The Genom of Homo sapiens.pdf

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CENTROMERE ANNOTATION 149Schueler M.G., Higgins A.W., Rudd M.K., Gustashaw K., andWillard H.F. 2001. Genomic and genetic definition of a functionalhuman centromere. Science 294: 109.Skaletsky H., Kuroda-Kawaguchi T., Minx P.J., Cordum H.S.,Hillier L., Brown L.G., Repping S., Pyntikova T., Ali J., BieriT., Chinwalla A., Delehaunty A., Delehaunty K., Du H.,Fewell G., Fulton L., Fulton R., Graves T., Hou S.F., LatrielleP., Leonard S., Mardis E., Maupin R., McPherson J., andMiner T., et al. 2003. The male-specific region of the humanY chromosome is a mosaic of discrete sequence classes. Nature423: 825.Smith G.P. 1976. Evolution of repeated DNA sequences by unequalcrossover. Science 191: 528.Sonnhammer E.L. and Durbin R. 1995. A dot-matrix programwith dynamic threshold control suited for genomic DNA andprotein sequence analysis. Gene 167: 1.Spence J.M., Critcher R., Ebersole T.A., Valdivia M.M., EarnshawW.C., Fukagawa T., and Farr C.J. 2002. Co-localizationof centromere activity, proteins and topoisomerase II within asubdomain of the major human X alpha-satellite array. EMBOJ. 21: 5269.Stankiewicz P. and Lupski J.R. 2002. Molecular-evolutionarymechanisms for genomic disorders. Curr. Opin. Genet. Dev.12: 312.Sullivan B.A. and Willard H.F. 1998. Stable dicentric X chromsomeswith two functional centromeres. Nat. Genet. 20: 227.Sullivan B.A., Blower M.D., and Karpen G.H. 2001. Determiningcentromere identity: Cyclical stories and forking paths.Nat. Rev. Genet. 2: 584.Sun X., Le H.D., Wahlstrom J.M., and Karpen G.H. 2003. Sequenceanalysis of a functional Drosophila centromere.Genome Res. 13: 182.Tanaka T.U. 2002. Bi-orienting chromosomes on the mitoticspindle. Curr. Opin. Cell Biol. 14: 365.Trask B.J. 2002. Human cytogenetics: 46 chromosomes, 46years and counting. Nat. Rev. Genet. 3: 769.Tyler-Smith C., Oakey R.J., Larin Z., Fisher R.B., Crocker M.,Affara N.A., Ferguson-Smith M.A., Muenke M., Zuffardi O.,Jobling M.A. 1993. Localization of DNA sequences requiredfor human centromere function through an analysis of rearrangedY chromosomes. Nat. Genet. 5: 368.Vafa O. and Sullivan K.F. 1997. Chromatin containing CENP-Aand alpha satellite DNA is a major component of the innerkinetochore plate. Curr. Biol. 7: 897.Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., SuttonG.G., Smith H.O., Yandell M., Evans C.A., Holt R.A.,Gocayne J.D., Amanatides P., Ballew R.M., Huson D.H.,Wortman J.R., Zhang Q., Kodira C.D., Zheng X.H., Chen L.,Skupski M., Subramanian G., Thomas P.D., Zhang J., GaborMiklos G.L., and Nelson C., et al. 2001. The sequence of thehuman genome. Science 291: 1304.Warburton P.E. and Willard H.F. 1990. Genomic analysis of sequencevariation in tandemly repeated DNA. Evidence for localizedhomogenous sequence domains within arrays of alphasatelliteDNA. J. Mol. Biol. 216: 3._______ . 1995. Interhomologue sequence variation of alphasatellite DNA from human chromosome 17: Evidence forconcerted evolution along haplotypic lineages. J. Mol. Evol.41: 1006._______ . 1996. Evolution of centromeric alpha satellite DNA:Molecular organization within and between human and primatechromosomes. In Human genome evolution (ed. S.T.Jackson and G. Dover), p. 121. BIOS Scientific Publishers,Oxford, United Kingdom.Waterston R.H., Lindblad-Toh K., Birney E., Rogers J., AbrilJ.F., Agarwal P., Agarwala R., Ainscough R., AlexanderssonM., An P., Antonarakis S.E., Attwood J., Baertsch R., BaileyJ., Barlow K., Beck S., Berry E., Birren B., Bloom T., BorkP., Botcherby M., Bray N., Brent M.R., Brown D.G., andBrown S.D., et al. (Mouse Genome Sequencing Consortium).2002. Initial sequencing and comparative analysis of themouse genome. Nature 420: 520.Waye J.S. and Willard H.F. 1986. Structure, organization, andsequence of alpha satellite DNA from human chromosome17: Evidence for evolution by unequal crossing-over and anancestral pentamer repeat shared with the human X chromosome.Mol. Cell. Biol. 6: 3156.Wevrick R. and Willard H.F. 1989. Long-range organization oftandem arrays of alpha satellite DNA at the centromeres ofhuman chromosomes: High frequency array-length polymorphismand meiotic stability. Proc. Natl. Acad. Sci. 86: 9394._______ . 