List of RNAs

The following is a list of RNAs in nature. Some of these categories are broad, while others are single RNA families.

RNAs involved in protein synthesis
Type Abbr. Function Distribution Ref.
Messenger RNA mRNA Codes for protein All organisms
Ribosomal RNA rRNA Translation All organisms
Signal recognition particle RNA 7SL RNA or SRP RNA Membrane integration All organisms [1]
Transfer RNA tRNA Translation All organisms
Transfer-messenger RNA tmRNA Rescuing stalled ribosomes Bacteria [2]
RNAs involved in post-transcriptional modification or DNA replication
Type Abbr. Function Distribution Ref.
Small nuclear RNA snRNA Splicing and other functions Eukaryotes and archaea [3]
Small nucleolar RNA snoRNA Nucleotide modification of RNAs Eukaryotes and archaea [4]
SmY RNA SmY mRNA trans-splicing Nematodes [5]
Small Cajal body-specific RNA scaRNA Type of snoRNA; Nucleotide modification of RNAs
Guide RNA gRNA mRNA nucleotide modification Kinetoplastid mitochondria [6]
Ribonuclease P RNase P tRNA maturation All organisms [7]
Ribonuclease MRP RNase MRP rRNA maturation, DNA replication Eukaryotes [8]
Y RNA RNA processing, DNA replication Animals [9]
Telomerase RNA Component TERC Telomere synthesis Most eukaryotes [10]
Spliced Leader RNA SL RNA mRNA trans-splicing, RNA processing
Regulatory RNAs
Type Abbr. Function Distribution Ref.
Antisense RNA aRNA, asRNA Transcriptional attenuation / mRNA degradation / mRNA stabilisation / Translation block All organisms [11][12]
Cis-natural antisense transcript cis-NAT Gene regulation
CRISPR RNA crRNA Resistance to parasites, by targeting their DNA Bacteria and archaea [13]
Long noncoding RNA lncRNA Regulation of gene transcription, epigenetic regulation Eukaryotes
MicroRNA miRNA Gene regulation Most eukaryotes [14]
Piwi-interacting RNA piRNA Transposon defense, maybe other functions Most animals [15][16]
Small interfering RNA siRNA Gene regulation Most eukaryotes [17]
Short hairpin RNA shRNA Gene regulation Most eukaryotes [18]
Trans-acting siRNA tasiRNA Gene regulation Land plants[19]
Repeat associated siRNA rasiRNA Type of piRNA; transposon defense Drosophila [20]
7SK RNA 7SK negatively regulating CDK9/cyclin T complex
Enhancer RNA eRNA Gene regulation [21]

http://www.nature.com/nrg/journal/v17/n4/abs/nrg.2016.4.html

Parasitic RNAs
Type Function Distribution Ref.
Retrotransposon Self-propagating Eukaryotes and some bacteria [22]
Viral genome Information carrier Double-stranded RNA viruses, positive-sense RNA viruses, negative-sense RNA viruses, many satellite viruses and reverse transcribing viruses
Viroid Self-propagating Infected plants [23]
Satellite RNA Self-propagating Infected cells
Other RNAs
Type Abbr. Function Distribution Ref.
Vault RNA vRNA, vtRNA Expulsion of xenobiotics (conjectured) [24]

