The Genom of Homo sapiens.pdf

MOUSE GENOME ENCYCLOPEDIA PROJECT 199tained 33,994 unique sequences. We had intentionallyavoided redundant efforts to sequence the known genespresent in public databases, so by adding 44,122 redundantsequences of cDNA known in public databases, weestablished a database carrying 36,830 unique sequences.This we named Representative Transcript and Protein Set(RTPS). RTPSs are the unique FL cDNA sequences encodingprotein coding or protein noncoding transcriptssupported by physical clones.In the process of selecting the 60,770 sequences to subjectto full-stretch sequencing, many unique sequences,contained by 1,916,592 clones of the original masterbank, were missed. Using the new version (MGSCv3) ofthe mouse genome sequence database that was providedby the Mouse Genome Sequence Consortium (MGSC) asa part of the collaboration, it was concluded that at least43,000 unique transcripts are encoded in the mousegenome. It was estimated that the total number of“genes,” a word that should be used very carefully (seethe next section), is around 60,000.TRANSCRIPTIONAL UNITTo analyze the total number of genes for subsequent research,words with ambiguous definitions, such as“gene,” “locus,” and so on, should be avoided. In thegenome community, the word “gene” is used for “the protein-codinggenes (or loci)”. This was tacitly defined dueto the convenience of computer-assisted exon prediction,but genome sequences do not give any proof of the existenceof transcripts. Computer prediction of exons isbased on open reading frames (ORF). However, in transcriptomeanalysis, we meet a lot of “noncoding genes,”which should also be incorporated into the transcriptome.Thus, we should not use the word “gene” or “locus” todiscuss a genomic region which is transcribed, the socalled“gene” in the past definition.For this reason, we coined a new term, transcriptionalunit (TU). TU is defined as a segment of the genomeflanked by the most distal exons from which transcriptsare generated. This term can be used as purely computationaland unequivocal. The transcripts sharing any exonare encoded by a single TU. If two transcripts do not shareany single exon, these two transcripts are in different TUs,even if one is localized in the intron of the other. Wheretwo transcripts encode the sense and antisense strands, respectively,in the same region of genomic DNA, these twogenomic segments are different TUs. Thus, by the definitionof the new term “TU,” we could count the number ofso-called “genes” (Okazaki et al. 2002).Figure 5. Contribution of RIKEN FANTOM2 clones in theworld. The FANTOM2 collection covers 90% of all TU publishedin the world.CONTRIBUTION OF RIKEN FANTOM2CLONES INTERNATIONALLY (APRIL 2003)After our contribution to the world-wide mouse gene(TU) database, the number in the RTPS has increased to37,086. As shown in Figure 5, the Riken FANTOM2 collectioncovers 90% of the total TUs (33,459/37,086); althoughthe remaining 10%, including many known TUs,were covered by our master bank, they were not sequencedto avoid the redundant efforts. A significant proportion(24% of TUs; 8,898/37,086) of the RTPS is alsocovered by the Mammalian Gene Collection (MGC) supportedby the National Institutes of Health (Strausberg etal. 2002). From this analysis, we estimate that a significantproportion of mouse TUs have still not been covered,much less the whole transcriptome, which includes varianttranscripts with alternative splicing and differential 5´and 3´ sites.FUNCTIONAL CLASSIFICATION OF MOUSETRANSCRIPTOME AND NONPROTEINCODING TRANSCRIPTSAll sequence data were classified by level of homologyFigure 6. The breakdown of RIKEN FANTOM2 clones to thecategories defined below. (1) Directly assigned by MGI, (2)Mouse DNA Hit (>98% ID, >100 bp) Complete, (3) MouseDNA Hit (>98% ID, >100 bp) Partial, (4) Protein Hit (>98% ID,>100% length, mouse) Complete, (5) Protein Hit (>85% ID,>90% length) Complete, (6) Protein Hit (>85% ID, >90%length) Partial, (7) Protein Hit (>70% ID, >70% length) Complete,(8) Protein Hit (>70% D, >70% length) Partial, (9) ProteinHit (>50% ID, >50% length) Complete, (10) Protein Hit (>50%ID, >50% length) Partial, (11) Inferred from TIGR/UniGeneCluster, (12) Inferred from UniGene Cluster, (13) Inferred fromTIGR Cluster, (14) InterPro domain/motif containing, (15)MDS domain/motif containing, (16) SCOP structural domain/motifcontaining, (17) hypothetical protein, (18) EST hit,(19) unclassifiable.