1、General organization of the human genome,20 000,Organization of the human genome,Genome structure Nuclear vs. mitochondrial genomes Gene families Transposable elements Other repeated sequences,Organization of the human genome,Nuclear genome 3000 Mb 23 (XX) or 24 (XY) linear chromosomes 20-23,000 gen

2、es 1 gene/40kb Introns 3% coding Repetitive DNA sequences (45%) Recombination Mendelian inheritance (X + auto, paternal Y),Organization of the human genome,Contrasting gene densities Some regions of the genome are gene-rich and others are gene-poor HLA high density Dystrophin low density,Histone gen

3、e distribution,Gene Structure and Expression,2.2 Gene and genome,Human Gene Intron Structure,15 nt,7 nt,6 nt,Gene Sizes Vary a Lot,Organization of the human genome,Gene families Thought to be generated by gene duplication Functionally similar genes are occasionally clustered, but usually dispersed t

4、hroughout the genome,Organization of the human genome,Genes vary in size and exon content A general inverse relationship.,09_07.jpg,Exon content vs. length,09_07_2.jpg,09_07_3.jpg,Organization of the human genome,Genes within genes Intron 26 of the NF1 gene contains three internal genes.,Organizatio

5、n of the human genome,Gene families: defined by extensive DNA similarity Alpha and Beta globin genes defined by large highly conserved domains defined by conserved amino acid motifs DEAD box WD repeats,Organization of the human genome,Superfamilies Common structural features Ig superfamily Cell surf

6、ace receptors,Organization of the human genome,HLA heavy chain gene cluster: an example Gene fragments Pseudogenes Truncated genes,Organization of the human genome,Processed pseudogenes Originate by reverse transcription of a processed transcript TPRT,Organization of the human genome,Mitochondrial g

7、enome: Origin Endosymbiont Hypothesis Ancient archaeal cell engulfed a proteobacterium and eventually came to rely on the symbiont for survival. Evidence Circular genome Autonomous ribosomes,Organization of the human genome,Mitochondrial genome Small (16.5 kb) circular DNA 1 gene/0.45 kb Very few re

8、peats No introns 93% coding Heavy and Light strands,Organization of the human genome,Mitochondrial genes rRNA, tRNA and protein encoding genes (37) 28 encoded by the heavy strand 24 RNA products and (23s, 16s, tRNAs) 13 protein coding genes,Organization of the human genome,Mitochondrial genes rRNA,

9、tRNA and protein encoding genes (37) 28 encoded by the heavy strand 24 RNA products and (23s, 16s, tRNAs) 13 protein coding genes Genes are transcribed as two transcription units and cleaved afterwards Genes may overlap,Organization of the human genome,Limited autonomy of mt genomesmt encodednuclear

10、 NADH dehydrog 7 subunits41 subunits Succinate CoQ red0 subunits4 subunits Cytochrome b-c1 comp1 subunit10 subunits Cytochrome C oxidase 3 subunits10 subunits ATP synthase complex2 subunits14 subunits tRNA components22 tRNAsnone rRNA components 2 componentsnone Ribosomal proteins none 80 Other mt pr

11、oteinsnonemtDNA pol, RNA pol etc.,Organization of the human genome,Special Features Mitochondrial genetic code (reduced selection) Two extra stop codons: AGA and AGG UGA = tryptophan, AUA = Methionine/start No recombination Maternal inheritance,Organization of the human genome,Mitochondrial genome r

12、eplication OH Origin of heavy strand replication OL Origin of light strand replication D-loop,2.7 Polymorphism,Multiple functional alleles at a frequency of 1% in a population A population may have extensive polymorphism at the level of genotype It may offer a diagnostic procedure for detecting the

13、disease It may lead to isolation of the gene,Restriction Fragment Length Polymorphism (RFLP),Short Tandem Repeat Polymorphism (STRP) / microsatellite marker,A polymorphic locus consisting of a variable number of tandemly repeated binucleotide, trinucleotide, or tetranucleotide units such as (TG)n, (

14、CAA)n, or (GATA)n,Single Nucleotide Polymorphism (SNP) A polymorphism in DNA sequence consisting of variation in a single base. Single Nucleotide Variation (SNV) A variation in DNA sequence consisting of a single base.,DNA Mutation,Mutations change the sequence of DNA: Spontaneous and induced; Germ-

15、line and somatic; Large scale and small scale Point mutations (nucleotide substitutions), deletions, insertions.,DNA Mutation,(1) Nucleotide Substitutions (Point Mutations) Missense mutations (amino acid substitutions) Nonsense mutations (premature stop codons) RNA processing mutations (destroy cons

16、ensus splice sites, cap sites, and polyadenylation sites or create cryptic sites) Splice-site mutations leading to Indel, frameshift mutations and premature stop codons. Regulatory mutations affecting transcription factor binding, transcriptional control, or other aspects of gene expression. 6 Silen

17、ce mutations (nucleiotide changed, but not amino acid ） (2) Deletions and Insertions (Indel) Addition or deletion of a small number of bases: Larger scale gene deletions, duplications, and inversions, translocation, fusions : Expansion of trinucleotide repeat sequences: dynamic mutation,Where can a

