Attaching the ENCODE track hub in human
(a) Add the ENCODE Track Hub to the Region in Detail View for the genomic region surrounding the BRCA2 gene. Hint: You will need to add and view this Track Hub to the human GRCh37 genome assembly.
(b) Turn on all the available tracks relating to Histone Modification Peaks and Transcription Factor Peaks in HeLa-S3 cells.
(c) Which Transcription Factors and Histone Modifications have features in this region?
(d) Add the Tracks showing Signals for the Histone Modifications and Transcription Factors that have peaks in this region. Compare the signal intensity to the location of annotated peaks.
(e) Remove the ENCODE Track Hub from your list of custom tracks.
(a) There are two ways to add the ENCODE Track Hub to view in Ensembl.
- Search for Encode from the Track Hub Registry home page. From the search results, find the Encode Analysis Hub and select Ensembl in the View in Genome Browser list.
- Search for the BRCA2 gene in the GRCh37 human genome assembly. Switch to the Location Tab. Click on Custom tracks in the side panel. Click Track Hub Registry Search and Search for Encode. Click Attach this hub in the ENCODE Analysis Hub option.
(b) Go to Configure this page and click on ENCODE Histone Modification Peaks under ENCODE Analysis Hub. Turn on all available tracks for HeLaS3 cells by selecting HeLaS3 from the Cell Line tab and clicking Select all in the Factor tab. Go to the second step 2. Refine selection and make sure all tracks are on (blue colour). You can go to the third step to change the track display (3. Configure track display).
Click on ENCODE Transcription Factor Peaks now. Turn on all available tracks for HeLaS3 cells by selecting HeLaS3 from the Cell Line tab and clicking Select all in the Factor tab. Go to the second step 2. Refine selection and make sure all tracks are on (blue colour). You can go to the third step to change the track display (3. Configure track display) or proceed straight to View tracks.
(c) There are features for a number of different Transcription Factors and Histone modifications, mainly surrounding the BRCA2 5’ region.
Transcription Factors: CTCF, USF2, TBP, STAT1, MAX, POL2S2, POLR2A, POL2, POL2B, MXI1, INI1, E2F1, E2F4, E2F6, HAE2F1, ELK4, MYC, CMYC, CEBPB, TAF1, TFAP2A, TFAP2C, AP2alpha and AP2gamma.
Histone Modifications: H3K4me3, H3K9ac, H3K79me2, H3K4me3, H3K4me2, H3K36me3, H3K27ac
(d) Go to Configure this page and click on ENCODE Histone Modifications Signal. Turn on all available tracks for HeLaS3 cells by selecting HeLaS3 from the Cell Line tab and clicking Select all in the Factor tab. Go to the second step 2. Refine selection and make sure all tracks are on (blue colour). You can go to the third step to change the track display (3. Configure track display).
Go to Configure this page and click on ENCODE Transcription Factor Signal. Turn on all available tracks for HeLaS3 cells by selecting HeLaS3 from the Cell Line tab and clicking Select all in the Factor tab. Go to the second step 2. Refine selection and make sure all tracks are on (blue colour). You can go to the third step to change the track display (3. Configure track display) or proceed straight to View tracks.
By comparing the signal intensity and annotated peaks for each of the Histone Modifications and Transcription factors, you can see that the increased signal intensity corresponds to the regions where a peak has been annotated.
(e) Go to Custom tracks and click the Trash icon from the Actions section of the ENCODE Track Hub.
