Glimpses of a little literature on small RNA

Zhaoyanlin

readpaper@hotmail.com

The antiquity of RNA-based evolutionGerald F. JoyceDepartments of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute,

10550 North Torrey Pines Road, La Jolla, California 92037, USA (e-mail: gjoyce@scripps.edu)

NATURE | VOL 418 | 11 JULY 2002 |

The dawn of darwinian evolution

A cluttered path to RNA

RNA-catalysed RNA replication

Metabolic function in the RNA world

Transition to the DNA–protein world

1982 Ribozyme ribonuclerase RNAse

The discovery of RNA interference

petunias 1990

(PTGS)

1960‘s ncRNA RNA, that catalyse nucleotide synthesis RNA polymerization,aminoacylation of transfer RNA and peptide bond formation

Some titles concerning about the small

RNAfRNA

sRNA

smRNA

ncRNA

siRNA

RNAi

stRNA

snmRNA

snRNA (small nucleus)

scRNA

snoRNA( small nucleolar RNAs)

Recent efforts of several laboratories have brought together two fascinating forms of gene regulation: silencing genes by degrading their mRNAs,and blocking translation of specific mRNAs during development.Both of these processes involve very small RNAs,about 22nt in length.

RNA interferenceGregory J. Hannon

Cold Spring Harbour Laboratory, 1 Bungtown Road, Cold Spring Harbour, New York 11724, USA (e-mail: hannon@cshl.org)

NATURE | VOL 418 | 11 JULY 2002

RNA interference: It’s a small RNA worldEric G. Moss

Current Biology 2001, 11:R772–R775

Short RNAs regulate gene expression in many species. Some are generated from any double-stranded RNA and degrade complementary RNAs; others are encoded by genes and repress specific mRNAs. Both, it turns out, are processed and handled by similar proteins. These pathways offer a glimpse into a world of small RNAs.

To identify more small regulatory RNAs of the lin-4/let-7 class in C. elegans, we used informatics and cDNA cloning to select C. elegans genomic sequences that exhibited four characteristics of lin-4 and let-7: (i) expression of a mature RNA of ;22 nt in of a mature RNA of ;22 nt incoding) sequences; (iii) high DNA se-quence similarity between orthologs in C. elegans and a related species, Caenorhabditis briggsae; and (iv) processing of the ;22-ntmature RNA from a stem-loop precursor transcript of ;65 nt (2, 3).An Extensive Class of Small RNAs in Caenorhabditis elegansRosalind C. Lee and Victor Ambros*SCIENCE VOL 294 26 OCTOBER 2001

The first of these was that let-7 RNA is phylogenetically conserved—in size and nucleotide sequence- in essentially all the bilaterally symmetric animals (Pasquinelli et al., 2000 Nature).

A second discovery that supported the relative ubiq-uity of tiny RNAs like lin-4 (1993)and let-7(2000) was the finding that small antisense RNAs of about 22 nt in length (called siRNAs) are central to RNA interference (RNAi) (see Sharp, 2001 Gene Dev. and references therein).

For example, exons can be extended or shortened, skipped or included, and introns can be removed or retained in the mRNA

alternative splicing

A general mechanisms of alternative splicing

RNA Silencing: The Genome’s

Immune SystemRonald H. A. Plasterk

Scienc vol 296 2002

Genomes are databases sensitive to invasion by viruses. In recent years, a

defense mechanism has been discovered, which turns out to be conserved

among eukaryotes. The system can be compared to the immune system in

several ways: It has speciÞcity against foreign elements and the ability to

amplify and raise a massive response against an invading nucleic acid. The

latter property is beginning to be understood at the molecular level.

Over the years, a number of RNAs that do not function as messenger RNAs (mRNAs), transfer RNAs (tRNAs), or ribosomal RNAs (rRNAs) have been discovered,mostly fortuitously. The non-mRNAs have been given a variety of names (1, 2); the term small RNAs (sRNAs) has been pre-dominant in bacteria, whereas the term noncoding RNAs (ncRNAs) has been pre-dominant in eukaryotes and will be used here. ncRNAs range in size from 21 to 25 nt for the large family of microRNAs (miRNAs) that modulate development in Caenorhabditis elegans, Drosophila, and mammals (3–8), up to ;100 to 200 nt for sRNAs commonly found as translational regulators in bacterial cells (9, 10) and to 10,000 nt for RNAs involved in gene silencing in higher eukaryotes (11–13). The functions described for ncRNAs thus far `are extremely varied (Table 1).

