COM.on C.A.4:e6/34-41
Online published on Jun.2, 2010.WANG Chuanchao,LI Hui
MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China.
Key words: Ancient DNA, Molecular cloning, Polymerase chain reaction (PCR), Next generation DNA sequencing techniques, Primer extension capture (PEC), Array hybridization capture(AHC).
Recieved: May.10, 2010 Accepted: May.25, 2010 Corresponding: lihui.fudan@gmail.com
《现代人类学通讯》第四卷e6篇 第34-41页 2010年6月2日网上发行
专题综述
古DNA分析技术发展的三次革命
王传超, 李辉
复旦大学现代人类学教育部重点实验室,上海200433.
摘要:古DNA研究以分子生物学技术为基础,以古生物的DNA为研究对象,是一个新兴领域。20余年来,古DNA实验技术不断发展。分子克隆、PCR、下一代测序技术、引物延伸捕获和芯片杂交捕获等扩增和测序技术的不断涌现,分别引领了古DNA研究的三次革命,极大推动古DNA研究发展、成熟。从229bp斑驴的mtDNA到尼安德特人基因组草图,古DNA研究取得一系列的突出成果, 解开了众多千万年来的谜题。
关键词:古DNA;分子克隆;聚合酶链式反应(PCR);下一代测序技术;引物延伸捕获(PEC);芯片杂交捕获(AHC)
参考文献 References
1.Poinar HN (1999)
DNA from fossils : The past and the
future. Acta Paediat rica. 88
:133-140.
2.Hofreiter M, Serre D, Poinar HN, Kuch
M, Pääbo S (2001)
Aneient DNA. Nat Rev Genet
2:353-359.
3.Willerslev E, Cooper A (2005)
Ancient DNA. Proc Biol Sci 272:3-16.
4.Hunan Medical College (1981) Study of
an ancient cadaver in Mawangtui tomb No.
1 of the Han Dynasty in Changsha. New
York : Ancient Memorial Press.184-187.
5.Higuchi R,Bowman B,Freiberger M,Ryder
OA,Wilson AC (1984)
DNA sequences from the quagga,an extinct
member of the horse family. Nature
312:282-284.
6.Pääbo S (1985)
Molecular cloning of Aneient Egyptian
mummy DNA. Nature 314:644一645.
7.Handt O,Richards M,Trommsdorff
M,Kilger C, Simanainen J, Georgiev O,
Bauer K, Stone A, Hedges R, Schaffner W
(1994)
Molecular genetic analyses of the
Tyrolean Ice Man. Science
264:1775-1778.
8.Handt O, Krings M, Ward RH, Pääbo S
(1996)
The retrieval of ancient human DNA
sequences.
Am J Hum Genet 59:368-376.
9.Graziano P,Cecilia S (2001)
A Novel method for estimating
substitution rate variation among sites
in a large dataset of homologous DNA
sequences.
Genetics 157:859-865.
10.Wandeler P, Smith S, Morin PA,
Pettifor RA, Funk SM (2003)
Patterns of nuclear DNA Degeneration
over time-a case study in historic teeth
samples. Mol Ecol 12:1087-1093.
11.Pääbo S, Higuchi RG, Wilson AC (1989)
Aneient DNA and the polymerase chain
reaction.The emerging field of molecular
archaeology. J Biol Chem
264:9709-9712.
12.Greer S, Zamenhof S (1962)
Studies on depurination of DNA by heat.
J Mol Biol 4:123-141.
13.Poinar HN (2002)
The genetic secrets some fossils hold.
Acc Chem Res 35:676-684.
14.Saiki RK, Scharf S, Faloona F, Mullis
KB, Horn GT, Erlich HA, Arnheim N (1985)Enzymatic
amplification of beta-globin genomic
sequences and restriction site analysis
for diagnosis of sickle cell anemia.
Science 230:1350 -1354.
15.Mullis KB, Faloona FA (1987)
Specific synthesis of DNA in vitro via a
polymerase-catalyzed chain reaction.
Methods Enzymol 155:335-350.
16.Pääbo S, John A. Gifford, Allan C
(1988)
Wilson Mitochondrial DNA sequences from
a 7000-year old brain. Nucleic Acids
Research 16(20): 9775-9787.
17.Golenberg EM, Giannasi DE, Clegg MT,
Smiley CJ, Durbin M (1990)
Chloroplast DNA sequence from a miocene
Magnolia species. Nature
344:656-658.
18.Woodward SR, Weyand NJ, Bunnell M
(1994)
DNA sequence from Cretaceous period Bone
fragments. Science 266:1229-1232.
19.Desalle R, Gatesy J, Wheeler W,
Grimaldi D (1992)
DNA sequences from a fossil termite In
Oligo-Miocene amber and their
phylogenetic implications. Science
257:1933-1936.
20.Desalle R, Bareia M, Wray C (1993)
PCR jumping in clones of
30-million-year-old DNA fragments from
amber preserved termites (Mastotermes
electrodominicus).
Experientia 49:906-909.
