Profile of methylation about the centromeres/telomeres of human

Question

[dongqingyang7]

Human centromeres are located at repetitive alpha satellite DNA arrays that compose approximately 5% of the genome. Is this the reason why we can't find methylation info in centromeres?

Refer the paper "Human DNA methylomes at base resolution show widespread epigenomic differences", the Fig 1 d shows the human DNA methylomes in chromosome 12, the black rectangle is where the centromere located. So, how to understand this?

[stolarek.ir]

if you will lay your hands on dataset from illumina moleculo, you will get near perfect >1 kb reads spanning centromeres from both ends. Beside that you could also look into data from 10X <- it's also a sequencing done in a limited space and then assembled and given to you as reads

Answer 1

[Devon Ryan]

You'll only get multimappers in those regions and you typically ignore multimappers when determining methylation.

[dongqingyang7]

What you mean that it is the reason of mapper (like Bismark) which didn't map to the centromere? CpGi existed centromere area?

[Devon Ryan]

Bismark et al. can map there, but when a methylation extractor (either bismark's or a different one) is run on the alignment results it'll normally skip multimappers. I haven't a clue if there are any CpG islands in the centromere, I've never looked.

[dongqingyang7]

I see. Thank you so much for your prompt answer! That's very appreciated!