2Section 1** Basic concept, specificity and modality of gene expression Section 2** Basic principle of gene expression regulationSection 3** Regulation of gene expression in prokaryoteSection 4** Regulation of gene expression in eukaryote
3Section 1The basic concept, specificity and modality of gene expression
41.1 The concept of gene expression =transcriptiontranslation
5Interaction among large biomolecules 1 proteins2 RNAs1 proteins2 RNAsDNAs RNAs ProteinsInteraction among large biomolecules
61.2 The specificity ofgene expression in thetime and the space
71.2.1 The temporal specificity of gene expression The temporal specificity is that some specific genes in genome are expressed in order of specific timeThe temporal specificity is also stage specifi-city in the polycellular biosomesThe expressed genes in early developmental steps are more than in other steps in polycellular biosomesThe expressed genes relate with biological function.
81.2.2 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.
91.3 Modality of gene expression Constitutive gene expressionInductive and repressivegene expression
101.3.1 constitutive gene expression Some genes in genome are known ashousekeeping genes. The expression of housekeeping genes ingenome are also called constitutive geneexpression. Constitutive gene expression iscontinual in most cells.
11less effected by environment factors. The expressive products of constitutivegenes are absolutely necessary in all overlife process. The expression of constitutive genes areless effected by environment factors. The constitutive gene expression are onlyeffected by interacting between promoterand RNA polymerase.
121.3.2 Inductive and repressive gene expression The expression of some genes in genomeare more effected by environment factors. The increase of gene expression which iseffected by environment factors are calledinduction, in contrast, the decrease of thatare repression.
13genes are regulated by other factors, The expression of induced or repressedgenes are regulated by other factors,besides interaction between promoter andRNA polymerase. The special elements are located in theregulation region of induced or repressedgenes. Induction and repression of geneexpression correspond with each other.
141.4 Biological significance of gene expression regulation acclimation keep growth and proliferation keep individual developmentand differentiation
15Section 2Basic principle of gene expressionregulation
162.1 multilevel regulation of gene expression check pointactivity of gene structure in genomeDNA amplificationDNA rearangementDNA methylation initiation of RNA transcription* process of RNA post-transcription transport of RNA post-process initiation of protein translation process of protein post-translation
172.2 basic factors of gene expression regulation regulation proteinRNA polymerasespecific DNA sequence
182.2.1 specific DNA sequence -35 region -10 region promoter of prokaryotic genesspacerATTTACATATGATN7N16TATGTTN6N17TTGATATATAATCTGACGTACTGTN18TTGACATTAACTtranscriptionalinitiation sitetRNATyrtrplacrecAara BAC+1“TTGACA”“TATAAT”consensus sequence
126.96.36.199 the prokaryotic operon in 1961 by Jacob and Monod. The concept of the operon was first proposedin 1961 by Jacob and Monod. An operon is a whole unit of prokaryotic geneexpression which includes a set of structuralgenes and its promoter, operator and othercontrol elements which are recognized andbond by regulatory gene products.
20Structural genes region 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 regionInhibitor geneGene 1Gene 2Gene 3Structural genes regionOp3’5’i gene regionrepressorRNA polymerase
188.8.131.52 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 mechanismabout gene expression regulation of operons, butthe negative regulation is .
184.108.40.206 cis-acting elements of eukaryotic gene The cis-acting elements are DNA fragments. The cis-acting elements are the regulator ofeukaryotic gene transcription There are cis-acting elements in the flakings or theintrons of eukaryotic gene. The cis-acting elements include promoter,enhancer,silencer and so on.
23eukaryotic genome RNA polymerase gene coding regionenhancersilencerpromoter3’5’exon intron exonRNA polymerase The eukaryotic genes are monocistron. there are not the operons structure ineukaryotic genome
242.2.2.1 regulation protein of prokaryotic genes specific factors：decide identification and bind between RNApolymerase and specific promoter repressor：bind operator and repress gene transcription activator:bind a special DNA sequence next to promoteradvance to bind between RNA polymerase and promoterand to form transcription initiation complex.
