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Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences

Marin, Marilyn
Barde, Isabelle
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Published in PloS one. 2011, vol. 6, no. 3, e17634
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.
Keywords AnimalsBase SequenceChromosomes, Human/chemistry/geneticsConserved Sequence/geneticsDNA, Circular/geneticsDNA, Intergenic/geneticsGenome, Human/geneticsHumansK562 CellsLocus Control Region/geneticsMiceNucleic Acid ConformationOligodendroglia/metabolismOpen Reading Frames/geneticsBeta-Globins/genetics
PMID: 21408183
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Research group Pathologie Moléculaire de la Trisomie 21 et le Génome Humain (248)
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ROBYR, Daniel et al. Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. In: PloS one, 2011, vol. 6, n° 3, p. e17634. doi: 10.1371/journal.pone.0017634 https://archive-ouverte.unige.ch/unige:34664

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Deposited on : 2014-03-07

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