BMS8110复习（十一）：Lecture 11 - DNA Methylation

Contents

• Epigenetics
• DNA Methylation
• Measuring DNA Methylation
• Methylation arrays
• Methylation sequencing
• Case Study

What is epigenetics?

• Epigenetics refers to stable heritable traits not explained by changes in DNA sequence
• Chromosome modifications that affect gene expression
• Essential for nomal development
• Can be modified by environment
• Can be disrupted in disease

Epigenetics brings DNA to life! Important in all species.

Epigenetics is very complicated!

• New sequencing & microarray technologies are enabling us to learn a lot more about epigenetics
• Different data types need different analysis.

What is DNA methylation?

• DNA methylation primarily occurs at CpG dinucleotides(核苷酸).

DNA methylation in the genome

• The human genome contains ~30,000,000 CpGs
• CpGs are not evenly spaced across the genome
• CpG methylation is spatially correlated

Methylation can regulate gene expression

Finding methylation differences can tell us a lot

• Methylation is critical in determining cell type
• Methylation can be disrupted in disease
• Methylation is affected by the environment

Epigenome-wide association studies (EWAS)

• Similar to GWAS 
• Compare lots of cases to lots of controls
• Need lots of samples

How do we measure methylation?

• Bisulphite conversion 亚硫酸氢盐转换
  • Create "SNPs"
• Single nucleotide resolution
  • Arrray
  • Seuqencing
• Enrichment of methylated DNA
  • Restriction enzymes
  • Affinity
• Regional resolution
  • Array
  • Sequencing

Methylation arrays

• Methylation arrays are based on SNP array technology
• Methylation array analysis is very mature: lots of methods

Two main types of bisulphite sequencing

• Whole-genome bisulphite sequencing (BS-seq)
• Targeted BS-seq

What are the challenges?

• Like calling SNPs, methylation in BS-seq inferred by comparison to uncoverted reference sequence
  • Correct alignment is critical
• More challenging than usual
  • Aligned sequences do not exactly match reference
  • Complexity of libraries is reduced
• Methylation is not symmetrical
  • Two strands of DNA in the reference genome must be considered separately