High DNA melting temperature predicts transcription start site location in human and mouse.

Hdl Handle:
http://hdl.handle.net/10147/93888
Title:
High DNA melting temperature predicts transcription start site location in human and mouse.
Authors:
Dineen, David G; Wilm, Andreas; Cunningham, Pádraig; Higgins, Desmond G
Affiliation:
Complex and Adaptive Systems Laboratory (CASL), University College Dublin, Belfield, Dublin 4, Ireland. david.dineen@ucd.ie
Citation:
High DNA melting temperature predicts transcription start site location in human and mouse. 2009, 37 (22):7360-7 Nucleic Acids Res.
Journal:
Nucleic acids research
Issue Date:
Dec-2009
URI:
http://hdl.handle.net/10147/93888
DOI:
10.1093/nar/gkp821
PubMed ID:
19820114
Abstract:
The accurate computational prediction of transcription start sites (TSS) in vertebrate genomes is a difficult problem. The physicochemical properties of DNA can be computed in various ways and a many combinations of DNA features have been tested in the past for use as predictors of transcription. We looked in detail at melting temperature, which measures the temperature, at which two strands of DNA separate, considering the cooperative nature of this process. We find that peaks in melting temperature correspond closely to experimentally determined transcription start sites in human and mouse chromosomes. Using melting temperature alone, and with simple thresholding, we can predict TSS with accuracy that is competitive with the most accurate state-of-the-art TSS prediction methods. Accuracy is measured using both experimentally and manually determined TSS. The method works especially well with CpG island containing promoters, but also works when CpG islands are absent. This result is clear evidence of the important role of the physical properties of DNA in the process of transcription. It also points to the importance for TSS prediction methods to include melting temperature as prior information.
Language:
en
MeSH:
Algorithms; Animals; CpG Islands; DNA; Humans; Mice; Nucleic Acid Denaturation; Promoter Regions, Genetic; Temperature; Transcription Initiation Site
ISSN:
1362-4962

Full metadata record

DC FieldValue Language
dc.contributor.authorDineen, David Gen
dc.contributor.authorWilm, Andreasen
dc.contributor.authorCunningham, Pádraigen
dc.contributor.authorHiggins, Desmond Gen
dc.date.accessioned2010-03-08T16:46:07Z-
dc.date.available2010-03-08T16:46:07Z-
dc.date.issued2009-12-
dc.identifier.citationHigh DNA melting temperature predicts transcription start site location in human and mouse. 2009, 37 (22):7360-7 Nucleic Acids Res.en
dc.identifier.issn1362-4962-
dc.identifier.pmid19820114-
dc.identifier.doi10.1093/nar/gkp821-
dc.identifier.urihttp://hdl.handle.net/10147/93888-
dc.description.abstractThe accurate computational prediction of transcription start sites (TSS) in vertebrate genomes is a difficult problem. The physicochemical properties of DNA can be computed in various ways and a many combinations of DNA features have been tested in the past for use as predictors of transcription. We looked in detail at melting temperature, which measures the temperature, at which two strands of DNA separate, considering the cooperative nature of this process. We find that peaks in melting temperature correspond closely to experimentally determined transcription start sites in human and mouse chromosomes. Using melting temperature alone, and with simple thresholding, we can predict TSS with accuracy that is competitive with the most accurate state-of-the-art TSS prediction methods. Accuracy is measured using both experimentally and manually determined TSS. The method works especially well with CpG island containing promoters, but also works when CpG islands are absent. This result is clear evidence of the important role of the physical properties of DNA in the process of transcription. It also points to the importance for TSS prediction methods to include melting temperature as prior information.-
dc.language.isoenen
dc.subject.meshAlgorithms-
dc.subject.meshAnimals-
dc.subject.meshCpG Islands-
dc.subject.meshDNA-
dc.subject.meshHumans-
dc.subject.meshMice-
dc.subject.meshNucleic Acid Denaturation-
dc.subject.meshPromoter Regions, Genetic-
dc.subject.meshTemperature-
dc.subject.meshTranscription Initiation Site-
dc.titleHigh DNA melting temperature predicts transcription start site location in human and mouse.en
dc.contributor.departmentComplex and Adaptive Systems Laboratory (CASL), University College Dublin, Belfield, Dublin 4, Ireland. david.dineen@ucd.ieen
dc.identifier.journalNucleic acids researchen

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