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Sunday, June 1, 2014

Visualize CTCF Binding Sites in UCSC Genome Browser

The Encyclopedia of DNA Elements (ENCODE) Consortium has recently added some new and exciting information to the University of California Santa Cruz (UCSC) genome browser relating to CTCF binding sites.  CTCF is a transcriptional repressor encoded by the CTCF gene that regulates the 3 dimensional (3D) structure of chromatin.  CTCF mediated changes in chromatin structure can lead to insulator activity, transcriptional regulation, and changes in RNA splicing.  CTCF binding sites typically have a CCCTC motif used by CTCF to bind together strands of DNA.  Changes in gene expression can result from the bound CTCF sites insulating the activity of an enhancer from a gene's promoter site.

The UCSC genome browser has two tracks that aid in identifying CTCF binding sites in the genome.  The two tracks are the Transcription Factor ChIP-seq track and the Genome Segmentations from ENCODE track.  Both UCSC data tracks use ChIP-seq data and can be filtered to localize CTCF binding sites.  The Transcription Factor ChIP-seq track shows CTCF binding sites from a large collection of ChIP-seq experiments.  The Genome Segmentation track takes things a step further by segmenting the genome into a variety of functionally relevant segments (ex: insulators, enhancers, promoters) using two bioinformatic algorithms (ChromHMM and Segway).

A helpful link to visualize CTCF insulator sites in the UCSC genome browser is here.  This will link to a session where the two above described ENCODE tracks are selected in the browser window.  It should look something like the picture above the post.  If you are aware of other resources or other UCSC data tracks that localize genomic insulators such as CTCF binding sites, please share in the comments below.

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