Tutorial



  • Select Genome


    Genome: mm10

  • Enter gene, SNP, genomic coordinate, or rank


    genomic region: chr1:134054000-134071000

  • Choose assays used to determine enhancer-like elements

    assays: DNase + H3K27ac

  • Select cell types of interest


    cell types: hindbrain, midbrain, neural tube, and lung

  • Display on genome browser


    UCSC

Exercises

Exercise #1

You are a graduate student working on the mechanistic role and therapeutic potential of microRNA-122 (MIR122) in alcoholic liver disease. Are there any enhancers nearby that you could potentially study?
Visualize on Genome Browser There appear to be several enhancer-like regions within 1Mb of MIR122.

Exercise #2

In Flavahan, Drier, et al., Nature 2015, compromised CTCF binding was demonstrated to allow a constitutive enhancer to interact with an oncogene in IDH gliomas. The enhancer is ~50Kb upstream of the oncogene PDGFRA. Is this constitutive enhancer also potentially found in other ENCODE brain-related cell types?
Visualize on Genome Browser There appear to be enhancer-like regions within 100Kb of PDGFRA in astrocytes.

Exercise #3

Breast cancer risk SNP rs4784227 has been demonstrated to change TOX3 gene expression, and thus alter chromatin structure (Cowper-Sal.lari, et. al., Nature Genetics 2012; Huang and Ovcharenko, NAR 2014). Are there any potential regulatory elements at this SNP location in an ENCODE breast cancer cell line?
Visualize on Genome Browser The SNP appears to be in a regulatory-like element.