一、Term
Nucleosome核小体
Metaphase中期
Interphase间期
HAT (histone acetyltransferase)组蛋白乙酰转移酶
HDAC (histone deacetylase)组蛋白去乙酰酶
Acetylated乙酰化
Unacetylated去乙酰化/未乙酰化
Chromatin remodelling factors染色质重塑因子
Mediator中介体
DNMT – DNA methyltransferase DNA甲基转移酶
SAM: S-adenosylmethionine S-腺苷甲硫氨酸（甲基供体）
covalent modification共价修饰
Phosphorylation磷酸化
kinase激酶
ubiquitin泛素
Ubiquitination泛素化
Sumoylation SUMO化
Acetylation乙酰化
Nuclear receptors核受体
二、Chromatin mediated transcription control染色质介导的转录调控
Chromatin remodelling factors
- Chromatin remodellig factors are multiprotein complexes with some subunits showing helicase activity染色质重塑因子是具有一些亚单位显示解旋酶活性的多蛋白复合体。可能导致转录抑制或激活
- Chromatin remodelling complex SWI/SNF transiently dissociates DNA from the surface of nucleosomes, decondensing the chromatin and making the DNA more accessible to transcription factors
- The activity of complex may also result in transcription repression, probably by exposing the histone tails to deacetylases or by assisting in folding of chromatin into higher-order structures
三、Mediators
Composed of ~20 subunits which are arranged in modules
Some subunits interact with RNA Pol II, others with activators
One subunit has histone acetylase activity which might keep the promoter region in hyperacetylated state
有些subunits是对所有基因的表达都是必须的，有些则是specific的
四、Epigenetic control mechanisms
Transcription control through DNA methylation and histones
Methylation of CpG islands can block transcription by two distinct pathways:
1. Direct blocking of TFIID binding
2. Recruitment募集 of histone deactylases
招募组蛋白去乙酰化，就会使DNA与histones结合更紧密，从而抑制转录
维持甲基化：DNA methyltransferase I
转录因子的活性调节：
(1) covalent modification (phosphorylation, acetylation, ubiquitination, sumolation etc.)
共价修饰(磷酸化、乙酰化、泛素化、总和等)
(2) by binding to ligands (nuclear receptors)
通过与配体(核受体)结合
五、Methods for detecting changes in transcription level
- Northern blot
- RT-PCR
- Real time quantitative RT-PCR
- In situ hybridization (ISH, FISH)
- Micro-array
- Deep sequencing (transcriptome)深度测序，可确定转录组及表观遗传修饰
- Next generation sequencing (High-throughput sequencing)下一代测序
六、Methods for detecting DNA protein interaction
- Chromatin immunoprecipitation (ChIP)（in vivo）
- Gel shift assay (Electrophoretic mobility shift assay, EMSA)
- DNase footprinting
- Y1H
- Filter-Binding Assays
Filter-Binding Assays 亦即亲和力分析，是分析蛋白与核酸相互作用的一种方法。由于蛋白质一般带正电荷，而核酸则由于磷酸基团的存在带负电荷。在该实验中，我们用到的硝化纤维膜带负电荷。实验开始之前，先用同位素标记待研究的DNA片段，将其与研究蛋白共同孵育，然后过柱。与DNA能够结合的蛋白质则会留在消化纤维的表面，而那些不能结合的DNA，则被洗掉。通过仪器放射性，便可了解其结合情况。
七、Applications of ChIP, ChIP-Chip, and ChIP-Seq
- Target Gene Identification (individual and global)
- Binding Site Consensus Identification
- DNA (RNA)--Protein Interactions
- Analysis of Epigenetic Phenomenon表观遗传分析 (eg, methylation, silencing)
1、CHIP
2、ChIP-chip
3、ChIP-Seq
