Presentation on theme: "1 Gene expression regulation *** Enmin Li 2 Section 1** Basic concept, specificity and modality of gene expression Section 2** Basic principle of."— Presentation transcript:
1 Gene expression regulation *** Enmin Li
2 Section 1** Basic concept, specificity and modality of gene expression Section 2** Basic principle of gene expression regulation Section 3** Regulation of gene expression in prokaryote Section 4** Regulation of gene expression in eukaryote
3 Section 1 The basic concept, specificity and modality of gene expression
4 1.1 The concept of gene expression gene expression transcription translation = +
5 DNAs RNAs Proteins 1 proteins 2 RNAs 1 proteins 2 RNAs Interaction among large biomolecules
6 1.2 The specificity of gene expression in the time and the space
7 1.2.1 The temporal specificity of gene expression The temporal specificity is that some specific genes in genome are expressed in order of specific time The temporal specificity is also stage specifi- city in the polycellular biosomes The expressed genes in early developmental steps are more than in other steps in polycellular biosomes The expressed genes relate with biological function.
8 1.2.2 The spatial specificity of gene expression In the polycellular biosomes the spatial speci- ficity of gene expression is that one or some specific genes in the genome are expressed in different systems, organs, tissues and cells in order of space. The spatial specificity of gene expression is also known as tissue specificity or cell specificity. The expressed genes relate with biological function.
9 1.3 Modality of gene expression 1.3.1 Constitutive gene expression 1.3.2 Inductive and repressive gene expression
10 1.3.1 constitutive gene expression Some genes in genome are known as housekeeping genes. The expression of housekeeping genes in genome are also called constitutive gene expression. Constitutive gene expression is continual in most cells.
11 The expressive products of constitutive genes are absolutely necessary in all over life process. The expression of constitutive genes are less effected by environment factors. The constitutive gene expression are only effected by interacting between promoter and RNA polymerase.
12 1.3.2 Inductive and repressive gene expression The expression of some genes in genome are more effected by environment factors. The increase of gene expression which is effected by environment factors are called induction, in contrast, the decrease of that are repression.
13 The expression of induced or repressed genes are regulated by other factors, besides interaction between promoter and RNA polymerase. The special elements are located in the regulation region of induced or repressed genes. Induction and repression of gene expression correspond with each other.
14 1.4 Biological significance of gene expression regulation acclimation keep growth and proliferation keep individual development and differentiation
15 Section 2 Basic principle of gene expression regulation
16 2.1 multilevel regulation of gene expression check point v activity of gene structure in genome v DNA amplification v DNA rearangement v DNA methylation initiation of RNA transcription* process of RNA post-transcription transport of RNA post-process initiation of protein translation process of protein post-translation
17 2.2 basic factors of gene expression regulation regulation protein RNA polymerase specific DNA sequence
18 -35 region -10 region 2.2.1 specific DNA sequence 18.104.22.168 promoter of prokaryotic genes spacer ATTTACATATGAT N7N7 N 16 ATTTACATATGTT N6N6 N 17 ATTGATATATAAT N7N7 N 16 ACTGACGTACTGT N6N6 N 18 ATTGACATTAACT N7N7 N 17 transcriptional initiation site tRNA Tyr trp lac recA ara BAC +1 “TTGACA”“TATAAT” consensus sequence
19 22.214.171.124 the prokaryotic operon The concept of the operon was first proposed in 1961 by Jacob and Monod. An operon is a whole unit of prokaryotic gene expression which includes a set of structural genes and its promoter, operator and other control elements which are recognized and bond by regulatory gene products.
20 The operator is a site bond with the repressor. The operator mediates a negative regulation of operon. The operator is next to the promoter. The operator sites in downstream of the promoter. The operator overlaps partly with the promoter some time. Regulatory region Inhibitor gene Gene 1Gene 2Gene 3 Structural genes region O p 3’3’ 5’5’ i gene region repressor RNA polymerase
21 126.96.36.199 Other regulator of prokaryotic operons special DNA sequence in some prokaryotic operons can bind with activator of RNA polymerase increase transcription of operons mediate positive regulation of operons The positive regulation is not main mechanism about gene expression regulation of operons, but the negative regulation is.
