Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22.

Despite the publication of a highly accurate human genome sequence (International Human Genome Sequencing Consortium [IHGSC] 2004) with comprehensive annotation (Hubbard et al. 2002; Kent et al. 2002), the functional definition of a mammalian gene remains in flux (Okazaki and Hume 2003), in part because more of the genome is transcribed than is accounted for by reference protein-coding gene sets. Sequencing random clones from normalized and subtracted high-quality cDNA libraries continues to uncover previously uncharacterized transcripts, many of which do not correspond to mRNAs of conserved protein-coding genes (Carninci et al. 2003). The continued growth of dbEST has resulted in the availability of >2 million sequences not matching any annotated genes (Larsson et al 2005) and has facilitated definition of ∼25,000 transcript models distinct from known genes (Shklar et al 2005). Since the loci encoding such transcripts may not fit conventional definitions of a gene, the term transcriptional unit (TU) has been introduced (Carninci et al. 2003). Transcriptome hybridization to genomic tiling arrays suggests that noncoding TUs are surprisingly widespread and that existing annotations greatly underestimate the number of transcribed features (Shoemaker et al. 2001; Kapranov et al. 2002; Rinn et al. 2003). Functions have been identified for some non-coding RNAs. They can serve as hosts of intron-encoded snoRNAs (Numata et al. 2003) and as host genes or direct precursors of small trans-acting microRNAs, which themselves constitute an extremely important functional class of noncoding RNAs (Rodriguez et al. 2004). They can also be involved in mRNA processing, transcription factor recruitment, and chromatin remodeling, suggesting that an extensive RNA-based regulatory network may exist in higher organisms (Mattick 2003). In addition, ORFless functional RNAs encoding telomerase and endoribonuclease components have been reported (Topper and Clayton 1990; Feng et al. 1995), emphasizing the significance of noncoding TUs. A second intriguing feature of genome organization emerging from cDNA discovery projects is the abundance of unconventional gene pairs (UGPs), each comprised of two transcripts that overlap or are in close proximity to one another, in a manner suggesting coordinated regulation of gene expression. These UGPs include naturally occurring cis-antisense pairs, as well as genes and/or TUs that share a putative bidirectional promoter. Noncoding TUs and UGPs may be functionally linked in that many noncoding RNAs are antisense to coding genes and have been shown to regulate gene expression in many species (Hildebrandt and Nellen 1992; Delihas and Forst 2001; Lee and Ambros 2001; Misra et al. 2002; Kramer et al. 2003; Numata et al. 2003). In humans, naturally occurring cis-antisense transcripts are relevant to diverse aspects of genome dynamics, including imprinting (Sleutels et al. 2002); pathogenesis of neurodegenerative disorders (Andres et al. 2003); methylation in inherited anemia (Tufarelli et al. 2003); gene vestigialization (Millar et al. 1999); splicing regulation, X-inactivation, and RNA editing (Shendure and Church 2002); and retrotransposition (Ejima and Yang 2003) leading to de novo generation of primate-specific genes expressed in the brain (Courseaux and Nahon 2001). We define a TU as one or more flcDNA-supported and/or EST-supported transcripts mapping to the same locus and sharing exonic sequence on the same strand. In this report, we refer to TUs identical to known genes as “known genes,” or simply “genes,” and to TUs identified by our analysis but devoid of known-gene identities and public-database annotations as “novel TUs,” or simply “TUs.” The goal of the present study was to annotate TUs and UGPs on chromosome 22 (chr22) and to characterize their incidence, evolutionary conservation, and distribution along the genomic landscape of the chromosome.