The four Rs of RNA-directed evolution

Abstract

The read-out of genetic information in eukaryotes is not only more complex than previously realized, but also more dynamic. Much of the information is 'soft-wired' , with extensive RNA processing necessary to generate phenotypes 10 . A subset of the RNA, referred to here as coRNA ( Fig. 1), coordinates the read-out of genetic information and reconciles regulatory inputs. For each cell type, the sum of these interactions defines a distinct RNA profile or ribotype 10 . RNA-based processes also facilitate replication of ribotypes in subsequent generations. The flexibility of these programs allows soft-wired organisms to evolve in a more rapid and dynamic way than 'hard-wired' organisms constrained by DNA mutation 10 . Together, the actions of reading, 'riting, 'rithmetic and replication constitute the four Rs of RNA-directed evolution. Here, we describe roles for coRNAs and SATs (Fig. 2) in these events. RNA-directed RNA readoutRNA coregulates the sequence-specific read-out of genetic information from RNA by targeting the evolutionarily conserved machinery of RNA interference (RNAi) 11 and translational repression. RNAi leading to post-transcriptional gene silencing (PTGS) is induced by doublestranded RNA (dsRNA) arising from infection by dsRNA viruses, senseantisense transcription pairs, transcription of inverted repeats and delivery of dsRNAs manufactured in vitro 12 . Both endogenous and exogenous dsRNAs are processed cytoplasmically by RNase III dicer paralogs into small interfering RNAs (siRNAs) that are 21-25 bases long 12,13 . These siRNAs are incorporated into an RNA-induced silencing complex (RISC) that targets any RNA with a sequence complementary to the siRNA 12,14 . The target RNA is cleaved by RISC, which has endonucleolytic and presumed exonucleolytic activity 12,15 . Each cycle results in the destruction of the target RNA and the regeneration of an active RISC 16,17 .In Neurospora crassa 18,19 , plants 20 , Schizosaccharomyces pombe 21 and Caenorhabditis elegans 22 , but not in flies, humans or mouse oocyctes 18,19,23,24 , PTGS can also be initiated by an RNA-dependent RNA polymerase (RdRP) that synthesizes complementary RNA from highly expressed transcripts to generate dsRNA. This process can spread from the 3´ to the 5´ end of the mRNA, leading to progressive silencing of a gene and other mRNAs with exons in common (transitive RNAi) 18,22 . From the evolutionary viewpoint, transitive RNAi favors the generation of new phenotypes, as related genes in species with polyploid genomes will escape cosuppression by sequence divergence, resulting in altered function or expression.The number of dicer paralogs also differs between species. Arabidopsis, which has at least four dicer family members, seems to use different enzymes to defend against viruses and to process endogenously produced dsRNA 13,25 . In humans, mice and worms, there is only one dicer ortholog, suggesting that any pathway-specific functions are guided by ancillary regulatory proteins associated with RISC. These ancillary proteins include me...

Expanding the ‘central dogma’: the regulatory role of nonprotein coding genes and implications for the genetic liability to schizophrenia

“…In higher organisms only a minority of genetic transcripts (2-3%) code for proteins. 1,2 Nonprotein coding RNA (ncRNA) refers to mRNA that is transcribed from DNA but not translated into protein. Rather than being 'junk' DNA (ie an evolutionary relic) some nonprotein coding transcripts may in fact play a critical role in regulating gene expression and so organizing the development and maintenance of complex life.…”

“…9 These newly discovered control mechan-isms for protein expression are often referred to as the 'tip of the iceberg', anticipating that yet undiscovered regulatory functions of ncRNAs are likely to be critical to the development and function of complex organisms. 2 In classical Mendelian disorders, mutations generally lead to striking alterations in protein structure that impair function, resulting in disease. This theoretical perspective has led investigators to emphasize investigation of nonsynonymous base pair (bp) changes as candidate disease genes.…”

“…In a series of insightful studies, it was discovered that a region of the lin-4 gene codes for a miRNA (cel-lin-4) whose mature region binds to Figure 1 ncRNA and mRNA interactions. mRNA transcribed from a protein coding gene (1) may be translated into a protein (2). siRNA and miRNA interact with RISC (3).…”

Natural Antisense Transcripts

“…This lead to the speculation that the vast amount of untranslated RNA produced during transcription could give rise to regulatory output-possibly also in the form of microRNAs. 98,99 RNA editing. Primary transcripts that include repetitive elements may form long imperfect hairpins that are recognized by ADAR (Fig.…”

Repetitive sequences that shape the human transcriptome

“…Hence, there are thousands of different transcriptomes in hundreds of different cell types and organs in their various physiological and pathological states. The variety of transcripts as compared to genes increases by about 50% due to alternative splicing [4,5], the numerous antisense transcripts are synthesized [6], and all non-protein-coding RNAs [7,8] including the recently recognized microRNA family [9] also make a significant contribution to the pool of human transcripts.…”