RNA polymerase II

RNA polymerase II (RNAP II and Pol II) is a

Discovery

Early studies suggested a minimum of two RNAPs: one which synthesized rRNA in the

The eukaryotic core RNA polymerase II was first purified using transcription assays.^[10] The purified enzyme has typically 10–12 subunits (12 in humans and yeast) and is incapable of specific promoter recognition.^[11] Many subunit-subunit interactions are known.^[12]

• DNA-directed RNA polymerase II subunit RPB1 – an
  transcribed into RNA.^[14] It strongly interacts with RPB8.^[12]
• RPB2 (POLR2B) – the second-largest subunit that in combination with at least two other polymerase subunits forms a structure within the polymerase that maintains contact in the active site of the enzyme between the DNA template and the newly synthesized RNA.^[15]
• RPB3 (POLR2C) – the third-largest subunit. Exists as a heterodimer with another polymerase subunit, POLR2J forming a core subassembly. RPB3 strongly interacts with RPB1-5, 7, 10–12.^[12]
• RNA polymerase II subunit B4 (RPB4) – encoded by the POLR2D gene^[16] is the fourth-largest subunit and may have a stress protective role.
• RPB5 – In humans is encoded by the POLR2E gene. Two molecules of this subunit are present in each RNA polymerase II.^[17] RPB5 strongly interacts with RPB1, RPB3, and RPB6.^[12]
• RPB6 (POLR2F) – forms a structure with at least two other subunits that stabilizes the transcribing polymerase on the DNA template.^[18]
• RPB7 – encoded by POLR2G and may play a role in regulating polymerase function.^[19] RPB7 interacts strongly with RPB1 and RPB5.^[12]
• RPB8 (POLR2H) – interacts with subunits RPB1-3, 5, and 7.^[12]
• RPB9 – The groove in which the DNA template is transcribed into RNA is composed of RPB9 (POLR2I) and RPB1.
• RPB10 – the product of gene POLR2L. It interacts with RPB1-3 and 5, and strongly with RPB3.^[12]
• RPB11 – the RPB11 subunit is itself composed of three subunits in humans: POLR2J (RPB11-a), POLR2J2 (RPB11-b), and POLR2J3^[20] (RPB11-c).
• RPB12 – Also interacts with RPB3 is RPB12 (POLR2K).^[12]

Assembly

RPB3 is involved in RNA polymerase II assembly.^[21] A subcomplex of RPB2 and RPB3 appears soon after subunit synthesis.^[21] This complex subsequently interacts with RPB1.^[21] RPB3, RPB5, and RPB7 interact with themselves to form homodimers, and RPB3 and RPB5 together are able to contact all of the other RPB subunits, except RPB9.^[12] Only RPB1 strongly binds to RPB5.^[12] The RPB1 subunit also contacts RPB7, RPB10, and more weakly but most efficiently with RPB8.^[12] Once RPB1 enters the complex, other subunits such as RPB5 and RPB7 can enter, where RPB5 binds to RPB6 and RPB8 and RPB3 brings in RPB10, RPB 11, and RPB12.^[12] RPB4 and RPB9 may enter once most of the complex is assembled. RPB4 forms a complex with RPB7.^[12]

Kinetics

Bacterial RNA polymerase, a relative of RNA Polymerase II, switches between inactivated and activated states by translocating back and forth along the DNA.[23] Concentrations of [NTP]_eq = 10 μM GTP, 10 μM UTP, 5 μM ATP and 2.5 μM CTP, produce a mean elongation rate, turnover number, of ~1 bp (NTP)⁻¹ for bacterial RNAP, a relative of RNA polymerase II.^[23]

RNA polymerase II undergoes extensive co-transcriptional pausing during transcription elongation.^[24][25] This pausing is especially pronounced at nucleosomes, and arises in part through the polymerase entering a transcriptionally incompetent backtracked state.^[24] The duration of these pauses ranges from seconds to minutes or longer, and exit from long-lived pauses can be promoted by elongation factors such as TFIIS.^[26] In turn, the transcription rate influences whether the histones of transcribed nucleosomes are evicted from chromatin, or reinserted behind the transcribing polymerase.^[27]

Alpha-Amanitin

RNA polymerase II is inhibited by α-Amanitin^[28] and other amatoxins. α-Amanitin is a highly poisonous substance found in many mushrooms.^[5] The mushroom poison has different effects on each of the RNA Polymerases: I, II, III. RNAP I is completely unresponsive to the substance and will function normally while RNAP III has a moderate sensitivity. RNAP II, however, is completely inhibited by the toxin. Alpha-Amanitin inhibits RNAP II by strong interactions in the enzyme's "funnel", "cleft", and the key "bridge α-helix" regions of the RPB-1 subunit.^[29]

Holoenzyme

RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells.^[11] It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as SRB proteins.

Part of the assembly of the holoenzyme is referred to as the

• Chromatin structure oriented factors:
  (HMTs (Histone MethylTransferases)):
  COMPASS§† – (COMplex of Proteins ASsociated with Set1) – Methylates lysine 4 of histone H3: Is responsible of repression/silencing of transcription. A normal part of cell growth and transcription regulation within RNAP II.[30]
• Set2 – Methylates lysine 36 of histone H3: Set2 is involved in regulation transcription elongation through its direct contact with the CTD.^[31]
  (interesting irrelevant example: Dot1*‡ – Methylates lysine 79 of histone H3.)
• Bre1 – Ubiquinates (adds ubiquitin to) lysine 123 of histone H2B. Associated with pre-initiation and allowing RNA Pol II binding.

C-terminal Domain

The

Oxidative DNA damage may block RNA polymerase II transcription and cause strand breaks. An RNA templated transcription-associated recombination process has been described that can protect against DNA damage.^[34] During the G1/G0 stages of the cell cycle, cells exhibit assembly of homologous recombination factors at double-strand breaks within actively transcribed regions. It appears that transcription is coupled to repair of DNA double-strand breaks by RNA templated homologous recombination. This repair process efficiently and accurately rejoins double-strand breaks in genes being actively transcribed by RNA polymerase II.

See also

• Eukaryotic transcription
• Post-transcriptional modification
• RNA polymerase I
• RNA polymerase II holoenzyme
• RNA polymerase III
• Transcription (genetics)

References