252.2.2.2 regulation protein of eukaryotic genes transcription factor, it is also trans-acting factor. cis-acting proteinprotein Atrans-acting proteintrans-acting factortrans-regulationPAAPBBprotein B cis-acting proteincis-regulation
2220.127.116.11 promoter of prokaryotes/eukaryotes effect on RNA polymerase The promoter of prokaryotes/eukaryotes is consistof transcription initiation site, RNA polymeraseidentification and binding site and other regulationelements. The promoter of eukaryotes is more complicated thanthat of prokaryotes.
27polymerase effects directly on frequency of gene The sequence of different promoter is certaindifferent. The affinity of prokaryotic promoter with RNApolymerase effects directly on frequency of genetranscription initiation The affinity between eukaryotic RNA polymeraseand promoter is less, when RNA polymerase issingle. The eukaryotic RNA polymerase can bind withpromoter after forming complex with basictranscription factor.
218.104.22.168 regulation proteins effect on activity of RNA polymerase Specific promoter decides basic transcriptionfrequency of genes. The regulation proteins can change transcription The conformation or the expression level in the cellof regulation proteins gets a change understimulation of environment signal.
29interaction in transcription regulation of eukaryotic genes DNA-protein and protein-proteininteraction in transcription regulation ofeukaryotic genesDNA-protein interaction Identification and bind between cis-acting proteinsor trans-acting factors and cis-acting elements Its interaction is a non-covalent bond. Form DNA-protein complex finally
302.2.4.2 protein-protein interaction The most regulation protein can form homodimer,heterodimer, homopolymer or heteropolymer beforebinding with cis-acting element. Ability of some regulation protein to bind with itscis-acting element is increased or decreased afterpolymerization. Some regulation protein don’t bind with DNA, butcan effect the activity binding between DNA andother regulation protein by protein-proteininteraction.
31Section 3Regulation of prokaryotic gene expression3.1 Characters of transcribed regulation inprokaryotic genes3.2 Regulation of transcribed initiation in3.3 Regulation of transcribed termination in3.4 Regulation of proteic translation in prokaryote
323.1 characters of transcriptional regulation in prokaryotic genes The function of factorsThe factors bind a special element in 5’ flaking region of genes in the stage of transcribed initiationThe factors decide the specificity of transcribed genesThe factors mediate holoenzyme of RNA polymerase binding to specific promoter of genesDifferent factors decide transcription of different genes.
333.1.2 universality of operon model the most prokaryotic genes There are many operons in order in prokaryoticgenome. Don’t discover operon in eukaryotic genome.3.1.3 universality of repression mechanism The repression mechanism is the main mechanism oftranscriptional regulation of prokaryotic genes
343.2 regulation of transcribed initiation in prokaryotic genes
36Primary structure of lac operon regulation region Catabolite geneactivation protein site-10 site-35 siteCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGAGCGGATAACAATTTCACACCTCATTAGGACTCGATTGAGTGTAATTA5’3’Operon region20bpRNA polymerase binding region or promoter regionPrimary structure of lac operon regulation region5’ TATAAT 3’Pribnow box
39+ 3.2.3 correspond between negative regulation of repressor and positive regulation of CAP ingene transcription control of lac operonCAP site5’3’-35-10RNA polymeraseinhibitor geneglucose concentration is lower and lactoseconcentration is higherRepressor(4 polymer)+galactosecAMPat glucose absentsCAP
40+ 22.214.171.124 glucose concentration is higher and lactose CAP site5’3’-35-10RNA polymeraseinhibitor genecAMPat glucose presentsCAP+glucose concentration is higher and lactoseconcentration is lowerRepressor(4 polymer)
41The 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.
