Quantitative modeling of transcription factor binding specificities using DNA shape
نویسندگان
چکیده
منابع مشابه
Quantitative modeling of transcription factor binding specificities using DNA shape.
DNA binding specificities of transcription factors (TFs) are a key component of gene regulatory processes. Underlying mechanisms that explain the highly specific binding of TFs to their genomic target sites are poorly understood. A better understanding of TF-DNA binding requires the ability to quantitatively model TF binding to accessible DNA as its basic step, before additional in vivo compone...
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Although the proteins that read the gene regulatory code, transcription factors (TFs), have been largely identified, it is not well known which sequences TFs can recognize. We have analyzed the sequence-specific binding of human TFs using high-throughput SELEX and ChIP sequencing. A total of 830 binding profiles were obtained, describing 239 distinctly different binding specificities. The model...
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Transcription factors (TFs) are regulatory proteins that bind DNA in promoter regions of the genome and either promote or repress gene expression. Here, we predict analytically that enhanced homooligonucleotide sequence correlations, such as poly(dA:dT) and poly(dC:dG) tracts, statistically enhance nonspecific TF-DNA binding affinity. This prediction is generic and qualitatively independent of ...
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Motivation Transcription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of adjacent base pairs, etc. Several methods have been developed to jointly account for DNA sequence and shape properties in predicting TF binding affi...
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Today, annotated amino acid sequences of more and more transcription factors (TFs) are readily available. Quantitative information about their DNA-binding specificities, however, are hard to obtain. Position frequency matrices (PFMs), the most widely used models to represent binding specificities, are experimentally characterized only for a small fraction of all TFs. Even for some of the most i...
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ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 2015
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.1422023112