Editing Messenger RNA (section)

==Synthesis==
[[File:DNA transcription.svg|thumb|RNA polymerase transcribes a DNA strand to form mRNA]]
The brief existence of an mRNA molecule begins with transcription, and ultimately ends in degradation. During its life, an mRNA molecule may also be processed, edited, and transported prior to translation. Eukaryotic mRNA molecules often require extensive processing and transport, while [[prokaryotes|prokaryotic]] mRNA molecules do not. A molecule of [[Eukaryote|eukaryotic]] mRNA and the proteins surrounding it are together called a [[messenger RNP]].{{cn|date=February 2024}}

===Transcription===
{{main|Transcription (genetics)}}
Transcription is when RNA is copied from DNA in the nucleus. During transcription, [[RNA polymerase]] makes a copy of a gene from the DNA to mRNA as needed. This process differs slightly in eukaryotes and prokaryotes. One notable difference is that prokaryotic RNA polymerase associates with DNA-processing enzymes during transcription so that processing can proceed during transcription. Therefore, this causes the new mRNA strand to become double stranded by producing a complementary strand known as the tRNA strand, which when combined are unable to form structures from base-pairing. Moreover, the template for mRNA is the complementary strand of tRNA, which is identical in sequence to the anticodon sequence that the DNA binds to. The short-lived, unprocessed or partially processed product is termed ''precursor mRNA'', or ''[[pre-mRNA]]''; once completely processed, it is termed ''[[mature mRNA]]''.{{cn|date=February 2024}}

===Uracil substitution for thymine===
mRNA uses uracil (U) instead of thymine (T) in DNA. uracil (U) is the complementary base to adenine (A) during transcription instead of thymine (T). Thus, when using a template strand of DNA to build RNA, thymine is replaced with uracil. This substitution allows the mRNA to carry the appropriate genetic information from DNA to the ribosome for translation. Regarding the natural history, uracil came first then thymine; evidence suggests that RNA came before DNA in evolution.<ref>{{Cite web |title=The Information in DNA Is Decoded by Transcription {{!}} Learn Science at Scitable |url=http://www.nature.com/scitable/topicpage/the-information-in-dna-is-decoded-by-6524808 |access-date=2024-05-03 |website=www.nature.com |language=en}}</ref> The [[RNA World]] hypothesis proposes that life began with RNA molecules, before the emergence of DNA genomes and coded proteins. In DNA, the evolutionary substitution of thymine for uracil may have increased DNA stability and improved the efficiency of DNA replication.<ref>{{Cite web |title=RNA world (article) {{!}} Natural selection |url=https://www.khanacademy.org/science/ap-biology/natural-selection/origins-of-life-on-earth/a/rna-world |access-date=2024-05-03 |website=Khan Academy |language=en}}</ref><ref>{{Cite web |title=The presence of thymine the place of uracil also confers additional stability to DNA. How? |url=https://www.toppr.com/ask/question/the-presence-of-thymine-at-the-place-of-uracil-also-confers-additional-stability-to-dna/ |access-date=2024-05-04 |website=Toppr Ask |language=en}}</ref>

=== Eukaryotic pre-mRNA processing ===
{{main|Post-transcriptional modification}}
[[File:Gene structure eukaryote 2 annotated.svg|thumb|DNA gene is transcribed to pre-mRNA, which is then processed to form a mature mRNA, and then lastly translated by a ribosome to a protein]]
Processing of mRNA differs greatly among [[eukaryote]]s, [[bacteria]], and [[archaea]]. Non-eukaryotic mRNA is, in essence, mature upon transcription and requires no processing, except in rare cases.<ref>{{Cite book| vauthors = Watson JD |author-link=James Watson |title=Molecular Biology of the Gene, 7th edition|publisher=Pearson Higher Ed USA|date=February 22, 2013|isbn=9780321851499}}</ref> Eukaryotic pre-mRNA, however, requires several processing steps before its transport to the cytoplasm and its translation by the ribosome.

