functional genomics | epigenomic annotations
剛入行的總是一頭霧水，對這些表觀的標記一點興趣都沒有，種類繁多，總是記不住，這里我就做一個常識性的總結，不搞太多術語。
需要了解的也不多，常見的就那么幾個，搞懂ENCODE和ROADMAP上有的就行。細節頗多，需要一點耐心。
各種類型的數據可以直接在這個genome browser里瀏覽：http://genomebrowser.wustl.edu/
注意：
- 所有的表觀或轉錄組都具有非常強的組織（cell type）特異性
- ChIP-seq最大的特點就是需要input，作為對照
- ChIP-seq可以Identify direct and indirect protein-DNA interactions
- ChIP-seq preferred for functional information
原始數據：
- DHSs
- H3K4me3
- H3K9ac
- H3K27ac
- H3K4me1
處理后數據：
- Enhancer
- TFBSs
主要是ChIP-seq（immunological assays）占了很大一類，把它搞懂就行。
另一類non-immunological assays：ATAC-seq, MNase-seq, DNase-seq, and FAIRE-seq。
DHSs
DNase I hypersensitive site
DNase-seq
FAIRE-Seq is a successor
genome-wide DNA footprints
Deoxyribonuclease 脫氧核糖核酸酶
DNase I hypersensitive sites (DHSs) are regions of chromatin that are sensitive to cleavage by the DNase I enzyme. In these specific regions of the genome, chromatin has lost its condensed structure, exposing the DNA and making it accessible. This raises the availability of DNA to degradation by enzymes, such as DNase I. These accessible chromatin zones are functionally related to transcriptional activity, since this remodeled state is necessary for the binding of proteins such as transcription factors.
ChIP-seq
Basically,
- "encc-enhancer.bed" is enhancers defined with H3K27ac & H3K4me1 activity
- "encc-enhancer-atac.bed" is enhancers defined with H3K27ac & H3K4me1 activity as well as open chromatin (ATAC-seq) signal summits.
不同ChIP-seq的功能，一圖勝千言：【我們用了第一行和最后一行，效率最高】
不同表觀注釋的比較：
待續~
快速使用epigenomic annotations data：
有個叫做baseline_v1.1的文件，里面包含了各種整理好的表觀注釋數據。
https://data.broadinstitute.org/alkesgroup/LDSCORE/baseline_v1.1_bedfiles.tgz
~/project2/CPloci/Evo/ENCODE/
包含的數據類型：
- Coding
- Intron
- Transcribe
- Conserved
- DGF
- DHS
- H3K9ac
- H3K27ac
- H3K4me1
- H3K4me3
- CTCF
- TFBS
- TSS
- Promoter
- Enhancer
- SuperEnhancer
- WeakEnhancer
- Repressed
- UTR_5
- UTR_3
算是種類非常多了，如果對精度沒有要求，就可以直接用了，全部是bed格式的。
參考：
Chromatin accessibility and the regulatory epigenome
Identifying and mitigating bias in next-generation sequencing methods for chromatin biology - 劉小樂
Chromatin Structure Research Methods
Introduction to ChIP-seq and ATAC-seq - 非常贊
Mapping DNA-protein interactions via ChIP-seq - 非常詳細
如何通過CHIP-seq分析鑒別基因啟動子和增強子 - ChIP-seq詳解
ChIP-seq實踐(H3K27Ac,enhancer的篩選和enhancer相關基因的GO分析) - 實戰