BMS8110复习（八）：Lecture 8- Epigenetics and Epigenomics

Outline

• Introduction to the concept of epigenetics and epigenomics
• Tissue specific transcriptional regulation
  • Chromatin accessibility
  • Histone Modifications 组蛋白修饰
  • DNA Methylation
  • Chromatin three-dimensional structure
• Introduction to useful database
  • ENCODE
  • Roadmap Epigenome
  • 4DN

What is (Epi)genetics?

• The study of changes in organisms caused by modification of gene expression rather than alteration of the genetic codeitself.
• Key features of epigenetics
  • Inheritable
  • No change of DNA sequences
  • Related to gene expression
  • Cell-to-Cell variation

What determines the cell types?

• Every cell has the same copy of genome
  • They share the same DNA sequences
• The expression level of individual genes is different
  • The cell type is determined by the regulation of gene expression
  • Cell type specific regulatory elements ---enhancers
• Epigeneticsfocuses on processes that regulatehowand whencertain genes are turned onand turned off ---gene regulation (irrelevant to sequence)
  • Quantity
  • Spatial and Temporal

Regulatory Elements

• Pormoters
  • A promoter is a region of DNA that leads to initation of transcription of a particular gene.
  • Promoters are located near the transcription start sites of genes, upstream on the DNA (towards the 5' region of the sense strand)
  • Promoters can be about 100-1000 base pairs long.
• Enhancers
  • An enhancer is a short (50–1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur.
  • These proteins are usually referred to as transcription factors. Enhancers are cis-acting.
  • They can be located up to 1 Mbp(1,000,000 bp) away from the gene, upstream or downstream from the start site.
  • There are hundreds of thousands of enhancers in the human genome.
  • They are found in both prokaryotes and eukaryotes.
• Insulators
  • An insulator is a genetic boundary element that blocks the interaction between enhancers and promoters.
  • It is thought that an insulator must reside between the enhancer and promoter to inhibit their  subsequent interactions.
  • Insulators therefore determine the set of genes an enhancer can influence.
• Repressors

Epigenetics

• Epi- means "above" or "on top of"
• Epigenetic literally means "above" or "on top of" genetics
• It refers to external modifications to DNA that turn "on" or "off" gene expression.
• These modifications do not change the DNA sequence, but instead, they affect how cells "read" genes.
• Epigenomicspertains to analysis of epigenetic changes across many genes in a cell or entire organism.
• The epigenomecan mark DNA in two ways, both of which play a role in turning genes off or on.
  • The first occurs when certain chemical tags called methyl groups attach to the backbone of a DNA molecule. –-DNA methylation (CpG)
  • The second occurs when a variety of chemical tags attach to the tails of histones, which are spool-like proteins that package DNA neatly into chromosomes. This action affects how tightly DNA is wound around the histones. ---Histone tail modifications (methylation or acetylation乙酰化作用)

How is DNA organized in cells?

• Nucleosomes(核小体)
  • DNA (~147 bp)
  • Histones
    • H2A
    • H2B
    • H3
    • H4
  • Histones compete with other regulatory proteins for DNA binding
  • Regulatory proteins, such as RNA polymerase and transcription factors can only bind to DNA when it is accessible

How to identify accessible chromatin?

• ChIP-seq
  • Histone marks
• Dnase I Hypersensitive Region
• FAIRE-seq: Formaldehyde-Assisted Isolation of Regulatory Elements 甲醛辅助分离调控元件
• ATAC-seq: Assay for Transposase-Accessible Chromatin with high-throughput sequencing

DNA Methylation

• Two of DNA's four bases, cytosine and adenine, can be methylated. Mostly related to Cytosine 5-methylation.
• Highly frequently happens at CpGmotif
• Happens in most Prokaryotes and Eukaryotes
• Differ greatly between species:
  • 75% in mammals
  • 14% in Arabidopsis thaliana
  • 8% in Physarum
  • 2.3% in Escherichia coli
  • 0.03% in Drosophila
  • 0.006% in Dictyostelium
  • virtually none (< 0.0002%) in Caenorhabditisor yeast species such as Saccharomyces cerevisiae and S. pombe(but not N. crassa)

Promoter Methylation and Human Diseases

• In cancers, loss of expression of genes occurs about 10 times more frequently by hyper-methylation of promoter CpGislands than by mutations.
• Compared with adjacent normal tissues, the tumorsare heavily methylated at thousands of CpGsites, causing reduction of hundreds of genes in cancer cells.
• DNA repair genes are frequently repressed in cancers due to hypermethylationof CpGislands within their promoters, leading to DNA damage and tumorigenesis

How to detect DNA methylation?

• Antibody to detect methylcytosine(甲基胞嘧啶)
• Methylcytosine sensitive restriction enzyme treatment
• Sodium bisulfite conversion 亚硫酸氢钠转换

Chromatin High-Order Structure

Hi-C Data Analysis

• Mapping
• Genome segmentation
• Normalization
  • Distance
  • GC content
  • Enzyme site frequency
• 2*2 Matrix  generation

TAD

• is a self-interacting genomic region, meaning that DNA sequences within a TAD physically interact with each other more frequently than with sequences outside the TAD.
• These three-dimensional chromosome structures are present in animals as well as some plants, fungi, and bacteria. TADs can range in size from thousands to millions of DNA bases.
• They are highly conserved across species and invariant across tissue types.

Compartment A/B

Chromatin loop

ENCODE(Encyclopedia of DNA Elements) Consortium Project (NIH)

Roadmap EpigenomeConsortium

4D NucleomeConsortium