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Encyclopedia > RNA polymerase II

RNA polymerase II (also called RNAP II and Pol II) transcribes DNA to synthesize precursors of mRNA and most snRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to its promoters and begin transcription. Transcription is the process through which a DNA sequence is enzymatically copied by an RNA polymerase to produce a complementary RNA. Or, in other words, the transfer of genetic information from DNA into RNA. In the case of protein-encoding DNA, transcription is the beginning of the process that ultimately... The general structure of a section of DNA Deoxyribonucleic acid (DNA) is a nucleic acid —usually in the form of a double helix— that contains the genetic instructions specifying the biological development of all cellular forms of life, and most viruses. ... The interaction of mRNA in a eukaryote cell. ... Ribonucleic acid (RNA) is a nucleic acid consisting of a string of covalently-bound nucleotides. ... Possible meanings: Kachin Defense Army Kentucky Distillers Association Kongsberg Defence & Aerospace This page expands a three-character combination which might be any or all of: an abbreviation, an acronym, an initialism, a word in English, or a word in another language. ... To meet Wikipedias quality standards, this article or section may require cleanup. ... In the context of genetics, a transcription factor is a regulatory protein that initiates the transcription of certain genes upon binding with DNA. The binding of a transcription factor to a specific DNA sequence can result in either an increased rate of transcription of the gene, known as activated transcription... In genetics, a promoter is a DNA sequence that enables a gene to be transcribed. ... Transcription is the process through which a DNA sequence is enzymatically copied by an RNA polymerase to produce a complementary RNA. Or, in other words, the transfer of genetic information from DNA into RNA. In the case of protein-encoding DNA, transcription is the beginning of the process that ultimately...


In the process of transcription (by any polymerase) there are three main stages: Transcription is the process through which a DNA sequence is enzymatically copied by an RNA polymerase to produce a complementary RNA. Or, in other words, the transfer of genetic information from DNA into RNA. In the case of protein-encoding DNA, transcription is the beginning of the process that ultimately...

  1. Initiation; requiring construction of the RNA polymerase complex on the gene's promoter.
  2. Elongation; the writing of the RNA transcript, highly moderated by several methods.
  3. Termination; the finishing of RNA writing and disassembly of the RNA polymerase complex.

Due to the range of genes PolII transcribes this is the polymerase that experiences greatest regulation, by a range of factors, at each stage of transcription. It is also one of the most complex in terms of polymerase cofactors involved. In genetics, a promoter is a DNA sequence that enables a gene to be transcribed. ...

Contents


Pol II Initiation

Preinitiation complex (PIC): the construction of the polymerase complex on the promoter. There is one common main conserved DNA sequence in the promoter, the TATA box where binding of the complex generally starts. The sequence TATA is located ‘-30’ nucleotides upstream of the Transcription Start Point (TSP). In addition, there are also some weakly conserved features including the B-Recognition Element (BRE), approximately 5 nucleotides upstream of the TATA box. A preinitiation complex (abbreiviated PIC) is an ordered combination of six general transcription factors: TFIIA TFIIB TFIID TFIIE TFIIF TFIIH The preinitiation complex combines with RNAP near the transcriptional start site, to support a basal level of transcription. ... A TATA box (also called Hogness box) is a DNA sequence (cis-element) found in the promoter region of most genes (it is considered to be a promoter sequence). ...


The following is the order in which the TAFs (TBP Associated Factors) attach:

