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#RNA polymerase II

9 public questions tagged with this topic.

Transcription in Eukaryotes

Termination of RNA pol II transcription occurs

Termination of RNA polymerase II transcription is coupled to three prime end processing and occurs after recognition of polyadenylation signal AAUAAA. CPSF-CstF machinery cleaves nascent RNA downstream of signal while polymerase continues transcribing one to two kilobases beyond cleavage site. Uncapped five prime monophosphate of downstream fragment becomes substrate for nuclear 5' to 3' exonuclease Xrn2 Rat1 torpedo that degrades RNA faster than elongation, eventually catching polymerase and triggering dissociation. Allosteric model also proposes conformational change after polyadenylation signal causing loss of elongation factors.

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 10: Pol II termination after polyadenylation signal; Alberts et al., Torpedo model of termination

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Transcription in Eukaryotes

Phosphorylation of Ser2 in CTD is associated with

During transition to productive elongation, CDK9 cyclin-dependent kinase of P-TEFb complex and later CDK12 phosphorylate serine two of CTD heptad repeats YSPTSPS, creating high density pattern near three prime end of gene body. Serine2-P CTD recruits histone chaperone FACT, Spt6, chromatin modifier Set2 responsible for H3K36 trimethylation, and cleavage and polyadenylation factors CPSF and CstF for messenger RNA three prime end formation. Exchange from serine five to serine two ensures temporal coupling of elongation, chromatin restoration, and termination. Phosphatase Fcp1 recycles polymerase after termination releasing from DNA.

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 10: Ser2-P marks elongation; J Biol Chem, CTD Ser2 phosphorylation elongation

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Transcription in Eukaryotes

Phosphorylation of Ser5 in CTD is associated with

Phosphorylation of CTD heptad serine five by TFIIH CDK7 occurs early during transcription, peaking within fifty base pairs downstream of promoter. Serine5-phosphorylated CTD serves as landing pad for capping enzyme complex containing RNA triphosphatase, guanylyltransferase, N7-methyltransferase activities, stimulating cotranscriptional cap addition when transcript reaches twenty to thirty nucleotides. Marker also recruits early spliceosome components and H3K4 methyltransferase Set1 complex via interaction with Paf1 elongation complex. Phosphatases Ssu72 and Rtr1 later dephosphorylate serine five as serine two phosphorylation rises during elongation progression toward gene end.

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 6: Ser5-P associated with initiation and promoter escape; PLoS Biology CTD phosphorylation dynamics

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Transcription in Eukaryotes

Heptapeptide repeat in CTD of RNA pol II is

Largest subunit of eukaryotic RNA polymerase II possesses unique C-terminal domain extension absent in Pol I and Pol III. Domain consists of tandem repeats of conserved heptapeptide Tyr-Ser-Pro-Thr-Ser-Pro-Ser, written YSPTSPS, twenty-six copies in yeast Saccharomyces cerevisiae and fifty-two copies in mammals providing extended tail. Conserved tyrosine one, serines two, five, seven can be phosphorylated, threonine four phosphorylated, prolines three and six isomerized, lysine seven acetylated, creating combinatorial CTD code read by processing factors coordinating transcription with capping, splicing, and termination.

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 10: Heptapeptide repeat YSPTSPS in CTD; Cell Biology of CTD code

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Transcription in Eukaryotes

TFIIH also has kinase activity for phosphorylation of

TFIIH includes CAK subcomplex cyclin activating kinase comprising CDK7 kinase, cyclin H, MAT1 assembly factor stabilizing kinase module. After promoter melting, CDK7 phosphorylates serine five residues within YSPTSPS heptad repeats of RPB1 C-terminal domain, converting initiation complex to early elongation state. Serine5 phosphorylation reduces affinity for Mediator, facilitating promoter escape, and creates binding site for capping enzymes and Set1 methyltransferase depositing H3K4 trimethylation. Later transcription factor P-TEFb containing CDK9 phosphorylates serine two to promote productive elongation and recruitment of polyadenylation and splicing machineries.

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 6: TFIIH kinase phosphorylates CTD Ser5; Lodish 9th ed., CTD code

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Transcription in Eukaryotes

TAFs are associated with

TAFs, TBP-associated factors, are integral components of TFIID assembling with TBP via histone-fold dimerization domains mimicking H3-H4 octamer structure and wrapping DNA. Human TFIID includes TAF1 largest with acetyltransferase and kinase activity recognizing initiator element, TAF2, TAF4, TAF6, TAF9 interacting with downstream promoter element, TAF3 recognizing H3K4 trimethylation. TAFs function as coactivators bridging enhancer-bound activators to basal machinery, with bromodomains binding acetylated histone tails and PHD fingers reading methylation marks, thereby integrating chromatin signaling into transcription initiation decisions at specific promoters spatially.

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 6: TAFs associated with TFIID; Lodish 9th ed., TAF coactivator functions

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Transcription in Eukaryotes

Core promoter of RNA pol II generally lies between

The functional core promoter of RNA polymerase II extends approximately from minus forty to plus forty relative to transcription start site plus one, sufficient to direct accurate basal transcription in vitro with purified general factors. This minimal region integrates potentially TATA box at minus thirty, BRE elements upstream and downstream, initiator Inr spanning plus one, downstream promoter element DPE at plus twenty-eight to thirty-two, and GC-rich SP1 binding sites. Combinatorial presence dictates affinity for TFIID and positioning of polymerase active site precisely over initiator nucleotide for initiation.

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 10: Core promoter -40 to +40; Alberts 7th ed., Eukaryotic promoter architecture and elements

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Transcription in Eukaryotes

TBP is a component of

TATA-binding protein functions within multisubunit TFIID complex comprising TBP plus thirteen to fourteen TBP-associated factors TAF1 to TAF14 forming lobe-like structures visible by electron microscopy. TFIID is first general transcription factor to bind core promoter, recognizing TATA box via TBP, initiator via TAF1 and TAF2, downstream promoter element via TAF6 and TAF9. TFIIA stabilizes TFIID-DNA interaction while TFIIB joins. Formation of TBP-TFIID promoter complex is rate-limiting step regulated by activators, coactivators like Mediator, and chromatin remodeling events controlling polymerase recruitment.

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 6: TFIID contains TBP and TAFs; Lodish 9th ed., Assembly of Pol II preinitiation complex

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Transcription in Eukaryotes

RNA polymerase II transcribes

RNA polymerase II is the central eukaryotic polymerase responsible for synthesizing messenger RNA precursors, long noncoding RNAs, many small nuclear RNAs such as U1, U2, U4, U5, and microRNA primary transcripts. Its unique largest subunit RPB1 harbors C-terminal domain of heptapeptide repeats YSPTSPS that undergoes dynamic phosphorylation regulating transcription cycle. Serine5 phosphorylation by TFIIH marks initiation and capping, serine2 phosphorylation by P-TEFb marks elongation and 3' processing. Polymerase II is extremely sensitive to amatoxin alpha-amanitin at 0.01 microgram per milliliter, causing liver failure due to transcriptional arrest.

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 10: RNA Pol II transcribes mRNA and snRNA; CTD code coupling

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