HELP assay

The HELP Assay is HpaII-tiny fragment Enrichment by Ligation-mediated PCR.

Additional recommended knowledge

Daily Visual Balance Check

Don't let static charges disrupt your weighing accuracy

What is the Correct Way to Check Repeatability in Balances?

To study cytosine methylation throughout the genome, techniques usually involve the use of restriction enzymes or proteins with affinity for 5-methylcytosine.

The HELP assay [1] compares representations generated by HpaII and by MspI digestion of the genome followed by ligation-mediated PCR. As HpaII only digests 5'-CCGG-3' sites when the cytosine in the central CG dinucleotide is unmethylated, the HpaII representation is enriched for the hypomethylated fraction of the genome. The MspI representation is a control for copy number changes and PCR amplification difficulties.

It was recently shown [2] that cytosine methylation patterns tend to be concordant over short (~1 kb) regions. The patterns represented by the HpaII sites therefore tend to be representative of other CG dinucleotides locally.

The protocol for the HELP assay is available from [3].