The Genom of Homo sapiens.pdf

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Identification of Novel Functional Elementsin the Human GenomeZ. LIAN,* † G. EUSKIRCHEN,* ‡ J. RINN,* R. MARTONE,* ‡ P. BERTONE,* ‡ S. HARTMAN, ‡T. ROYCE, K. NELSON, ‡ F. SAYWARD, § N. LUSCOMBE, J. YANG, § J.-L. LI, § P. MILLER, §A.E. URBAN, ‡ M. GERSTEIN, S. WEISSMAN, † AND M. SNYDER ‡† Department of Genetics, ‡ Department of Molecular, Cellular and Developmental Biology, Department of Molecular Biophysics and Biochemistry, and § Department of Anesthesiology,Yale University, New Haven, Connecticut 06520Recently, a nearly complete draft of the human genomehas been determined, producing an enormous wealth ofinformation (Olivier et al. 2001). However, the sequenceby itself reveals little about the critical elements encodedin the DNA, and consequently, it is paramount to identifythe functional elements encoded in the 3 billion base pairsand to determine how they work together to mediate complexprocesses such as development and responses to environmentalalterations. Two essential tasks toward thisgoal are the identification of coding and transcriptionallyactive regions in the human genome and determining howthey are regulated. The identification of these regions isan essential first step for the comprehensive and systematicanalysis of gene and protein function. Thus far, a varietyof different approaches have been used for identificationof coding sequences and other functional elementsin genomic DNA (Snyder and Gerstein 2003). Geneshave been identified by generating and sequencing ofcDNAs, expressed sequence tags (ESTs), and related approaches,and then mapping the mRNA coding sequencesonto genomics DNA (Lander et al. 2001). Genes havealso been identified by computational methods such asmotif searches, identification of long open readingframes, and comparative genomic studies to identify conservedsequences, particularly those predicted to encodeproteins (Lander et al. 2001; Venter et al. 2001; Waterstonet al. 2002). The availability of the full genomicDNA sequence allows the direct identification of transcribedsequences by globally interrogating all regions ofthe genome using genomic DNA microarrays.In addition to identification of genes, it is also of highinterest to identify the elements that regulate their expression.Such information is crucial for understandinghow the activity of genes is controlled and thereby whatis essential for understanding cell proliferation and differentiation.Approaches to analyze gene regulation in thepast have been hampered by the fact that the approachesare either not comprehensive or are indirect. For example,comparative analysis of gene expression using DNA microarraysin lines expressing or lacking a factor of interestis indirect—changes in gene expression may be due todownstream effects of the factor.*These authors contributed equally to this work.Recently, we have developed an approach for identifyingthe binding sites of transcription factors on a globalscale (Iyer et al. 2001; Horak et al. 2002). This procedureinvolves immunoprecipitation of chromatin (ChIP) associatedwith a transcription factor of interest and using theassociated DNA to probe a genomic DNA array containingthe regulatory sequences or large segments of thegenome. Thus, in one experiment, many binding sites fora transcription factor can be identified.Below we describe the comprehensive analysis of transcribedregions and transcription factor-binding sites on aglobal scale. We have constructed an array containingmost of the sequences of human Chromosome 22 andused it to identify novel transcribed regions and transcriptionfactor-binding sites. These approaches are expectedto be of broad utility for understanding the functionand regulation of the human genome.CONSTRUCTION OF A HUMANCHROMOSOME 22 ARRAYWe have prepared an array containing nearly all of theunique sequences of human Chromosome 22 (Dunham etal. 1999; Rinn et al. 2003). Chromosome 22 contains 35.XMbp of DNA; approximately one-half comprises repetitiveDNA, and it contains 545 annotated genes (Sanger release2.3). To prepare the array, the repetitive DNA of humanchromosome was detected computationally andsubtracted from the total sequence. The remaining singlecopyDNA sequence was amplified in 0.3- to 1.4-kb segments(mean size 820 bp) using oligonucleotide primersand PCR; 21, 024 PCR products were attempted and 93%were successful. The DNA products were printed in duplicateonto 2.5 slides. Sequencing of several hundredproducts has revealed that 95% of the sequences are identicalor close matches to the expected fragments.IDENTIFICATION OF NOVELTRANSCRIBED REGIONSThe chromosome 22 array was probed with a cDNAprobe prepared from placental poly(A) + RNA (Rinn et al.2003). The RNA had been purified three times usingoligo(dT) cellulose. Labeled single-stranded cDNA wassynthesized using a 50:50 mixture of oligo(dT) and ran-Cold Spring Harbor Symposia on Quantitative Biology, Volume LXVIII. © 2003 Cold Spring Harbor Laboratory Press 0-87969-709-1/04. 317
318 LIAN ET AL.0 12 34 5 6 78 9 1011 12 13 1415 16 1718 19 20 2122 23 2425 26 27 2829 30 3132 33 34The top gray bar represents the sequence on Chromosome 22, ordered from centromere to telomere(unit: Mega bp).Sanger Centre release 2.3 annotated genes in human Chromosome 22.the value of the number of positive hybridizing fragments divided by the total number of fragments in a 100-kb window.Figure 1. The human Chromosome 22 placental transcriptome.dom primers. Six sets of slides were probed, and 2470fragments exhibited a significant signal in five or morereplicas. The results are shown in Figure 1. Matching ofthe Sanger 2.3 annotation to the arrays revealed that 946fragments corresponded to known exons; ~60% of knowngenes on Chromosome 22 were expressed in placentalRNA. Importantly, more than half (1307 fragments) didnot correspond to known exons or other annotations.These novel transcribed regions are designated TARs, fortranscriptionally active regions.To determine whether the novel TARs encoded discretetranscripts, 118 fragments were labeled and used to probeRNA blots of placental poly(A) + RNA (Rinn et al. 2003).Thirty (27%) reacted primarily with one RNA band, indi-
