Editing Messenger RNA (section)

== Structure ==
[[File:MRNA structure.svg|thumb|700px|center|The structure of a mature eukaryotic mRNA. A fully processed mRNA includes a [[5' cap]], [[5' UTR]], [[coding region]], [[3' UTR]], and poly(A) tail.]]

=== Coding regions ===
{{main|Coding region}}
Coding regions are composed of [[codons]], which are decoded and translated into proteins by the ribosome; in eukaryotes usually into one and in prokaryotes usually into several. Coding regions begin with the [[start codon]] and end with a [[stop codon]]. In general, the start codon is an AUG triplet and the stop codon is UAG ("amber"), UAA ("ochre"), or UGA ("opal"). The coding regions tend to be stabilised by internal base pairs; this impedes degradation.<ref>{{cite journal | vauthors = Shabalina SA, Ogurtsov AY, Spiridonov NA | title = A periodic pattern of mRNA secondary structure created by the genetic code | journal = Nucleic Acids Research | volume = 34 | issue = 8 | pages = 2428–2437 | year = 2006 | pmid = 16682450 | pmc = 1458515 | doi = 10.1093/nar/gkl287 }}</ref><ref>{{cite journal | vauthors = Katz L, Burge CB | title = Widespread selection for local RNA secondary structure in coding regions of bacterial genes | journal = Genome Research | volume = 13 | issue = 9 | pages = 2042–2051 | date = September 2003 | pmid = 12952875 | pmc = 403678 | doi = 10.1101/gr.1257503 }}</ref> In addition to being protein-coding, portions of coding regions may serve as regulatory sequences in the [[pre-mRNA]] as [[exonic splicing enhancer]]s or [[exonic splicing silencer]]s.

=== Untranslated regions ===
{{main|5' UTR|3' UTR}}
[[File:Fbioe-09-718753-g002.jpg|thumb|Universal structure of eukaryotic mRNA, showing the structure of the 5' and 3' UTRs.]]
Untranslated regions (UTRs) are sections of the mRNA before the start codon and after the stop codon that are not translated, termed the [[five prime untranslated region]] (5' UTR) and [[three prime untranslated region]] (3' UTR), respectively. These regions are transcribed with the coding region and thus are [[exon]]ic as they are present in the mature mRNA. Several roles in gene expression have been attributed to the untranslated regions, including mRNA stability, mRNA localization, and [[translational efficiency]]. The ability of a UTR to perform these functions depends on the sequence of the UTR and can differ between mRNAs. Genetic variants in 3' UTR have also been implicated in disease susceptibility because of the change in RNA structure and protein translation.<ref>{{cite journal | vauthors = Lu YF, Mauger DM, Goldstein DB, Urban TJ, Weeks KM, Bradrick SS | title = IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance | journal = Scientific Reports | volume = 5 | pages = 16037 | date = November 2015 | pmid = 26531896 | pmc = 4631997 | doi = 10.1038/srep16037 | bibcode = 2015NatSR...516037L }}</ref>

The stability of mRNAs may be controlled by the 5' UTR and/or 3' UTR due to varying affinity for RNA degrading enzymes called [[ribonuclease]]s and for ancillary proteins that can promote or inhibit RNA degradation. (See also, [[C-rich stability element]].)

Translational efficiency, including sometimes the complete inhibition of translation, can be controlled by UTRs. Proteins that bind to either the 3' or 5' UTR may affect translation by influencing the ribosome's ability to bind to the mRNA. [[MicroRNA]]s bound to the [[3' UTR]] also may affect translational efficiency or mRNA stability.

Cytoplasmic localization of mRNA is thought to be a function of the 3' UTR. Proteins that are needed in a particular region of the cell can also be translated there; in such a case, the 3' UTR may contain sequences that allow the transcript to be localized to this region for translation.

Some of the elements contained in untranslated regions form a characteristic [[secondary structure]] when transcribed into RNA. These structural mRNA elements are involved in regulating the mRNA. Some, such as the [[SECIS element]], are targets for proteins to bind. One class of mRNA element, the [[riboswitch]]es, directly bind small molecules, changing their fold to modify levels of transcription or translation. In these cases, the mRNA regulates itself.

===Poly(A) tail===
{{main|Polyadenylation}}
The 3' poly(A) tail is a long sequence of [[adenine]] nucleotides (often several hundred) added to the [[3' end]] of the pre-mRNA. This tail promotes export from the nucleus and translation, and protects the mRNA from degradation.

