The Genom of Homo sapiens.pdf

MOUSE GENOME ENCYCLOPEDIA PROJECT 201One remarkable finding of the FANTOM2 research isthat the genome of higher organisms, including humansand mice, can encode much more information than suggestedby the number of TUs (genes). To control suchenormously complex biological systems, dynamic variationis employed at the transcriptional level, since genomicinformation itself is very static. In our database, wefound an unexpectedly large number of 5´ and 3´ endvariations and alternatively spliced sequences. Variationat the 5´ end is mainly due to differences in gene promoters,which are regulated in a tissue- and stage-specificmanner. 3´-end variation is so common that it is also verylikely to be functional. When classified by 3´-end sequence,our original 1,916,592 clones fell into 188,000clusters. When analyzed in terms of complexity, these188,000 3´-end variations are equivalent to ~60,000 TUs.Each TU therefore has more than three 3´-end variationson average. In the 3´-end untranslated region (UTR),many consensus sequences with clear functions areknown. One good example is the small stretch “UUAU-UUAUU.” When included in a 3´-end variation, this motifappears to be the target attacked by endonucleases.mRNAs with the “UUAUUUAUU” motif are degradedvery rapidly, and the half-life of such transcripts is veryshort, whereas mRNAs without this motif have a longhalf-life. 3´-end variation, therefore, is clearly functional.Living cells control the selection and ordering of exonsusing tissue- and stage-specific splicing machinery. Ourclones were collected using normalization and subtractionmethods to cover a greater variety of TUs. If our subtractionsystem had worked perfectly, we would not havecollected any alternatively spliced transcripts. However,the system is leaky; given the large-scale collection of FLcDNA, plenty of alternatively spliced transcripts wereisolated in FANTOM2 analysis. Surprisingly, more than41% of all TUs encode alternatively spliced forms, and79% of alternatively spliced TUs alter the amino acid sequencesof CDSs. Thus, the number of transcripts andproteins is much larger than the number of TUs (genes).This mechanism allows living cells to expand their genomicinformation to finely control their life processes.THE DISTRIBUTION SYSTEM FOR THE POST-GENOME RESOURCE (DNABOOK)The Riken Mouse Genome Encyclopedia Project producedtwo major resources: the transcriptome databaseand the mouse FL cDNA clone bank. These two resourcesare key platforms for use in post-genome andpost-transcriptome life science. The distribution of theseresources is therefore very important in facilitating researchin the 21st century. The FANTOM2 database waspublished on the Internet on December 5, 2002. However,at that point, the clone bank of 60,770 FL cDNAclones still had to be shipped in a box with 100 kg of dryice, a very inconvenient and tedious process.We have solved this problem by developing a newtechnology for the distribution of FL cDNA clones(Hayashizaki and Kawai 2003; Hayashizaki et al. 2003;Kawai and Hayashizaki 2003). The DNA is printed ontoFigure 7. The cover design represents full-length cDNA analyzedby RIKEN Integrated Sequence Analyzer (RISA) andFANTOM computer system. Designed by Dr. Chie Owa.paper sheets and may be shipped as a bound “DNA-Book.” This idea was first conceived at the beginning ofthis project. Figure 7 shows the cover of the first editionof the Riken Mouse Encyclopedia DNABook and has beenused from the start of this project as the title slide in ourpresentations. This design illustrates the following: All ofthe FL cDNAs were fed into the RISA system, many sequenceshave come out of RISA, and the database wassubsequently established on computer hard disk. An imageof the hard-copy encyclopedia “book” is also includedin this figure.We tested the performance of the DNA printed sheetunder various conditions of temperature, humidity, pressure,and other environmental factors, and its resistanceto scratching or touching. Under normal conditions, webelieve it possible for cDNA clones to be maintained onthe paper sheet for at least several years.The DNABook has the potential to significantly improvethe processes of storing and shipping genome resources.Traditionally, a large dry-ice box for shippingand a large freezer at –80ºC for storage are required.Shipping and handling times are typically one or twoweeks. The DNABook, however, can be shipped as easilyas printed material. Once a user has the encyclopediaDNABook, clones may be obtained by simply punchingout the relevant spots and subjecting them to PCR. Clonesare available for experiments within two hours. One bookcan replace a freezer full of clones.In the pre-genome era (before about 1995), we man-