What does a CpG island do?
CpG islands are DNA methylations regions in promoters known to regulate gene expression through transcriptional silencing of the corresponding gene. DNA methylation at CpG islands is crucial for gene expression and tissue-specific processes.
What is a CpG shore?
Shores are the regions immediately flanking CpG islands (CGI) the consensus definition of a CpG shore is up to 2kbp away from the CGI. To generate a list of shore coordinates, go to UCSC table browser (https://genome.ucsc.edu/cgi-bin/hgTables?command=start). You can find CGI coordinates under the “regulation” menu.
What is methylated in CpG?
Methylation of CpG islands stably silences genes In humans, DNA methylation occurs at the 5 position of the pyrimidine ring of the cytosine residues within CpG sites to form 5-methylcytosines. The presence of multiple methylated CpG sites in CpG islands of promoters causes stable silencing of genes.
How do you calculate CpG?
Observed CpG is the number of CpG dinucleoetides in a segment and expected CpG is calculated by multiplying the number of ‘C’s and the number of ‘G’s in a segment and then dividing the product by length of the segment.
Are CpG islands transcriptionally repressed?
Methylation of CpG islands is an established transcriptional repressive mechanism and is a feature of silencing in X chromosome inactivation.
How CpG islands are detected?
Most currently used methods for detecting methylated-CpG islands are based on sodium bisulfite conversion of genomic DNA, followed by PCR reactions. Specifically bound DNA is eluted from the matrix and gene-specific PCR reactions are performed to detect CpG island methylation.
How do you check methylation status?
Currently, there are three primary methods to identify and quantify DNA methylation. These are: sodium bisulfite conversion and sequencing, differential enzymatic cleavage of DNA, and affinity capture of methylated DNA (1). Restriction enzyme based differential cleavage of methylated DNA is locus-specific.