  1. TBP (TATA Binding Protein, see TATA Binding Protein) and an attached complex TAFs, collectively known as TFIID (Transcription Factor for polymerase II D), bind at the TATA box.†
  2. TFIIA (three subunits) binds TFIID and DNA, stabilising the first interactions.
  3. TFIIB binds between TFIID and the location of Pol II binding in the near future. TFIIB binds partially sequence specifically, with some preference for BRE.
  4. TFIIF and Pol II (two subunits, RAP30 and RAP74, showing some similarity to bacterial sigma factors) enter the complex together. TFIIF helps to speed up the polymerization process.
  5. TFIIE enters the complex, and helps to open and close the PolII’s ‘Jaw’ like structure, which enables movement down the DNA strand. TFIIE and TFIIH enter concomitantly.
  6. Finally TFIIH binds. TFIIH is a large protein complex that contains among others the CDK7/cyclin H kinase complex and a DNA helicase. TFIIH has three functions: it binds specifically to the template strand to ensure that the correct strand of DNA is transcribed and melts or unwinds the DNA (ATP dependently) to separate the two strands using its Helicase activity. It has a kinase activity that phosphorylates the C-terminal domain (CTD) of Pol II at the amino acid serine. This switches the RNA polymerase to start producing RNA, which marks the end of initiation and the start of elongation. Finally it is essential for Nucleotide Excision Repair (NER) of damaged DNA. TFIIH and TFIIE strongly interact with one another. TFIIE affects TFIIH’s catalytic activity. Without TFIIE, TFIIH will not unwind the promoter.
  7. Mediator then encases all the transcription factors and the Pol II. Mediator interacts with enhancers, areas very far away (upstream or downstream) that help regulate transcription.

†Occasionally there is no TATA box at the promoter. In this case a TAF will bind sequence specifically, and force the TBP to bind non sequence specifically. TAFs are highly variable, and add a level of control to the initiation. Cartoon of the TATA binding protein structure. ... Helicases are a class of enzymes vital to all living organisms. ... // Nucleotide Excision Repair DNA constantly requires repair due to chemical damage that can occur to bases, and nucleotide excision repair (NER) is one of the mechanisms by which the cell can prevent unwanted mutations caused by base damage (see also Base excision repair). ... In genetics, an enhancer is a short region of DNA that can be bound with proteins (namely, the trans-acting factors, much like a set of transcription factors) to enhance transcription levels of genes (hence the name) in a gene-cluster. ...


Pol II Initiation Regulation

Initiation is regulated by many mechanisms. These can be separated into two main categories:

  1. Protein interference.
  2. Chromatin structure inhibition.

Protein interference is the process where some signaling protein interacts, either with the promoter or some stage of the partially constructed complex, to prevent further construction of the polymerase complex, so preventing initiation. This is generally a very rapid response and is used for fine level, individual gene control and for 'cascade' processes for a group of genes useful under a specific conditions (for example DNA repair genes or heat shock genes) Chromatin is the structural building block of a chromosome. ...


Chromatin structure inhibition is the process where the promoter is hidden by chromatin structure. Chromatin structure is controlled by post-transcriptional modification of the histones involved and leads to gross levels of high or low transcription levels. See: chromatin, histone and nucleosome. For a detailed treatment of a single example see: RNA polymerase control by chromatin structure. Chromatin is the structural building block of a chromosome. ... Chromatin is the structural building block of a chromosome. ... In biology, histones are the chief proteins of chromatin. ... Chromatin is the structural building block of a chromosome. ... In biology, histones are the chief proteins of chromatin. ... A nucleosome is a unit made of DNA and histones. ... This is an outline of an example mechanism of yeast cells by which chromatin structure and histone posttranslational modification help regulate and record the transcription of genes by RNA polymerase II. This pathway gives examples of regulation at these points of transcription: Pre-initiation (promotion by Bre1, histone modification) Initiation...


These methods of control can be combined in a modular method, aloowing very high specificity in transcription initiation control.


Regulation by phosphorylation

The largest subunit of Pol II (Rpb1) has a domain at its C-terminus that is called the CTD. This is the target of kinases and phosphatases. The phosphorylation of the CTD is an important regulation mechanism, as this allows attraction and rejection of factors that have a function in the transcription process. The CTD can be considered as a platform for transcription factors. A protein kinase is an enzyme that modifies other proteins by chemically adding phosphate groups to them (phosphorylation). ... A phosphatase is an enzyme that hydrolyses phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxy group. ... In the context of genetics, a transcription factor is a regulatory protein that initiates the transcription of certain genes upon binding with DNA. The binding of a transcription factor to a specific DNA sequence can result in either an increased rate of transcription of the gene, known as activated transcription...


The CTD consists of repetitions of an amino acid motif, out of which serines and threonines get phosphorylated. The amount of these repetitions varies. The yeast protein counts less repetitions than the mammalian one. There are many different combinations of phosphorylations possible on these repeats and these can change rapidly during transcription. The regulation of these phosphorylations and the consequences for the association of transcription factors plays a major role in the regulation of transcription. An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond. ... Serine is one of the 20 natural amino acids. ... Threonine is one of the 20 natural amino acids. ... Phosphorylation is the addition of a phosphate (PO4) group to a protein or a small molecule or the introduction of a phosphate group into an organic molecule. ...


