Additional material
September 1st, 2005 (Eastern Time, USA)The discovery of a novel RNA Continent through comprehensive
analyses of mammalian transcriptomes.
The FANTOM Consortium for Genome Exploration Research Group, RIKEN
Genomic Sciences Center (GSC), RIKEN Yokohama Institute and Genome Science
Laboratory, Discovery and Research Institute, RIKEN Wako Institute (GenomeNetwork Core Group), involving researchers from Australia, Italy, Germany, Greece,Singapore, South Africa, Switzerland, Sweden, UK and the United States, has published
two milestone papers this week in the prestigious journal Science, which transform ourunderstanding of the information content of the mammalian genome.
The past 5 years have seen the completion of several mammalian genome sequences, butthese are of limited value unless we can decode the way that they are translated intofunctions required to create a mature animal. Only around 2% of the genome is translated
into proteins, the building blocks of the cells that make up our bodies. But which 2%, andhow is it controlled? The key intermediate is the transcriptome.
The transcriptome is made of many individual RNA molecules (transcripts), which arecopied from DNA, and in many cases, translated into proteins. Transcriptome analysis ismuch more demanding than genome sequencing, since thousands of RNA molecules
must be individually isolated and sequenced. The FANTOM Consortium analyzed over 2
million sequences of RNAs produced from the mouse genome, obtaining more than
100,000 full length copies of these RNAs, and used several new technologies (CAGE(cap analysis gene expression), GIS (gene identification signature, in collaboration with
the Genome Institute of Singapore) and GSC (gene signature cloning)), to generate morethan 20 million tags representing their starts and ends in a technical tour-de-force thatprovides an amazing new view of our genome.

Another aspect of our study is the analysis of sense and antisense transcription
overlapping in the genome. In particular, the analysis of physical cDNA clones, sequencetags and Expressed Sequence Tags (EST), provides compelling evidence that overlapping
sense-antisense (S/AS) from both strands is almost universal in the genome. S/AS areespecially abundant in imprinted loci, keeping with the putative role of non-coding RNA
in gene silencing. We also provide experimental evidence that perturbation of anantisense RNA can alter the expression of sense mRNAs, suggesting that antisensetranscription contributes to the control of transcriptional output in mammals.
The data taken together provides the biomedical research community with the tools tounderstand the control networks that are needed to create a mammal. A genome
sequence contains not only the code for making the parts (proteins) of a mammal, butalso the code for making the right forms, in the right amounts, in the right place, at theright time. The FANTOM data provide the most complete overview of a transcriptome
in any species. Since mammals only have slightly more conventional genes (around22,000) than a simple worm, the results of the FANTOM Consortium study clearly
indicate that while proteins comprise the essential components of our cells, thedevelopment of multicellular organisms like mammals is controlled by vast amounts ofregulatory noncoding RNAs that until recently was not suspected to exist or be relevant
to our biology.
Moreover, since most proteins are similar among mammals it also suggests that many ofthe differences between species may be embedded in the differences in the RNA
regulatory control systems, which are evolving much faster than the protein components.
If correct, these findings will radically alter our understanding of genetics and how
information is stored in our genome, and how this information is transacted to control theincredibly complex process of mammalian development, with enormous implications forthe future of biological research, medicine and biotechnology.
[Future directions]With this study we challenge the concept of a gene as declared in the central dogma, agene is no longer only the section of DNA that is transcribed to RNA, to be translated
into a protein; we now declare that RNA is not simply an intermediary between DNA andfunctional protein, but has a multitude of intrinsic functions and activities.
This discovery of the “RNA Continent” consisting of the gigantic amount and varieties ofmRNA and non-coding RNAs, is in contrast to the previous view of the genome
consisting of transcriptional forests (many transcription starts) located between
transcriptional deserts (no transcription starts). From this on, new studies will include
ncRNA as a primary target to further unveil the transcription/regulation mechanisms in
mammals.
Currently, the systematic analysis of the transcriptome is in its infancy. Comparison withindependent tiling array experiments reveals that we currently target around 50% of all
polyA RNAs using full-length cDNA sequencing. Other predictions indicate that thenumber of non polyA transcripts is close to the number of polyA transcripts. Thus, this is
only the beginning systematic transcriptome analysis. Today we have two dimensions ingenome analysis: time and location. In the future we will have to consider the cell age,development and tissue differentiation to be able to encompass this new, dynamic field oftranscriptome analysis. Transcriptome analysis is the next new and powerful tool to apply
to our understanding of gene functions, and ultimately; the secrets of life.

These studies have been carried out mainly in mice; the most widely used experimental
mammalian species. Equivalent human data is not far behind, and RIKEN and many
FANTOM members are actively involved in the next phase, the Genome Network
consortium, which aims to use these new tools to understand human development anddisease. Associated with the publication of the Science papers, all of the information will
be publicly released on Internet in a unique user-friendly format. (On the servers ofDDBJ, National Institute of Genetics and RIKEN; http://www.ddbj.nig.ac.jp/,
http://fantom3.gsc.riken.jp/, http://www.ddbj.nig.ac.jp/whatsnew/050124-e.html)

[New concept of genes]