==== Splicing ====
{{main|RNA splicing}}
The extensive processing of eukaryotic pre-mRNA that leads to the mature mRNA is the [[RNA splicing]], a mechanism by which [[intron]]s or [[outron]]s (non-coding regions) are removed and [[exon]]s (coding regions) are joined.<ref>{{cite journal | url=https://www.nature.com/articles/s41580-022-00545-z | doi=10.1038/s41580-022-00545-z | title=The physiology of alternative splicing | date=2023 | journal=Nature Reviews Molecular Cell Biology | volume=24 | issue=4 | pages=242–254 | pmid=36229538 | vauthors = Marasco LE, Kornblihtt AR }}</ref><ref>{{cite journal | url=https://www.nature.com/articles/s41576-022-00556-8 | doi=10.1038/s41576-022-00556-8 | title=Regulation of pre-mRNA splicing: Roles in physiology and disease, and therapeutic prospects | date=2023 | journal=Nature Reviews Genetics | volume=24 | issue=4 | pages=251–269 | pmid=36526860 | vauthors = Rogalska ME, Vivori C, Valcárcel J }}</ref>

==== 5' cap addition ====
{{main|5' cap}}
[[File:5' cap labeled.svg|thumb|5' cap structure]]
A ''5' cap'' (also termed an RNA cap, an RNA [[7-methylguanosine]] cap, or an RNA m<sup>7</sup>G cap) is a modified guanine nucleotide that has been added to the "front" or [[5' end]] of a eukaryotic messenger RNA shortly after the start of transcription. The 5' cap consists of a terminal 7-methylguanosine residue that is linked through a 5'-5'-triphosphate bond to the first transcribed nucleotide. Its presence is critical for recognition by the [[ribosome]] and protection from [[RNase]]s.{{cn|date=February 2024}}

Cap addition is coupled to transcription, and occurs co-transcriptionally, such that each influences the other. Shortly after the start of transcription, the 5' end of the mRNA being synthesized is bound by a [[Capping enzyme|cap-synthesizing complex]] associated with [[RNA polymerase]]. This [[enzyme|enzymatic]] complex [[catalyze]]s the chemical reactions that are required for mRNA capping. Synthesis proceeds as a multi-step [[biochemistry|biochemical]] reaction.{{cn|date=February 2024}}

====Editing====
In some instances, an mRNA will be [[RNA editing|edited]], changing the nucleotide composition of that mRNA. An example in humans is the [[apolipoprotein B#RNA editing|apolipoprotein B]] mRNA, which is edited in some tissues, but not others. The editing creates an early stop codon, which, upon translation, produces a shorter protein. Another well-defined example is A-to-I (adenosine to inosine) editing, which is carried out by double-strand specific adenosine-to inosine editing (ADAR) enzymes. This can occur in both the open reading frame and untranslated regions, altering the structural properties of the mRNA. Although essential for development, the exact role of this editing is not fully understood <ref>{{cite journal | doi=10.1186/gm508 | doi-access=free | title=Adenosine-to-inosine RNA editing and human disease | date=2013 | journal=Genome Medicine | volume=5 | issue=11 | page=105 | pmid=24289319 | pmc=3979043 | vauthors = Slotkin W, Nishikura K }}</ref>

