Transcription factors
In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The f ...
are proteins that bind genomic regulatory sites. Identification of
genomic regulatory elements is essential for understanding the dynamics of developmental, physiological and pathological processes. Recent advances in
chromatin immunoprecipitation Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. It aims to determine whether specific proteins are associated with specific genom ...
followed by sequencing (
ChIP-seq
ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated prote ...
) have provided powerful ways to identify genome-wide profiling of
DNA-binding protein
DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, becau ...
s and
histone
In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn ar ...
modifications.
The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.
Transcription factor binding site databases
Comprehensive List of transcription factor binding sites (TFBSs) databases based on ChIP-seq data as follows:
References
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Bioinformatics
Genetics databases