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Global analysis of inverted repeat sequences in human gene promoters reveals their non-random distribution and association with specific biological pathways
V. Brázda, M. Bartas, J. Lýsek, J. Coufal, M. Fojta
Jazyk angličtina Země Spojené státy americké
Typ dokumentu časopisecké články, práce podpořená grantem
NLK
Free Medical Journals
od 2006 do Před 18 měsíci
Elsevier Open Access Journals
od 2005-12-01
ROAD: Directory of Open Access Scholarly Resources
od 1987
Elsevier Open Archive Journals
od 2005-12-01 do Před 18 měsíci
- MeSH
- analýza hlavních komponent MeSH
- lidé MeSH
- obrácené repetice * MeSH
- počátek transkripce MeSH
- promotorové oblasti (genetika) * MeSH
- shluková analýza MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Inverted repeats (IR) play important roles in specific DNA-dependent processes in simple prokaryotes to complex eukaryotes. They are recognized by a variety of proteins including restriction enzymes, helicases and transcription factors. We evaluate the presence and localization of IRs in all validated human promoter sequences within 1000 bp upstream and downstream of the transcription start site (TSS). The occurrence of 7 bp and longer IRs is located non-randomly in promoter regions, with enrichment within 200 bp upstream of the TSS. The highest frequency of IRs is just before TSS for repeats of 8 bp or longer. A comparison of promoters divided according to the occurrence of five individual promoter motifs shows unique location patterns of IRs. Principal component analyses and hierarchical clustering of IRs abundance demonstrated that they are depleted and/or not enriched in the promoters of stably expressed genes, but show significant enrichments for specific dynamically regulated biological pathways.
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- $a Brázda, Václav $u Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 612 65, Czech Republic. Electronic address: vaclav@ibp.cz
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- $a Global analysis of inverted repeat sequences in human gene promoters reveals their non-random distribution and association with specific biological pathways / $c V. Brázda, M. Bartas, J. Lýsek, J. Coufal, M. Fojta
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- $a Inverted repeats (IR) play important roles in specific DNA-dependent processes in simple prokaryotes to complex eukaryotes. They are recognized by a variety of proteins including restriction enzymes, helicases and transcription factors. We evaluate the presence and localization of IRs in all validated human promoter sequences within 1000 bp upstream and downstream of the transcription start site (TSS). The occurrence of 7 bp and longer IRs is located non-randomly in promoter regions, with enrichment within 200 bp upstream of the TSS. The highest frequency of IRs is just before TSS for repeats of 8 bp or longer. A comparison of promoters divided according to the occurrence of five individual promoter motifs shows unique location patterns of IRs. Principal component analyses and hierarchical clustering of IRs abundance demonstrated that they are depleted and/or not enriched in the promoters of stably expressed genes, but show significant enrichments for specific dynamically regulated biological pathways.
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- $a Bartas, Martin $u Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava 710 00, Czech Republic
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- $a Lýsek, Jiří $u Mendel University in Brno, Zemědělská 1, Brno 613 00, Czech Republic
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