Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites
نویسندگان
چکیده
منابع مشابه
Distinct properties of cell-type-specific and shared transcription factor binding sites.
Most human transcription factors bind a small subset of potential genomic sites and often use different subsets in different cell types. To identify mechanisms that govern cell-type-specific transcription factor binding, we used an integrative approach to study estrogen receptor α (ER). We found that ER exhibits two distinct modes of binding. Shared sites, bound in multiple cell types, are char...
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Transcription of a gene is cued by the binding of a protein to a binding site. Transcription factors bind to specific binding sites (TFBSs), of which there may be many for a single transcription factor (1). However, these TFBSs often exhibit a considerable amount of variability, as the sequences consist of similar nucleotides rather than complete replicas of a TFBS (1). The ability to model the...
متن کاملUsing Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites
An important step in understanding gene regulation is to identify the DNA binding sites recognized by each transcription factor (TF). Conventional approaches to prediction of TF binding sites involve the definition of consensus sequences or position-specific weight matrices and rely on statistical analysis of DNA sequences of known binding sites. Here, we present a method called SiteSleuth in w...
متن کاملMaterial for Predicting tissue specific transcription factor binding sites
Our k-mer based PBM model (Figure 1a in main text) is motivated by the biophysics of TF binding to the probes in PBM experiments. Following Zhao et al. [1], we denote by Yi the experimentally measured intensity of the i-Th. probe on the PBM array. We denote by F (i) the (unobserved) binding probability of the TF to this probe. While these two quantities are related, due to experiential errors a...
متن کاملEvolution of transcription factor DNA binding sites.
In bioinformatics, binding of transcription regulatory factors to the cognate binding sites is usually described by sequence-specific binding energy, which is estimated from a training sample of sites. This model implies that all binding sites with binding energy above some threshold are functional and site sequence variations should be considered neutral until they do not reduce this energy be...
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ژورنال
عنوان ژورنال: Molecular Cell
سال: 2013
ISSN: 1097-2765
DOI: 10.1016/j.molcel.2013.08.037