22 188.8.131.52 cis-acting elements of eukaryotic gene The cis-acting elements are DNA fragments. The cis-acting elements are the regulator of eukaryotic gene transcription There are cis-acting elements in the flakings or the introns of eukaryotic gene. The cis-acting elements include promoter,enhancer, silencer and so on.
23 gene coding region enhancer silencer enhancer silencerpromoter 3’3’ 5’5’ exon intron exon RNA polymerase The eukaryotic genes are monocistron. there are not the operons structure in eukaryotic genome
24 2.2.2 regulation protein 184.108.40.206 regulation protein of prokaryotic genes specific factors ： decide identification and bind between RNA polymerase and specific promoter repressor ： bind operator and repress gene transcription activator: bind a special DNA sequence next to promoter advance to bind between RNA polymerase and promoter and to form transcription initiation complex.
25 220.127.116.11 regulation protein of eukaryotic genes transcription factor, it is also trans-acting factor. cis-acting protein PBPB BPAPA A protein A trans-acting protein trans-acting factor protein B cis-acting protein trans-regulation cis-regulation
26 2.2.3 RNA polymerase 18.104.22.168 promoter of prokaryotes/eukaryotes effect on RNA polymerase The promoter of prokaryotes/eukaryotes is consist of transcription initiation site, RNA polymerase identification and binding site and other regulation elements. The promoter of eukaryotes is more complicated than that of prokaryotes.
27 The sequence of different promoter is certain different. The affinity of prokaryotic promoter with RNA polymerase effects directly on frequency of gene transcription initiation The affinity between eukaryotic RNA polymerase and promoter is less, when RNA polymerase is single. The eukaryotic RNA polymerase can bind with promoter after forming complex with basic transcription factor.
28 22.214.171.124 regulation proteins effect on activity of RNA polymerase Specific promoter decides basic transcription frequency of genes. The regulation proteins can change transcription frequency of genes. The conformation or the expression level in the cell of regulation proteins gets a change under stimulation of environment signal.
29 2.2.4 DNA-protein and protein-protein interaction in transcription regulation of eukaryotic genes 126.96.36.199 DNA-protein interaction Identification and bind between cis-acting proteins or trans-acting factors and cis-acting elements Its interaction is a non-covalent bond. Form DNA-protein complex finally
30 188.8.131.52 protein-protein interaction The most regulation protein can form homodimer, heterodimer, homopolymer or heteropolymer before binding with cis-acting element. Ability of some regulation protein to bind with its cis-acting element is increased or decreased after polymerization. Some regulation protein don’t bind with DNA, but can effect the activity binding between DNA and other regulation protein by protein-protein interaction.
31 Section 3 Regulation of prokaryotic gene expression 3.1 Characters of transcribed regulation in prokaryotic genes 3.2 Regulation of transcribed initiation in prokaryotic genes 3.3 Regulation of transcribed termination in prokaryotic genes 3.4 Regulation of proteic translation in prokaryote
32 3.1 characters of transcriptional regulation in prokaryotic genes 3.1.1 The function of factors The factors bind a special element in 5’ flaking region of genes in the stage of transcribed initiation The factors decide the specificity of transcribed genes The factors mediate holoenzyme of RNA polymerase binding to specific promoter of genes Different factors decide transcription of different genes.
