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. 2011 Mar 7;6(3):e17634.
doi: 10.1371/journal.pone.0017634.

Chromosome Conformation Capture Uncovers Potential Genome-Wide Interactions Between Human Conserved Non-Coding Sequences

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Free PMC article

Chromosome Conformation Capture Uncovers Potential Genome-Wide Interactions Between Human Conserved Non-Coding Sequences

Daniel Robyr et al. PLoS One. .
Free PMC article

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.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Interaction map of the beta-globin locus control region (LCR).
The blue bars correspond to the number of sequence tags (log 2 transformed) found in the library generated with HS5 (black arrow) in the indicated cell line. The red arrow corresponds to regions of the locus where interactions were described in earlier studies. The genes found in the region are displayed at the bottom of the map. The image was generated with the UCSC genome browser (http://genome.ucsc.edu/). The DNaseI hypersensitivity heat map was obtained through the UCSC browser.
Figure 2
Figure 2. Circular representation of the interactions identified for all CNCs.
All chromosomes are drawn to scale with the exception of chromosome 21. Lines are connecting the specified CNC with the DpnII fragments observed at least 50 times in trans. Dots in blue in the scatter plot inside the circles represent sequences observed less than 50 times, whereas red dots correspond to sequences observed at least 50 times (in cis or trans). The images were generated with the circos software package (http://mkweb.bcgsc.ca/circos/) . The numbers shown below each interaction map correspond to the percentage of trans CIRs (threshold of 50 observations).
Figure 3
Figure 3. Circular representation of the interactions identified for all nonCNCs.
All chromosomes are drawn to scale with the exception of chromosome 21. Lines are connecting the specified CNC with the DpnII fragments observed at least 50 times in trans. Dots in blue in the scatter plot inside the circles represent sequences observed less than 50 times, whereas red dots correspond to sequences observed at least 50 times (in cis or trans). The images were generated with the circos software package (http://mkweb.bcgsc.ca/circos/) . The numbers shown below each interaction map correspond to the percentage of trans CIRs (threshold of 50 observations).
Figure 4
Figure 4. Enrichment of conserved regions.
A) Comparisons of the quantile distributions of the distances (bp) between all DpnII fragments and their nearest conservation block. 10000 DpnII fragments were sampled from the genome for the “simulation” distribution. The dashed lines correspond to the expected plot if the distributions are equal. The P-value (two sample Wilcoxon test) of the divergence between two distributions is displayed at the bottom-right of each plot. B) Lines are connecting DpnII fragments that are within 5 kb of the interrogated CNC and non-CNCs in any of the other libraries analyzed in this study. The red lines connect interacting CNCs whereas the green lines represent interactions observed between CNCs and non-CNCs. The image was generated with the circos software package (http://mkweb.bcgsc.ca/circos/) .
Figure 5
Figure 5. Several CNCs are potential regulators of the Olig genes.
A) Interaction map of CNC8 (black arrow) with regions in cis in K562 cells. The blue bars correspond to the number of sequences tags (log 2 transformed) found in the library generated with CNC8. The genes in the region are displayed at the bottom of the map. The image was generated with the UCSC genome browser (http://genome.ucsc.edu/). B) Sagital and dorsal view of mouse embryos at E11.5 stained for LacZ expression after injection of CNC8 fused to LacZ in a lentiviral vector. 4 of the 45 embryos that have integrated the construct are shown here. C) Lines are connecting CNCs with fragments within their libraries that are less than 5 kb (upper) or 10 kb (lower) away from either OLIG1 (blue) or OLIG2 (orange). Images were generated with the circos software package (http://mkweb.bcgsc.ca/circos/) .

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References

    1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921. - PubMed
    1. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. The sequence of the human genome. Science. 2001;291:1304–1351. - PubMed
    1. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15:1034–1050. - PMC - PubMed
    1. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007;447:799–816. - PMC - PubMed
    1. Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH. Local DNA topography correlates with functional noncoding regions of the human genome. Science. 2009;324:389–392. - PMC - PubMed

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