協(xié)和單獨(dú)遺傳genemutation

1、Gene Structure &Pathogenic DNA VariantsDepartment of Medical GeneticsYaping Liu (劉雅萍) Human Molecular Genetics (4th Edition) by Tom Strachan and Andrew Read Part I:Gene StructureDepartment of Medical GeneticsYaping Liu (劉雅萍) Human Molecular Genetics (4th Edition) by Tom Strachan and Andrew Read Defi

2、nition of GeneDefinition of GeneGene: a unit of heredity composed of DNA occupying a fixed position on a chromosome, it may determine a characteristic of an individual by specifying a polypeptide chain that forms a protein or part of a protein (structural gene); or encode an RNA molecule; or regulat

3、e the operation of other genes or repress such operationA modern working definition of a gene: a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence regionsDefinition of GeneG

4、enes are transcribed into segments of RNA, some of which are translated into proteins. Both RNA and proteins are products of the expression of the geneGene ProductCarrier of the information: DNA/RNA sequencesUnit of the function: product (protein or RNA)Two Key Points of Defining A Gene2022/8/248Gen

5、eProtein-coding geneStructural GeneRegulatory geneRNA-codinggenetRNA generRNA genemicroRNARegulatory sequencesType of GenesA unique abbreviation of a gene name consisting of italicized UPPERCASE Latin letters and Arabic numbers (e.g. PAH, MFR1) formally assigned by the HUGO Gene Nomenclature Committ

6、ee after a gene has been identifiedGene SymbolChromosomal Architecture of An Eukaryotic GenesA Typical Human Gene 10000bpProtein-Coding GenesHuman proteinSize of protein (no. of amino acid)Size of gene (Kb)No. of exonsCoding DNA(%)Average size of exon (bp)Average size of intron (bp)SRY2040.9194850-G

7、lobin1461.6338150490p161567.43174063064Serum albumin6091814121371100Type VII collagen2928311182977190p53393391062363076Complement C3164141298.6122900Apolipoprotein B45634529314871103Phenylalanine Hydroxylase452902633757100Factor VIII2351186263963500Huntingtin31441896782012361RB1 retinoblastoma prote

8、in928198272.41796668CFTR1480250272.42279100Tltin3435028336340315466Utrophin3433567742.21687464Dystrophin36852400790.618030770Independent Of gene sizedependent Of gene size珠蛋白基因結(jié)構(gòu)模式圖 加強(qiáng)子；啟動(dòng)子；RNA 5 端；起始密碼子；剪接信號(hào)：給點(diǎn)、分枝點(diǎn)、受點(diǎn)；終止密碼子； Poly A加接信號(hào)；轉(zhuǎn)錄終止信號(hào)； 編碼序列； 內(nèi)含子； 分別為3不翻譯區(qū)和5不翻譯區(qū)； 35PromoterPromoter ElementsP

9、romoterExon: Coding sequence of DNA present in mature messenger RNA Intron: Non-coding sequence of DNA removed from mature messenger RNA prior to translationExon & Intron內(nèi)含子-外顯子交界類型Splicing Signal Splicing: The process by which introns, non-coding regions, are excised out of the primary messenger RN

10、A transcript, and exons (i.e., coding regions) are joined together to generate mature messenger RNA Genetic CodePoly A信號(hào)和轉(zhuǎn)錄終止信號(hào)Gene Expression In A Human CellDNARNAProtein基因組學(xué)轉(zhuǎn)錄本組學(xué)蛋白質(zhì)組學(xué)中 心 法 則Alternative PromoterAlternative SplicingAlternative Splicing14a.a.Epstein et al. 1994Consequence of Alternat

11、ive SplicingIsoforms: The protein products of different versions of messenger RNA created from the same gene by employing different promoters, alternative splicing, which causes transcription to skip certain exons. Since the promoters are tissue-specific, different tissues express different protein

12、products of the same gene Consequence of Alternative SplicingIn contravention of the Central Dogma, there are examples in which the DNA sequence of a gene does not fully determine the sequence of its transcriptInvolves the insertion, deletion, or modification of specific nucleotides in the primary t

13、ranscriptHappens on a large scale in the mitochondria and chloroplasts of vascular plants; In mammals, no evidence for insertion or deletion RNA editing, but modification of nucleotides has been observedRNA EditingRNA EditingDistal Regulatory ElementsLocus control region (LCRs)Allow tissue-specific

14、expression and development switching of genes in the clusterDistal Regulatory Elements EnhancerHeterozygous LOF mutations in the PAX6 gene on chr11p15 cause aniridia. Some patients with aniridia have no mut in PAX6 but have translocations with breakpoints up to 125kb downstream of the last PAX6 exon

