The Genom of Homo sapiens.pdf

462 LIPOVICH AND KINGtions that create or destroy polyadenylation signals in thegenomic DNA sequence (Dan et al. 2002), in the generationof lineage-specific cis-antisense UGPs. Against abackground of evidence for substantial numbers of lineage-specificgenes in completely sequenced prokaryotic(Jordan et al. 2001) and eukaryotic (Lespinet et al. 2002)genomes, human–mouse comparisons have shown thateven in two species sharing a common ancestor only ~ 70mya, lineage-specific members of gene families related totranscription regulation, olfaction, behavior, and immunityhave appeared (Young et al. 2002; Emes et al. 2003;Shannon et al. 2003), spurring an entire field of “genomezoology” focused on the genomic basis for interspecificdifferences (Emes et al. 2003).The present study began more than 4 years ago as asimple attempt to construct and refine a comprehensive insilico physical and transcript map of a 5.5-Mb human genomicregion at 5q31. At the time, the genome draft washighly fragmented, the cDNA databases rudimentary, andpublished analyses of TUs and UGPs beyond isolated single-locusexamples practically nonexistent. Nevertheless,our extensive manual annotation uncovered substantialevidence for the existence of numerous TUs and UGPs inthe region. As our in silico models of these TUs andUGPs continued to be supported by progressively largeramounts of increasingly higher-quality genomic andcDNA sequences over time, even while gap-filling by theHuman Genome Project permitted completion of the dataset with additional genes mapping to our 5q31 region, weset out to determine whether the patterns of incidence andgenomic distribution of TUs and UGPs observed at 5q31would be also detectable over larger intervals elsewherein the genome. Our development of an automated TU andUGP discovery pipeline and subsequent validation of the5q31 observations over the entire 35-Mb euchromatic sequenceof human chromosome 22 constitute the balanceof the study.OPERATIONAL DEFINITIONS1. Transcriptional unit (TU). A TU is a transcribed featurein the genome other than a known gene. It is predictedin silico from analyzing EST-to-genomic DNAalignments in which the ESTs do not correspond toknown or undocumented exons of known genes. ESTscomprising a TU must be canonically spliced (GT-AGintrons) and/or canonically polyadenylated(AATAAA or ATTAAA polyadenylation signalwithin 40 bp of the submitter-indicated 3´ end). Indefining TUs, we excluded ESTs from the ORESTESdata set (Strausberg et al. 2002) and the RAGE data set(Harrington et al. 2001) because the former containslarge numbers of unspliced, singleton, and chimericESTs, and the latter is derived from cell lines with artificialpromoter insertions and therefore is not representativeof naturally occurring transcription.Since our definition of a TU was developed prior toand independently from that of Carninci et al. (2003),it is not identical to that of Carninci et al. Due to theabsence of an experimental component, our analysiscannot distinguish functionally important TUs fromnonfunctional, stochastically transcribed TUs.2. Unconventional gene pair (UGP) type 1: cis-antisense.The term “cis-antisense” means that both membersof the pair are encoded within the same genomiclocus. cis-antisense overlaps included in this analysismust be exon-to-exon, meaning that the predicted matureRNAs must overlap (intronic intercalation aloneis insufficient). Two transcribed features cis-antisenseto one another, residing on the opposite strands of thesame locus, may be two genes, two TUs, or one ofeach. If only the first exons of the two features overlap,then the overlap is categorized as head-to-head. Ifonly the last exons overlap, then the overlap is tail-totail.The “other” category is for all remaining possibilities.3. Unconventional gene pair (UGP) type 2: putative promoter-sharing.This is a pair of divergently transcribedfeatures whose transcription start sites are separatedby 100 amino acids in length, and most of its ORFs were eitherunique or located inside expressed repetitive elements,supporting the notion that if this TU is functional,its function is not to encode a protein. The TU is cis-antisenseto an internal, translated exon of the TTID gene,which may be unusual because most cis-antisense in hu-