1991. Physical map of the centromeric region of humanchromosome 7: Relationship between two distinct alpha satellitearrays. Nucleic Acids Res. 19: 2295.Wevrick R., Earnshaw W.C., Howard-Peebles P.N., and WillardH.F. 1990. Partial deletion of alpha satellite DNA associatedwith reduced amounts of the centromere protein CENP-B in amitotically stable human chromosome rearrangement. Mol.Cell. Biol. 10: 6374.Willard H.F. 1998. Centromeres: The missing link in the developmentof human artificial chromosomes. Curr. Opin. Genet.Dev. 8: 219.Willard H.F. and Waye J.S. 1987. Hierarchical order in chromosome-specifichuman alpha satellite DNA. Trends Genet. 3:192.Willard H.F., Smith K.D., and Sutherland J. 1983. Isolation andcharacterization of a major tandem repeat family from the humanX chromosome. Nucleic Acids Res. 11: 2017.Zhong C.X., Marshall J.B., Topp C., Mroczek R., Kato A., NagakiK., Birchler J. A., Jiang J., and Dawe R.K. 2002. Centromericretroelements and satellites interact with maize kinetochoreprotein CENH3. Plant Cell 14: 2825.
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ForewordIn 2001, as we considered t
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The Finished Genome Sequence of Hom
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4 ROGERSFigure 2. Accumulation of h
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6 ROGERSFigure 4. Sequencing center
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8 ROGERSabcFigure 5. Ensembl view o
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10 ROGERS2000. Analysis of vertebra
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The Human Genome: Genes, Pseudogene
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VARIATION ON CHROMOSOME 7 15rived f
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VARIATION ON CHROMOSOME 7 17DNAs an
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VARIATION ON CHROMOSOME 7 19expecte
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VARIATION ON CHROMOSOME 7 21Drosoph
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Mutational Profiling in the Human G
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HUMAN MUTATIONAL PROFILING 25Anothe
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HUMAN MUTATIONAL PROFILING 27Figure
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HUMAN MUTATIONAL PROFILING 29Rieder
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32 SCHMUTZ ET AL.algorithm itself,
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34 SCHMUTZ ET AL.Figure 2. Genomic
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36 SCHMUTZ ET AL.compared. Some of
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Human Subtelomeric DNAH. RIETHMAN,
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HUMAN SUBTELOMERIC SEQUENCES 41The
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HUMAN SUBTELOMERIC SEQUENCES 43cate
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HUMAN SUBTELOMERIC SEQUENCES 45Figu
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HUMAN SUBTELOMERIC SEQUENCES 47pres
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50 COLLINSand expand the genomics r
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52 COLLINSFigure 2. A public-sector
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54 COLLINSdefine all the parts of t
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56 BENTLEYmon over many generations
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58 BENTLEYTable 1. Genetic Disease
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60 BENTLEY(Clark et al. 1998; Reich
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62 BENTLEYACKNOWLEDGMENTSThe author
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SNP Genotyping and Molecular Haplot
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GENETIC ANALYSIS OF DNA POOLS 67gen
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70 FAN ET AL.matrix is then mated t
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72 FAN ET AL.Figure 3. Views of gen
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74 FAN ET AL.including 32 duplicate
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76 FAN ET AL.Figure 7. Allele-speci
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78 FAN ET AL.microsphere-based assa
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80 BERTRANPETIT ET AL.function, may
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82 BERTRANPETIT ET AL.diversity in
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84 BERTRANPETIT ET AL.gree of block
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86 BERTRANPETIT ET AL.Figure 1. Dec
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88 BERTRANPETIT ET AL.1999. Populat
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90 WINDEMUTH ET AL.Expression data.
