Monday, August 11, 2008

This Week's Citation Classic

This week's citation classic is relatively new, but has outsized importance, and should result in a future Nobel Prize for its primary author. The paper is Lee RC, Feinbaum RL and Ambros V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-85.

Geraldine Seydoux once wrote about Ambros' discovery, "In 1990, Victor Ambros faced a conundrum. The search for the heterochronic gene lin-4 had led him to a 700-bp DNA fragment. This fragment could rescue a lin-4 mutant but contained no apparent open reading frame (ORF). The few small ORFs that could be detected were either not conserved in other nematodes or not essential for rescue. Two years and several RNAse protection experiments later, Victor Ambros was forced to conclude that the lin-4 gene product was not a protein at all, but a very small 20-base RNA—the first microRNA!"

Yeah so...

Yeah so Ambros et al. discovered an entirely new form of genetic regulation. At first, it was thought to be some "weird worm thing", a quirky aspect of the genetics of the roundworm C. elegans. That is, until Gary Ruvkun of Massachusetts General Hospital BLASTed another miRNA called Let-7. "Bingo" said Ruvkun, "up came the fly with a perfect match and the human [was another close match]. Within minutes I knew exactly what we were going to be doing for the next year." To date, 678 miRNA's have been discovered and it is believed that there are probably hundreds more.

Each miRNA can affect dozens or more mRNA's and alter gene expression with significant consequences for organismal function. "The miRNAs collectively have much of the genome under their influence," says Ambros. "They can affect almost any aspect of the biology of a cell or organism."

miRNA's and other small RNA molecules have made the science of gene regulation bewilderingly complex, but they also have opened up a window of opportunity for new types of therapies. To design an artificial miRNA or anti-miRNA, you need only know the sequence of the microRNA whose action you want to block or mimic. This may eventually lead to treatments for many diseases such as hepatitis C and cancer.

Figure: The secondary structure of a precursor microRNA sequence from Brassica oleracea, as predicted by MFOLD ( by M. Zuker. GIF generation by plt22gif, D. Stewart and M. Zuker 2007.


  1. Yeah so Ambros et al. discovered an entirely new form of genetic regulation

    Really? What about antisense RNA in bacteriophage lambda? The expression of the Q gene is blocked by synthesis of an antisense RNA. We've known about it for three decades. It was in all the textbooks before the recent purging of prokaryotic molecular biology that occurred in the 1990's.

    I used to teach about the bacterial antisense RNA back in the early 1980's.

    And what about control of DNA replication in ColE2 plasmids? Synthesis of the Rep protein is controlled by an antisense RNAI made by the plasmid.

    These, and other systems have also been known for three decades. Here's the opening paragraph of a 1993 paper ...

    A number of cases have been known in which small RNAs are revealed or suggested to control DNA replication or gene expression (for reviews; 1, 2). These small RNAs are termed 'antisense RNA', because the RNAs are in part or entirely complementary to the functional 'sense RNA', whose expression is regulated. In all of these antisense RNA regulatory systems except for that of ColEl DNA replication, antisense RNAs regulate syntheses of the proteins from the target genes. The molecular mechanism of inhibition of the protein synthesis by binding of the antisense RNA to the target mRNA, however, is only elucidated for the clI gene expression of bacteriophage lambda (3), the transposase gene expression of Tn1O (4) and the rep gene expression of plasmids pTl81 (5) and ColIb-P9 (6).

    This is just one example of a disturbing trend. Today's scientists seem to have completely forgotten all the fundamental work on molecular biology that was done with bacteria and bacteriophage.

  2. Yes, you are right! I forgot that phage antisense RNA was discovered before Ambros et al. I should have know this.