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

Robyr, Daniel; Friedli, Marc; Gehrig, Corinne; Arcangeli, Mélanie; Marin, Marilyn; Guipponi, Michel; Farinelli, Laurent Luca Denis; Barde, Isabelle; Verp, Sonia; Trono, Didier; Antonarakis, Stylianos

doi:10.1371/journal.pone.0017634

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Title		Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences
Authors		Robyr, Daniel Friedli, Marc Gehrig, Corinne Arcangeli, Mélanie Marin, Marilyn Guipponi, Michel Farinelli, Laurent Luca Denis Barde, Isabelle Verp, Sonia Trono, Didier Antonarakis, Stylianos show all authors [1 - 11]
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		Animals — Base Sequence — Chromosomes, Human/chemistry/genetics — Conserved Sequence/genetics — DNA, Circular/genetics — DNA, Intergenic/genetics — Genome, Human/genetics — Humans — K562 Cells — Locus Control Region/genetics — Mice — Nucleic Acid Conformation — Oligodendroglia/metabolism — Open Reading Frames/genetics — Beta-Globins/genetics
Identifiers		DOI: 10.1371/journal.pone.0017634 PMID: 21408183
Full text		Article (Published version) (1.8 MB) - Free access
Structures		Faculté de médecine / Section de médecine fondamentale / Département de médecine génétique et développement
Research group		Pathologie Moléculaire de la Trisomie 21 et le Génome Humain (248)
Citation (ISO format)		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