15、 The role of SHH gene is very important in limb development. Another gene, LMBR1, is located 1mb away from the SHH gene on chr7q36. several deletions, insertions, or translocation breakpoints in the LMBR1 gene in humans or mice cause various limb abnormalities. It was natural to assume that these we

16、re the result of a loss of function of LMBR1-but point mutations in LMBR1 had no effect on limb development. Instead, these changes disrupt a series of enhancers of SHH that happen to be located in introns of LMBR1Red box: DNase hypersensitive sitesDNA methylationChromatin ConformationHistone codeCh

17、romatin ConformationChromatin ConformationDNA methylation changes during mammalian development Epigenetic Control of Gene ExpressionX chromosome inactivation. In the zygote, both the maternally and paternally derived X chromosomes (Xm and Xp) are active. Early in development, one of the two X chromo

18、somes in each cell is inactivated (indicated as the dark chromosome). This X chromosome remains inactive in all the descendants of that cell.Epigenetic Control of Gene ExpressionConcept of genomic imprinting. In this example, the paternally derived copy of a gene is not expressed, whereas the matern

19、ally inherited copy is expressed. The imprint is reset in the germ line, so that in the next generation, the active copy of the gene depends on the parent of origin, not on whether that copy was active in the parent. Epigenetic Control of Gene ExpressionSmall RNA Regulate Gene ExpressionPart II：Path

20、ogenic DNA VariantsDepartment of Medical GeneticsYaping Liu (劉雅萍) Human Molecular Genetics (4th Edition) by Tom Strachan and Andrew Read A Typical Human GeneFrom InternetGenetic VariationMutationGenome MutationChromosome MutationGene Mutation 突變與致病突變Mutation: Any alteration in a gene from its natura

21、l state; may be disease-causing or a benign, normal variant Disease-causing mutation: A gene alteration that causes or predisposes an individual to a specific disease Type of mutation Percentage of live births Gene mutation Autosomal dominant 0.90 Autosomal recessive0.25 X linked0.05 Total gene muta

22、tion: 1.20 Chromosome mutation Autosomal trisomies (mainly Down syndrome) 0.14 Other unbalanced autosomal aberrations0.06 Balanced autosomal aberrations0.19 Sex chromosomes XYY, XXY, and other0.17 XO, XXX, and other0.05 Total chromosome mutation:0.61 Type of MutationsTranslocation: A chromosome alte

23、ration in which a whole chromosome or segment of a chromosome es attached to or interchanged with another whole chromosome or segment, the resulting hybrid segregating together at meiosis; Balanced translocations (in which there is no net loss or gain of chromosome material) are usually not associat

24、ed with phenotypic abnormalities, although gene disruptions at the breakpoints of the translocation can, in some cases, cause adverse effects, including some known genetic disorders;Unbalanced translocations (in which there is loss or gain of chromosome material) nearly always yield an abnormal phen

25、otype Chromosome MutationsInversion: A chromosomal rearrangement in which a segment of a chromosome has inverted from end to end, and re-inserted into the chromosome at the same breakage site. Balanced inversions (in which no net loss or gain of genetic material occurs) are usually not associated wi

26、th phenotypic abnormalities, however, in some cases, gene disruptions at the breakpoints can cause adverse phenotypic effects, including some known genetic diseases. Unbalanced inversions (in which loss or gain of chromosome material occurs) nearly always yield an abnormal phenotype. 融合(fusion)Chrom

27、osome MutationsChromosome Mutations SRY TranslocationChromosome Mutations SRY TranslocationPh1 ablbcrChromosome Mutations Ph ChromosomeChromosome Mutations Fusion geneChromosome Mutations Fusion geneDeletion/InsertionDeletion: Absence of a segment of DNA; may be as small as a single base or as large

28、 as one or more genesInsertion: A mutation in which a segment of DNA is inserted into a gene or other segment of DNA, potentially disrupting the coding sequenceChanges in gene dosageAt a particular locus heterozygous for a deleterious mutant allele and a normal allele, a deletion or other mutational

29、 event within the normal allele renders the cell either hemizygous (one deleterious allele and one deleted allele) or homozygous for the deleterious allele Loss of Heterozygosity (LOH)Changes In Gene Dosage Non-allelic homologous binationAlso called contiguous gene deletion syndrome. A syndrome caus

30、ed by a chromosomal deletion spanning several genes that is too small to be detected under the microscope using conventional cytogenetic methods. The phenotype usually depends on dosage effects of more than one gene and is not seen in people with a point mutation in just one of the genesMicrodeletio

31、n syndromeMicrodeletion SyndromeDeletion on X chromosomePatients 1-3 show a nested series CGS; Patient 4 shows a different CGS.Only gene A5 is dosage sensitive. Patients 5-7 with different sized deletions all show the same phenotype as patient 8, who is a het for a LOF point mutation in the gene A5O