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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
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98 WINDEMUTH ET AL.Table 6. List of
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100 WINDEMUTH ET AL.Table 6. (Conti
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102 WINDEMUTH ET AL.Table 6. (Conti
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104 WINDEMUTH ET AL.much of a surpr
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106 WINDEMUTH ET AL.Given our resul
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Genetic Variation and the Control o
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GENETIC CONTROL OF TRANSCRIPTION 11
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GENETIC CONTROL OF TRANSCRIPTION 11
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Genome-wide Detection and Analysis
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RECENT SEGMENTAL DUPLICATIONS 117Fi
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RECENT SEGMENTAL DUPLICATIONS 119St
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RECENT SEGMENTAL DUPLICATIONS 121Co
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RECENT SEGMENTAL DUPLICATIONS 123Ho
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The Effects of Evolutionary Distanc
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EVOLUTIONARY DISTANCE AND GENE PRED
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EVOLUTIONARY DISTANCE AND GENE PRED
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Lineage-specific Expansion of KRAB
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EVOLUTION OF ZNF GENES 133Figure 2.
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EVOLUTION OF ZNF GENES 135Figure 4.
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EVOLUTION OF ZNF GENES 137get gene,
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EVOLUTION OF ZNF GENES 139Y., Goodw
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Sequence Organization and Functiona
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CENTROMERE ANNOTATION 143THE CENTRO
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CENTROMERE ANNOTATION 145Figure 4.
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CENTROMERE ANNOTATION 147CONCLUSION
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CENTROMERE ANNOTATION 149Schueler M
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152 PARKHILL AND THOMSONFigure 1. T
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154 PARKHILL AND THOMSONshow very h
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156 PARKHILL AND THOMSONGene Loss a
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158 PARKHILL AND THOMSONYersinia ad
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160 MCKAY ET AL.Choosing Candidate
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162 MCKAY ET AL.new comparative too
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164 MCKAY ET AL.rich. Based on a th
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166 MCKAY ET AL.Embryonic Muscle an
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168 MCKAY ET AL.native polyadenylat
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Building Comparative Maps Using 1.5
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HUMAN CHROMOSOME 1p IN THE DOG 1731
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HUMAN CHROMOSOME 1p IN THE DOG 175(
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HUMAN CHROMOSOME 1p IN THE DOG 177l
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180 GEORGES AND ANDERSSON5. There i
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182 GEORGES AND ANDERSSONplied to r
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184 GEORGES AND ANDERSSONbe common
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186 GEORGES AND ANDERSSONin humans
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Evolving Methods for the Assembly o
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ASSEMBLING LARGE GENOMES 191Figure
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ASSEMBLING LARGE GENOMES 193tant ad
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Mouse Genome Encyclopedia ProjectY.
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MOUSE GENOME ENCYCLOPEDIA PROJECT 1
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DNA Sequence Assembly and Multiple
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EULERIAN ASSEMBLY AND MULTIPLE ALIG
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Ensembl: A Genome InfrastructureE.
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ENSEMBL 215projects often submit th
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218 ZHANGthe majority of these are
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220 ZHANGFigure 2. Demonstration of
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222 ZHANG(G.X. Chen et al., in prep
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224 ZHANGWe are waiting for experim
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Ontologies for Biologists: A Commun
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ONTOLOGIES FOR BIOLOGISTS 229al. 20
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ONTOLOGIES FOR BIOLOGISTS 231TOPIC
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ONTOLOGIES FOR BIOLOGISTS 233a.b.Fi
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ONTOLOGIES FOR BIOLOGISTS 2352003.
