Finding features that regulate genes – the Ensembl Regulatory Build
Exercise 1 – Gene regulation: Human
(a) Find the Location tab (Region in detail page) for the STX7 gene. Are there any predicted promoters in this gene region?
(b) Click Configure this page and on the Regulatory features menu in the left hand side. Turn on Regulatory features for HUVEC, HeLa-S3 and HepG2 cell types. Is the predicted promoter active in any of these cell lines?
(c) Use Configure this page to add supporting data indicating open chromatin for HeLa-S3, HUVEC and HepG2 cells. Are there sites enriched for marks of open chromatin (DNase1) in these cells at the 5' end of STX7?
(d) Configure this page once again to add histone modification supporting data for the same cell type as above. Which ones are present at the 5’ end of STX7?
(e) Do any data support methylated CpG sites in this region (5’ end) of STX7 in Jurkat cells?
Exercise 2 – Regulatory features in human
(a) Go to the Location tab (Region in detail page) for human APOE and zoom out a little to see the flanking region. Is there a regulatory feature annotated at the 5' end of the gene? What kind of feature is it and what is its stable ID? Does it contain any transcription factor binding motifs?
(b) In which cell types is this feature active? And poised?
(c) Are there any transcription factor binding motifs in this feature? For what transcription factor?
(d) Can you observe binding of this transcription factor in any cell types? What other transcription factors are also found at this location in this/these cell type(s)?
Exercise 3 – Finding regulatory features with BioMart
An ~80 kb deletion on chromosome 18 (11874760-11954376) has been identified in a patient with blood defects. This region is non-genic and you suspect it may contain a CTCF binding site.
(a) Use BioMart to export a list of CTCF binding sites within this locus.
(b) You are particularly interested in CTCF binding sites that are active in eosinophil:VenousBlood cells, studied by Blueprint. Which of the CTCF binding sites in this region have evidence of activity in these cells?
(c) Click through from the active CTCF binding site to the Regulation tab. Can you find what histone modifications occur in this locus in this cell type?