==== Polyadenylation ====
{{main|Polyadenylation}}
[[File:Polyadenylation.png|thumb|Polyadenylation]]
Polyadenylation is the covalent linkage of a polyadenylyl moiety to a messenger RNA molecule. In eukaryotic organisms most messenger RNA (mRNA) molecules are polyadenylated at the 3' end, but recent studies have shown that short stretches of uridine (oligouridylation) are also common.<ref name="Choi_2012">{{cite journal | vauthors = Choi YS, Patena W, Leavitt AD, McManus MT | title = Widespread RNA 3'-end oligouridylation in mammals | journal = RNA | volume = 18 | issue = 3 | pages = 394–401 | date = March 2012 | pmid = 22291204 | pmc = 3285928 | doi = 10.1261/rna.029306.111 }}</ref> The [[messenger RNA#Poly(A) tail|poly(A) tail]] and the protein bound to it aid in protecting mRNA from degradation by exonucleases. Polyadenylation is also important for transcription termination, export of the mRNA from the nucleus, and translation. mRNA can also be polyadenylated in prokaryotic organisms, where poly(A) tails act to facilitate, rather than impede, exonucleolytic degradation.{{cn|date=February 2024}}

Polyadenylation occurs during and/or immediately after transcription of DNA into RNA. After transcription has been terminated, the mRNA chain is cleaved through the action of an endonuclease complex associated with RNA polymerase. After the mRNA has been cleaved, around 250 adenosine residues are added to the free 3' end at the cleavage site. This reaction is catalyzed by [[polyadenylate polymerase]]. Just as in [[alternative splicing]], there can be more than one polyadenylation variant of an mRNA.

Polyadenylation site mutations also occur. The primary RNA transcript of a gene is cleaved at the poly-A addition site, and 100–200 A's are added to the 3' end of the RNA. If this site is altered, an abnormally long and unstable mRNA construct will be formed.

===Transport===
Another difference between eukaryotes and prokaryotes is mRNA transport. Because eukaryotic transcription and translation is compartmentally separated, eukaryotic mRNAs must be exported from the [[cell nucleus|nucleus]] to the [[cytoplasm]]—a process that may be regulated by different signaling pathways.<ref name=Quaresma2013>{{cite journal | vauthors = Quaresma AJ, Sievert R, Nickerson JA | title = Regulation of mRNA export by the PI3 kinase/AKT signal transduction pathway | journal = Molecular Biology of the Cell | volume = 24 | issue = 8 | pages = 1208–1221 | date = April 2013 | pmid = 23427269 | pmc = 3623641 | doi = 10.1091/mbc.E12-06-0450 }}</ref> Mature mRNAs are recognized by their processed modifications and then exported through the [[nuclear pore]] by binding to the cap-binding proteins CBP20 and CBP80,<ref name=kierzkowski2009>{{cite journal | vauthors = Kierzkowski D, Kmieciak M, Piontek P, Wojtaszek P, Szweykowska-Kulinska Z, Jarmolowski A | title = The Arabidopsis CBP20 targets the cap-binding complex to the nucleus, and is stabilized by CBP80 | journal = The Plant Journal | volume = 59 | issue = 5 | pages = 814–825 | date = September 2009 | pmid = 19453442 | doi = 10.1111/j.1365-313X.2009.03915.x | doi-access = free }}</ref> as well as the transcription/export complex (TREX).<ref name=strausser2002>{{cite journal | vauthors = Strässer K, Masuda S, Mason P, Pfannstiel J, Oppizzi M, Rodriguez-Navarro S, Rondón AG, Aguilera A, Struhl K, Reed R, Hurt E | title = TREX is a conserved complex coupling transcription with messenger RNA export | journal = Nature | volume = 417 | issue = 6886 | pages = 304–308 | date = May 2002 | pmid = 11979277 | doi = 10.1038/nature746 | bibcode = 2002Natur.417..304S | s2cid = 1112194 }}</ref><ref name=katahira2014>{{cite journal | vauthors = Katahira J, Yoneda Y | title = Roles of the TREX complex in nuclear export of mRNA | journal = RNA Biology | volume = 6 | issue = 2 | pages = 149–152 | date = 27 October 2014 | pmid = 19229134 | doi = 10.4161/rna.6.2.8046 | doi-access = free }}</ref> Multiple mRNA export pathways have been identified in eukaryotes.<ref name="Cenik2011">{{cite journal | vauthors = Cenik C, Chua HN, Zhang H, Tarnawsky SP, Akef A, Derti A, Tasan M, Moore MJ, Palazzo AF, Roth FP | title = Genome analysis reveals interplay between 5'UTR introns and nuclear mRNA export for secretory and mitochondrial genes | journal = PLOS Genetics | volume = 7 | issue = 4 | pages = e1001366 | date = April 2011 | pmid = 21533221 | pmc = 3077370 | doi = 10.1371/journal.pgen.1001366 | doi-access = free }}</ref>

