Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure

The postgenomic era is all about learning about function by comparing genomic sequences within and between organisms. This review describes an approach that applies detailed thermodynamic information, as opposed to sequence motif searches, to analyze genomes (thermogenomics) for the occurrence of se...

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Bibliographic Details
Published in:Methods (San Diego, Calif.) Calif.), 2009-03, Vol.47 (3), p.159-167
Main Author: Ho, P. Shing
Format: Article
Language:English
Subjects:
Algorithms
Binding Sites - genetics
DNA - chemistry
DNA - metabolism
DNA, Z-Form - chemistry
DNA, Z-Form - metabolism
Genomics - methods
NFI Transcription Factors - metabolism
Nuclear factor I
Nucleic Acid Conformation
Phylogeny
Software
Thermodynamics
Transcription regulation
Z-DNA
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Summary:The postgenomic era is all about learning about function by comparing genomic sequences within and between organisms. This review describes an approach that applies detailed thermodynamic information, as opposed to sequence motif searches, to analyze genomes (thermogenomics) for the occurrence of sequences with the potential to form left-handed Z-DNA and those that bind the eukaryotic nuclear factor I (NFI) transcriptional regulators. Such thermogenomic strategies allow us to address the questions of whether Z-DNA forming sequences can potentially function in regulating transcription of eukaryotic genes and how such function may emerge relative to other GC-rich elements, such as NFI recognition sites, to become a transcriptional coactivator.
ISSN:1046-2023
1095-9130
DOI:10.1016/j.ymeth.2008.09.007