See also

References

  1. ↑ Gribaldo S, Brochier-Armanet C (2006). "The origin and evolution of Archaea: a state of the art". Philos Trans R Soc Lond B Biol Sci. 361 (1470): 1007–22. doi:10.1098/rstb.2006.1841. PMC 1578729Freely accessible. PMID 16754611.
  2. ↑ Gillet R, Felden B (2001). "Emerging views on tmRNA-mediated protein tagging and ribosome rescue". Molecular Microbiology. 42 (4): 879–85. doi:10.1046/j.1365-2958.2001.02701.x. PMID 11737633.
  3. ↑ Thore S, Mayer C, Sauter C, Weeks S, Suck D (2003). "Crystal Structures of the Pyrococcus abyssi Sm Core and Its Complex with RNA". J. Biol. Chem. 278 (2): 1239–47. doi:10.1074/jbc.M207685200. PMID 12409299.
  4. ↑ Kiss T (2001). "Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs". The EMBO Journal. 20 (14): 3617–22. doi:10.1093/emboj/20.14.3617. PMC 125535Freely accessible. PMID 11447102.
  5. ↑ Jones TA, Otto W, Marz M, Eddy SR, Stadler PF (2009). "A survey of nematode SmY RNAs". RNA Biol. 6 (1): 5–8. doi:10.4161/rna.6.1.7634. PMID 19106623.
  6. ↑ Alfonzo JD, Thiemann O, Simpson L (1997). "The mechanism of U insertion/deletion RNA editing in kinetoplastid mitochondria". Nucleic Acids Research. 25 (19): 3751–59. doi:10.1093/nar/25.19.3751. PMC 146959Freely accessible. PMID 9380494.
  7. ↑ Pannucci JA, Haas ES, Hall TA, Harris JK, Brown JW (1999). "RNase P RNAs from some Archaea are catalytically active". Proc Natl Acad Sci USA. 96 (14): 7803–08. doi:10.1073/pnas.96.14.7803. PMC 22142Freely accessible. PMID 10393902.
  8. ↑ Woodhams MD, Stadler PF, Penny D, Collins LJ (2007). "RNase MRP and the RNA processing cascade in the eukaryotic ancestor". BMC Evolutionary Biology. 7: S13. doi:10.1186/1471-2148-7-S1-S13. PMC 1796607Freely accessible. PMID 17288571.
  9. ↑ Perreault J, Perreault JP, Boire G (2007). "Ro-associated Y RNAs in metazoans: evolution and diversification". Molecular Biology and Evolution. 24 (8): 1678–89. doi:10.1093/molbev/msm084. PMID 17470436.
  10. ↑ Lustig AJ (1999). "Crisis intervention: The role of telomerase". Proc Natl Acad Sci USA. 96 (7): 3339–41. doi:10.1073/pnas.96.7.3339. PMC 34270Freely accessible. PMID 10097039.
  11. ↑ Brantl S (2002). "Antisense-RNA regulation and RNA interference". Biochimica et Biophysica Acta. 1575 (1–3): 15–25. doi:10.1016/S0167-4781(02)00280-4. PMID 12020814.
  12. ↑ Brantl S (2007). "Regulatory mechanisms employed by cis-encoded antisense RNAs". Curr. Opin. Microbiol. 10 (2): 102–9. doi:10.1016/j.mib.2007.03.012. PMID 17387036.
  13. ↑ Brouns SJ, Jore MM, Lundgren M, et al. (August 2008). "Small CRISPR RNAs guide antiviral defense in prokaryotes". Science. 321 (5891): 960–4. doi:10.1126/science.1159689. PMID 18703739.
  14. ↑ Lin SL, Miller JD, Ying SY (2006). "Intronic microRNA (miRNA)". Journal of Biomedicine and Biotechnology. 2006 (4): 1–13. doi:10.1155/JBB/2006/26818. PMC 1559912Freely accessible. PMID 17057362.
  15. ↑ Horwich MD, Li C, Matranga C, Vagin V, Farley G, Wang P, Zamore PD (2007). "The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC". Current Biology. 17 (14): 1265–72. doi:10.1016/j.cub.2007.06.030. PMID 17604629.
  16. ↑ Ghildiyal M, Zamore PD (February 2009). "Small silencing RNAs: an expanding universe". Nat. Rev. Genet. 10 (2): 94–108. doi:10.1038/nrg2504. PMC 2724769Freely accessible. PMID 19148191.
  17. ↑ Ahmad K, Henikoff S (2002). "Epigenetic consequences of nucleosome dynamics". Cell. 111 (3): 281–84. doi:10.1016/S0092-8674(02)01081-4. PMID 12419239.
  18. ↑ Ahmad K, Henikoff S (2002). "Epigenetic consequences of nucleosome dynamics". Cell. 111 (3): 281–84. doi:10.1016/S0092-8674(02)01081-4. PMID 12419239.
  19. ↑ Vazquez F, Vaucheret H (2004). "Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs". Mol. Cell. 16: 69–79. doi:10.1016/j.molcel.2004.09.028. PMID 15469823.
  20. ↑ Desset S, Buchon N, Meignin C, Coiffet M, Vaury C (2008). Volff J, ed. "In Drosophila melanogaster the COM locus directs the somatic silencing of two retrotransposons through both Piwi-dependent and -independent pathways". PLoS ONE. 3 (2): e1526. doi:10.1371/journal.pone.0001526. PMC 2211404Freely accessible. PMID 18253480.
  21. ↑ "Enhancers as non-coding RNA transcription units: recent insights and future perspectives". Nat Rev Genet. doi:10.1038/nrg.2016.4L3.
  22. ↑ Boeke JD (2003). "The unusual phylogenetic distribution of retrotransposons: a hypothesis". Genome Research. 13 (9): 1975–83. doi:10.1101/gr.1392003. PMID 12952870.
  23. ↑ Flores R, Hernández C, Martínez de Alba AE, Daròs JA, Di Serio F (2005). "Viroids and viroid-host interactions". Annual Review of Phytopathology. 43: 117–39. doi:10.1146/annurev.phyto.43.040204.140243. PMID 16078879.
  24. ↑ Gopinath SC, Matsugami A, Katahira M, Kumar PK (2005). "Human vault-associated non-coding RNAs bind to mitoxantrone, a chemotherapeutic compound". Nucleic Acids Res. 33 (15): 4874–81. doi:10.1093/nar/gki809. PMC 1201340Freely accessible. PMID 16150923.

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