Exercise solutions

Finding features that regulate genes – the Ensembl Regulatory Build

 

Exercise 1 – Gene regulation: Human STX7

(a) Search for human STX7 from the home page. Click on 6:132445867-132513198:-1 below STX7 (Human Gene).

Regulatory features from the Ensembl 'regulatory build' are based on indicators of open chromatin such as CTCF binding sites, DNase I hypersensitive sites, and Transcription Factor binding sites. The Regulatory features are turned on by default in the Region in detail view.

There is one promoter predicted in the region of STX7.

Click on the Reg. Feats track name to jump to an article explaining the underlying data. Click and drag the Reg. Feats track next to the Genes track to better compare where the Regulatory features are in the gene.

(b) See the legend below the Region in detail view to find the predicted promoter is coloured red or purple in the different cell lines chosen. The purple colouring of the predicted promoter in the HUVEC cell type (out of the three cells chosen) indicates that this promoter is 'poised'. The red colouring of the predicted promoter in the HeLa-S3 and HepG2 cell lines indicates that these promoters are 'active'.

(c) Configure this page and click on Open chromatin & TFBS. Turn on both peaks and signal for DNase 1 in HeLa-S3, HUVEC and HEPG2 cells (the boxes in this configure this page window will turn blue. For more information on how to select and view the supporting data, click on Show tutorial in the pop up window). Close the menu.

There’s a DNase1 hypersensitive site in the first exon of STX7 that is detected in HUVEC and HepG2 cells; a second DNase1-hypersensitive site in exon 2 is detected in HUVEC cells. Click on the coloured block to find out that the DNase1 enriched sites come from the ENCODE project.

(d) Configure this page and click on Histones & polymerases. Change the Filter by menu from All classes to Histone. Select all the histone modifications available for HeLa-S3, HepG2 and HUVEC cells (some of them might be on by default). Save and close the menu.

H2AZ, H3K27me3, H3K4me1, H3K4me2, H3K4me3, H3K79me2, H3K9ac and H4K20me1 sites have been found in the 5' region of STX7 in HepG2 cells.

(e) Click on Configure this page and choose the DNA Methylation menu. Turn on the track Jurkat RRBS ENCODE. Save and close the menu.

Some CpG sites at the 5' end of STX7 are not highly methylated (note the yellow bars) whilst others are (blue bars). See the Methylation Legend, at bottom, for more details. Additional information on human DNA methylation tracks can be found at

www.ensembl.org/info/docs/funcgen/index.html

 

Exercise 2 – Regulatory features in human

(a) Search for human APOE from the home page. Click on Location in the search results and zoom out to view the genomic region surrounding the APOE gene. The gene is positive stranded so look for features at the left hand side. Click on the features to get their IDs.

There is a pink promoter flank at the 5’ end of APOE. Click on it to get a pop-up with its ID: ENSR00000110117.

(b) Click on the stable ID ENSR00000110117. Click on the ID to go to the regulation tab.

ENSR00000110117 is active in 18/68 cell types studied and poised in 32.

(c) Click on the promoter to see a list of its TF motifs.

There are SP1 motifs in this promoter.

(d) Click on Details by cell type, then open the Select cells menu. Choose ALL ON to select all cell types, then close the menu. Open the Select evidence menu and choose SP1 only, then close.

SP1 binding is only observed in H1ESC cells.

Open Select evidence again and choose all the transcription factors, then close. You may find it easier to see if you also go into Select cells and turn the cell types ALL OFF, then turn on H1ESC only.

TAF7 and USF1 also bind to this locus.

 

Exercise 3 – Finding regulatory features with BioMart

(a) Start at ensembl.org/biomart/martview. Choose the ENSEMBL Regulation database. Choose the Homo sapiens Regulatory Features dataset.

Click on Filters in the left panel. Select Chromosome – 18. Select Base Pair and input the coordinates. Select Feature Type – CTCF binding site.

Click on Attributes in the left panel. Select Regulatory stable ID along with the default attributes.

Click the Results button on the toolbar. Select View All rows as HTML or export all results to a file.

(b) Click on Filters again. Select Epigenome: eosinophil (VB).

Click on Attributes. Select Activity.

Click the Results button.

There is one active CTCF binding site in this region in eosinophil:VenousBlood cells: ENSR00000285159.

(c) Click on the reg-feat ID ENSR00000285159 to get to the regulation tab. Go to Details by cell type.

Go to Select cells then select eosinophil (VB). Save and close the menu. Open the Select evidence menu and choose all the histone modification, then save and close.

The site has the histone modification H3K4me1 in eosinophil (VB) cells, which is known to be associated with activation.