Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding
نویسندگان
چکیده
منابع مشابه
Nonspecific transcription-factor-DNA binding influences nucleosome occupancy in yeast.
Quantitative understanding of the principles regulating nucleosome occupancy on a genome-wide level is a central issue in eukaryotic genomics. Here, we address this question using budding yeast, Saccharomyces cerevisiae, as a model organism. We perform a genome-wide computational analysis of the nonspecific transcription factor (TF)-DNA binding free-energy landscape and compare this landscape w...
متن کاملIdentification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices
Accurate prediction of transcription factor binding sites (TFBSs) is a prerequisite for identifying cis-regulatory modules that underlie transcriptional regulatory circuits encoded in the genome. Here, we present a computational framework for detecting TFBSs, when multiple position weight matrices (PWMs) for a transcription factor are available. Grouping multiple PWMs of a transcription factor ...
متن کاملIncorporating Nucleosome Occupancy to Predict Transcription Factor Binding Sites
Bo Jiang April 29, 2007 ABSTRACT Traditional methods to identify potential binding sites of known transcription factors usually neglect abundant information hidden in a large genomic scale. Recent researches, however, reveal that the intrinsic nucleosome organization in genome can be predicted and may help in directing transcription factors towards their target sites. In this paper, we present ...
متن کاملPrediction of Nucleosome Positioning Based on Transcription Factor Binding Sites
BACKGROUND The DNA of all eukaryotic organisms is packaged into nucleosomes, the basic repeating units of chromatin. The nucleosome consists of a histone octamer around which a DNA core is wrapped and the linker histone H1, which is associated with linker DNA. By altering the accessibility of DNA sequences, the nucleosome has profound effects on all DNA-dependent processes. Understanding the fa...
متن کاملDiscovering Transcription Factor Binding Motif Sequences
Introduction In biology, sequence motifs are short sequence patterns, usually with fixed lengths, that represent many features of DNA, RNA, and protein molecules. Sequence motifs can represent transcription factor binding sites for DNA, splice junctions for RNA, and binding domains for proteins. Thus, discovering sequence motifs can lead to a better understanding of transcriptional regulation, ...
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ژورنال
عنوان ژورنال: BMC Genomics
سال: 2013
ISSN: 1471-2164
DOI: 10.1186/1471-2164-14-428