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92 WINDEMUTH ET AL.Table 1. A Summa
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94 WINDEMUTH ET AL.Table 2. Signifi
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96 WINDEMUTH ET AL.Table 3. Summary
Page 105 and 106: 98 WINDEMUTH ET AL.Table 6. List of
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Page 111 and 112: 104 WINDEMUTH ET AL.much of a surpr
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Page 116 and 117: Genetic Variation and the Control o
Page 118 and 119: GENETIC CONTROL OF TRANSCRIPTION 11
Page 120 and 121: GENETIC CONTROL OF TRANSCRIPTION 11
Page 122 and 123: Genome-wide Detection and Analysis
Page 124 and 125: RECENT SEGMENTAL DUPLICATIONS 117Fi
Page 126 and 127: RECENT SEGMENTAL DUPLICATIONS 119St
Page 128 and 129: RECENT SEGMENTAL DUPLICATIONS 121Co
Page 130 and 131: RECENT SEGMENTAL DUPLICATIONS 123Ho
Page 132 and 133: The Effects of Evolutionary Distanc
Page 134 and 135: EVOLUTIONARY DISTANCE AND GENE PRED
Page 136 and 137: EVOLUTIONARY DISTANCE AND GENE PRED
Page 138 and 139: Lineage-specific Expansion of KRAB
Page 140 and 141: EVOLUTION OF ZNF GENES 133Figure 2.
Page 142 and 143: EVOLUTION OF ZNF GENES 135Figure 4.
Page 144 and 145: EVOLUTION OF ZNF GENES 137get gene,
Page 146 and 147: EVOLUTION OF ZNF GENES 139Y., Goodw
Page 148 and 149: Sequence Organization and Functiona
Page 150 and 151: CENTROMERE ANNOTATION 143THE CENTRO
Page 152 and 153: CENTROMERE ANNOTATION 145Figure 4.
