and stability of TAD locations. This has suggested further hypotheses about the still elusive origin of CNEs, and has provided a comparative genomics-based method of estimating the position of TADs around developmentally regulated genes in genomes where chromatin conformation capture data is missing. To enable researchers in gene regulation and chromatin biology to start deciphering this phenomenon, we developed CNEr, a R/Bioconductor toolkit for large-scale identification of CNEs and for studying their genomic properties. We apply CNEr to two novel genome comparisons-fruit fly vs tsetse fly, and two sea urchin genomes-and report novel insights gained from their analysis. We also show how to reveal interesting characteristics of CNEs by coupling CNEr with existing Bioconductor packages. CNEr is available at Bioconductor (https://bioconductor.org/packages/CNEr/) and maintained at github (https://github.com/ge11232002/CNEr).
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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.