GC skew is a conserved property of unmethylated CpG island promoters across vertebrates
In: Nucleic Acids Research, Jg. 43 (2015-11-16), Heft 20
Online
academicJournal
- 9729 - 9741
GC skew is a measure of the strand asymmetry in the distribution of guanines and cytosines. GC skew favors R-loops, a type of three stranded nucleic acid structures that form upon annealing of an RNA strand to one strand of DNA, creating a persistent RNA:DNA hybrid. Previous studies show that GC skew is prevalent at thousands of human CpG island (CGI) promoters and transcription termination regions, which correspond to hotspots of R-loop formation. Here, we investigated the conservation of GC skew patterns in 60 sequenced chordates genomes. We report that GC skew is a conserved sequence characteristic of the CGI promoter class in vertebrates. Furthermore, we reveal that promoter GC skew peaks at the exon 1/ intron1 junction and that it is highly correlated with gene age and CGI promoter strength. Our data also show that GC skew is predictive of unmethylated CGI promoters in a range of vertebrate species and that it imparts significant DNA hypomethylation for promoters with intermediate CpG densities. Finally, we observed that terminal GC skew is conserved for a subset of vertebrate genes that tend to be located significantly closer to their downstream neighbors, consistent with a role for R-loop formation in transcription termination.
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GC skew is a conserved property of unmethylated CpG island promoters across vertebrates
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Autor/in / Beteiligte Person: | Hartono, Stella R ; Korf, Ian F ; Chédin, Frédéric |
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Zeitschrift: | Nucleic Acids Research, Jg. 43 (2015-11-16), Heft 20 |
Veröffentlichung: | eScholarship, University of California, 2015 |
Medientyp: | academicJournal |
Umfang: | 9729 - 9741 |
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