33 3.1.2 universality of operon model the most prokaryotic genes There are many operons in order in prokaryotic genome. Don’t discover operon in eukaryotic genome. 3.1.3 universality of repression mechanism The repression mechanism is the main mechanism of transcriptional regulation of prokaryotic genes
34 3.2 regulation of transcribed initiation in prokaryotic genes
35 3.2.1 stucture of lactose operon C regulatory region Inhibitor gene Gene ZGene YGene A structural genes region O p 3’3’ 5’5’ i gene region 1000bp 100bp 3520bp 760bp810bp base pair: peptide : (MW kDa) 37 repressor (4 polymer) 32 30 135 -galactosidase (4 polymer) lactose cell galactose + acetyl CoA acetylgalactose + glucose galactose lactose - galactoside transacetylase (2 polymer) lactose permease (2 polymer)
36 Catabolite gene activation protein site - 10 site - 35 site CACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGAGCGGA TAACAATTTCACACTAACAATTTCACAC CTCATTAGGCTCATTAGG ACTCGATTGAGTGTAATTA 5’ 3’ Operon region 20bp RNA polymerase binding region or promoter region Primary structure of lac operon regulation region 5’ TATAAT 3’ Pribnow box
37 z y ai o p repressor (4 polymer) RNA polymerase z y ai o p repressor (4 polymer) RNA polymerase + galactose mRNA 3.2.2 regulated mechanism of lac operon genes 184.108.40.206 repressor regulate negatively transcription of lac operon genes
38 3. 2.2.2 catabolite gene activation protein(CAP) regulate positively transcription of lac operon genes CAP site - 35 - 10 1 5’ 3’ RNA polymerase - 35 - 10 CAP cAMP at glucose absents CAP cAMP CAP + at glucose presents
39 3.2.3 correspond between negative regulation of repressor and positive regulation of CAP in gene transcription control of lac operon CAP site 0 5’ 3’ - 35 - 10 RNA polymerase inhibitor gene 220.127.116.11 glucose concentration is lower and lactose concentration is higher Repressor (4 polymer) + galactose cAMP at glucose absents CAP cAMP CAP + cAMP
40 CAP site 0 5’ 3’ - 35 - 10 RNA polymerase inhibitor gene cAMP at glucose presents CAP cAMP CAP + 18.104.22.168 glucose concentration is higher and lactose concentration is lower Repressor (4 polymer)
41 The negative regulation mechanism of the repressor cooperate with the positive regulation mechanism of the CAP control gene transcription of lac operon by kind and concentration of carbohydrate from the environment.
42 3.3 regulation of transcribed termination in prokaryotic genes
43 5’ c 3.3.1 Dependent upon factor 5’ Promoter Gene RNA polymerase Terminator c new RNA
44 RNA polymerase 5’ coding strand template strand new RNA transcript 3.3.2 model about transcription termination for independent to factor
45 GACCGCCGGACCGCCG CUGGCGGCCUGGCGGC A U U U U-OH 3’5’ U U C G G 5’…GCCGCCAGUUCGGCUGGCGGCAUUUU…3’ RNA 5’…GCCGCCAGTTCGGCTGGCGGCATTTT… 3’terminator The RNA made from the DNA palindrome is self- complementary and so formed a internal hairpin structure followed by a few U bases. The signals that terminates transcri- ption are localized in the gene 3’ end. A simple termination signal is a GC- rich region that is a palindrome, followed by AT-rich sequence. DNA
46 Synthesis of tryptophan in E. coli O HO H2CH2C COOH C Chorismic acid COOH NH 2 Anthranilic acid synthetase CH 2 N CH OH O P CH Indolglycerol phosphate Indoglycerol phosphate synthetase NH 2 N CH CH 2 COOH Tryptophan synthetase 3.3.3 attenuation regulation mechanism of gene transcription of trp operon in E.coli L Trp operon REDCBA p O Attenuater
47 The regulation mechanism of trp operon at a few tryptophans present or tryptophans absent L Inactive repressor REDCBA p O whole mRNA at a lot of tryptophans present L Inactive repressor Trp + Repressor REDCBA p O RNA polymerase or fragmentary mRNA
