Speakers: 黄渊华 (HUANG Yuanhua)

古梦婷 (GU Mengting)

方荣欣 (FANG Rongxin)

What is DNA methylation?

2DNA methylation from Wikipedia

• A biochemical process: an addition of methyl group to cytosine or adenine.• Stably alters the genes expression as cells divide and differentiate.

•In adult somatic cells, DNA methylation typically occurs in a CpG (CG) dinucleotide context; •non-CpG methylation is prevalent in embryonic stem cells. www.web-books.com

What are CpG site and CpG island?

www.mad-cow.org/exon2

• CpG sites or CG sites: a cytosine nucleotide occurs next to a guanine nucleotide in DNA sequence.•CpG islands or CG islands (CGI): genomic regions that contain a high frequency of CpG sites.

How to detect DNA methylation?

whole-genome bisulphite sequencing (BisSeq)

4Bisulfite sequencing from Wikipedia

•Highly parallel sequencing in the article.

Blue Nucleotides are unmethylated cytosines converted to uracils by bisulfite, Red nucleotides are 5-methylcytosines resistant to conversion.

Mouse methylome

Using Bis-Seq to obtain base-pair-resolution methylomes of mouse from embryonic stem (ES) cells and neuronal progenitors (NP).

77.3 billion mappable methylome bases by High-coverage Illumina sequencing.

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Features of the mouse methylome

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Bimodal distribution

Distribution: not randomly but cluster locally

Hidden Markov Model for classifying DNA methylation regions: fully methylated regions (FMRs)unmethylated regions (UMRs)low-methylated regions (LMRs)

LMRs are generally not CpG islands:• Lower CpG content;• Shorter; • Further reside distal to transcriptional start sites(TSS).

Features of the mouse methylome

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Composite profile of CpG methylation

A small percentage of LMRs overlap with CpG islands

Distribution of the regions throughout the genome.

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ES-specific

NP-specific

Why?

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Finds

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