Editing Primary transcript (section)

== Production ==
{{main|Transcription (genetics)}}

The steps contributing to the production of primary transcripts involve a series of molecular interactions that initiate transcription of DNA within a cell's nucleus. Based on the needs of a given cell, certain DNA sequences are transcribed to produce a variety of RNA products to be translated into functional proteins for cellular use. To initiate the transcription process in a cell's nucleus, DNA double helices are unwound and [[hydrogen bond]]s connecting compatible nucleic acids of DNA are broken to produce two unconnected single DNA strands.<ref name="StrachanRead2004">{{cite book| vauthors = Strachan T, Read AP |title=Human Molecular Genetics 3|url=https://books.google.com/books?id=g4hC63UrPbUC|date=January 2004|publisher=Garland Science|isbn=978-0-8153-4184-0|pages=16–17}}</ref> One strand of the DNA template is used for transcription of the single-stranded primary transcript mRNA. This DNA strand is bound by an [[RNA polymerase]] at the [[promoter (genetics)|promoter]] region of the DNA.<ref name="Alberts3rd">{{cite book| vauthors = Alberts B |title=Molecular Biology of the Cell |chapter=RNA Synthesis and RNA Processing | edition = 3rd |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK28319/| via = NCBI |date=1994 |publisher=New York: Garland Science}}</ref>
[[File:Transcription.jpg|thumb|Transcription of DNA by RNA polymerase to produce primary transcript]]
In eukaryotes, three kinds of RNA—[[rRNA]], [[tRNA]], and mRNA—are produced based on the activity of three distinct RNA polymerases, whereas, in [[prokaryotes]], only one RNA polymerase exists to create all kinds of RNA molecules.<ref>{{cite web| vauthors = Griffiths AJ |title=An Introduction to Genetic Analysis |url= https://www.ncbi.nlm.nih.gov/books/NBK21853/|work=NCBI|date=2000 |publisher=New York: W.H. Freeman}}</ref> RNA polymerase II of eukaryotes transcribes the primary transcript, a transcript destined to be processed into mRNA, from the [[antisense]] DNA template in the 5' to 3' direction, and this newly synthesized primary transcript is complementary to the antisense strand of DNA.<ref name="StrachanRead2004" /> RNA polymerase II constructs the primary transcript using a set of four specific [[ribonucleoside]] monophosphate residues ([[adenosine monophosphate]] (AMP), [[cytidine monophosphate]] (CMP), [[guanosine monophosphate]] (GMP), and [[uridine monophosphate]] (UMP)) that are added continuously to the 3' hydroxyl group on the 3' end of the growing mRNA.<ref name="StrachanRead2004" />

Studies of primary transcripts produced by RNA polymerase II reveal that an average primary transcript is 7,000 [[nucleotide]]s in length, with some growing as long as 20,000 nucleotides in length.<ref name="Alberts3rd"/> The inclusion of both [[exon]] and [[intron]] sequences within primary transcripts explains the size difference between larger primary transcripts and smaller, mature mRNA ready for translation into protein.{{cn|date=July 2024}}

===Regulation===

A number of factors contribute to the activation and inhibition of transcription and therefore regulate the production of primary transcripts from a given DNA template.{{cn|date=July 2024}}

Activation of RNA polymerase activity to produce primary transcripts is often controlled by sequences of DNA called [[enhancers]]. [[Transcription factors]], proteins that bind to DNA elements to either activate or repress transcription, bind to enhancers and recruit enzymes that alter [[nucleosome]] components, causing DNA to be either more or less accessible to RNA polymerase. The unique combinations of either activating or inhibiting transcription factors that bind to enhancer DNA regions determine whether or not the gene that enhancer interacts with is activated for transcription or not.<ref name="Gilbert2013">{{cite book| vauthors = Gilbert SF |title=Developmental Biology|url=https://books.google.com/books?id=-e_bmgEACAAJ|date=15 July 2013|publisher=Sinauer Associates, Incorporated|isbn=978-1-60535-173-5|pages=38–39, 50}}</ref> Activation of transcription depends on whether or not the transcription elongation complex, itself consisting of a variety of transcription factors, can induce RNA polymerase to dissociate from the [[Mediator (coactivator)|Mediator]] complex that connects an enhancer region to the promoter.<ref name="Gilbert2013" /> [[File:Role of transcription factor in gene expression regulation.svg|thumb|Role of transcription factors and enhancers in gene expression regulation]]

