Mammalian Transcriptome Mapped, and It Makes Antisense

By Jason Socrates Bardi

The FANTOM Consortium for Genome Exploration Research Group, a large international collection of scientists that includes researchers at The Scripps Research Institute's Florida campus, is reporting the results of a massive multi-year project to map the mammalian "transcriptome" in this week's issue of the journal Science.

The transcriptome, or transcriptional landscape as it is sometimes called, is the totality of RNA transcripts produced from DNA, by the cell in any tissue at any given time. It is a measure of how human genes are expressed in living cells, and its complete mapping gives scientists major insights into how our genome works.

"This is arguably the next major step after the human genome project," says Professor Claes Wahlestedt, who is the director of Pharmacogenomics at Scripps Florida. Wahlestedt is also a professor at the Karolinska Institute in Sweden, and is adjunct chief scientist at RIKEN Institutes, Japan. "Our Japanese collaborators, headed by Professor Yoshihide Hayashizaki, should be credited for their long-standing focus on generating novel data on the transcriptome," Wahlestedt continues.

The mammalian transcriptome has already revealed a number of new and startling things about the nature of mammalian biology. One of the most significant of these findings, about "antisense transcription," appears in a separate article by Wahlestedt and his colleagues in the same issue of Science.

Antisense transcription (see section below) was once thought to be rare, but the transcriptome reveals that it takes place to an extent that few could have imagined. "Instead of it being a rare phenomenon, we are showing that it is a massively abundant phenomenon," says Wahlestedt. "It is the rule rather than the exception."

This discovery has significant implications for the future of biological research, medicine, and biotechnology because antisense genes are likely to participate in the control of many, perhaps all, cell and body functions. 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 the incredibly complex process of mammalian development.

How They Mapped the Transcriptome

The results that appear in a special section in the journal Science are part of an international effort that represents an enormous body of work —one that has been going on for about a decade, but really took off in the last four years following the completion of the Human Genome Project in early 2001.

Like the genome project, the transcriptome project constituted another massive sequencing effort. Instead of DNA, though, it was concerned with RNA, the genetic material that is transcribed from DNA. Basically, the project amounted to fishing all the RNA out of a variety of tissues and cells and sequencing the pieces that were found.

While genomic DNA is comprised of some 3 billion "nucleotide" bases in humans and other mammals, RNA transcripts may be anywhere from a few dozen to several thousand nucleotides. Or, to describe the difference in terms of an analogy, if a cell were a music library, then the genome would be the complete collection of recordings, the genes would be like the master tapes of individual songs, and the RNA transcripts would be like dubbed copies, ready to play.

One big surprise about the recent transcriptome results is the amount of noncoding RNA expressed in cells. (Noncoding RNA does not encode for proteins and therefore does not fit into the classical definition of a gene.) While Wahlestedt and his consortium colleagues found 20,714 protein-encoding RNA transcripts—which was what the scientists expected, since there are about 22,000 genes in the human genome—they found an even larger number of noncoding RNAs in mammalian cells, 22,839 in all.

No doubt, many of the noncoding RNA play a number of different regulatory roles, and now that the sequences of these noncoding RNA molecules are known, scientists can begin to look for their cellular functions.

In fact, a third article in this week's issue of the journal Science by a team of researchers at The Scripps Research Institute and the Genomics Institute of the Novartis Research Foundation have discovered a way to screen through hundreds of RNA molecules for their functions within cells. For details on these results, see " Mysterious Molecules Begin to Yield Their Secrets."

Antisense Transcription—What Is It?

Another major finding of the transcriptome project is that there are far more antisense genes than anyone ever knew. Some genes have been known for a long time to have antisense counterparts, but the extent to which antisense expression exists has never been guessed at before. The stunning thing is that the majority of genes are seen to have an antisense counterpart.

To get an idea of what antisense RNA is, it's necessary to understand something about how and why RNA is made in the cell. The why is simple—or at least it used to be. The "central dogma" of molecular biology states that DNA genes are transcribed into RNA transcripts that are then translated into proteins. The RNA, from this point of view, is there to take a gene from DNA to protein, the building blocks of our cells that in turn make up our bodies.

RNA, which is a single strand of nucleotides, is made by enzymes as an exact base-to-base copy of DNA. Since DNA is double-stranded, only one of these strands, the so-called sense strand, encodes for proteins. In normal DNA transcription, the two strands are split apart, and only the sense strand is copied. The other DNA strand, the "antisense" strand, can also be transcribed into RNA. Antisense transcription is the "reverse" expression of genomic DNA. If the same molecule of DNA is transcribed into antisense RNA, then the transcript has the reverse sequence as the original DNA sequence.

Antisense RNA transcripts can exert function because they can bind to the RNA transcripts for which they are complementary messengers and modulate their expression into proteins. In fact, synthetic antisense molecules have been widely used to inhibit conventional genes, including applications as anti-viral and anti-cancer drugs, which are currently on the market or in clinical trials.

With such a widespread occurrence of antisense sequences, says Wahlestedt, the transcriptional landscape of mammals shows this same principle may be used by nature on a massive scale to extensively modulate the gene expression within in our cells.

It's still unclear whether the majority of antisense sequences are involved in regulation or in some other biology, he adds, but this result is likely to fuel research for years to come.

The article, "Antisense Transcription in the Mammalian Genome" is authored by S. Katayama, Y. Tomaru, T. Kasukawa, K. Waki, M. Nakanishi, M. Nakamura, H. Nishida, C.C. Yap, M. Suzuki, P. Carninci, Y. Hayashizaki, C. Wells, M. Frith, T. Ravasi, K.C. Pang, J. Hallinan, J. Mattick, D.A. Hume, L. Lipovich, P.G. Engstrom, Y. Mizuno, M.A. Faghihi, A. Sandelin, A.M. Chalk, S. Mottagui-Tabar, Z. Liang, B. Lenhard and C. Wahlestedt and appears in the September 2, 2005 issue of the journal Science. See: www.sciencemag.org.

This work was primarily supported by a Research Grant for the Genome Network Project from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT), the RIKEN Genome Exploration Research Project from MEXT, Advanced and Innovational Research Program in Life Science, National Project on Protein Structural and Functional Analysis from MEXT, Presidential Research Grant for Intersystem Collaboration of RIKEN, Scripps Florida and grants from the Swedish Research Council and from the Wallenberg Foundation of Sweden on natural antisense transcripts.

Send comments to: jasonb@scripps.edu