Pol II Elongation

The process of elongation is the synthesis of a copy of the DNA into messenger RNA. RNA Pol II matches complementary RNA nucleotides to the template DNA by Watson-Crick base pairing. These RNA nucleotides are ligated and this results in a strand of messenger RNA. In genetics, a double-stranded DNA or RNA strand consists of two complementary strands of base pairs, which are non-covalently connected via two or three hydrogen bonds. ... Headline text this website sucks your mothers dickIn molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). ... The life cycle of an mRNA in a eukaryotic cell. ...


Pol II Elongation Regulation

RNA Pol II elongation promoters can be summarised in 3 classes:

  1. Drug/sequence-dependent arrest affected factors. Eg. SII (TFIIS) and PTEF-b protein families.
  2. Chromatin structure oriented factors. Based on histone post translational modifications - phosphorylation, acetylation, methylation and ubiquination.
    See: chromatin, histone, and nucleosome
  3. RNA Pol II catalysis improving factors. Improve the Vmax or Km of RNA Pol II, so inproving the catalytic quality of the polymerase enzyme. Eg. TFIIF, Elongin and ELL families.
    See: Enzyme kinetics, Henri-Michaelis-Menten kinetics, Michaelis constant, and Lineweaver-Burke diagram

As for initiation, protein interference, seen as the "drug/sequence-dependent arrest affected factors" and "RNA Pol II catalysis improving factors" provide a very rapid response and is used for fine level individual gene control. Elongation downregulation is also possible, in this case usually by blocking polymerase progress or by deactivating the polymerase. Chromatin is the structural building block of a chromosome. ... In biology, histones are the chief proteins of chromatin. ... A nucleosome is a unit made of DNA and histones. ... It has been suggested that this article or section be merged with Enzyme. ... Michaelis-Menten kinetics describe the rate of enzyme mediated reactions for many enzymes. ... Michaelis-Menten kinetics describe the rate of enzyme mediated reactions for many enzymes. ... In biochemistry, a Lineweaver-Burke diagram (also called a Lineweaver-Burke plot or double reciprocal plot) is a graphical representation of the Lineweaver-Burke equation of enzyme kinetics: where v is the reaction velocity, Km is the Michaelis-Menten constant, vmax is the maximum reaction velocity, and [S] is the...


Chromatin structure oriented factors are more complex than for initiation control. Often the chromating altering factor becomes bound to the polymerase complex, altering the histones as they are encountered and providing a semi-permenant 'memory' of previous promotion and transcription. For detailed treatment of an example see: RNA polymerase control by chromatin structure. This is an outline of an example mechanism of yeast cells by which chromatin structure and histone posttranslational modification help regulate and record the transcription of genes by RNA polymerase II. This pathway gives examples of regulation at these points of transcription: Pre-initiation (promotion by Bre1, histone modification) Initiation...


Pol II Termination

Termination is the process of breaking up of the polymerase complex and ending of the RNA strand. In eukaryotes using RNA Pol II this termination is very variable (up to 2000 bases), relying on post transcriptional modification. See: Messenger RNA and Polyadenylation. Kingdoms Eukaryotes are organisms with complex cells, in which the genetic material is organized into membrane-bound nuclei. ... The life cycle of an mRNA in a eukaryotic cell. ... Polyadenylation is the covalent linkage of a polyadenylyl moiety to a messenger RNA molecule. ...


Little regulation occurs at termination, although it has been proposed newly transcribed RNA is held in place if proper termination is inhibited, allowing very fast expression of genes given a stimulus. This has not been demonstrated in eukaryotes as of yet. Kingdoms Eukaryotes are organisms with complex cells, in which the genetic material is organized into membrane-bound nuclei. ...


  Results from FactBites:
 
B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. (346 words)
B2 RNA binds directly to RNA polymerase II to repress transcript synthesis.
B2 RNA is a small noncoding RNA polymerase III transcript that represses mRNA transcription in
Once B2 RNA is removed from preinitiation complexes, transcriptional activity is restored.
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