Inhibition of RNA polymerase activity can also be regulated by DNA sequences called [[silencer (DNA)|silencer]]s. Like enhancers, silencers may be located at locations farther up or downstream from the genes they regulate. These DNA sequences bind to factors that contribute to the destabilization of the initiation complex required to activate RNA polymerase, and therefore inhibit transcription.<ref>{{cite book| vauthors = Brown TA | title=Genomes | chapter=Assembly of the Transcription Initiation Complex | date=2002 | edition = 2nd |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK21115/ | location = Oxford |publisher= Wiley-Liss}}</ref>

[[Histone]] modification by transcription factors is another key regulatory factor for transcription by RNA polymerase. In general, factors that lead to histone [[acetylation]] activate transcription while factors that lead to histone [[deacetylation]] inhibit transcription.<ref name="Lodish2008">{{cite book| vauthors = Lodish H |title=Molecular Cell Biology|url=https://books.google.com/books?id=K3JbjG1JiUMC|year=2008|publisher=W. H. Freeman|isbn=978-0-7167-7601-7|pages=303–306}}</ref> Acetylation of histones induces repulsion between negative components within nucleosomes, allowing for RNA polymerase access. Deacetylation of histones stabilizes tightly coiled nucleosomes, inhibiting RNA polymerase access. In addition to acetylation patterns of histones, methylation patterns at promoter regions of DNA can regulate RNA polymerase access to a given template. RNA polymerase is often incapable of synthesizing a primary transcript if the targeted gene's promoter region contains specific methylated cytosines— residues that hinder binding of transcription-activating factors and recruit other enzymes to stabilize a tightly bound nucleosome structure, excluding access to RNA polymerase and preventing the production of primary transcripts.<ref name="Gilbert2013" />

===R-loops===

[[R-loop]]s are formed during transcription. An R-loop is a three-stranded nucleic acid structure containing a DNA-RNA hybrid region and an associated non-template single-stranded DNA.  Actively transcribed regions of [[DNA]] often form R-loops that are vulnerable to [[DNA damage (naturally occurring)|DNA damage]].  Introns reduce R-loop formation and DNA damage in highly expressed yeast genes.<ref name="pmid28757210">{{cite journal | vauthors = Bonnet A, Grosso AR, Elkaoutari A, Coleno E, Presle A, Sridhara SC, Janbon G, Géli V, de Almeida SF, Palancade B | title = Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability | journal = Molecular Cell | volume = 67 | issue = 4 | pages = 608–621.e6 | date = August 2017 | pmid = 28757210 | doi = 10.1016/j.molcel.2017.07.002 | doi-access = free }}</ref>

===Transcription stress===

[[DNA damage (naturally occurring)|DNA damages]] arise in each cell, every day, with the number of damages in each cell reaching tens to hundreds of thousands, and such DNA damages can impede primary transcription.<ref name = Milano2024>{{cite journal |vauthors=Milano L, Gautam A, Caldecott KW |title=DNA damage and transcription stress |journal=Mol Cell |volume=84 |issue=1 |pages=70–79 |date=January 2024 |pmid=38103560 |doi=10.1016/j.molcel.2023.11.014 |url=}} {{CC-notice|cc=by4}}</ref>  The process of [[gene expression]] itself is a source of endogenous DNA damages resulting from the susceptibility of single-stranded DNA to damage.<ref name = Milano2024/>  Other sources of DNA damage are conflicts of the primary transcription machinery with the [[DNA replication]] machinery, and the activity of certain enzymes such as [[topoisomerase]]s and [[base excision repair]] enzymes.  Even though these processes are tightly regulated and are usually accurate, occasionally they can make mistakes and leave behind DNA breaks that drive [[chromosomal rearrangement]]s or [[cell death]].<ref name = Milano2024/>