Editing Transcription (biology) (section)

=== Initiation ===
{{Multiple image
| direction         = vertical
| total_width       = 300
| image1            = Transcription initiation eukaryote A.svg
| caption1          = The regulatory sequence elements (yellow) at the start of a eukaryotic protein-coding gene, can be immediately upstream of the open read frame (ORF, red), or many kilobases away (upstream or downstream). Promoter and enhancer regions up-regulate (and silencers downregulate) transcription from DNA to mRNA. The 5' and 3' untranslated regions of that mRNA (UTR, blue) then regulate translation into the final protein product.<ref name="10.26826/1017">{{Cite book |last1=Pakay |first1=Julian |title=Threshold Concepts in Biochemistry |last2=Duivenvoorden |first2=Hendrika |last3=Shafee |first3=Thomas |last4=Clarke |first4=Kaitlin |publisher=La Trobe eBureau |year=2023 |isbn=978-0-6484681-9-6 |doi=10.26826/1017|s2cid=258899183 }}</ref>
| image2            = Transcription initiation eukaryote B.svg
| caption2          = During transcription initiation, proteins (dark grey semi-circles) bound to the DNA can be brought into proximity with each other since the intervening DNA can loop back on itself. In this way, the basal transcription machinery can interact with distant activators and repressors many kilobases upstream or downstream of the open reading frame.<ref name="10.26826/1017"/>
| footer            =
}}
Transcription begins with the RNA polymerase and one or more [[transcription factor|general transcription factors]] binding to a DNA [[Promoter (genetics)|promoter]] sequence to form an RNA polymerase-promoter closed complex. In the closed complex, the promoter DNA is still fully double-stranded.<ref name="MBOG"/>

RNA polymerase, assisted by one or more general transcription factors, then unwinds approximately 14 base pairs of DNA to form an RNA polymerase-promoter open complex. In the open complex, the promoter DNA is partly unwound and single-stranded. The exposed, single-stranded DNA is referred to as the "[[transcription bubble]]".<ref name="MBOG"/>

RNA polymerase, assisted by one or more general transcription factors, then selects a '''transcription start site''' in the transcription bubble, binds to an initiating [[Nucleoside triphosphate|NTP]] and an extending [[Nucleoside triphosphate|NTP]] (or a short RNA [[Primer (molecular biology)|primer]] and an extending NTP) complementary to the transcription start site sequence, and catalyzes bond formation to yield an initial RNA product.<ref name="MBOG"/>

In [[bacteria]], RNA polymerase [[holoenzyme]] consists of five subunits: 2 α subunits, 1 β subunit, 1 β' subunit, and 1 ω subunit. In bacteria, there is one general RNA transcription factor known as a [[sigma factor]]. RNA polymerase core enzyme binds to the bacterial general transcription (sigma) factor to form RNA polymerase holoenzyme and then binds to a promoter.<ref name="MBOG"/>
(RNA polymerase is called a holoenzyme when sigma subunit is attached to the core enzyme which is consist of 2 α subunits, 1 β subunit, 1 β' subunit only). Unlike eukaryotes, the initiating nucleotide of nascent bacterial mRNA is not capped with a modified guanine nucleotide. The initiating nucleotide of bacterial transcripts bears a 5′ triphosphate (5′-PPP), which can be used for genome-wide mapping of transcription initiation sites.<ref name="Boutard2016">{{cite journal|last1=Boutard|first1=Magali|title=Global repositioning of transcription start sites in a plant-fermenting bacterium|journal=Nature Communications|volume=7|year=2016|page=13783|doi=10.1038/ncomms13783|pmid=27982035|pmc=5171806|bibcode=2016NatCo...713783B|doi-access=free}}</ref>

In [[archaea]] and [[eukaryotes]], RNA polymerase contains subunits [[Sequence homology|homologous]] to each of the five RNA polymerase subunits in bacteria and also contains additional subunits. In archaea and eukaryotes, the functions of the bacterial general transcription factor sigma are performed by multiple general transcription factors that work together.<ref name="MBOG"/> In archaea, there are three general transcription factors: [[TATA-binding protein|TBP]], [[Archaeal transcription factor B|TFB]], and [[2,2,2-Trifluoroethanol|TFE]]. In eukaryotes, in [[RNA polymerase II]]-dependent transcription, there are six general transcription factors: [[TFIIA]], [[TFIIB]] (an [[orthologous|ortholog]] of archaeal TFB), [[TFIID]] (a multisubunit factor in which the key subunit, [[TATA-binding protein|TBP]], is an [[orthologous|ortholog]] of archaeal TBP), [[TFIIE]] (an [[orthologous|ortholog]] of archaeal TFE), [[TFIIF]], and [[TFIIH]]. The TFIID is the first component to bind to DNA due to binding of TBP, while TFIIH is the last component to be recruited. In archaea and eukaryotes, the RNA polymerase-promoter closed complex is usually referred to as the "[[Transcription preinitiation complex|preinitiation complex]]".<ref name="Roeder1991">{{cite journal|last1=Roeder|first1=Robert G.|title=The complexities of eukaryotic transcription initiation: regulation of preinitiation complex assembly|journal=Trends in Biochemical Sciences|volume=16|year=1991|issue=11|pages=402–8 |doi=10.1016/0968-0004(91)90164-Q|pmid=1776168}}</ref>

Transcription initiation is regulated by additional proteins, known as [[activator (genetics)|activators]] and [[repressor]]s, and, in some cases, associated [[coactivator]]s or [[coactivator|corepressors]], which modulate formation and function of the transcription initiation complex.<ref name="MBOG"/>

{{anchor|Promoter clearance}}