48 M K A I F L K G 1 2 3 4 ribosome Try code RNA polymerase RNA DNA M K A I F L K G 1 3 4 ribosome Try code RNA polymerase 2 W W R DNA RNA tryptophans absent lot of tryptophans
49 3.4 regulation of proteic translation in prokaryote
50 3.4.1 autoregulation/autogenous control Protein mRNA DNA same mRNA 5’ 3’ started region
51 3.4.2 antisene control Protein mRNA DNA 5’ 3’ started region Antisens RNA
52 Section 4 Regulation of eukaryotic gene expression 4.1 character of eukaryotic genomic structure 4.2 character of expressional regulation of eukaryotic genes 4.3 regulation of transcription for RNA pol I and RNA pol III 4.4 regulation of transcriptional initiation for RNA pol II 4.5 regulation of transcriptional termination for RNA pol II 4.6 regulation of past-transcription for RNA 4.7 regulation of translation for protein
53 4.1 Character of eukaryotic genomic structure The eukaryotic genome is very great. The structure of eukaryotic genome is very complex. There is only a gene in a transcriptional unit of eukaryotic genome. There are a lot of repeat sequences in eukaryotic genome. Gene are discontinuous, there are noncoding sequences in the most eukaryotic gene.
54 4.2 character of transcription regulation of eukaryotic genes 4.2.1 three RNA polymerases in eukaryote RNA polymerase Ⅰ， 45s-rRNA(28S, 18S, 5.8S) RNA polymerase Ⅱ * ， hnRNA(mRNA), a part of snRNA RNA polymerase Ⅲ， 5s-rRNA, tRNA, a part of snRNA
55 The every RNA polymerase is consist of about 10 subunits. The some subunits are in common for every RNA polymerase, for example TATA box-binding protein (TBP). The some subunits are special for a RNA polymerase. TF Ⅱ D is core of polymerase Ⅱ. TF Ⅱ D is consist of TBP and TBP-related factor.
56 4.2.2 structural character of active gene region There are hypersensitive sites of DNase Ⅰ in the flanking regions of active gene, near regulation protein binding sites. Gene coding region Promoter Silencer or Enhancer Silencer or Enhancer site
59 When gene is activated, topology structure of transcription region DNA in front of RNA polymerase is positive superhelix conformation,that one in back of RNA polymerase is negative superhelix conformation. RNA polymerase negative superhelix positive superhelix
60 GCGCGCGC The negative superhelix conformation of DNA is propitious to form nucleosomes again, positive one is propitious to separate histone in nucleosomes The methylation of CpG sequence in active gene flaking region is lower. Gene
61 The histons in active gene region change often as follows: The histons is prone to be modified, in result its structure becomes instability. The dimer H2A-H2B is prone to be replaced out from nucleosome. The instability of dimer H2A-H2B is increased. The rich-Lys H1-like histons are decreased.
62 4.2.3 The positive regulation is main in gene transcription regulation of eukaryotes The most transcriptional regulation proteins are transcription activation proteins. The affinity between RNA polymerase and promoter in eukaryotes is very weaker or not. RNA polymerase must depend on one or many activation proteins to bind with promoter. The positive regulation is universality in gene transcription regulation of eukaryotes.
63 The eukaryotic genome is very great. There are many cis-acting elements in a gene regulation region, in result that specificity of interaction between activation protein and DNA is increased. Many activation proteins regulate a gene, therefore the regulation efficiency is higher. A activation proteins regulate many gene, therefore the regulation is more economical.
64 4.2.4 The transcription and the translation are separated in different area, this is prone to regulate exactly in gene transcription 4.2.5 The process of post-transcription modification is more complex and perfect, therefore links of gene expression regulation is increased.