423.3 regulation of transcribed termination in prokaryotic genes
433.3.1 Dependent upon factor 5’cDependent upon factorPromoterGeneRNA polymeraseTerminatornew RNA
44coding strand template strand RNA polymerase5’coding strandtemplate strandnew RNA transcript3.3.2 model about transcription terminationfor independent to factor
45GA CCU GA U U U U-OH 3’5’U5’…GCCGCCAGUUCGGCUGGCGGCAUUUU…3’RNA5’…GCCGCCAGTTCGGCTGGCGGCATTTT… 3’terminatorThe 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
463.3.3 attenuation regulation mechanism of gene transcription of trp operon in E.coliLTrp operonREDCBApOAttenuaterSynthesis of tryptophan in E. coliOHOH2CCOOHCChorismic acidNH2Anthranilic acidsynthetaseCH2NCHOHPIndolglycerolphosphateIndoglycerol phosphate synthetaseTryptophan
47The regulation mechanism of trp operon at a few tryptophans present or tryptophans absentLInactiverepressorREDCBApOwhole mRNAat a lot of tryptophans presentTrp+RepressorRNA polymeraseorfragmentary mRNA
48tryptophans absent ribosome RNA polymerase RNA DNA lot of tryptophans KAIFLG1234ribosomeTry codeRNA polymeraseRNADNAWRtryptophans absentlot of tryptophans
493.4 regulation of proteic translation in prokaryote
503.4.1 autoregulation/autogenous control DNAstarted regionmRNA5’3’same mRNAProtein
513.4.2 antisene control Antisens RNA DNA started region 5’ 3’ mRNA ProteinmRNADNA5’3’started regionAntisens RNA
52Section 4 Regulation of eukaryotic gene expression 4.1 character of eukaryotic genomic structure4.2 character of expressional regulation ofeukaryotic genes4.3 regulation of transcription for RNA pol I and RNApol III4.4 regulation of transcriptional initiation forRNA pol II4.5 regulation of transcriptional termination for4.6 regulation of past-transcription for RNA4.7 regulation of translation for protein
534.1 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.
544.2 character of transcription regulation of eukaryotic genes three RNA polymerases in eukaryote RNA polymerase Ⅰ，45s-rRNA(28S, 18S,5.8S)RNA polymerase Ⅱ*，hnRNA(mRNA), a partof 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 forevery RNA polymerase , for exampleTATA box-binding protein (TBP). The some subunits are special for a RNApolymerase. TFⅡD is core of polymeraseⅡ. TFⅡD is consist of TBP and TBP-relatedfactor.
564.2.2 structural character of active gene region There are hypersensitive sites of DNaseⅠinthe flanking regions of active gene, nearregulation protein binding sites.Gene coding regionPromoterSilencer orEnhancersite
58activity of gene structure dsDNAsupersolenoidchromatidchromosomesolenoidchromatinnucleosomestranscriptionbubbleRNAactivity of gene structure213456
59of transcription region DNA in front of RNA When gene is activated, topology structureof transcription region DNA in front of RNApolymerase is positive superhelixconformation,that one in back of RNApolymerase is negative superhelixconformation.RNApolymerasenegative superhelixpositive superhelix
60DNA is propitious to form nucleosomes GCGCGCGC The negative superhelix conformation ofDNA is propitious to form nucleosomesagain, positive one is propitious to separatehistone in nucleosomes The methylation of CpG sequence in activegene flaking region is lower.Gene
61The 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.
624.2.3 The positive regulation is main in gene transcription regulation of eukaryotesThe 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.
63The 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.
644.2.4 The transcription and the translation are separated in different area , this isprone to regulate exactly in genetranscriptionThe process of post-transcriptionmodification is more complex andperfect, therefore links of geneexpression regulation is increased.
654.3 regulation of transcription for RNA polⅠ and RNA pol Ⅲ
664.3.1 control of transcription for RNA polⅠ rDNA genecore elementupstream control elementrRNARNA polⅠupstream binding factor 1, UBF-1selectivity factor 1, SL-1
674.3.2 control of transcription for RNA pol Ⅲ TGGCNNAGTGGGGTTCGANNCCtRNA+1tDNA geneTF Ⅲ CRNA pol ⅢTF Ⅲ B
68+1 TF Ⅲ B TF Ⅲ C RNA pol Ⅲ tRNA TGGCNNAGTGG tDNA gene GGTTCGANNCC
69+15s rDNA geneTF Ⅲ ATF Ⅲ BTF Ⅲ CRNA pol Ⅲ5s rRNA
704.4 regulation of transcriptional initiation for RNA polⅡ
714.4.1 cis-acting elementaccording to function, main includingpromoter, enhancer, silencer and so on
73promoterIt 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.