32、n the autosome, contiguous gene syndrome (CGS) are rare because of the balancing effect of the second chromosome.Imprinting DisordersA Recurrent Microdeletion Causing PWS & AS15q11-134.2 MbPWS-AS critical regionLow copy repeat+The Imprinted Gene Cluster at 15q11-q13 That is deleted in PWS or ASIC ma

33、rks an imprinting control center, a sequence that is differentially methylated in males and females and that seems to control overall imprinting of the region.遺傳印記無論從染色體水平還是等位基因水平，遺傳物質(zhì)的表現(xiàn)取決于它的親代來源，父源和母源的遺傳物質(zhì)表達(dá)不同。這種由雙親性別決定的基因功能上的差異被稱之為遺傳印記(genetic imprinting)或親代印記(parental imprinting, PI)。遺傳印跡在減數(shù)分裂中重

34、置Human Genes Showing Tissue-Specific & Developmental Stage-Specific ImprintingPWS與AS Autosomal dominant Gene is maternally expressed Affected when mutation inherited from mother NOT affected when mutation inherited from fatherAngelman SyndromeDevelopmental delayMental retardationSevere speech impari

35、mentGait ataxia, tremulousness of limbsAbnormal behavior, happy, laughing frequently,smiling, excitableAngelman Syndrome1-2% Mutation: affected only when mutation inherited from mother; paternal gene is normal70% 15q11.2-q13 Microdeletion: affected if active gene is deleted from maternal chromosome;

36、 paternal gene is normal5% Uniparental disomy: affected if both copies of chromosome or segment are inherited from father secondary to nondisjunctionDiagnostic testing11% UBE3A mutations78% methylation parent-specific abnormalityAngelman Syndrome Autosomal dominant Gene is paternally expressed Affec

37、ted when mutation inherited from father NOT affected when mutation inherited from motherPrader-Willi SyndromeEarly infancy: Severe hypotoniaFeeding difficultiesLater infancy and early childhood:Excessive eatingMorbid obesityCognitive impairment Prader-Willi Syndrome1-2% Mutation: affected only when

38、mutation inherited from father; maternal gene is normal70% 15q11.2-q13 microdeletion: affected if active gene is deleted from paternal chromosome; maternal gene is normal30% uniparental disomy: affected if both copies of chromosome or segment are inherited from mother secondary to nondisjunctionDiag

39、nostic testing99% methylation parent-specific abnormalityPrader-Willi SyndromeIn-frame mutation: A mutation that does not cause a shift in the triplet reading frame; such mutations can, however, lead to the synthesis of an abnormal protein product Frameshift mutation: An insertion or deletion involv

40、ing a number of base pairs that is not a multiple of three and consequently disrupts the triplet reading frame, usually leading to the creation of a premature termination (stop) codon and resulting in a truncated protein product Deletion/Insertion In Coding RegionBMDDMDConsequence of Deletion In Dyt

41、rophin GeneDuplication: The presence of an extra segment of DNA, resulting in redundant copies of a portion of a gene, an entire gene, or a series of genes, usually caused by unequal crossing-over during gene replication when gametes are formed in meiosisChanges in gene dosageDuplicationDAX1重復(fù)導(dǎo)致性別發(fā)育

42、異常 Type of Gene MutationsPoint Mutation Deletion Insertion Dynamic MutationSplicing Mutation Regulatory MutationType of Gene MutationsPromoter mutationsLead to increased or decreased levels of transcriptionMutations within the exonCause changes of amino acid sequence or premature termination of tran

43、slationMutations at intron-exon bordersMay affect the splicing process Wild-Type Allele M Y I Q I S H I G H ATG TAC ATC CAG ATA TCC CAT ATT GGC CAC Samesense or Silent Mutation M Y I Q I S H I G H ATG TAC ATC CAG ATA TCC CAC ATT GGC CAC Nonsense Mutation M Y I X I S H I G H ATG TAC ATC TAG ATA TCC C

44、AT ATT GGC CAC Missense Mutation M Y L Q I S H I G H ATG TAC CTC CAG ATA TCC CAT ATT GGC CAC Frameshift Mutation M Y S R Y P I L A T ATG TAC TCC AGA TAT CCC ATA TTG GCC AC Dynamic Mutation M Y I Q Q Q Q Q Q I S H I G H ATG TAC ATC CAG CAG CAG CAG CAG CAG ATA TCC CAT ATT GGC CACMutations In Coding Se

45、quencesHave an impact on protein functionHave no impact on protein functionMay create a cryptic splice site leading to abnormal splicingLead to premature termination of translation Alter the amino acid sequence, and usually results in production of a stop codon A mutation that substitutes amino acid

