The Genom of Homo sapiens.pdf

Comparative Analysis of Human Chromosome 22q11.1-q12.3with Syntenic Regions in the Chimpanzee, Baboon, Bovine,Mouse, Pufferfish, and Zebrafish GenomesB.A. ROE,* C. LAU,* S. OOMMEN,* J. LI,* A. HUA,* H.S. LAI,* S. KENTON,*J. WHITE,* AND H. WANG †*Department of Chemistry and Biochemistry and † Department of Zoology, University of Oklahoma,Norman, Oklahoma 73019It has been over three decades since the initial publicationof the methods for DNA sequencing that were developedindependently by Sanger, Nicklen, and Coulson atthe Medical Research Council Laboratory of MolecularBiology in Cambridge, England (Sanger et al. 1977) andby Maxam and Gilbert (1977) in the biology departmentat Harvard University in Cambridge, Massachusetts.Since then, the Sanger dideoxynucleotide sequencingmethod has become the method of choice for large-scaleDNA sequencing, has been automated by Lee Hood’sgroup (Smith et al. 1986) and others (Ansorge et al. 1987;Prober et al. 1987; Brumbaugh et al. 1988; Kambara andTakahahi 1993), and commercially developed into a stableplatform for large-scale, highly accurate, and rapid sequencedata collection with robust sequencing chemistry.Today, because of these improvements, DNA sequencingalmost is taken for granted. In this volume, we celebratethe completion of the entire human genomic DNA sequence,almost 50 years after the initial publication of thedouble-helix structure of DNA and its implications (Watsonand Crick 1953a,b), and we look forward to the completionof the genomes of other organisms that eitherpresently are in working draft form (Waterston et al.2002) or whose sequence is being contemplated (J.E.Collins et al. 2003).Although there is an ever-growing compilation ofDNA sequence data, fewer than half of the predicted humangenes, and ironically, a similar percentage of genesfrom bacteria and other model organisms, have been assignedwell-defined functions (Lander et al. 2001; Shoemakeret al. 2001; Zhang 2002; Waterston et al. 2002;F.S. Collins et al. 2003). The challenge now is to developmethods and approaches that will result in detailed understandingof the regions contained within the humangenome, whether they be exons coding for functionalproteins, regions encoding the genes for stable RNAs,regulatory regions, or regions involved in regulating geneexpression and other genome-specific functions. One approachthat has emerged as a powerful tool for genomicfunctional annotation is to compare the sequences of orthologousregions that are syntenic to segments of the humangenome (Jan et al. 1999; Lund et al. 2000; Footz etal. 2001; Ji et al. 2001; Deschamps et al. 2003; Thomas etal. 2003; Ureta-Vidal et al. 2003). Then, based on the hypothesisthat if a region has been conserved over evolutionarytime its structure contains important features requiredto maintain biological function, it is possible to illuminatethese genomic features; e.g., genes, regulatoryregions including antisense RNAs, and conserved evolutionarybreakpoints which can be related directly to conservedbiological functions that occur in evolutionarilydistant organisms (Thomas et al. 2003; Ureta-Vidal et al.2003). Once discovered, the function of these conservedpredicted features must be confirmed, through gene expressionstudies to determine when during developmentand in what cells the gene is transcribed, to infer whenand where its biological function(s) is performed. Thisknowledge is a natural prelude to the eventual detailedanalysis of both the biochemical and biophysical propertiesof the genomic region and its final gene product, be ita stable RNA or functional protein.Our laboratory has played a role in the developmentand implementation of DNA sequencing methods overthe past 30 years (Chissoe et al. 1991; Bodenteich et al.1994). This stems from my (B.A.R.) initial introductionto DNA sequencing as a member of the human mitochondrialgenome sequencing project during my first sabbaticalin Fred Sanger’s laboratory (Anderson et al. 1981,1982), through sequencing the genomic regions involvedin the Philadelphia chromosomal translocation (Chissoeet al. 1995), and culminating in sequencing a significantportion of the upper half of human Chromosome 22(Dunham et al. 1999) as a member of the internationalconsortium that reported the sequence of this first completedhuman chromosome. More recently, we have focusedour efforts on comparative genomics, prompted bythe observation that although 598 protein-coding genesand 228 pseudogenes have been predicted on humanChromosome 22, only about half of the protein-codinggenes have both a known function and expression profiles,one-quarter of the predicted genes have an unknownfunction but are expressed in one or more tissues and developmentalstages, and one-quarter have neither aknown function nor a known expression profile (Dunhamet al. 1999; Shoemaker et al. 2001; J.E. Collins et al.2003). These studies are revealing the identity of evolutionarilyconserved structures in the upper third of humanChromosome 22 genes corresponding to both coding andCold Spring Harbor Symposia on Quantitative Biology, Volume LXVIII. © 2003 Cold Spring Harbor Laboratory Press 0-87969-709-1/04. 265