In spatially complex cells, some mRNAs are transported to particular subcellular destinations. In mature [[neuron]]s, certain mRNA are transported from the [[Soma (biology)|soma]] to [[dendrite]]s. One site of mRNA translation is at polyribosomes selectively localized beneath synapses.<ref>{{cite journal | vauthors = Steward O, Levy WB | title = Preferential localization of polyribosomes under the base of dendritic spines in granule cells of the dentate gyrus | journal = The Journal of Neuroscience | volume = 2 | issue = 3 | pages = 284–291 | date = March 1982 | pmid = 7062109 | pmc = 6564334 | doi = 10.1523/JNEUROSCI.02-03-00284.1982 }}</ref> The mRNA for [[Arc/Arg3.1]] is induced by synaptic activity and localizes selectively near active [[synapse]]s based on signals generated by [[NMDA receptor]]s.<ref>{{cite journal | vauthors = Steward O, Worley PF | title = Selective targeting of newly synthesized Arc mRNA to active synapses requires NMDA receptor activation | journal = Neuron | volume = 30 | issue = 1 | pages = 227–240 | date = April 2001 | pmid = 11343657 | doi = 10.1016/s0896-6273(01)00275-6 | s2cid = 13395819 | doi-access = free }}</ref> Other mRNAs also move into dendrites in response to external stimuli, such as [[β-actin]] mRNA.<ref name=Job1912>{{cite journal | vauthors = Job C, Eberwine J | title = Localization and translation of mRNA in dendrites and axons | journal = Nature Reviews. Neuroscience | volume = 2 | issue = 12 | pages = 889–898 | date = December 2001 | pmid = 11733796 | doi = 10.1038/35104069 | author-link2 = James Eberwine | s2cid = 5275219 }}</ref> For export from the nucleus, actin mRNA associates with [[ZBP1]]<ref name=Oleynikov2003>{{cite journal | vauthors = Oleynikov Y, Singer RH | title = Real-time visualization of ZBP1 association with beta-actin mRNA during transcription and localization  | journal = Current Biology | volume = 13 | issue = 3 | pages = 199–207 | date = February 2003 | pmid =  12573215 | pmc = 4765734 | doi = 10.1016/s0960-9822(03)00044-7 | bibcode = 2003CBio...13..199O }}</ref> and later with [[Eukaryotic small ribosomal subunit (40S)|40S subunit]]. The complex is bound by a [[motor protein]] and is transported to the target location ([[Neurite|neurite extension]]) along the [[cytoskeleton]]. Eventually ZBP1 is [[Phosphorylation|phosphorylated]] by [[Src family kinase|Src]] in order for translation to be initiated.<ref name="Hüttelmaier_2005">{{cite journal | vauthors = Hüttelmaier S, Zenklusen D, Lederer M, Dictenberg J, Lorenz M, Meng X, Bassell GJ, Condeelis J, Singer RH | display-authors = 6 | title = Spatial regulation of beta-actin translation by Src-dependent phosphorylation of ZBP1 | journal = Nature | volume = 438 | issue = 7067 | pages = 512–515 | date = November 2005 | pmid = 16306994 | doi = 10.1038/nature04115 | s2cid = 2453397 | bibcode = 2005Natur.438..512H }}</ref> In developing neurons, mRNAs are also transported into growing [[axon]]s and especially growth cones. Many mRNAs are marked with so-called "zip codes", which target their transport to a specific location.<ref name=Oleynikov1998>{{cite journal | vauthors = Oleynikov Y, Singer RH | title = RNA localization: different zipcodes, same postman? | journal = Trends in Cell Biology | volume = 8 | issue = 10 | pages = 381–383 | date = October 1998 | pmid =  9789325 | pmc = 2136761 | doi = 10.1016/s0962-8924(98)01348-8 }}</ref><ref name=Ainger1997>{{cite journal | vauthors = Ainger K, Avossa D, Diana AS, Barry C, Barbarese E, Carson JH | title = Transport and localization elements in myelin basic protein mRNA | journal = The Journal of Cell Biology | volume = 138 | issue = 5 | pages = 1077–1087 | date = September 1997 | pmid = 9281585 | pmc = 2136761 | doi = 10.1083/jcb.138.5.1077 }}</ref> mRNAs can also transfer between mammalian cells through structures called [[tunneling nanotube]]s.<ref>{{cite journal | vauthors = Haimovich G, Ecker CM, Dunagin MC, Eggan E, Raj A, Gerst JE, Singer RH | title = Intercellular mRNA trafficking via membrane nanotube-like extensions in mammalian cells | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 114 | issue = 46 | pages = E9873–E9882 | date = November 2017 | pmid = 29078295 | pmc = 5699038 | doi = 10.1073/pnas.1706365114 | bibcode = 2017PNAS..114E9873H | doi-access = free }}</ref><ref>{{Cite journal | vauthors = Haimovich G, Dasgupta S, Gerst JE  |title=RNA transfer through tunneling nanotubes | journal = Biochemical Society Transactions | date = February 2021| volume = 49 | issue = 1 | pages = 145–160 |url=https://portlandpress.com/biochemsoctrans/article-abstract/49/1/145/227426/RNA-transfer-through-tunneling-nanotubes |doi=10.1042/BST20200113|pmid=33367488 |s2cid=229689880 }}</ref>

