RNA polymerase II

RNA polymerase II (RNAP II or Pol II) is a eukaryotic enzyme that plays a central role in the transcription of protein-coding genes. Using genomic DNA as a template, RNA polymerase II synthesizes matrix RNA precursor (mRNA), as well as most mRNAs and miRNAs. [2] [3]
RNA polymerase II is a highly conserved protein whose three-dimensional structure and mechanism of action in the major their features have not changed from yeast to mammals. [4]
RNA polymerase of yeast consists of 12 subunits having a total molecular weight of 550 kDa. RNA polymerase II is the most studied RNA polymerase. A large number of accessory proteins, mainly transcription factors, are required to initiate transcription involving RNA polymerase II.
Content
1 Subunit
2 Formation
3 Haloenzyme 4 Dependence on Chromatin Structure
5 Links
Subunits
"Core" of Purified Eukaryotic RNA Polymerase II (the eukaryotic core RNA polymerase II) [5] consists of 10-12 subunits (12 in human and yeast) and is not capable of independently recognizing promoter gene sequences. [6] The method of interaction of different subunits with each other has been studied in detail. [7]
RPB1-subunit with domains: green - RPB1-domain 1, blue - RPB1-domain 2
sand - RPB1-domain 3 < bractin - RPB1-domain 4
brown - RPB1-domain 6
pink - RPB1 CTD.
RPB1 (DNA-dependent RNA polymerase subunit 1) is an enzyme encoded in the human genome by the POLR2A gene and the RPO21 gene in yeast. RPB1 is the largest subunit of RNA polymerase II. In combination with some other subunits, RPB1 forms the DNA-binding site of the polymerase, a recess in which DNA is read into an RNA molecule. [8] The major interaction partner is RPB8. [7]
The subunit of RPB1 is the largest and contains a large number of C-terminal domains (up to 52 units per person, 26 per yeast). the seven-peptide repeats of Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7, which are critical for polymerase activity. [9] In general, this domain is quite evolutionarily conservative. Modifications such as phosphorylation are important modifiers of polymerase activity. Thus, at transcription initiation, high levels of Ser5 phosphorylation and low levels of Tyr1 and Ser2 phosphorylation are important, which must be phosphorylated, on the contrary, for transcription termination. [10]
Also, the C-terminal domain is a platform for interacting with many other proteins, involved in RNA transcription and processing: capsule, splicing, polyadenylation, etc. [10]. The RPB2 subunit is encoded by the POLR2B gene and is the second largest RNA polymerase II complex. In combination with at least two other subunits, it forms a structure that maintains contact between the DNA template and the newly synthesized RNA at the active site of the polymerase. [11] The RPB3 subunit is encoded by the POLR2C gene and is the third largest in the complex. It exists in the form of a subunit heterodimer, supporting the architecture of the polymerase nucleus. RPB3 interacts with RPB1-5, 7, 10-12. [7]
RPB4 - the fourth largest subunit encoded by the POLR2D gene, [12] performs stabilizing functions. RPB5 - encoded by the POLR2E gene. Two such subunits are present in RNA polymerase II. [13] RPB5 interacts directly with RPB1, RPB3, and RPB6. [7]
RPB6 is encoded by the POLR2F gene - stabilizes the position of the complex on the DNA template. [14]
RPB7 - is encoded by the POLR2G gene and probably plays a role in regulating polymerase activity. [15] RPB7 interacts with RPB1 and RPB5. [7]
RPB8 (POLR2H gene) - interacts with subunits RPB1-3, 5, and 7. [7]
RPB9 is a recess into which the DNA template enters and where it is read (transcribed) into an RNA product; formed by the subunits of RPB9 (POLR2I gene) and RPB1.
RPB10 - Encoded by POLR2L gene. It interacts with RPB1-3 and 5 subunits, as well as strongly with RPB3. [7]
RPB11 - a human being has three smaller subunits: POLR2J (RPB11-a), POLR2J2 (RPB11-b), and POLR2J3 [16] (RPB11-c).
RPB12 - a subunit interacts with RPB3 and RPB12 (POLR2K gene). [7]
Formation of RPB3 is involved in the assembly of RNA polymerase II. [17] The RPB2 and RPB3 subunits are combined immediately after biosynthesis of the polymerase components. [17] They in turn interact with RPB1. [17] RPB3, RPB5, and RPB7 interact with each other to form homodimers, after which RPB3 together with RPB5 are able to merge all other subunits except RPB9. [7] Only RPB1 interacts strongly with RPB5. [7] The RPB1 subunit interacts with RPB7, RPB10, and to some extent with RPB8. [7] As soon as RPB1 joins the complex, other subunits, such as RPB5 and RPB7, may also be part of it; in turn, RPB5 joins RPB6 and RPB8, and RPB3 joins RPB10, RPB 11, and RPB12. [7] RPB4 and RPB9 join in the final assembly phase. RPB4 binds to RPB7. [7]
Holoenzyme
The holoenzyme RNA polymerase II is a complex consisting of the polymerase itself, transcription factors and other regulatory proteins to initiate transcription at the promoters of protein-coding genes. [6]
The part of the holoenzyme is called the preinitiation complex, because it is this complex of proteins that is formed before transcription begins. The mediator complex acts as a mediator between RNA polymerase II and transcription factors.
Chromatin structure dependence
RNA polymerase II activity is indirectly dependent on local chromatin structure, namely, post-translational histone modifications.
References
↑ Meyer PA, Ye P, Zhang M, Suh MH, Fu J (Jun 2006). Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model. Structure. 14 (6). with. 973–82. doi: 10.1016 / j.str.2006.04.003. PMID 16765890.
↑ Kornberg R (1999).
↑ Sims, R. J. 3rd; Mandal, S. S.; Reinberg, D. (June 2004). ↑ Carrie Bernecky, Franz Herzog, Wolfgang Baumeister, Jürgen M. Plitzko, Patrick Cramer. Structure of transcribing mammalian RNA polymerase II // Nature. - 2016. - Vol. 529. P. 551–554. - DOI: 10.1038 / nature16482.
↑ Sawadogo M, Sentenac A (1990).
My a b Myer VE, Young RA (October 1998). Acker J, de Graaff M, Cheynel I, Khazak V, Kedinger C, Vigneron M (Jul 1997).
↑ "Entrez Gene: POLR2A polymerase (RNA) II (DNA directed) polypeptide A, 220kDa".
↑ Brickey WJ, Greenleaf AL (June 1995).
Od a b Odil Porrua & amp; Domenico Libri (March 2015). Transcription termination and transcriptome control: why, where and how to stop. Nature reviews. Molecular cell biology 16 (3). with. 190–202. doi: 10.1038 / nrm3943. PMID 25650800.
↑ «Entrez Gene: POLR2B polymerase (RNA) II (DNA directed) polypeptide B, 140kDa».
↑ Khazak V, Estojak J, Cho H, Majors J, Sonoda G, Testa JR, Golemis EA (May 1998). ↑ «Entrez Gene: POLR2E polymerase (RNA) II (DNA directed) polypeptide E, 25kDa ».
↑ «Entrez Gene: POLR2F polymerase (RNA) II (DNA directed) polypeptide F».
↑ «Entrez Gene: POLR2G polymerase (RNA) II (DNA directed) polypeptide G».
↑ «POLR2J3 polymerase (RNA) II (DNA directed) polypeptide J3».


