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
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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