What is a transcription factor motif?

In Silico Detection of Transcription Factor Binding Sites. We define TF binding motifs as sets of DNA sequences having high affinity for binding TFs. Each occurrence of a sequence from the binding motif in a genomic region is referred to as a motif instance.

What is a transcription factor DNA binding motif?

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. Transcription factors are members of the proteome as well as regulome.

What are the two main categories of motif discovery algorithms?

There are two principal types of motif discovery algorithms; i.e. enumeration approach and probabilistic technique.

Do transcription factors bind to DNA?

Transcription factors are proteins involved in the process of converting, or transcribing, DNA into RNA. One distinct feature of transcription factors is that they have DNA-binding domains that give them the ability to bind to specific sequences of DNA called enhancer or promoter sequences.

Where do most transcription regulators bind?

How or where do most transcription regulators bind? Most transcriptional regulator proteins bind DNA as dimers. Dimerization roughly doubles the area of contact with the DNA, making the interaction tighter and more specific.

What is motif finding problem?

Given a set of DNA sequences (promoter region), the motif finding problem is the task of detecting overrepresented motifs as well as conserved motifs from orthologous sequences that are good candidates for being transcription factor binding sites. A large number of algorithms for finding DNA motifs have been developed.

How do you identify motifs in a query sequence?

To know the motifs that our problem sequence has: guessing about function. Search with a protein query sequence against a database of regular expressions (PROSITE) or profiles (PROSITE profiles or Pfam). The result provides a description of the motivs found in the sequence.

How does an activator DNA transcription factor activate transcription?

Most activators function by binding sequence-specifically to a regulatory DNA site located near a promoter and making protein–protein interactions with the general transcription machinery (RNA polymerase and general transcription factors), thereby facilitating the binding of the general transcription machinery to the …

What are the three phases of transcription?

It involves copying a gene’s DNA sequence to make an RNA molecule. Transcription is performed by enzymes called RNA polymerases, which link nucleotides to form an RNA strand (using a DNA strand as a template). Transcription has three stages: initiation, elongation, and termination.

Where do most transcription factors bind?

Transcription factors are proteins that bind to the upstream regulatory elements of genes in the promoter and enhancer regions of DNA and stimulate or inhibit gene expression and protein synthesis.

How are transcription factors binding beyond binding site motifs?

Transcription factor-DNA binding: beyond binding site motifs Sequence-specific transcription factors (TFs) regulate gene expression by binding to cis-regulatory elements in promoter and enhancer DNA.

Is there a transcription factor binding site prediction tool?

I looked online and found this transcription factor binding site prediction tool called TFSEARCH. It’s very straight-forward; all you have to do is input a sequence, which may explain its popularity (based on the site’s counter and Google’s pagerank for the site).

Where do transcription factors bind to cis-regulatory elements?

Sequence-specific transcription factors (TFs) regulate gene expression by binding to cis-regulatory elements in promoter and enhancer DNA. While studies of TF-DNA binding have focused on TFs’ intrinsic preferences for primary nucleotide sequence motifs, recent studies have elucidated additional laye …

How does TF-DNA binding affect gene expression?

Sequence-specific transcription factors (TFs) regulate gene expression by binding to cis-regulatory elements in promoter and enhancer DNA. While studies of TF-DNA binding have focused on TFs’ intrinsic preferences for primary nucleotide sequence motifs, recent studies have elucidated additional layers of complexity that modulate TF-DNA binding.