Editing RNA (section)

==RNA synthesis and processing==
===Synthesis===
Synthesis of RNA typically occurs in the cell nucleus and is usually catalyzed by an enzyme—[[RNA polymerase]]—using DNA as a template, a process known as [[Transcription (genetics)|transcription]]. Initiation of transcription begins with the binding of the enzyme to a [[promoter (biology)|promoter]] sequence in the DNA (usually found "upstream" of a gene). The DNA double helix is unwound by the [[helicase]] activity of the enzyme. The enzyme then progresses along the template strand in the 3’ to 5’ direction, synthesizing a complementary RNA molecule with elongation occurring in the 5’ to 3’ direction. The DNA sequence also dictates where termination of RNA synthesis will occur.<ref>{{cite journal | vauthors = Nudler E, Gottesman ME | title = Transcription termination and anti-termination in E. coli | journal = Genes to Cells | volume = 7 | issue = 8 | pages = 755–68 | date = August 2002 | pmid = 12167155 | doi = 10.1046/j.1365-2443.2002.00563.x | s2cid = 23191624 | doi-access =  }}</ref>

[[Primary transcript]] RNAs are often [[Post-transcriptional modification|modified]] by enzymes after transcription. For example, a [[poly(A) tail]] and a [[5' cap]] are added to eukaryotic [[pre-mRNA]] and [[intron]]s are removed by the [[spliceosome]].

There are also a number of [[RNA-dependent RNA polymerase]]s that use RNA as their template for synthesis of a new strand of RNA. For instance, a number of [[Orthornavirae|RNA viruses]] (such as poliovirus) use this type of enzyme to replicate their genetic material.<ref>{{cite journal | vauthors = Hansen JL, Long AM, Schultz SC | title = Structure of the RNA-dependent RNA polymerase of poliovirus | journal = Structure | volume = 5 | issue = 8 | pages = 1109–22 | date = August 1997 | pmid = 9309225 | doi = 10.1016/S0969-2126(97)00261-X | doi-access = free }}</ref> Also, RNA-dependent RNA polymerase is part of the [[RNA interference]] pathway in many organisms.<ref>{{cite journal | vauthors = Ahlquist P | title = RNA-dependent RNA polymerases, viruses, and RNA silencing | journal = Science | volume = 296 | issue = 5571 | pages = 1270–73 | date = May 2002 | pmid = 12016304 | doi = 10.1126/science.1069132 | bibcode = 2002Sci...296.1270A | s2cid = 42526536 }}</ref>

=== RNA processing ===
[[File:Synthesis of Pseudouridine.svg|class=skin-invert-image|thumb|Uridine to pseudouridine is a common RNA modification.]]
Many RNAs are involved in modifying other RNAs.
[[Intron]]s are [[Splicing (genetics)|spliced]] out of [[pre-mRNA]] by [[spliceosome]]s, which contain several [[small nuclear RNA]]s (snRNA),<ref name=Biochemistry/> or the introns can be ribozymes that are spliced by themselves.<ref>{{cite journal | vauthors = Steitz TA, Steitz JA | title = A general two-metal-ion mechanism for catalytic RNA | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 90 | issue = 14 | pages = 6498–502 | date = July 1993 | pmid = 8341661 | pmc = 46959 | doi = 10.1073/pnas.90.14.6498 | bibcode = 1993PNAS...90.6498S | doi-access = free }}</ref>
RNA can also be altered by having its nucleotides modified to  nucleotides other than [[adenosine|A]], [[cytidine|C]], [[guanosine|G]] and [[uridine|U]].
In eukaryotes, modifications of RNA nucleotides are in general directed by [[small nucleolar RNA]]s (snoRNA; 60–300&nbsp;nt),<ref name=transcriptome>{{cite book|title=Mining the transcriptome&nbsp;– methods and applications|url=http://kth.diva-portal.org/smash/get/diva2:10803/FULLTEXT01 | vauthors = Wirta W |date=2006|isbn=978-91-7178-436-0|publisher=School of Biotechnology, Royal Institute of Technology|location=Stockholm|oclc=185406288}}</ref> found in the [[nucleolus]] and [[Cajal body|cajal bodies]]. snoRNAs associate with enzymes and guide them to a spot on an RNA by basepairing to that RNA. These enzymes then perform the nucleotide modification. rRNAs and tRNAs are extensively modified, but snRNAs and mRNAs can also be the target of base modification.<ref>{{cite journal | vauthors = Xie J, Zhang M, Zhou T, Hua X, Tang L, Wu W | title = Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs | journal = Nucleic Acids Research | volume = 35 | issue = Database issue | pages = D183–87 | date = January 2007 | pmid = 17099227 | pmc = 1669756 | doi = 10.1093/nar/gkl873 }}</ref><ref>{{cite journal | vauthors = Omer AD, Ziesche S, Decatur WA, Fournier MJ, Dennis PP | title = RNA-modifying machines in archaea | journal = Molecular Microbiology | volume = 48 | issue = 3 | pages = 617–29 | date = May 2003 | pmid = 12694609 | doi = 10.1046/j.1365-2958.2003.03483.x | s2cid = 20326977 | doi-access =  }}</ref> RNA can also be methylated.<ref>{{cite journal | vauthors = Cavaillé J, Nicoloso M, Bachellerie JP | title = Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides | journal = Nature | volume = 383 | issue = 6602 | pages = 732–35 | date = October 1996 | pmid = 8878486 | doi = 10.1038/383732a0 | bibcode = 1996Natur.383..732C | s2cid = 4334683 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Kiss-László Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T | title = Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs | journal = Cell | volume = 85 | issue = 7 | pages = 1077–88 | date = June 1996 | pmid = 8674114 | doi = 10.1016/S0092-8674(00)81308-2 | s2cid = 10418885 | doi-access = free }}</ref>