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
cis-level regulation.
Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 2007 Jun;17(6):898-909.
Hudson ME, Snyder M. High-throughput methods of regulatory element discovery. Biotechniques. 2006 Dec;41(6):673, 675, 677 passim.