21.Handt O, Hss M, Krings M, Pbo S
(1994)
Aneient DNA: methodological challenges.
ExPerientia 50:524-529.
22.Poinar HN, Hss M, Bada JL, Pbo S
(1996)
Amino acid racemization and the
preservation of aneient DNA. Science
272:864-866.
23.Kumar SS, Nasidze I, Walimbe SR,
Stoneking M (2000)
Brief communication: discouraging
prospects for aneient DNA from India.
Am J Phys Anthropol 113:129-133.
24.徐智(2008)中国西北地区古代人群的DNA研究.博士毕业论文.复旦大学.
25.Gutierrez G, Marin A (1998)
The most ancient DNA reeovered from
anamber-preserved specimen may not be as
ancient as it seems. Mol Biol Evol
15:926-929.
26.Cano RJ, Poinar HN, Pieniazek NJ,
Acra A, Poinar GO (1993)
Amplification and sequencing of DNA from
a 120–135-million-year-old weevil.
Nature 363:536–538.
27. Ohuchi S, Nakano H, Yamane T (1998)
In vitro method for the generation of
protein libraries using PCR
amplification of a single DNA molecule
and coupled transcription/translation.
Nucleic Acids Res 26(19):4339-434
28.Nakano M, Komatsu J, Matsuura S,
Takashima K, Katsura S, Akira Mizuno
(2003)
Single-Molecule PCR using water-in-oil
emulsion. J Biotechnol 102:117-124.
29.Rmpler H, Dear PH, Krause J, Meyer
M, Rohland N, Schneberg T, Spriggs H,
Stiller M, Hofreiter M (2006)
Multiplex amplification of ancient DNA.
Nat Protoc 1(2) : 720-728.
30.Krause J , Dear P H , Pollack J L,
Slatkin M, Spriggs H, Barnes I, Lister
AM, Ebersberger I, Pbo S, Hofreiter M
(2006)
Multiplexed amplification of the mammoth
mitochondrial genome and the evolution
of Elephantidae. Nature 439:724-727.
31.Endicott P, Metspalu M, Stringer C,
Macaulay V, Cooper A, Sanchez J (2006)
Multiplexed SNP typing of ancient DNA
clarifies the origin of andaman mtDNA
haplogroups amongst South Asian tribal
populations.
PloS ONE 1:e81.
32.Cooper A (2006)
The year of the mammoth. PLoS Biol.
4:e78
33.Margulies M, Egholm M, Altman W E
(2005)
Genome sequencing in microfabricated
high idensity picolitre reactors.
Nature 437: 376-380.
34.Ju J,Kim DH,Bi L, Meng QL, Bai XP ,
Li ZM, Li XX, Marma MS, Shi S, Wu J,
Edwards JR, Romu A, Turro NJ (2006)
Four-color DNA sequencing by synthesis
using cleavable fluorescent nucleotide
reversible terminators. Proc Natl
Acad Sci USA 103:19635-19640.
35.Shendure J , Porreca GJ , Reppas NB ,
Lin XX, McCutcheon JP, Rosenbaum AM,
Wang MD, Zhang K, Mitra RD, Church GM
(2005)
Accurate multiplex polony sequencing of
an evolved bacterial genome.
Science 309:1728-1732.
36.Mitchelson KR (2007) New high
throughput technologies for DNA
sequencing and genomics.
Capitalbio Corporation Beijing
China:1-20.
37.Korlach J , Marks P J , Cicero R L ,
et al (2008)
Selective aluminum passivation for
targeted immobilization of single DNA
polymerase molecules in zero mode
waveguide nanostructures. Proc Natl
Acad Sci USA , , 105 (4) : 1176-1181
38.Handelsman J, Rondon MR, Brady SF,
Clardy J, Goodman RM (1998)
Molecular biological acccss to the
chemistry of unkown soil microbes:a new
frontier for natural products.
Chem.Biol 5(10):245-249.
39.Hoelzel AR (2005)
Ancient genomes. Genome Biology
6:239.
40.Noonan JP, Hofreiter M, Smith D,
Priest JR, Rohland N (2005)
Genomic sequencing of Pleistocene cave
bears. Science 309:597-599.
41.Green RE,Krause J,Ptak SE,Briggs
AW,Ronan MT, Simons JF, Du L, Egholm M,
Rothberg JM, Paunovic M, Pääbo S (2006)
Analysis of one million base pairs of
Neanderthal DNA.
Nature 444:330-336.
42.Poinar HN, Schwarz C, Qi J, Shapiro
B, Macphee RD, Buigues B, Tikhonov A,
Huson DH, Tomsho LP, Auch A, Rampp M,
Miller W, Schuster SC (2006)
Metagenomics to paleogenomics:
large-scale sequencing of mammoth DNA.
Science 311:392-394.
43.Blow MJ, Zhang T, Woyke T, Spelle CF,
Krivoshapkin A, Yang DY, Derevianko A,
Rubin EM (2008)
Identifieation of the source of ancient
remains through genomic sequeneing.
