Orphan CpG islands identify numerous conserved promoters in the mammalian genome

Bird lab paper featured in PLoS Genetics.

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Image from paper, PLoS Genetics 2010

Authors

Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R, Bird AP.

Summary

The Bird Lab identified all CpG islands in the human and mouse genomes using a CpG affinity column plus high throughput sequencing (CAP). Surprisingly, half are not at known gene promoters, but lie within or between genes. Nevertheless, many of these “orphan CpG islands” have the characteristics of promoters, including transcripts independently identified by cap affinity (CAGE) or nuclear run-on (NRO) technologies, bound RNA polymerase II (RNAPII) or methylation of lysine 4 of histone H3.

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