Published in: Nature Genetics, vol. 36 no. 1 pp, 19-25 (January, 2004).
doi:10.1038/ng1275
http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v36/n1/abs/ng1275.html


"The four Rs of RNA-directed evolution".

Alan Herbert

Department of Genetics and Genomics, Boston University School of Medicine, 715 Albany Street, Boston, Massachusetts 02118, USA.
e-mail:    aherbert@bu.edu


Summary:

The way we quantify the human genome has changed markedly. The estimated percentage of the genome derived from retrotransposition has increased (now 45%; refs. [1,2]), as have the estimates for alternative splicing (now 41–60% of multiexon genes) [3, 4], antisense transcription (now 10–20% of genes) [5, 6] and non–protein coding RNA (now 7% of full-length cDNAs) [7]. Concomitantly, the estimated number of protein-coding genes (now 24,500) has decreased [8]. These numbers support an RNA-centric view of evolution in which phenotypic diversity arises through extensive RNA processing and widespread RNA-directed rewriting of DNA enables dissemination of 'selfish' RNAs associated with successful outcomes [9]. The numbers also indicate important roles for sense-antisense transcription units (SATs) and coregulatory RNAs (coRNAs) in directing the read-out of genetic information, in reconciling different regulatory inputs and in transmitting epigenetic information to progeny. Together, the actions of reading, 'riting, 'rithmetic and replication constitute the four Rs of RNA-directed evolution.


References:

1. Jordan I.K., Rogozin I.B., Glazko G.V. & Koonin E.V., Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet. 19, 68–72 (2003).

2. Brosius J., The contribution of RNAs and retroposition to evolutionary novelties. Genetica 118, 99–116 (2003).

3. Black D.L., Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72, 291–336 (2003).

4. Zavolan M., et al., Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res. 13, 1290–1300 (2003).

5. Yelin R., et al., Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol. 21,
379–386 (2003).

6. Kiyosawa H., Yamanaka I., Osato N., Kondo S., & Hayashizaki Y., Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res. 13, 1324–1334 (2003).

7. Numata K., et al., Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res. 13, 1301–1306 (2003).

8. Pennisi E., Human genome. A low number wins the GeneSweep Pool. Science 300, 1484 (2003).

9. Orgel L.E. & Crick F.H., Selfish DNA: the ultimate parasite. Nature 284, 604–607 (1980).

10. Herbert A. & Rich A., RNA processing and the evolution of eukaryotes. Nat. Genet. 21, 265–269 (1999). 

Additional References:

1. Brosius J, "Gene duplication and other evolutionary strategies: from the RNA world to the future", Journal of Structural and Functional Genomics, vol. 3, pp. 1-17, (2003).

2. Topics in:  Euchromatin,  active DNA, and  RNA  ribo-regulators:

Reviews and Research:

Links to Euchromatin Activator RNA Reviews:
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"Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".
 


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