Page 154 and 155: CENTROMERE ANNOTATION 147CONCLUSION
Page 158 and 159: Evolutionary Strategies of Human Pa
Page 160 and 161: EVOLUTION OF HUMAN PATHOGENS 153Fig
Page 162 and 163: EVOLUTION OF HUMAN PATHOGENS 155rol
Page 164 and 165: EVOLUTION OF HUMAN PATHOGENS 157in
Page 166 and 167: Gene Expression Profiling of Cells,
Page 168 and 169: GENE EXPRESSION PROFILING IN C. ELE
Page 176: GENE EXPRESSION PROFILING IN C. ELE
Page 179 and 180: 172 GUYON ET AL.Table 1. Map Statis
Page 181 and 182: 174 GUYON ET AL.only in one of the
Page 183 and 184: 176 GUYON ET AL.million reads (mean
Page 186 and 187: Positional Identification of Struct
Page 188 and 189: IDENTIFYING LIVESTOCK QTN 181initia
Page 190 and 191: IDENTIFYING LIVESTOCK QTN 183tation
Page 192 and 193: IDENTIFYING LIVESTOCK QTN 185The fa
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Page 197 and 198: 190 GIBBS AND WEINSTOCKBACATLASWGSF
Page 199 and 200: 192 GIBBS AND WEINSTOCKsentation of
Page 201 and 202: 194 GIBBS AND WEINSTOCKCONCLUSIONSE
Page 203 and 204: 196 HAYASHIZAKIFigure 1. Strategy f
Page 205 and 206: 198 HAYASHIZAKIpasses per day. Ther
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200 HAYASHIZAKIto known genes. As s
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202 HAYASHIZAKIaged small amounts o
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204 HAYASHIZAKIanalysis of more tha
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206 ZHANG AND WATERMAN(a)Repeat Rep
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208 ZHANG AND WATERMAN501234301245(
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210 ZHANG AND WATERMANing and Green
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212 ZHANG AND WATERMANACKNOWLEDGMEN
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214 BIRNEY ET AL.Table 1. General I
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Prediction, Annotation, and Analysi
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ANALYSIS OF HUMAN PROMOTERS 219Inte
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ANALYSIS OF HUMAN PROMOTERS 221Figu
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ANALYSIS OF HUMAN PROMOTERS 223nacc
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ANALYSIS OF HUMAN PROMOTERS 225E2F
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228 ASHBURNER ET AL.cally meaningfu
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230 ASHBURNER ET AL.man protein ann
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232 ASHBURNER ET AL.associations be
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234 ASHBURNER ET AL.cabulary for th
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The Genome Knowledgebase: A Resourc
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THE GENOME KNOWLEDGEBASE 239Figure
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THE GENOME KNOWLEDGEBASE 241by the
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THE GENOME KNOWLEDGEBASE 243Karp P.
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246 CHIAROMONTE ET AL.We make no pa
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248 CHIAROMONTE ET AL.Figure 1. Smo
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250 CHIAROMONTE ET AL.can use this
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252 CHIAROMONTE ET AL.However, we c
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254 CHIAROMONTE ET AL.Ihaka R. and
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256 MARGULIES ET AL.HumanMouseFuguR
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258 MARGULIES ET AL.Base Position 1
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260 MARGULIES ET AL.Figure 4. Gener
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262 MARGULIES ET AL.CONCLUSIONSWith
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Comparative Analysis of Human Chrom
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COMPARATIVE GENOMIC ANALYSIS 267aBa
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COMPARATIVE GENOMIC ANALYSIS 269µg
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COMPARATIVE GENOMIC ANALYSIS 271aHu
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COMPARATIVE GENOMIC ANALYSIS 273___
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Genome-wide Analyses Based on Compa
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WHOLE-GENOME COMPARISONS 277Figure
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WHOLE-GENOME COMPARISONS 279Table 2
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WHOLE-GENOME COMPARISONS 281models
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Comparative Genomic Tools for Explo
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COMPUTATIONAL TOOLS FOR ANALYZING G
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294 ROGOZIN ET AL.BeTs are combined
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296 ROGOZIN ET AL.Dm Hs Ce Sc Sp Ec
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298 ROGOZIN ET AL.Dm Ag Hs Ce Sc Sp
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300 ROGOZIN ET AL.gene lossgene gai
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Human-Mouse Comparative Genomics: S
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HUMAN-MOUSE COMPARATIVE GENOMICS 30
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MOUSE KNOCKOUTS ILLUSTRATE FUNCTION
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MOUSE KNOCKOUTS ILLUSTRATE FUNCTION
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318 LIAN ET AL.0 12 34 5 6 78 9 101
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320 LIAN ET AL.90 minutes and the c
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322 LIAN ET AL.Iyer V.I., Horak C.A
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324 LI ET AL.Figure 1. Array-based
