Московский семинар по биоинформатике - 18 марта 2010

Юлия Медведева, ГосНИИГенетика

Межгенные, терминальные, и внутригенные CpG островки в геноме человека

Четверг, 18 марта 2010, 18.00
Институт молекулярной биологии (Вавилова, 32), к. 309.
Yulia Medvedeva


Intergenic, gene terminal, and intragenic CpG islands in the human genome

Recently, it has been discovered that the human genome contains hundred times more transcription start sites (TSSs) then protein-coding genes. At least part of those TSSs associated with non-coding RNA of different functions. Regulatory regions related to transcription of such RNAs are poorly studied. Some of these regulatory regions may be associated with CpG islands located far from transcription start-sites of any protein coding gene. The human genome contains many such CpG islands; however, until now their properties were not systematically studied.
We studied CpG islands located in different regions of the human genome using methods of bioinformatics and comparative genomics. We have observed that CpG islands have a preference to overlap with exons, including exons located far from TSS of the gene, but usually extend well into introns. Synonymous substitution rate of CpG-containing codons becomes substantially reduced in regions where CpG islands overlap with protein-coding exons, even if they are located far downstream from TSSs, which means that selection pressure on the nuclear acids level exists in CpG islands. CAGE tag analysis displayed frequent transcription start sites in all CpG islands, including those found far from transcription start sites of protein coding genes. Computational prediction and analysis of published ChIP-chip data revealed that CpG islands contain an increased number of sites recognized by Sp1 protein. CpG islands containing more CAGE tags usually also contain more Sp1 binding sites. This is especially relevant for CpG island
s located in 3' gene regions. Various examples of transcription, confirmed by mRNAs or ESTs, but with no evidence of protein coding genes, were found in CAGE-enriched CpG islands located far TSS of any known protein coding gene.
Summarizing, CpG islands located far from transcription start sites of protein coding genes have transcription initiation activity and display Sp1 binding properties. In exons, overlapping with these islands, the synonymous substitution rate of CpG containing codons is decreased. This suggests that such CpG islands are involved in transcription initiation, possibly of some non-coding RNAs.

Рабочий язык семинара – русский

Заседания семинара проходят в Институте молекулярной биологии им. Энгельгардта РАН, ул. Вавилова 32, комната 309.

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