ArticlePloS one2011
Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
8 citing papers in PubMed, 20 citations in OpenAlex.
- Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization.Cell reports · 2018Article
- Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences.Molecular biology and evolution · 2017Article
- The dynamic architectural and epigenetic nuclear landscape: developing the genomic almanac of biology and disease.Journal of cellular physiology · 2014Review
- The mystery of extreme non-coding conservation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Review
- Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods.BMC genomics · 2013Article
- TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed.The EMBO journal · 2012Article
- Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse.Human molecular genetics · 2012Article
- Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements.Bioinformatics (Oxford, England) · 2012Article
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comparative analyses of various mammalian genomes have identified numerous conserved non-coding (CNC) DNA elements that display striking conservation among species, suggesting that they have maintained specific functions throughout evolution. CNC function remains poorly understood, although recent studies have identified a role in gene regulation. We hypothesized that the identification of genomic loci that interact physically with CNCs would provide information on their functions. We have used circular chromosome conformation capture (4C) to characterize interactions of 10 CNCs from human chromosome 21 in K562 cells. The data provide evidence that CNCs are capable of interacting with loci that are enriched for CNCs. The number of trans interactions varies among CNCs; some show interactions with many loci, while others interact with few. Some of the tested CNCs are capable of driving the expression of a reporter gene in the mouse embryo, and associate with the oligodendrocyte genes OLIG1 and OLIG2. Our results underscore the power of chromosome conformation capture for the identification of targets of functional DNA elements and raise the possibility that CNCs exert their functions by physical association with defined genomic regions enriched in CNCs. These CNC-CNC interactions may in part explain their stringent conservation as a group of regulatory sequences.
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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.