Biomaterial Database

Genome-wide analysis of transcription factor binding sites and their characteristic DNA structures. 2015

Zhiming Dai, and Dongliang Guo, and Xianhua Dai, and Yuanyan Xiong

BACKGROUND Transcription factors (TF) regulate gene expression by binding DNA regulatory regions. Transcription factor binding sites (TFBSs) are conserved not only in primary DNA sequences but also in DNA structures. However, the global relationship between TFs and their preferred DNA structures remains to be elucidated. RESULTS In this paper, we have developed a computational method to generate a genome-wide landscape of TFs and their characteristic binding DNA structures in Saccharomyces cerevisiae. We revealed DNA structural features for different TFs. The structural conservation shows positional preference in TFBSs. Structural levels of DNA sequences are correlated with TF-DNA binding affinities. CONCLUSIONS We provided the genome-wide correspondences of TFs to DNA structures. Our findings will have implications in understanding TF regulatory mechanisms.

UI	MeSH Term	Description	Entries
D001665	Binding Sites	The parts of a macromolecule that directly participate in its specific combination with another molecule.	Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D012441	Saccharomyces cerevisiae	A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.	Baker's Yeast,Brewer's Yeast,Candida robusta,S. cerevisiae,Saccharomyces capensis,Saccharomyces italicus,Saccharomyces oviformis,Saccharomyces uvarum var. melibiosus,Yeast, Baker's,Yeast, Brewer's,Baker Yeast,S cerevisiae,Baker's Yeasts,Yeast, Baker
D014157	Transcription Factors	Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.	Transcription Factor,Factor, Transcription,Factors, Transcription
D016681	Genome, Fungal	The complete gene complement contained in a set of chromosomes in a fungus.	Fungal Genome,Fungal Genomes,Genomes, Fungal
D019295	Computational Biology	A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.	Bioinformatics,Molecular Biology, Computational,Bio-Informatics,Biology, Computational,Computational Molecular Biology,Bio Informatics,Bio-Informatic,Bioinformatic,Biologies, Computational Molecular,Biology, Computational Molecular,Computational Molecular Biologies,Molecular Biologies, Computational
D020218	Response Elements	Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.	Element, Response,Elements, Response,Response Element