Speakers : 黄渊华 (HUANG Yuanhua ) 古梦婷 (GU Mengting ) 方荣欣 (FANG Rongxin )
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Transcript of Speakers : 黄渊华 (HUANG Yuanhua ) 古梦婷 (GU Mengting ) 方荣欣 (FANG Rongxin )
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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