RNA polymerase II

RNA polymerase II
Name	RNA polymerase II
EC number	2.7.7.6
Caption	Crystal structure of Saccharomyces cerevisiae RNA polymerase II.
GO	0003899

RNA polymerase II. It is a multi-subunit enzyme responsible for transcribing all protein-coding genes in eukaryotic cells, as well as most snRNA and miRNA genes. This enzyme is a central component of the transcription machinery, synthesizing RNA molecules from a DNA template. Its activity is tightly regulated by a complex network of transcription factors and cofactors, making it a key focus of study in molecular biology and gene regulation.

Structure and subunits

The enzyme comprises twelve distinct subunits, designated Rpb1 through Rpb12 in yeast, with homologous counterparts in higher eukaryotes. The largest subunit, Rpb1, contains a unique C-terminal domain composed of heptapeptide repeats that are critical for recruiting processing factors. The overall architecture resembles a crab claw, with a central cleft that binds DNA and a secondary channel for nucleotide entry. Structural studies, including those by Roger Kornberg who won the 2006 Nobel Prize in Chemistry, have revealed detailed mechanisms of elongation and initiation. Key structural features are conserved from archaeal enzymes to the human enzyme, highlighting its fundamental role.

Transcription cycle

The cycle begins with pre-initiation complex assembly at promoter regions, guided by general transcription factors like TFIIB and TFIID. Following melting of the template, the enzyme initiates RNA synthesis, a step often regulated by the Mediator complex. During elongation, the enzyme processively moves along the DNA, a process aided by factors such as P-TEFb and DSIF. Termination is triggered by specific sequences and involves the cleavage and polyadenylation specificity factor, leading to the release of the nascent mRNA and dissociation of the enzyme from the DNA.

Regulation of activity

Activity is regulated at multiple levels, primarily through phosphorylation states of the C-terminal domain by kinases like CDK7 of TFIIH and CDK9 of P-TEFb. The Mediator complex integrates signals from sequence-specific activators such as p53 and estrogen receptor. Chromatin structure, modulated by complexes like SWI/SNF and histone modifications including acetylation by p300/CBP, also plays a critical role. Furthermore, non-coding RNAs and insulator elements can influence recruitment and progression.

Role in gene expression

It is indispensable for expressing the vast majority of eukaryotic genes, producing pre-mRNA transcripts that undergo 5' capping, splicing, and 3' polyadenylation. The C-terminal domain acts as a platform for recruiting RNA capping enzymes, the spliceosome, and polyadenylation factors, thereby coupling transcription with RNA processing. This coordination is essential for the proper maturation and export of mRNA to the cytoplasm for translation by the ribosome.

Diseases and clinical significance

Dysregulation is implicated in numerous diseases, including many cancers where mutations in subunits or associated factors like TFIIH are found. For example, mutations in the POLR2A gene encoding the largest subunit are linked to neurodevelopmental disorders. Inhibitors targeting its transcription, such as α-amanitin from the death cap mushroom and the drug triptolide, are used in research and have therapeutic potential. Aberrant activity is also associated with viral infections, as many viruses like HIV-1 and influenza A hijack the host enzyme for their replication.

Evolutionary conservation

The enzyme is highly conserved across the eukaryotic domain, with strong homology between the yeast and human enzymes. Its core structure and mechanism are also shared with the other eukaryotic RNA polymerases, I and III, and have origins in the simpler RNA polymerases of archaea and bacteria, such as those studied in E. coli. This deep conservation underscores its fundamental role in the central dogma of biology, from synthesizing messenger RNA to enabling complex gene regulatory networks.

Category:RNA polymerase