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238 JOSHI-TOPE ET AL.Figure 1. The
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240 JOSHI-TOPE ET AL.state of knowl
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242 JOSHI-TOPE ET AL.and co-immunop
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The Share of Human Genomic DNA unde
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DNA UNDER SELECTION FROM HUMAN-MOUS
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Detecting Highly Conserved Regions
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DETECTING MULTISPECIES CONSERVED SE
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Page 273 and 274: 266 ROE ET AL.noncoding regions. On
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Page 283 and 284: 276 JAILLON ET AL.Detection of Evol
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Page 291 and 292: 284 OVCHARENKO AND LOOTSdivergent r
Page 293 and 294: 286 OVCHARENKO AND LOOTSmodulation
Page 295 and 296: 288 OVCHARENKO AND LOOTSsequencing
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Page 302 and 303: EVOLUTION OF EUKARYOTIC GENES AND I
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Page 311 and 312: 304 PENNACCHIO, BAROUKH, AND RUBINA
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Page 328 and 329: FUNCTIONAL ELEMENTS IN HUMAN DNA 32
Page 330 and 331: High-resolution Human Genome Scanni
Page 332 and 333: HUMAN GENOME SCANNING 325false-posi
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Page 347 and 348: 340 HARDISON ET AL.CALIBRATION OF T
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Page 351 and 352: 344 HARDISON ET AL.cific chromosoma
Page 353 and 354: 346 WESTON ET AL.these differences
Page 355 and 356: 348 WESTON ET AL.els controlled by
Page 357 and 358: 350 WESTON ET AL.ures prominently i
Page 359 and 360: 352 WESTON ET AL.nal and Bop, which
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Page 363 and 364: 356 WESTON ET AL.like fold (Fig. 6)
Page 366 and 367: Implications of Genomics for Public
Page 368 and 369: GENETIC EPIDEMIOLOGY 361lytic epide
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PTC TASTE GENETICS 367Figure 2. Hap
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PTC TASTE GENETICS 369Table 2. Hapl
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PTC TASTE GENETICS 371the emergence
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374 MCCALLION ET AL.Figure 1. Schem
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376 MCCALLION ET AL.lier (Carrasqui
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378 MCCALLION ET AL.Table 3. HSCR A
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380 MCCALLION ET AL.Figure 3. Trans
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Genetics of Schizophrenia and Bipol
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SCHIZOPHRENIA AND BIPOLAR AFFECTIVE
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The Genetics of Common Diseases: 10
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GENETICS OF COMMON DISEASES 397with
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GENETICS OF COMMON DISEASES 399SELE
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GENETICS OF COMMON DISEASES 401F.,
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404 CHEUNG ET AL.netic analysis. Ex
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406 CHEUNG ET AL.Figure 3. The expr
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Regulation of α-Synuclein Expressi
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α-SYNUCLEIN EXPRESSION AND PD 411T
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1. The levels of α-synuclein prote
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α-SYNUCLEIN EXPRESSION AND PD 415g
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418 BOTSTEINFigure 1. (A) Blectron
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420 BOTSTEINFigure 3. Cluster diagr
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422 BOTSTEINFigure 6. Kaplan-Meier
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424 BOTSTEINGarber M.E., Troyanskay
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426 ANTONARAKIS ET AL.1316192225283
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428 ANTONARAKIS ET AL.Figure 5. Sam
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430 ANTONARAKIS ET AL.POPULATION VA
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432 JORGENSEN ET AL.tive small mole
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434 JORGENSEN ET AL.FLAG-tagged pro
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436 JORGENSEN ET AL.visualization t
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438 JORGENSEN ET AL.AArp2/3 Complex
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Pathway40S440 JORGENSEN ET AL.ANutr
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442 JORGENSEN ET AL.Giaever G., Chu
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Genomic Disorders: Genome Architect
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GENOME ARCHITECTURE AND GENOMIC DIS
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Human Versus Chimpanzee Chromosome-
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HUMAN VS. CHIMP CHROMOSOME COMPARIS
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HUMAN VS. CHIMP CHROMOSOME COMPARIS
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Novel Transcriptional Units and Unc
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TRANSCRIPTIONAL UNITS AND GENE PAIR
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mtDNA Variation, Climatic Adaptatio
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mtDNA VARIATION 473Figure 3. Region
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ANALYSIS OF ADAPTIVE SELECTION FORR
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mtDNA VARIATION 477Figure 8. Temper
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Positive Selection in the Human Gen
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HUMAN-SPECIFIC EVOLUTIONARY CHANGES
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488 UNDERHILLorigin episodes, each
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490 UNDERHILLhaplogroups C through
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492 UNDERHILLO (Fig. 2e) that share
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The New Quantitative BiologyM.V. OL
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NEW QUANTITATIVE BIOLOGY 497alone.
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NEW QUANTITATIVE BIOLOGY 499There w
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NEW QUANTITATIVE BIOLOGY 501ceded,
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