Which is a DNA binding motif?

The common motifs include the helix-turn-helix, the homeodomain, the leucine zipper, the helix-loop-helix, and zinc fingers of several types. The precise amino acid sequence that is folded into a motif determines the particular DNA sequence that is recognized.

What is a DNA binding sequence?

DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites can be thus defined as short DNA sequences (typically 4 to 30 base pairs long, but up to 200 bp for recombination sites) that are specifically bound by one or more DNA-binding proteins or protein complexes.

What is a transcription factor DNA binding motif?

Transcription factors (TFs) are proteins with DNA binding activity that are involved in the regulation of transcription. Generally, TFs modulate gene expression by binding to gene promoter regions or to distal regions called enhancers.

Where can I find transcription factor binding sites in promoters?

Go to Eukaryotic Promoter database, put in the NCBI accession number for your gene of interest and then search for the transcription factors of your interest for that promoter sequence. Promoter sequence can also be limited (eg. -500 to +100) or extended (-1000 to +1) the way you like.

Is Bromodomain a DNA binding motif?

We show that bromodomain-mediated DNA binding is conserved among members of the BET family, indicating that bivalent nucleosome recognition through simultaneous DNA and histone tail binding is an important component of nucleosome recognition by BET bromodomains and possibly in bromodomains beyond the BET family.

What does DNA-binding domain do?

The function of DNA binding is either structural or involves transcription regulation, with the two roles sometimes overlapping. DNA-binding domains with functions involving DNA structure have biological roles in DNA replication, repair, storage, and modification, such as methylation.

What are DNA-binding proteins and how do they work?

DNA-binding proteins are proteins that bind to single- or double-stranded DNA, generally in the major groove if the binding is sequence-specific – as with transcription factors that regulate expression of genes, and nucleases that cleave DNA between nucleotides.

What do transcription factors bind to?

Some transcription factors bind to a DNA promoter sequence near the transcription start site and help form the transcription initiation complex. Other transcription factors bind to regulatory sequences, such as enhancer sequences, and can either stimulate or repress transcription of the related gene.

How do I find my transcriptional start site?

The exact transcription start site is determined by comparing the size of the primer extension DNA strand to a sequencing ladder of the same region of DNA. The start site for transcription may be located by isolating mRNA and using reverse transcriptase to make complementary DNA.

What technique can be used to identify the binding sites of a transcription factor?

DNA footprinting is an in vitro technique used to examine the binding of proteins to specific regions of DNA. This technique cleverly exploits the fact that when a transcription factor is bound to DNA with a certain affinity, the DNA is protected from degradation by nucleases.

How is the motifmap system used in genomics?

The MotifMap system provides comprehensive maps of candidate regulatory elements encoded in the genomes of model species using databases of transcription factor binding motifs, refined genome alignments, and a comparative genomic statistical…

Is the Homer motif database based on published data?

A vast majority of motifs in the HOMER motif database are based on the analysis of published ChIP-Seq data. Only high-quality ChIP-Seq experiments where the top HOMER motif resembled the consensus site for factors with the given DNA binding domain were used.

How does motif search work in gene search?

Motif Search allows users to select a transcription factor, view its binding sequence logo, and list its genome-wide putative binding sites. Gene Search allows users to select a gene and search for transcription factor binding sites in regions upstream and downstream from its transcription start site.

How are motifs and motifs used in protein classification?

Motif is a region (a subsequence) of protein or DNA sequence that has a specific structure Motifs are candidates for functionally important sites Presence of a motif may be used as a base of protein classification