Transcription is regulated through the binding of transcription factor
proteins to specific cis-level regulatory sites in the DNA.
The nature of this regulation depends on the transcription factor.
For example, some proteins activate transcription by recruiting RNA
polymerase, some repress transcription by suppressing this
recruitment, and others insulate proximal regions from the activity of
nearby transcriptional activators or repressors.
A key characteristic of each transcription factor protein is its DNA
binding domain. Each DNA binding domain recognizes and interacts with
DNA that matches a specific nucleotide pattern, or motif. These
motifs tend to be short and degenerate, so even when the DNA binding
motif is known, one cannot generally predict where a given
transcription factor may bind. In general, transcription factor
binding is determined experimentally.
These tracks contain transcription factor binding sites determined by
ChIP-seq. This process involves fragmenting DNA, selecting the
fragments of DNA that are bound by a certain transcription factor, and
sequencing those DNA fragments. This generally yields a large library
of DNA sequences, including some that were bound by the transcription
factor directly, some that were bound indirectly via interactions with
other molecules, and some false positives (such as cases of
nonspecific binding). With the appropriate analysis methods, ChIP-seq can be
a valuable approach for elucidating transcription factor binding and
To view the full description, click here.