Genome Res 18: 1347-1353
44.Bentley DR, Balasubramanian S,
Swerdlow HP, Smith GP, Milton J(2008)
Accurate whole human genome sequencing
using reversible terminator chemistry.
Nature 456:53-59
45.Green RE, Malaspinas AS, Krause J,
Briggs AW, Johnson PL,et al.(2008)
A Complete Neandertal mitochondrial
genome sequence determined by
high-through put sequencing.
Cell 134:416-426.
46.Gilbert MT, Drautz DI, Lesk AM, Ho
SY,Qi J (2008)
Intraspecific phylogenetic analysis of
Siberian woolly mammoths using complete
mitochondrial genomes. Proc Natl
Aead Sci USA 105:8327-8332.
47.Mardis ER (2008)
Next-generation DNA sequencing methods.
Annu Rev Genomics Hum Genet
9:387-402.
48.Millar CD, Huynen L, Subramanian S,
Mohandesan E, Lambert DM (2008)
New evelopments in ancient genomics.
Trends Ecol Evol. 23(7):386-93.
49.Rasmussen M, Li YR, Lindgreen S,
Pedersen JS, Albrechtsen A,Moltke I,
Metspalu M, Metspalu E, Kivisild T,
Gupta R, Bertalan M, Nielsen K, Gilbert
MTP, Wang Y, Raghavan M, Campos PF, Kamp
HM, Wilson AS, Gledhill A, Tridico11 S,
Bunce M, Lorenzen ED, Binladen J, Guo
XS, Zhao J, Zhang XQ, Zhang H, Li Z,
Chen MF, Orlando L, Kristiansen K, Bak
M, Tommerup N, Bendixen C, Pierre TL,
Grnnow B, Meldgaard M, Andreasen C,
Fedorova SA, Osipova LP, Higham TFG,
Ramsey CB, Hansen TO,Nielsen FC,
Crawford MH, Brunak S, Sicheritz-Ponten
T, Villems R,Nielsen R, Krogh A, Wang J,
Willerslev E (2010)
Ancient human genome sequence of an
extinct Palaeo-Eskimo. Nature
463:757-762.
50.Briggs AW, Good JM, Green RE, Krause
J, Maricic T, Stenzel U, Lalueza-Fox C,
Rudan P, Brajkovi D, Kuan , Gui I,
Schmitz R, Doronichev VB, Golovanova LV,
Rasilla M, Fortea J, Rosas A, Pbo S
(2009)
Targeted Retrieval and Analysis of Five
Neandertal mtDNA Genomes. Science
325:318-321.
51.Krause J, Fu Q, Good JM, Viola B,
Shunkov MV, Derevianko AP, Pbo S
(2010)
The complete mitochondrial DNA genome of
an unknown hominin from southern Siberia.
Nature 464:894-897.
52.Hodges E, Xuan ZY, Balija V, Kramer
M, Molla MN, Smith SW, Middle CM,
Rodesch MJ, Albert TJ, Hannon1 GJ,
McCombie WR(2007)
Genome-wide in situ exon capture for
selective resequencing. Nature
Genetics 39:1522 – 1527.
53.Hodges E, Rooks M, Xuan ZY,
Bhattacharjee A, Gordon DB, Brizuela L,
McCombie WR, Hannon GJ(2009)
Hybrid selection of discrete genomic
intervals on custom-designed microarrays
for massively parallel sequencing.
Nature Protocols 4:960-974.
54.Burbano HA, Hodges E, Green RE,
Briggs AW, Krause J, Meyer M, Good JM,
Maricic T, Johnson PLF, Xuan ZY, Rooks
M, Bhattacharjee A, Brizuela L, Albert
FW, Rasilla de la M, Fortea J, Rosas A,
Lachmann M, Hannon GJ, Pbo S (2010)
Targeted Investigation of the Neandertal
Genome by Array-Based Sequence Capture.
Science 328:723-725.
55.Green RE, Krause J, Briggs AW,
Maricic T, Stenzel U, Kircher M,
Patterson Nick, L i H, Zhai WW,Fritz
MHY, Hansen NF, Durand EY, Malaspinas
AS, Jensen JD, Marques-Bonet T, Alkan C,
Prüfer Kay, Meyer M, Burbano HA, Good
JM, Schultz R, Aximu-Petri A, Butthof A,
Hber B, Hffner B, Siegemund M,
Weihmann A, Nusbaum C, Lander ES, Russ
C, Novod N, Affourtit J, Egholm M, Verna
C, Rudan P, Brajkovic Dejana, Kucan Ž,
Gušic I, Doronichev VB, Golovanova LV,
Lalueza-Fox C, Rasilla M, Fortea J,
Rosas A, Schmitz RW, Johnson PLF,
Eichler EE, Falush D, Birney E, Mullikin
JC, Slatkin M, Nielsen R, Kelso J,
Lachmann M, Reich D, Pbo S (2010)
A draft sequence of the Neandertal
genome. Science 328:710-722.