=== Monocistronic versus polycistronic mRNA ===
{{see also|Cistron}}
An mRNA molecule is said to be monocistronic when it contains the genetic information to [[Translation (genetics)|translate]] only a single [[protein]] chain (polypeptide). This is the case for most of the [[Eukaryote|eukaryotic]] mRNAs.<ref name="Kozak_1983">
{{cite journal | vauthors = Kozak M | title = Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles | journal = Microbiological Reviews | volume = 47 | issue = 1 | pages = 1–45 | date = March 1983 | pmid = 6343825 | pmc = 281560 | doi = 10.1128/MMBR.47.1.1-45.1983}}
</ref><ref>{{cite journal | vauthors = Niehrs C, Pollet N | title = Synexpression groups in eukaryotes | journal = Nature | volume = 402 | issue = 6761 | pages = 483–487 | date = December 1999 | pmid = 10591207 | doi = 10.1038/990025 | bibcode = 1999Natur.402..483N | s2cid = 4349134 }}</ref> On the other hand, polycistronic mRNA carries several [[open reading frame]]s (ORFs), each of which is translated into a polypeptide. These polypeptides usually have a related function (they often are the subunits composing a final complex protein) and their coding sequence is grouped and regulated together in a regulatory region, containing a [[Promoter (biology)|promoter]] and an [[Operator (biology)|operator]]. Most of the mRNA found in [[bacteria]] and [[archaea]] is polycistronic,<ref name="Kozak_1983"/> as is the human mitochondrial genome.<ref name="MercerNeph2011">{{cite journal | vauthors = Mercer TR, Neph S, Dinger ME, Crawford J, Smith MA, Shearwood AM, Haugen E, Bracken CP, Rackham O, Stamatoyannopoulos JA, Filipovska A, Mattick JS |author-link10=John Stamatoyannopoulos | title = The human mitochondrial transcriptome | journal = Cell | volume = 146 | issue = 4 | pages = 645–658 | date = August 2011 | pmid = 21854988 | pmc = 3160626 | doi = 10.1016/j.cell.2011.06.051 }}</ref> Dicistronic or bicistronic mRNA encodes only two [[protein]]s.

=== mRNA circularization ===
[[File:Fgene-10-00006-g001.jpg|thumb|mRNA circularisation and regulation]]
In eukaryotes mRNA molecules form circular structures due to an interaction between the [[eIF4E]] and [[poly(A)-binding protein]], which both bind to [[eIF4G]], forming an mRNA-protein-mRNA bridge.<ref>{{cite journal | vauthors = Wells SE, Hillner PE, Vale RD, Sachs AB | title = Circularization of mRNA by eukaryotic translation initiation factors | journal = Molecular Cell | volume = 2 | issue = 1 | pages = 135–140 | date = July 1998 | pmid = 9702200 | doi = 10.1016/S1097-2765(00)80122-7 | citeseerx = 10.1.1.320.5704 }}</ref> Circularization is thought to promote cycling of ribosomes on the mRNA leading to time-efficient translation, and may also function to ensure only intact mRNA are translated (partially degraded mRNA characteristically have no m7G cap, or no poly-A tail).<ref>{{cite journal | vauthors = López-Lastra M, Rivas A, Barría MI | title = Protein synthesis in eukaryotes: the growing biological relevance of cap-independent translation initiation | journal = Biological Research | volume = 38 | issue = 2–3 | pages = 121–146 | year = 2005 | pmid = 16238092 | doi = 10.4067/S0716-97602005000200003 | doi-access = free }}</ref>

Other mechanisms for circularization exist, particularly in virus mRNA. [[Poliovirus]] mRNA uses a cloverleaf section towards its 5' end to bind PCBP2, which binds [[poly(A)-binding protein]], forming the familiar mRNA-protein-mRNA circle. [[Barley yellow dwarf virus]] has binding between mRNA segments on its 5' end and 3' end (called kissing stem loops), circularizing the mRNA without any proteins involved.

RNA virus genomes (the + strands of which are translated as mRNA) are also commonly circularized.<ref>{{cite journal | vauthors = Zhang X, Liang Z, Wang C, Shen Z, Sun S, Gong C, Hu X | title = Viral Circular RNAs and Their Possible Roles in Virus-Host Interaction | journal = Frontiers in Immunology | volume = 13 | pages = 939768 | date = 2022 | pmid = 35784275 | pmc = 9247149 | doi = 10.3389/fimmu.2022.939768 | doi-access = free }}</ref> During genome replication the circularization acts to enhance genome replication speeds, cycling viral RNA-dependent RNA polymerase much the same as the ribosome is hypothesized to cycle.