65 4.3 regulation of transcription for RNA pol Ⅰ and RNA pol Ⅲ
66 4.3.1 control of transcription for RNA pol Ⅰ rDNA gene -45 +20-156 -107 core elementupstream control element rRNA RNA pol Ⅰ upstream binding factor 1, UBF-1 selectivity factor 1, SL-1 RNA pol Ⅰ
67 4.3.2 control of transcription for RNA pol Ⅲ TGGCNNAGTGGGGTTCGANNCC TGGCNNAGTGGGGTTCGANNCC tRNA +1 TGGCNNAGTGG tDNA gene GGTTCGANNCC TGGCNNAGTGGGGTTCGANNCC TF Ⅲ C RNA pol Ⅲ TF Ⅲ B
68 TGGCNNAGTGGGGTTCGANNCC TGGCNNAGTGGGGTTCGANNCC tRNA +1 TGGCNNAGTGG tDNA gene GGTTCGANNCC TGGCNNAGTGGGGTTCGANNCC TF Ⅲ C RNA pol Ⅲ TF Ⅲ B
69 5s rRNA +1 5s rDNA gene RNA pol Ⅲ TF Ⅲ A TF Ⅲ C TF Ⅲ B
70 4.4 regulation of transcriptional initiation for RNA pol Ⅱ
71 4.4.1 cis-acting element according to function, main including promoter, enhancer, silencer and so on
73 22.214.171.124 promoter It is consist of RNA polymerase binding site, a set of other functional elements which control transcription and a transcription initiation site at least. The length of every functional elements in the promoter is about 7-20 bp. Promoter sequence of different genes is a little different. Most gene promoter sequence have TATA box.
74 TATA box is the most basic and important functional element in the promoter. The consensus sequence of TATA box is TATAAAA locating in -25 -30 bp region of transcription start site upstream. TATA box controls veracity and frequency of gene transcription. GC box （ GGGCGG ） and CAAT box （ GCCAAT ） is more frequent in the promoter. GC box and CAAT box locate in -30 -110 bp region of transcription start site upstream.
75 The promoter locates in upstream of coding region of the gene certainly. The promoter has strict direction. The most simple promoter is consist of TATA box and transcription start site, but the typical promoter often contains also GC box and/or CAAT box in upstream of TATA box.
76 The promoter of some genes don’t contain TATA box. The promoter without TATA box always contains many transcription start sites, and contains rich-GC sometimes. The gene that contains the promoter without TATA box is house keeping gene or the gene which plays a role in fetation, tissue differentiation, tissue damage regeneration and so on.
77 126.96.36.199 enhancer The enhancer is a DNA fragment. The enhancer increases activation of gene transcription and decides space-time specificity of gene transcription. gene enhancer 5’ 3’ 72bp enhancer core sequence TGTGGAATTAG
78 The role of the enhancer don’t relate with its distance from transcription start site. The enhancer is very far from gene transcription start site(1~30/50kb) and locates not only in genic upstream, but also in genic downstream, sometimes in the intron. Some important functional elements ， for example core DNA sequence which is bond with special transcription factors, is in the enhancer and the promoter at same time. TATA box Enhencer-1 - 200 Enhancer-3 +10kb to +50kb Enhancer-2 - 10kb to - 50kb Gene regulatory proteins Gene regulatory proteins gene 5’ 3’ RNA pol II transcription initiation complex
79 promoterenhancergene The enhancer always interlinks or overlaps with the promoter. Sometimes the enhancer and the promoter too close in structure to differentiate definitely in space and function. The DNA structure of both the promoter and the enhancer is called space-time special promoter. space-time special promoter
80 Control of gene expression The action of enhancer is not strict specific. enhancer regulatory protein promoter transcription initiation complex 1 promoter transcription initiation complex 2 promoter transcription initiation complex n
81 The action of enhancer does not have strict direction. promoter gene 5’ 3’ GCGA…GCT ACGT...ACG enhancer gene 5’ 3’ TCG...AGCG GCA...TGCA
82 188.8.131.52 silencer The silencers are the negative elements in gene transcription regulation, in contrast to the enhancers. The gene transcription is suppressed when specific regulation protein have bound with the silencers. Some silencers play the role of enhancers sometime this mainly depends to the character of regulation proteins in the nucleus.