18、mutation locate?,Important to understand each type of mutations! - check the textbook,Gene Structure, Expression and Mutations,2.2 Gene and genome,Regulatory mutations,Missense Nonsense Indel Frameshift Trinucleotide repeat Expansion mutations,-AAAAA,“CAP”-,Splice-site mutation,Point mutation,HbS-CC

19、T GTG GAG- -Pro Val Glu-,HbA-CCT GAG GAG- -Pro Glu Glu-,Sickle cell anemia,Splicing Mutation,Gene Fusion,Mechanism of Large Scale Indel,More to Learn about Human Genome,“a complete human pan-genome would contain 1940Mb of novel sequence not present in the extant reference genome.”,28, 5763 (2010),A

20、Personal Genome = Reference genome + Read alignment + SNP/indel calls? +Segmental insertions/deletions/inversions/Complex rearrangements +Individual-specific sequences,Personal genome is personalized.,After all, you need a De Novo assembled genome for every individual!,Pilot project have identified

21、15M SNPs including 8.5M novel SNPs (left) Most novel SNPs are population specific (right),Nature. 464, 59-65(2010).,Our “other” Genome: Metagenomics,Metagenomics Research the study of metagenomes, genetic material recovered directly from environmental samples. The broad field may also be referred to

22、 as environmental genomics, ecogenomics or community genomics. Traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures. This relatively new field of genetic research enables studies of organisms that are not easily cultured in a laboratory as well as studies of

23、organisms in their natural environment.,Journal of Microbiological Methods. 79, 266-271(2009).,Nature. 464, 59-65(2010).,Andrologia. 40, 6671(2008).,PLoS ONE. 4, e4219(2009).,Genome Research. 18, 10431050(2008).,Metagenomics analysis of human disease,10 X human cells, 100 X human genes!,Microbial co

24、mmunity composition at different body locations in a healthy human,Gut microbial dysbiosis associated with disease,Assembly and stability of the gut microbiota, and environmental factors affecting the gut microbiome during life,Host genetic variants, their effects on the composition of the gut micro

25、biota, and the corresponding host disease state,International Human Genome Project (1990-2003),Genome: Blueprint of Life,Participant countries: USA, UK, GE, FR, JP, CN,Human Genome Project,Human genetic maps: Genetic maps are based on recombination frequencies between markers. Centimorgan: The dista

26、nce on a DNA molecule which have 1% recombinant frequency. 1 cM =1000kb. Physical Mapping: The physical maps depend on their physical distance apart on a DNA molecule. For example: Restriction Endonuclease physical map. DNA sequence itself is the finest physical map. markers RFLP markers: The first

27、human genetic marker map. Microsatellite markers: High resolution human genetic marker map. SNP: A new generation of human genetic marker map STS: sequence-tagged site. A short DNA sequence, readily located and amplified by PCR, that uniquely identifies a physical genomic location. Expressed sequenc

28、e tags (ESTs) are STSs obtained from cDNAs.,Center for Genomics, CAS GI was established in Aug, 1998,Bioinformatics Center, CAS / Huada Genome Center was established in Sept, 1999,寸草成簇根始深，寒冬未過(guò)便知春。 五駿齊趨何須顧，此行萬(wàn)里追鵬鯤。,立石銘 蒼天在上磐石作證此時(shí)此地一群普普通通的炎黃子孫用他們的淚汗心血和青春為他們古老的民族爭(zhēng)得了一個(gè)險(xiǎn)些失去的歷史機(jī)遇歲月無(wú)情他們和他們的支持者都將隨時(shí)光而逝去此心昭昭他

29、們的執(zhí)著奉獻(xiàn)和自信必將作為人類(lèi)基因圖的一小部分留駐歷史 楊煥明 一九九九年九月九日九時(shí)九分 華大成立,Important points of HVP,3000 mb, 20,000-25,000 genes Physical mapping STS / EST Genetic mapping Centigorgan: 1 cM = 1000kb Mapping marker: RFLP Microsatellite SNP,HGP to HapMap to HVP,10%,? %,1%,BIO-BANK AND GENETIC DATABASE OF MAJOR DISEASES IN CHI

30、NA,Ming Qi, PhD, FACMG, Dip ABMG Center for Genetic & Genomic Medicine James Watson Institute of Genomic Sciences & Medical School of Zhejiang University University of Rochester Medical Center,McGill University, Canada Feb 10, 2010,Initiation of HVP (China Consortium),Genetic & Genomic Medicine Anal

31、ytic Platform: ZJU CGGM Database & Bioinformatic Platform: Nat CompSci Ctr at ZJU Chinese Student Volunteer Club, internet-teleconference,HVP LOVD-CHINA,Understanding the Structure of Genomes,Understanding the Biology of Genomes,Understanding the Biology of Disease,Advancing the Science of Medicine,

32、Improving the Effectiveness of Healthcare,1990-2003 Human Genome Project,2004-2010,Genomic Accomplishments Across Domains,Courtesy from Eric Green, Director, NHGRI,Dr. Jim Watson s, Genome Sequenced for 2 Million Dollars announced on 5/30/2007,Cardiovascular genes,Tumer suppressor genes,Capability genes,Antitoxin genes,Alzheimer disease gene,co-discoverers of the structure of DNA,Dr. Venters Genome- Mapping own DNA changes scientists life,4.1 million DNA variants, 3,213,401 SNPs 22% events CNV, involved 74% bases His fathers fatal heart atta