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The DNA binding sites of 519 transcription factors were evaluated. [50] Of these, 169 transcription factors (33%) did not have CpG dinucleotides in their binding sites, and 33 transcription factors (6%) could bind to a CpG-containing motif but did not display a preference for a binding site with either a methylated or unmethylated CpG.
ChIPBase a database for Transcription factor-binding sites, motifs (~1290 transcription factors) and decoding the transcriptional regulation of LncRNAs, miRNAs and protein-coding genes from ~10,200 curated peak datasets derived from ChIP-seq methods in 10 species
DNA binding sites were finally confirmed in both systems [9] [10] [11] with the advent of DNA sequencing techniques. From then on, DNA binding sites for many transcription factors, restriction enzymes and site-specific recombinases have been discovered using a profusion of experimental methods.
TRANSFAC (TRANScription FACtor database) is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. The contents of the database can be used to predict potential transcription factor binding sites.
Regulatory elements are binding sites for transcription factors, which are involved in gene regulation. [1] Cis-regulatory modules perform a large amount of developmental information processing. [1] Cis-regulatory modules are non-random clusters at their specified target site that contain transcription factor binding sites. [1]
Activator-binding sites may be located very close to the promoter or numerous base pairs away. [2] [3] If the regulatory sequence is located far away, the DNA will loop over itself (DNA looping) in order for the bound activator to interact with the transcription machinery at the promoter site. [2] [3]
The Rb tumor suppressor protein (pRb) binds to the E2F1 transcription factor preventing it from interacting with the cell's transcription machinery. In the absence of pRb, E2F1 (along with its binding partner DP1) mediates the trans-activation of E2F1 target genes that facilitate the G1/S transition and S-phase.
A transcription factor is a protein that binds to specific DNA sequences (enhancer or promoter), either alone or with other proteins in a complex, to control the rate of transcription of genetic information from DNA to messenger RNA by promoting (serving as an activator) or blocking (serving as a repressor) the recruitment of RNA polymerase.
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