83 4.4.2 transcription regulation factors The transcription regulation factors are also called transcription factors (TF). Most transcription regulation factors are trans-acting factors, a few ones are cis- acting proteins.
84 TATA box various control element - 200 silencer +10kb to +50kb enhancer - 10kb to - 50kb gene 5’ 3’ RNA pol II transcription initiation complex Control of gene expression Trans-acting factor Gene regulatory proteins Gene regulatory proteins
85 184.108.40.206 type of transcription factors 220.127.116.11.1 general transcription factors It is necessary for the RNA polymerase bind with the promoter. It decides RNA transcription type. It is also regarded as a component of RNA polymerase.
86 Various transcription factors of RNA polymerase II TFMolecular weitht, kDFunction TF II A12, 19, 35 stabilize TF II D TF II B 33 accelerate that RNA pol II binding with DNA. TF II DTBP/38, TAP/15-250recognize TATA box TF II E 57( ), 34( ) ATPase TF II F30, 74 helicase TF II I120 accelerate that TF II D binding TATA TF II H35-89phosphorylation of carboxyl terminal domain of RNA pol II large subunit
87 18.104.22.168.2 special transcription factors It is necessary for individual gene transcription. It decided the specificity of gene transcription in the time and the space. Most special transcription factors are transcription activators, a few ones are transcription inhibitors.
88 Most transcription activators are the proteins binding with the enhancer. Most transcription inhibitors are the proteins binding with the silencer. Some transcription inhibitors don’t directly interact with DNA, but bind with the general transcription factor II-D or some transcription activators and decrease effective concentration of the latter in cell and suppress gene transcription.
89 22.214.171.124 structure of transcription factor Usually, a transcription factor contains a DNA binding domain and a transcription activation domain. Many transcription factors also contain a domain which mediate protein-protein interaction, for example dimerization domain.
90 126.96.36.199.1 DNA binding domain It is consist of 60~ 100 amino acid residues usually. the most familiar structures: zinc finger structure basic - helix structure other structures: basic leucine zipper structure ， bZIP basic helix-turn helix structure ， bHTH basic helix-loop-helix structure ， bHLH
91 zinc finger in TF III A C + C C C + + + + + + + + ++ + + + + + + + + Zn C + C H H + + + + + + + ++ + + + + + + + + C Y C H H + + + + L + + ++ F + + + + + + + ++ + COOH H2NH2N zinc finger in SP1 （ TF ） bind with GC box ， discovered the zinc finger early
93 basic - helix domain(bAH) DNA binding domain of CTF1 (transcription factor)
94 basic leucine zipper ， bZIP COOH NH 2 COOH NH 2 18 15 22 29 36 1 8 15 22 29 36 Leucine residue C N C O H CH 2 CH CH 3
97 188.8.131.52.2 transcription activation domain It is usually consist of 30 100 amino acid residues. It is divided three types as follows: acidic activation domain glutamine-rich domain proline-rich domain
98 184.108.40.206.3 dimerization domain It is the basic leucine zipper or basic helix loop helix in protein structure.
99 cis-acting elements the structure of gene in eukaryote, cis-acting element and trans or cis -acting factor exon intron ATG TAA Poly A site AATAAA, 30bp downstream enhancer terminator downstream silencer initiation site promoter upstream silencer upstream enhancer coding strand template strand 5’ 3’ 12n 12 n-1 TATA boxCAAT box GC box trans or cis-acting factors
100 gene TATA enhancer mRNA transcription activation and regulation 5’ 3’ promoter region EBP TF II A pol II TF II F TBP TAF TF II E TF II B
101 gene TATA enhancer 5’ 3’ promoter region EBP TF II A pol II TF II F TATA TAF TF II A pol II / TF II F PIC TBP TF II B TF II E TIC EBP enhancer TBP TAF TF II E TF II B