Your colleague professor Stu Dent generated a genome-wide DNA methylation map fo

Question

Your colleague professor Stu Dent generated a genome-wide DNA methylation map for normal colon cells using MRE-seq (a restriction enzyme approach) and MeDIPseq (an immunoprecipitation approach). In an intergenic region, he found an interesting locus. This locus is about 20kb. On one end of the locus, there is a 2kb CpG rich stretch that has both relatively low MRE-seq and MeDIP-seq signals. The rest 18kb has high level of MeDIP-seq signals.

(A) (3pt) Why might you suspect that this region encodes for a novel gene?

(B) (4pt) You decide to look at histone modification patterns across this region for more evidence. There are several genome-wide datasets available for this cell type: H3K4me1, H3K4me3, H3K27me3, H3K9me3, H3K36me3, and H3K9Ac. Which histone mark would you investigate for this locus and why?

(C) (3pt) Suggest at least one other source of data (NOT annotation or bisulfide sequencing) that may help you confirm or refute your suspicion, and why you think it may help?

Explanation / Answer

Your colleague professor Stu Dent generated a genome-wide DNA methylation map fo

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