Promoter-Enhancer Interactions: Resources

CAGE & FANTOM

Wikipedia: CAGE:

Cap Analysis of Gene Expression (CAGE) is a gene expression technique used in molecular biology to produce a snapshot of the 5′ end of the messenger RNA population in a biological sample. The small fragments (usually 27 nucleotides long) from the very beginnings of mRNAs (5’ ends of capped transcripts) are extracted, reverse-transcribed to DNA, PCR amplified and sequenced.

The output of CAGE is a set of short nucleotide sequences (often called tags) with their observed counts.

Using a reference genome, a researcher can usually determine, with some confidence, the original mRNA (and therefore which gene) the tag was extracted from.

Copy numbers of CAGE tags provide an easy way of digital quantification of the RNA transcript abundances in biological samples.

• 5’ end 指的是位置，5’ cap 指的是端点的那个结构
• 5‘ cap 中有一个 G，我们可以把它的 “position 7” (这是化学知识，我不懂) 甲基化 (添加一个 -CH3)，从而得到 “7-甲基鸟苷”，简称 m7G (甲基的英文是 methyl)
  • 这其实就是给 5’ cap 做了个标记，方便你观察、提取

Wikipedia: FANTOM:

FANTOM (Functional Annotation of the Mouse/Mammalian Genome) is an international research consortium first established in 2000 as part of the RIKEN research institute in Japan.

FANTOM-$n$ 后面的 $n$ 指的是这个 consortium 的 $n^{\text{th}}$ meeting，也拿来指 meeting 相关的 publications/data 等：

• FANTOM1: 2000
• FANTOM2: 2002
• FANTOM3: 2004
  • Introduction of CAGE
• FANTOM4: 2006
• FANTOM5: 2011
  • Aimed to provide insight into the regulatory landscape of the transcriptome across as many cell states as possible.
  • Phase 1: Focused on a steady state representation of cell states
    • Taking ‘snapshots’ of a wide range of steady state cell types using CAGE profiling across 975 human and 399 mouse samples, resulted in 2 Nature papers:
      • A promoter-level mammalian expression atlas
      • An atlas of active enhancers across human cell types and tissues
      • Together, they provide an atlas of promoters, enhancers and TSSs across diverse cell types, acting as a ‘baseline’ for studying the complex landscape of transcription regulation.
    • A new method to identify the CAGE peaks, Decomposition Peak Analysis
      • CAGE tags are clustered by proximity, followed by ICA (Independent Component Analysis) to decompose the peaks into non-overlapping regions.
      • An enrichment step is applied to ensure the peaks correspond to TSSs, and external data of EST (expressed sequence tag), histone H3 lysine 4 trimethylation marks and DNase hypersensitivity sites are used to support that the peaks are genuine TSSs.
    • A key finding showed that the typical mammalian promoter contains multiple TSSs with differing expression patterns across samples.
      • This implied that these TSSs are regulated separately, despite being within close proximity.
      • Ubiquitously expressed promoters had the highest conservation in their sequences, while cell-specific promoters were less conserved.
        • ubiquitous: present, appearing, or found everywhere
  • Phase 2: To explore the dynamic process of transitioning cell states through the use of temporal data
    • CAGE over 19 human and 14 mouse timecourses covering a range of cell types and biological stimuli that represented 408 distinct time points.
      • timecourse: (medicine) the varying activity of a medicine over time following administration; 这里应该是类似的意思
    • Unsupervised clustering was performed to identify a set of distinct response classes, examining patterns in expression fold changes compared to time 0
      • 不同时间点检测到的 tag 可能不同，从中可以推测 regulation 的 activitity
  • Tools:
    • ZENBU: 有点像 Genome Browser
    • SSTAR: Semantic catalog of Samples, Transcription initiation And Regulators
• FANTOM6: TBD
  • Aims to systematically characterize the role of lncRNA in the human genome.
  • Tools:
    • PrESSto: Promoter Enhancer Slider Selector Tool: 2016；我没有发现有 paper；是下面 SlideBase 的前身
    • SlideBase: 2016；这其实是个综合性的 database，查询 FANTOM5 数据只是它功能的一部分
      • Paper: On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

ENCODE DHS vs Roadmap Epigenomics DHS

DHS 的介绍在 Terminology Recap: DNase / DHS / Dnase-seq

• Epigenome: 表观基因组
  • The epigenome comprises all of the chemical compounds that have been added to the entirety of one’s DNA (genome) as a way to regulate the activity (expression) of all the genes within the genome.
  • The chemical compounds of the epigenome are not part of the DNA sequence, but are on or attached to DNA (“epi-“ means “above” in Greek)

ENCODE (Encyclopedia of DNA Elements) 和 Roadmap 这两个项目的区别

• Roadmap: research how epigenetics contributes to disease
• ENCODE: Creating comprehensive, high quality catalogs of functional elements
• Roadmap 研究 human primary cells and tissues
• ENCODE 偏 cancer cell lines

问题一：如何从 DHS 中划分 Promoter/Enhancer

如果 data source 只提供了 promoter 没有提供 enhancer 的话，那么 enhancer 一般可以这么定：

• 人为确定：比如非常粗暴地把 DHS 除 promoter 之外的部分都算是 enhancer，或是确定一个 window size，promoter 附件的 DHS 算 enhancer 子类的
• 通过 DHS 之外的技术确定，比如通过一个新的 data source 来做 intersection

问题二：如何确定 Promoter-Enhancer Interactions

这是个很大的问题，最近很多 paper 也在讨论。

人为的方法就是：用 window，promoter 附近的 enhancer 都是 candidate；或者以 TSS 为中心，window 内的 enhancer 为 candidate