[Gong, Shiaoching]

Dear Sir/Madam,

Good morning.

I want to know if I am able to search enhancer RNA for the gene of TNFAIP3. Could you please let me know which link I should choose?

Thank you very much and have a happy holidays and New Year.

Best,

Shiaoching

[Brian Lee]

Dear Shiaoching,

Thank you for using the UCSC Genome Browser and your question about enhancer RNA for the gene of TNFAIP3.

Please see this session where various ENCODE tracks are displayed around the gene TNFAIP3 indicating where DNase activity, Transcription Factor Binding, RNA transcription, and histone modification has been observed.

http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.TNFAIP3

Please move the cursor over the grey bar on the lefthand side of the image to click into the description page for these tracks where you can read more about the data presented. Alternatively you can click these below links:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeReg

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegMarkH3k27ac

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTxn

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegDnaseClustered

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeAwgSegmentation

The Overlayed H3K4Me1 and Overlayed H3K27Ac tracks show where modification of histone proteins is suggestive of enhancer and other regulatory activity. Investigating where RNA-seq signals overlap with Transcription Factor Binding upstream of TNFAIP3 transcription would appear to indicate possible eRNA locations and the segmentation track displays possible Strong and Weak Enhancers as calculated by the ChromHMM and Segway programs. You may be interested in reading the following ENCODE publication from 2012: http://www.nature.com/encode/threads/enhancer-discovery-and-characterization

Beyond the UCSC data in the browser, there are many externally hosted and maintained Public Hubs that can also display data in the browser, which may be of interest to your research. If you navigate to the Public Hubs page, http://genome.ucsc.edu/cgi-bin/hgHubConnect, you can enter "regulatory" in the box below "Enter search terms..." and then click "Search Public Hubs". Then you can click the "Connect" button and display further collections of data annotated to the genome that can help determine possible enhancer locations near TNFAIP3.

Lastly, please take a moment to review our archived list of previously answered mailing list questions where you might discover further topics of interest: https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!searchin/genome/enhancer

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genome Bioinformatics Group

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