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326 LI ET AL.Figure 4. Test of quan
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328 LI ET AL.Figure 5. Comparison o
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Annotation of Novel Proteins Utiliz
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FUNCTIONAL SHOTGUN SEQUENCING 333Fi
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Global Predictions and Tests of Ery
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PREDICTING GENE REGULATORY REGIONS
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Systems Approaches Applied to the S
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SYSTEMS BIOLOGY IN S. CEREVISIAE AN
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360 MERIKANGASidentification of gen
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362 MERIKANGASDay 1984; Ottman 1990
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364 MERIKANGASPrevention Research G
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366 DRAYNA ET AL.Figure 1. Distribu
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368 DRAYNA ET AL.Table 1. Summary o
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370 DRAYNA ET AL.Figure 5. Predicte
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Genomic Variation in Multigenic Tra
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GENOMIC VARIATION IN MULTIGENIC TRA
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384 PORTEOUS ET AL.of these devasta
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386 PORTEOUS ET AL.Figure 2. The t(
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388 PORTEOUS ET AL.Figure 3. DISC1
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390 PORTEOUS ET AL.cgi-bin/hgGatewa
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392 PORTEOUS ET AL.REFERENCESAshers
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394 PORTEOUS ET AL.Valles V., Van O
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396 GOLDSTEIN, CAVALLERI, AND AHMAD
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Genetics of Quantitative Variation
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HUMAN GENE EXPRESSION VARIATION 405
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HUMAN GENE EXPRESSION VARIATION 407
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410 CHIBA-FALEK AND NUSSBAUMconcent
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412 CHIBA-FALEK AND NUSSBAUMTable 4
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414 CHIBA-FALEK AND NUSSBAUMclein i
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Genomic Perspective and CancerD. BO
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GENOMIC PERSPECTIVE AND CANCER 419F
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GENOMIC PERSPECTIVE AND CANCER 421F
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GENOMIC PERSPECTIVE AND CANCER 423f
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Chromosome 21 and Down Syndrome: Th
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DOWN SYNDROME AND HUMAN CHROMOSOME
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DOWN SYNDROME AND HUMAN CHROMOSOME
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Harvesting the Genome’s Bounty: I
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INTEGRATIVE GENOMICS 433with high-d
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INTEGRATIVE GENOMICS 435497 baits3,
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INTEGRATIVE GENOMICS 437In contrast
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INTEGRATIVE GENOMICS 439Fly19,912Ye
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INTEGRATIVE GENOMICS 441IMPLICATION
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INTEGRATIVE GENOMICS 443gene intera
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446 STANKIEWICZ ET AL.Table 1. Sele
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448 STANKIEWICZ ET AL.al. 2002; Wal
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450 STANKIEWICZ ET AL.ate DNA rearr
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452 STANKIEWICZ ET AL.Figure 5. Sch
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454 STANKIEWICZ ET AL.Legius E. 200
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456 SAKAKI ET AL.determined. We pai
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458 SAKAKI ET AL.Table 2. Base Subs
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460 SAKAKI ET AL.D.R. 2003. Genomic
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462 LIPOVICH AND KINGtions that cre
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464 LIPOVICH AND KINGto-tail antise
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466 LIPOVICH AND KINGFigure 2. Perl
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468 LIPOVICH AND KINGtions. In inte
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470 LIPOVICH AND KINGOlson M.V. and
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472 WALLACE, RUIZ-PESINI, AND MISHM
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480 CLARK ET AL.Table 1. Derivation
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482 CLARK ET AL.Table 3. Biological
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484 CLARK ET AL.be under adaptive e
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Inferring Human History: Clues from
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Y-CHROMOSOME HAPLOTYPES AND GEOGRAP
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496 OLSONTable 1. Talks Grouped by
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498 OLSONbacterial lineages prosper
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500 OLSONwill respond to perturbati
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502 OLSONIn short, much remained to
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