===Translation===
{{main|Translation (biology)}}
[[File:Peptide syn.svg|thumb|Translation of mRNA to protein]]
Because prokaryotic mRNA does not need to be processed or transported, translation by the [[ribosome]] can begin immediately after the end of transcription. Therefore, it can be said that prokaryotic translation is ''coupled'' to transcription and occurs ''co-transcriptionally''. <ref>{{cite journal | doi=10.3389/fmicb.2020.624830 | doi-access=free | title=Coupled Transcription-Translation in Prokaryotes: An Old Couple with New Surprises | date=2021 | journal=Frontiers in Microbiology | volume=11 | vauthors = Irastortza-Olaziregi M, Amster-Choder O | pmid=33552035 | pmc=7858274 }}</ref>

Eukaryotic mRNA that has been processed and transported to the cytoplasm (i.e., mature mRNA) can then be translated by the ribosome. Translation may occur at ribosomes free-floating in the cytoplasm, or directed to the [[endoplasmic reticulum]] by the [[signal recognition particle]]. Therefore, unlike in prokaryotes, eukaryotic translation ''is not'' directly coupled to transcription. It is even possible in some contexts that reduced mRNA levels are accompanied by increased protein levels, as has been observed for mRNA/protein levels of [[Eukaryotic translation elongation factor 1 alpha 1|EEF1A1]] in [[breast cancer]].<ref name=Lin2018>{{cite journal | vauthors = Lin CY, Beattie A, Baradaran B, Dray E, Duijf PH | title = Contradictory mRNA and protein misexpression of EEF1A1 in ductal breast carcinoma due to cell cycle regulation and cellular stress | journal = Scientific Reports | volume = 8 | issue = 1 | pages = 13904 | date = September 2018 | pmid = 30224719 | pmc = 6141510 | doi = 10.1038/s41598-018-32272-x | bibcode = 2018NatSR...813904L }}</ref>{{Primary source inline|date=June 2021}}