46、s of similar chemical properties is described as conservative. Mutations In Coding SequencesPAH突變譜 （PKU）中國鑒定出60多種突變，大多數(shù)為中國人特有的突變珠蛋白基因突變譜 （地中海貧血）珠蛋白基因調(diào)控突變 （HPFH）珠蛋白基因突變頻率Missense Mutations Most amino acid substitutions probably have no effect on the function of a protein with some exceptionsNonsense

47、Mutations Trigger nonsense mediated decay or not?Splicing Mutations Splice sites can be strong or weak. Splicing enhancer or suppressor sequences modulate the strength of an adjacent splice site by binding proteins of the SR and hRNP Splicing MutationsSplicing MutationsFrameshift MutationsNormal L G

48、 G V N CTG GGG GGT GTG AACMutant L G V STOP CTG GGG GTG TGAEXON 1EXON 2Figure 13.15 A simple frameshiftA frameshiting deletion of one nucleotide in the GJB2 gene arises through replication slippage in a run of six G nucleotides. The mutation creates a premature stop codon in exon 2.Pathogenic Silent

49、 MutationsDynamic MutationsA special class of pathogenic STRPTrinucleotide repeat: Sequences of three nucleotides repeated a number of times in tandem within a gene. Normal polymorphic variation in repeat number with no clinical significance commonly occurs between individuals. Abnormally large alle

50、les are classified in increasing order of size as mutable normal allelesreduced penetrance allelesfull penetrance alleles e intensely unstable above a certain size repeat expansion動(dòng)態(tài)突變：脆X綜合征動(dòng)態(tài)突變：脆X綜合征 Expanded CGG repeat in Fragile X syndrome動(dòng)態(tài)突變一覽表（1）動(dòng)態(tài)突變一覽表（2）A phenomenon in which disease severity

51、 increases and/or age of onset of disease decreases from one generation to the next.Often observed in disorders resulting from the expression of a trinucleotide repeat mutation that tends to increase in size and have a more significant effect when passed from one generation to the next Anticipation

52、調(diào)控序列的突變Miao Sun, et al. J. Med. Genet. published online 16 Apr 2008; doi:10.1136/jmg.2008.0576467q36i5979 kbAn alteration in a gene that is present for the first time in one family member as a result of a mutation in a germ cell (egg or sperm) of one of the parents or in the fertilized egg itself De

53、 Novo Mutation De Novo MutationThe presence of an altered gene within the egg or sperm (germ cell), such that the altered gene can be passed to subsequent generations Germline Mutation Mutation NomenclatureAmino Acid SubstitutionInitiator methionine is codon 1;p.Arg117His or p.R117H : replace argini

54、ne by histidine;p.Gly542X or p.G542X : glycine 542 replaced by a stop codon.Nucleotide SubstitutionsThe A of the initiator ATG codon is +1;The immediate preceding base is 1;c.1162GA: replace guanine at position 1162 by adenine.Deletions and Insertionsp.Phe508del or p.F508del: delete phenylalanine 50

55、8;c.6232-6236del or c.6232-6236delATAAG: delete 5 nucleotides starting with nt 6232;c.409-410insC: insert C between nt 409 and 410c. for a coding DNA sequence (like c.76AT)g. for a genomic sequence (like g.76AT)m. for a mitochondrial sequence (like m.8993TC)r. for an RNA sequence (like r.76au)p. for

56、 a protein sequence (like p.K76A) Numbering coding DNA Reference Sequence 1. There is no nucleotide 0 2. Nucleotide 1 is the A of the ATG-translation initiation codon 3. The nucleotide 5 of the ATG-translation initiation codon is -1 4. The nucleotide 3 of the translation stop codon is *1 5. Intronic

57、 nucleotides:beginning of the intron; the number of the last nucleotide of the preceding exon, a plus sign and the position in the intron, like c.77+1G, c.77+2T, etc.end of the intron; the number of the first nucleotide of the following exon, a minus sign and the position upstream in the intron, lik

58、e c.78-1G.in the middle of the intron, numbering changes from c.77+. to c.78-.; for introns with an uneven number of nucleotides the central nucleotide is the last described with a +Description of Mutations at DNA LevelSubstitutions: c.76AC denotes that at nucleotide 76 an A is changed to a CDeletio

59、ns: c.76_78del (alternatively c.76_78delACT) denotes a ACT deletion from nucleotides 76 to 78 Duplications: c.77_79dup (or c.77_79dupCTG, c.77_79dup3) denotes that the three nucleotides 77 to 79 are duplicated Insertions: c.76_77insT denotes that a T is inserted between nucleotides 76 and 77 of the

60、coding DNA reference sequence Insertions / deletions (indels): c.112_117delinsTG (alternatively c.112_117delAGGTCAinsTG) denotes the replacement of nucleotides 112 to 117 (AGGTCA) by TG Inversions: c.203_506inv (or 203_506inv304) denotes that the 304 nucleotides from position 203 to 506 have been in