Table 1 Naturally occurring ribozymes and ribonucleoprotein enzymes

Ribozyme Sequenced Size Activity (reaction product)

examples (nt)

Hammerhead 11 40 Self-cleavage via

Hepatitis delta virus 2 90 transesterification (28,38 cyclic

Hairpin 1 70 phosphate)

Varkud satellite 1 160

Group I intron >1,500 210 Self-splicing via

Group II intron >700 500 transesterification (38-OH)

RNase P* >500 300 Pre-tRNA processing via

hydrolysis (38-OH)

Spliceosome* 70,50 180,100 RNA splicing via

(U2+U6 snRNAs) transesterification (38-OH)

Ribosome* >900 2,600 Peptidyl transfer (amide)

(23S rRNA)

Number of sequenced examples is a snapshot as of 2002 and is influenced by DNA-sequencing strategies and database upkeep; it may provide a rough indication of relative

abundance. RNAs in any group vary in size; the size provided here indicates the lower end of the length distribution for the natural examples.

Ribonucleoprotein enzymes. RNase P: bacterial and archaebacterial RNAs have the relevant activity in the absence of protein. Spliceosome: U2 and U6 small nuclear RNAs (snRNAs) alone show an activity related to the natural activity. Ribosome: no activity has yet been observed with protein-free, large-subunit rRNA.

The spreading signal may be the siRNAs itself, which could be continuously produced in cells that express dsRNA. It could also be envisioned that the siRNAs are replicated by the action of RdRPs.

Processes affected by ncRNAs.Process Example Function

Transcription 184-nt E. coli 6S Modulates promoter use

331-nt human 7SK Inhibits transcription elongation factor P-TEFb 875-nt human SRA Steroid receptor coactivator

Gene silencing 16,500-nt human Xist Required for X-chromosome I nactivation

100,000-nt human Air Required for autosomal gene imprinting Replication 451-nt human telomerase RNA Core of telomerase and telomere template

RNA processing 377-nt E. coli RNase P Catalytic core of RNase

186-nt human U2 snRNA Core of spliceosome

RNA modification 102-nt S. cerevisiae U18 C/D snoRNA Directs 2’-O-ribose methylation of target rRNA

189-nt S. cerevisiae snR8 H/ACA snoRNA Directs pseudouridylation of target rRNA

68-nt T. brucei gCYb gRNA Directs the insertion and excision of uridines

RNA stability 80-nt E. coli RyhB sRNA Targets mRNAs for degradation? Eukaryotic miRNA? Targets mRNAs for degradation?

mRNA translation 109-nt E. coli OxyS Represses translation by occluding ribosome binding 87-nt E. coli DsrA sRNA Activates translation by preventing formation of an inhibitory mRNA structure 22-nt C. elegans lin-4 miRNA Represses translation by pairing with 39 end of target mRNA

Protein stability 363-nt E. coli tmRNA Directs addition of tag to peptides on stalled ribosomesProtein Translocation 114-nt E. coli 4.5S RNA Integral component of signal recognition particle central to protein translocation across membranes

Table 1 Naturally occurring ribozymes and ribonucleoprotein enzymes

Ribozyme Sequenced Size Activity (reaction product)

Higher eukaryotes can mount antiviral immune responses induced by dsRNA. This process, called RNA interference, is sequence specific and can therefore be used to target gene expression.

Nature Immunology 3, 597 - 599 (2002) doi:10.1038/ni0702-597

1 According to one model for RNA silencing, there are two stages during which RNA is cleaved. a, In the first stage in Drosophila, the enzyme Dicer (identified by Bernstein et al.1) binds to double-stranded RNA produced by a virus or by mobile DNA, or introduced experimentally. Dicer cleaves the double-stranded RNA into fragments of 22 nucleotides each. b, Dicer then associates through its so-called PAZ domain with a relative of ARGONAUTE, another PAZ-domain-containing protein.c, This association would allow the 22-nucleotide RNA to be transferred to an RNase associated with the ARGONAUTE relative, guiding the RNase to single-stranded messenger RNAs that match the 22-nucleotide RNA. The RNase would then cleave the single-stranded RNAs (not shown).

Emerging clinical applications of RNA

RNA as a protein antagonist

Immunotherapy using mRNA-transfected dendritic cells

The small RNAs we know of ma

y only be the tip of an iceberg.

Our intention: