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Regulation of transcription


Regulation of transcription in prokaryotes (con’t)
Lac operon: utilization of the sugar lactose Ara operon: utilization of the sugar arabinose Trp operon: synthesis of the amino acid try

ptophan Polycistronic message (多顺反子): an mRNA bearing information from more than one gene Operator (操纵子): A DNA element found in prokaryotes that binds tightly to a specific repressor and thereby regulates the expression of adjoining genes

The ara operon

AraC protein as repressor, it binds to the operators in two sites and loop the 210bp DNA out Arabinose acts as inducers

? ?

Supercoiled DNA have a higher electroretic mobility than the same DNAs unlooped AraC can bind to the DNA in the site of araO and araL

Arabinose breaks the loop between araO2 and aral

ara operon
Positive control by CAP-cAMP complex, which is similar to Lac operon

The Trp Operon (反馈抑制)
Genes for enzymes making tryptophan Repression requires the binding of trp and aporepressor (辅阻遏蛋白) Aporepressor is inactive, only when it binds to tryptophan, act as a repressor. Low trp, no repression High trp, repression

Control the trp operon by attenuation
Attenuator: a region of DNA upstream of one or more structure genes, where premature transcription termination can occur Trp operon control 70 folds of transcription Attenuation controls additional 10 folds of transcription

Leading peptide

Attenuator

Looks like a terminator

Does not look like a terminator

Mechanism of attenuation

Stable structure

Less stable structure

Always off

Always on

Always on

Transcription in eukaryotes (真核生物基因的转录)

Basic machinery of transcription: Class II Promoter

Conserved modules
TATA Box (-25bp) CAAT Box GC Box

Sequence
TATAAA GGCCAATC TGGGCGG

Possible roles
Define transcription start site Define RNA Polymerase binding site Define RNA Polymerase binding site

Mutation in TATA box destroyed the promoter activity
-18---29

? ?

Done in frog Oocytes Two DNA template: 1. linker scanning mutated 2. WT different size

-80--105

-47--61

Upstream Elements
? CAT bos: an uostream motif, having sequence CCAAT, found in many eukaryotic promoters recognized by RNA ? GC box: a hexamer having the sequence of GGGCGG on one strand, which occurs in a nummber of mammalian structural gene promoter. It is the binding site for the transcription factor Sp1 ? It is orientation independent, but not position independent
-18---29 -80--105 -47--61

Class I promoter from rRNA gene
1. Per cell, there are hundreds of copies of rRNA genes 2. Each copy in the same species are the same 3. Huge variability exists among different species, not much conservative elements 4. One common feature : AT-rich initiator (rINR) which surrounds the transcription start site

Class I promoter

1. Two essential elements: 1. upstream control element:-107--156 2. core region: -45-20 2. Need to be apart: delete or add DNA fragment B/w the elements resulted in the decrease of promoter activity

Effect of spacing of the two rRNA promoter element

Class III Promoter:
sRNA and tRNA genes
Classic class III promoter: lie within the genes
(5S rRNAgene, tRNA gene)

Non-classic : similar to class II promoter
(U6 snRNA, 7SL RNA, 7SK RNA gene)

Effect of 5’-deletions on 5S rRNA gene

Effects of 3’-deletion on 5SrRNA gene transcription

Using cordycepin triphosphate (虫草菌素, 3’-dATP, no 3’ hydroxyl group) to terminate transcription at reproducible sites

Class III Promoter: sRNA and tRNA genes
Classic class III promoter: lie within the genes
(5S rRNAgene, tRNA gene)

Non-classic : similar to class II promoter
(U6 snRNA, 7SL RNA, 7SK RNA gene)

Cis-acting DNA elements (顺式作用元件)
Cis-acting DNA elements: genetic elements, such as enhancers,
promoters, operators, which are on the same chromosome of the regulating gene

Enhancer: A DNA element that strongly stimulates transcription of
a gene or genes.

Silencer: a DNA element that can act at a distance to decrease
transcription from a eukaryotic gene

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

Structure of SV 40 virus early control region: enhancers located upstream of the promoter enhancer enhancer

Enhancer could be within a gene (immunoglobulin) exons

How do enhancers stimulate transcription?
? Enhancers act through proteins that bind to them. ? These proteins named as: transcription factors, enhancerbinding protein, or activators.
Binding of specific proteins to an enhancer modulates the rate of transcription of the associated gene. TBP=TATA binding protein; TAF:TBP-associated protein; ENH=enhancer

Trans-acting factors: factors, usually considered to be proteins, that
bind to the cis-acting sequences to control gene expression

How do silencers work?
? silencers cause the chromatin to coil up into a condensed, inaccessible, and therefore inactive form, thereby preventing transcription of neighboring genes.

General Transcription factors
? General transcription factors: attract the RNA polymerases to their respective promoters with a weak extent. They support only a basal level of transcription. Cells exert exquisitely fine control over transcription through special transcription factors

? ?

Class II factors
Preinitiation complex: The combination of
RNA polymerase and general transcription factors assembled at promoter just before transcription begins

Order:
1. With help of TFII A, TFII D binds to TATA box 2. TFII B binds next, protein-DNA interaction 3. TFII F helps RNA polymerase bind to –34~+17 4. Remaining factors binds: TFII E & TFII H

Building the preinitiation complex
?TFIID is most important ?TFIIF is essential for the binding of RNA polymerase ?The preinitaition complex binds in TATA box region of a promoter

Binding of TFIID is on the minor groove of the TATA box, not in the major groove

TATA AAA

TFIID = a TATA-box binding protein (TBP) + 8-10TBP associated factors (TAFIIS)

TATA containing promoter

TATA less promoter w/i Inr & DPE

TATA less promoter w/i GC box

Binding of TFIID is on the minor groove of the TATA box, not in the major groove

TATA AAA

Class I factors
Two TFs:
1. core-binding factors:
SL1( human) TIF-IB (transcription initiation factor) Upstream-binding factor (UBF) or Upstream-activating factor (UAF)

2.

1. 2.

SL1 is required for the transcription SL1 is species-specific

1.

UBF1 or SL1 caused no footprint on its own UBF+SL1 caused footprint on UCE region of promoter

2.

Class III factors (TFIIIA, B, C)
1, -antibody, 2. +Irrelevant antibody, 3.+ TFIIIA antibody

?

TFIIIA is required for the synthesis of 5sRNA, but not tRNA TFIIIB and C are required by both 5srRNA gene and tRNA gene

?


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transcription | transcription factor | dna transcription | narrow transcription | transcription unit | broad transcription | transcription start | regulation |