Improved Methylation Protection-Based DNA Footprinting to Reveal Structural Distortion of DNA upon Transcription Factor Binding
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چکیده
منابع مشابه
Improved methylation protection-based DNA footprinting to reveal structural distortion of DNA upon transcription factor binding.
Mapping the precise DNA sequence to which transcription factors bind contributes significantly to understanding the regulation of gene expression. In vitro footprinting techniques are typically employed to examine DNA-protein contacts (3). Methylation protection-based footprinting (MeP) is specifically used to identify the guanine contacts by a transcription factor because DMS will uniformly me...
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MOTIVATION A key goal in molecular biology is to understand the mechanisms by which a cell regulates the transcription of its genes. One important aspect of this transcriptional regulation is the binding of transcription factors (TFs) to their specific cis-regulatory counterparts on the DNA. TFs recognize and bind their DNA counterparts according to the structure of their DNA-binding domains (e...
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MOTIVATION To understand transcription regulatory mechanisms, it is indispensable to investigate transcription factor (TF) DNA binding preferences. We noted that the generally acknowledged information of functional annotations of TFs as well as that of their target genes should provide useful hints in determining TF DNA binding preferences. RESULTS In this contribution, we developed an integr...
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MOTIVATION Comparative modelling is a computational method used to tackle a variety of problems in molecular biology and biotechnology. Traditionally it has been applied to model the structure of proteins on their own or bound to small ligands, although more recently it has also been used to model protein-protein interfaces. This work is the first to systematically analyze whether comparative m...
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: BioTechniques
سال: 2001
ISSN: 0736-6205,1940-9818
DOI: 10.2144/01301bm01