表观基因组

2018-02-11 本文已影响86人思考问题的熊

不同层次的表观

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Broadly, features at different levels of chromatin organization are generally associated with inactive (off) or active (on) transcription.
From the top, genomic DNA is methylated(Me) on cytosine bases in specific contexts and is packaged into nucleosomes, which vary in histone composition and histone modifications (for example, histone H3 lysine 9 trimethylation (H3K9me3)); these features constitute the primary layer of chromatinstructure.
Here, different histone modifications are indicated by coloured dots and histone variants such as H2A.Z are brown.
DNA in chromatin may remain accessible to DNA-binding proteins such as transcription factors (TFs) and RNA polymerase II (RNAPII)or may be further compacted.
Chromatin can also organize into higher-order structuressuch as nuclear lamina-associated domains and transcription factories.
DOI:10.1038/nrg2905

基因印迹

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A mitotically or meiotically heritable state of different gene activity and expression (phenotype) that is independent of differences in DNA sequence (genotype) – based on Conrad Waddington, 1942
The sum of the alterations to the chromatin template that collectively establish and propagate different patterns of gene expression (transcription) and silencing from the same genome.
Epigenetic changes influence the phenotype without altering the genotype.
While epigenetics often refers to the study of single genes or sets of genes, epigenomics refers to more global analyses of epigenetic changes across the entire genome.

The complete number,location, and types ofepigenetic modificationsthat occur in a given cell

Interaction between DNA methylation, histone modifications, and other players such as non-coding RNAs

Cell and tissue type specificity

Gene-environment interaction, disease susceptibility

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DNA methylation occurs mostly in CG context, but also non-CG sequences (mCHG, mCHH)
DNA methylation is generally depleted from promoters, and enriched within gene bodies
DNA methylation is partially depleted at regulatory element

基本原理

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比对的过程需要进行转换

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常用mapping软件算法

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Bisulfite seed table, using the original seed and bisulfite variants as keys and corresponding coordinates in the reference genome as values. Each read was looked up in the seed table for potential mapping positions.
A positional specific mask of the corresponding reference sequence was generated by setting 01 to C(light blue) and 11 to A, G, T(black). The original read was masked by a bitwise AND operation with the positional specific mask.
The reference sequence and the masked read were compared with a bitwise XOR operation. Non-zero XOR results were counted as mismatches (red). Bisulfite alignment is marked in green.

Unmethylated CpGs are identified by sequencing size selected fragments from parallel DNA digestions with the methyl-sensitive restriction enzymes (MREs)
没有甲基化的地方会有peak
甲基化敏感性限制酶测序(MRE-seq) 技术主要利用甲基化敏感性限制性酶(methylation-sensitive restriction enzyme, MRE) 对基因组 DNA 进行切割，未甲基化位点可以被酶切而产生不同长度的片段，然后，结合高通量测序技术获得序列的甲基化信息
和MeDIP结合使用
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plant DOI:10.1146/annurev-arplant-043014-114633
human DOI:10.1038/nature08514

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Promoters, gene bodies, an enhancer and a boundary element are indicated on a schematic genomic region.
Active promoters are commonly marked by H3K4me2, H3K4me3, acetylation (ac), and H2A.Z.
Transcribed regions are enriched for H3K36me3 and H3K79me2.
Repressed genes may be located in large domains of H3K9me2 and/or H3K9me3 or H3K27me3.
Enhancers are relatively enriched for H3K4me1, H3K4me2, H3K27ac and the histone acetyltransferase p300.
CTCF binds many sites that may function as boundary elements, insulators or structural scaffolds