Kolodziej PA, Young RA (Sep 1991).
n



Gene Expression - Basic Concepts
Nucleotide Sequence
Gene
Intron
Exon
Genetic code
Genome
Central molecular biology dogma
Standard direction: DNA (+ DNA) → mRNA → Protein
"Non-canonical" direction:
RNA → RNA
RNA → DNA
Protein → Protein
Transcription - Transcription Factors
Transcription Termination Factors
RNA Polymerase (Eukaryotic: I, II, III)
Promoter
Open Reading Frame - Operon - RNA Processing Pre-mRNA - Capsule - Splicing - Polyadenylation - Edit RNA Modification
RNA Modification
Pseudorudinylation
Broadcasting
Broadcasting Factors
FI
FE
FT
Ribosomes
tRNA
rRNA
Ribosomal Proteins [ en]
Posttranslational Modifications - Regulation of Gene Expression - Epigenetic Regulation - DNA Methylation
CpG Islet
Histone Methylation
Histone Acetylation and Deacetylation
Genomic Imprinting - Transcriptional Regulation - Regulatory Sequences - Activators
Enhancers - Repressors - Chromatin Remodeling
Post-Transcriptional Regulation
RNA Interference
miRNA
Al ternative splicing - Alternative polyadenylation - RNA degradation - Posttranslational regulation - Phosphorylation - Sumoylation - Glycosylation - Ubiquitination - Proteolysis


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