Editing Primary transcript (section)

==RNA processing==
{{Main|Post-transcriptional modification}}
Transcription, a highly regulated phase in gene expression, produces primary transcripts. However, transcription is only the first step which should be followed by many modifications that yield functional forms of RNAs.<ref name="Cooper GM">{{cite book| vauthors = Cooper GM |title=The Cell: A Molecular Approach |chapter=RNA Processing and Turnover |date=2000 | edition = 2nd |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK9864/ |publisher= Sunderland (MA): Sinauer Associates; 2000}}</ref> Otherwise stated, the newly synthesized primary transcripts are modified in several ways to be converted to their mature, functional forms to produce different proteins and RNAs such as mRNA, tRNA, and rRNA.{{cn|date=July 2024}}

===Processing===
The basic primary transcript modification process is similar for tRNA and rRNA in both eukaryotic and prokaryotic cells. On the other hand, primary transcript processing varies in mRNAs of prokaryotic and eukaryotic cells.<ref name="Cooper GM"/> For example, some prokaryotic bacterial mRNAs serve as templates for synthesis of proteins at the same time they are being produced via transcription. Alternatively, pre-mRNA of eukaryotic cells undergo a wide range of modifications prior to their transport from the nucleus to cytoplasm where their mature forms are translated.<ref name="Cooper GM"/> These modifications are responsible for the different types of encoded messages that lead to translation of various types of products. Furthermore, primary transcript processing provides a control for gene expression as well as a regulatory mechanism for the degradation rates of mRNAs. The processing of pre-mRNA in eukaryotic cells includes [[5' cap]]ping, [[polyadenylation|3' polyadenylation]], and [[alternative splicing]].{{cn|date=July 2024}}

===5' capping===
{{Main|Five-prime cap}}
Shortly after transcription is initiated in eukaryotes, a pre-mRNA's 5' end is modified by the addition of a [[5' cap|7-methylguanosine cap]], also known as a 5' cap.<ref name="Cooper GM"/> The 5' capping modification is initiated by the addition of a [[Guanosine triphosphate|GTP]] to the 5' terminal nucleotide of the pre-mRNA in reverse orientation followed by the addition of methyl groups to the G residue.<ref name="Cooper GM"/> 5' capping is essential for the production of functional mRNAs since the 5' cap is responsible for aligning the mRNA with the ribosome during translation.<ref name="Cooper GM"/>

===Polyadenylation===
{{Main|Polyadenylation}}
In eukaryotes, polyadenylation further modifies pre-mRNAs during which a structure called the [[poly-A tail]] is added.<ref name="Cooper GM"/> Signals for polyadenylation, which include several RNA sequence elements, are detected by a group of proteins which signal the addition of the poly-A tail (approximately 200 nucleotides in length). The polyadenylation reaction provides a signal for the end of transcription and this reaction ends approximately a few hundred nucleotides downstream from the poly-A tail location.<ref name="Cooper GM"/>

===Alternative splicing===
{{Main|Alternative splicing}}
Eukaryotic pre-mRNAs have their introns spliced out by [[spliceosome]]s made up of [[snRNP|small nuclear ribonucleoproteins]].<ref>{{cite book | vauthors = Weaver RF | date = 2005 | title = Molecular Biology | pages = 432–448 | publisher = McGraw-Hill| location = New York, NY| isbn = 0-07-284611-9}}</ref><ref>{{cite journal | vauthors = Wahl MC, Will CL, Lührmann R | title = The spliceosome: design principles of a dynamic RNP machine | journal = Cell | volume = 136 | issue = 4 | pages = 701–18 | date = February 2009 | pmid = 19239890 | doi = 10.1016/j.cell.2009.02.009 | hdl = 11858/00-001M-0000-000F-9EAB-8 | s2cid = 21330280 | hdl-access = free }}</ref>

In complex eukaryotic cells, one primary transcript is able to prepare large amounts of mature mRNAs due to alternative splicing. Alternative splicing is regulated so that each mature mRNA may encode a multiplicity of proteins. [[File:Alternativ splicing.png|thumb|Alternative splicing of the primary transcript]] The effect of alternative splicing in gene expression can be seen in complex eukaryotes which have a fixed number of genes in their genome yet produce much larger numbers of different gene products.<ref name="Cooper GM"/> Most eukaryotic pre-mRNA transcripts contain multiple introns and exons. The various possible combinations of 5' and 3' splice sites in a pre-mRNA can lead to different excision and combination of exons while the introns are eliminated from the mature mRNA. Thus, various kinds of mature mRNAs are generated.<ref name="Cooper GM"/> Alternative splicing takes place in a large protein complex called the [[spliceosome]]. Alternative splicing is crucial for tissue-specific and developmental regulation in gene expression.<ref name="Cooper GM"/> Alternative splicing can be affected by various factors, including mutations such as [[chromosomal translocation]].

In prokaryotes, splicing is done by [[autocatalytic]] cleavage or by endolytic cleavage. Autocatalytic cleavages, in which no proteins are involved, are usually reserved for sections that code for rRNA, whereas endolytic cleavage corresponds to tRNA precursors.