74TATA 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.
75The 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.
76The 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.
7126.96.36.199 enhancer The enhancer is a DNA fragment. The enhancer increases activation of gene transcription and decides space-time specificity of gene transcription.geneenhancer5’3’72bpcore sequenceTGTGGAATTAG
78 The role of the enhancer don’t relate with its distance from transcription start site. The enhancer is very far from genetranscription start site(1~30/50kb) and locates not only ingenic upstream, but also in genic downstream, sometimes inthe intron. Some important functional elements，for example coreDNA sequence which is bond with special transcriptionfactors, is in the enhancer and the promoter at same time.GeneregulatoryproteinsGeneregulatoryproteinstranscriptioninitiation complexRNA pol II5’3’Enhancer-2Enhencer-1geneEnhancer-3-10kbto -50kb-200TATA box+10kbto +50kb
79The enhancer always interlinks or overlaps with the promoter. geneThe 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
80Control of gene expression The action of enhancer is not strict specific.enhancerregulatoryproteinpromotertranscriptioninitiationcomplex12n
81 direction. The action of enhancer does not have strict promoter gene5’3’GCGA…GCTACGT...ACGenhancerTCG...AGCGGCA...TGCA
82silencerThe 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.
834.4.2 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.
84Control of gene expression TATA boxvariouscontrolelement-200silencer+10kbto +50kbenhancer-10kbto -50kbgene5’3’RNA pol IItranscriptioninitiation complexControl of gene expressionTrans-acting factorGeneregulatoryproteins
8188.8.131.52 type of transcription factors general transcription factorsIt 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.
86Various transcription factors of RNA polymerase II TFMolecular weitht, kDFunctionTF II A12, 19, 35stabilize TF II DTF II B33accelerate that RNA pol IIbinding with DNA.TF II DTBP/38, TAP/15-250recognize TATA boxTF II E57(), 34()ATPaseTF II F30, 74helicaseTF II I120accelerate that TF II Dbinding TATATF II H35-89phosphorylation of carboxyl terminal domain of RNA pol II large subunit
8184.108.40.206.2 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.
88Most 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.
8220.127.116.11 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.
90DNA 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
91F L + Y zinc finger in TF III A zinc finger in SP1（TF） ZnHYLFCOOHH2Nzinc finger in SP1（TF）bind with GC box，discovered the zincfinger early
918.104.22.168.2 transcription activation domain It is usually consist of 30100 amino acid residues . It is divided three types as follows: acidic activation domain glutamine-rich domain proline-rich domain
922.214.171.124.3 dimerization domain It is the basic leucine zipper or basic helix loop helix in protein structure.
99the structure of gene in eukaryote, cis-acting element and trans or cis -acting factorexonintronATGTAAPoly A siteAATAAA, 30bpdownstreamenhancerterminatorsilencerinitiation sitepromoterupstreamcoding strandtemplate strand5’3’12nn-1TATA boxCAAT boxGC boxcis-acting elementstrans or cis-acting factors
100mRNA transcription activation and regulation geneTATAenhancermRNA transcription activation and regulation5’3’promoter regionEBPTF II Apol IITF II FTBPTAFTF II ETF II B
101enhancer pol II / TF II F enhancer 5’ pol II TAF TBP 3’ gene TATATAFTF II Apol II / TF II FPICTBPTF II BTF II ETICEBPenhancergeneTATAenhancer5’3’promoter regionEBPpol IITF II FTBPTAFTF II ATF II BTF II E
102multilevel regulation of gene expression RNAdsDNAsupersolenoidchromatidchromosomesolenoidchromatinnucleosomesTranscriptionbubbleactivity of gene structure213456891011AAAAAhnRNA7proteinprecursorrRNArRNA MaturetRNAtRNA Mature12mature13mRNA Mature1416amino acidpolysome15functionmultilevel regulation of gene expression