一、Term
Cis-acting elements ( 顺式作用元件)
Enhancer增强子
Silencer沉默子
Trans-acting factors反式作用因子
Preinitiation complex预起始复合体
homeodomain ( 同源结构域 )
bZIP (leucine zipper ，亮氨酸拉链)
bHLH (helix-loop-helix)
二、Basic transcription machinery
1、RNA pol
2、Promoter
（1）Class II Promoter
Core Promoter：BRE、TATA box、Inr、DPE
Upstream Promoter Element：UPE，GC box、cat box.etc
Some class II promoters require the TATA box for function, but others need it only to position the transcription start site.
No TATA box, the specificity of transcription initiation is lost
At least one of these elements is missing in most promoters.
In fact, TATA-less promoters tend to have DPEs, at least in Drosophila.
Promoters for highly expressed specialized genes tend to have TATA boxes, promoters for housekeeping genes tend to lack them.
Some promoters (TdT) have only an initiator, possibly with a DPE.
（2）Class I promoter（rRNA）
Features：
Class I promoters are not well conserved in sequence
but the general architecture of the promoter is well conserved.
Two essential elements:
- upstream promoter element:-107- -156
- core element: -45-20
The spacing between the two elements is important：
delete or add DNA fragment B/w the elements resulted in the decrease of promoter activity
（3）Class III promoter（5s rRNA和tRNA）
Classic class III promoter: lie within the genes (5S rRNA gene, tRNA gene)
Non-classic : similar to class II promoter (U6 snRNA, 7SL RNA, 7SK RNA gene)
3、Cis-acting DNA elements顺式作用元件
genetic elements, such as enhancers, silencers, etc. which are on the same chromosome of the regulating gene位于调节基因的同一染色体上的遗传元件，如增强子、沉默子等
Enhancer: A DNA element that strongly stimulates transcription of a gene or genes.
增强子：强烈刺激一个或多个基因转录的DNA元件。
Silencer: a DNA element that can act at a distance to decrease transcription from a eukaryotic gene沉默子：一种可以远距离作用以减少真核基因转录的DNA元件。
（1）Enhancer
Enhancer and silencer are position and orientation independent.They are usually found upstream of the gene they influences, but they can also function at a distance or in either orientation增强子和抑制子是与位置和方向无关的，它们通常在它们影响的基因的上游被发现，但它们也可以在一定距离或在任何一个方向上发挥作用。
Enhancer也可以在基因内。
Enhancer通过结合蛋白来发挥作用，结合的蛋白比如有transcription factor转录因子、enhancer-binding protein、activator激活子等
Binding of specific proteins to an enhancer modulates the rate of transcription of the associated gene. 特定蛋白与增强子的结合能够调节相关基因的转录速度。
顺式作用元件本质上说是一段DNA序列，存在基因序列的上游或者是下游，来对基因的表达进行调控。
而反式作用因子实际上是一些可以调控基因表达的蛋白质分子，这些蛋白质通过与顺式作用元件发生作用来调控基因表达。
（2）Silencer
Silencers cause the chromatin to coil up into a condensed, inaccessible, and therefore inactive form, thereby preventing transcription of neighboring genes. 使染色质卷曲成浓缩的、不可接近的形式，从而阻止邻近基因的转录
4、General transcription factors
attract the RNA polymerases to their respective promoters with a weak extent.
They support only a basal level of transcription. 它们只支持基本水平的转录
Cells exert exquisitely fine control over transcription through special transcription factors细胞通过特殊的转录因子对转录进行精细控制
（1）Class II factors
- TFIID is most important TFIID是最重要的
- TFIIF is essential for the binding of RNA polymeraseTFIIF对于RNA聚合酶的结合是必不可少的
- The preinitaition complex binds in TATA box region of a promoter起始复合体结合在启动子的TATA box区域
TFIID ：a complex protein包括
TATA box-binding protein (TBP) and 8-10 TBP- associated factors (TAFs, more specifically, TAFIIs)
Binding of TFIID to the TATA box is on the minor groove of the TATA box, not in the major groove大沟突变不影响TFIID，说明TFIID结合小沟
（2）Class I factors
- core-binding factor: SL1( human) or TIF-IB (transcription initiation factor)
- Upstream-binding factor (UBF) or Upstream-activating factor (UAF)
（3）Class III factors (TFIIIA, B, C)
5s rRNA gene需要ABC，但tRNA gene只需要BC
（4）Transcription activators (Specific Transcription Factors)
基本的转录machinery只提供了一个很低的转录水平。需要transcription activators才能提高活跃基因的转录
Functions of transcription factors:
- Recognize target sequences in DNA
- Interact with other transcription factors
Control gene expression in following ways:
- Expressed in a specific tissue (spatial regulation)
- Expressed in at specific time (temporal regulation)
- Require modification (e.g. phosphorylation)
Two functional domains有两种功能域：
1. DNA-binding domain: well characterized structural motif
a. Zinc finger
b. homeodomains (HDs) helix-turn-helix
c. bZip (leucine zipper)
d. bHLH (basic helix-loop-helix)
2. Transcription-activating domain: not well-defined
a. Acidic domains
b. Glutamine rich domains
c. Proline rich domains
GAL4 protein：Transciptional factor
zinc-containing family
应用就是Y1H酵母单杂交和Y2H酵母双杂交