ArticleNucleic acids research2012
Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 40 citations in OpenAlex.
- The Value of Circulating microRNAs for Diagnosis and Prediction of Preeclampsia: a Meta-analysis and Systematic Review.Reproductive sciences (Thousand Oaks, Calif.) · 2022Pooled it
- Emerging Roles of ncRNAs in Type 2 Diabetes Mellitus: From Mechanisms to Drug Discovery.Biomolecules · 2024Review
- Blood and urine biomarkers of disease progression in IgA nephropathy.Biomarker research · 2024Review
- Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches inEcology and evolution · 2024Article
- PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters.Nucleic acids research · 2024Article
- Exploring the role of exosomal MicroRNAs as potential biomarkers in preeclampsia.Frontiers in immunology · 2024Review
- Novel insights regarding the role of noncoding RNAs in diabetes.World journal of diabetes · 2023Review
- Long non-coding RNA UCA1 enhances cervical cancer cell proliferation and invasion by regulating microRNA-299-3p expression.Oncology letters · 2021Article
- Long non-coding RNAs in metabolic disorders: pathogenetic relevance and potential biomarkers and therapeutic targets.Journal of endocrinological investigation · 2021Review
- Roles of noncoding RNAs in preeclampsia.Reproductive biology and endocrinology : RB&E · 2021Review
- Genome-wide analysis of European sea bass provides insights into the evolution and functions of single-exon genes.Ecology and evolution · 2021Article
- Article
- Regulation of Hippo, TGFβ/SMAD, Wnt/Frontiers in oncology · 2021Review
- Long Noncoding Competing Endogenous RNA Networks in Pancreatic Cancer.Frontiers in oncology · 2021Review
- Review
- Article
- Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium.PLoS pathogens · 2019Article
- Genome-wide identification of conserved intronic non-coding sequences using a Bayesian segmentation approach.BMC genomics · 2017Article
- Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle.Genome biology and evolution · 2016Article
- Genomic Views of Transcriptional Enhancers: Essential Determinants of Cellular Identity and Activity-Dependent Responses in the CNS.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2015Review
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
More than 98% of a typical vertebrate genome does not code for proteins. Although non-coding regions are sprinkled with short (<200 bp) islands of evolutionarily conserved sequences, the function of most of these unannotated conserved islands remains unknown. One possibility is that unannotated conserved islands could encode non-coding RNAs (ncRNAs); alternatively, unannotated conserved islands could serve as promoter-distal regulatory factor binding sites (RFBSs) like enhancers. Here we assess these possibilities by comparing unannotated conserved islands in the human and mouse genomes to transcribed regions and to RFBSs, relying on a detailed case study of one human and one mouse cell type. We define transcribed regions by applying a novel transcript-calling algorithm to RNA-Seq data obtained from total cellular RNA, and we define RFBSs using ChIP-Seq and DNAse-hypersensitivity assays. We find that unannotated conserved islands are four times more likely to coincide with RFBSs than with unannotated ncRNAs. Thousands of conserved RFBSs can be categorized as insulators based on the presence of CTCF or as enhancers based on the presence of p300/CBP and H3K4me1. While many unannotated conserved RFBSs are transcriptionally active to some extent, the transcripts produced tend to be unspliced, non-polyadenylated and expressed at levels 10 to 100-fold lower than annotated coding or ncRNAs. Extending these findings across multiple cell types and tissues, we propose that most conserved non-coding genomic DNA in vertebrate genomes corresponds to promoter-distal regulatory elements.
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Registered trials
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.