RNA polymerase II (Pol II) is a complex molecular machine found within the nucleus of eukaryotic cells, including animals, plants, and fungi. It is a fundamental enzyme that deciphers genetic instructions encoded in DNA. Pol II is responsible for the initial step of gene expression, a process that leads to the creation of proteins and other functional molecules that dictate a cell’s identity and activities. As a molecular reader, Pol II moves along a DNA strand and synthesizes a corresponding RNA molecule. Its precise and regulated operation is essential for all life processes, ensuring correct genetic information is accessed and utilized.
The Central Role of RNA Polymerase II in Gene Expression
RNA polymerase II holds a central position in the flow of genetic information by transcribing DNA into various types of RNA molecules. Its most recognized function is the synthesis of messenger RNA (mRNA) precursors, which carry the blueprints for protein synthesis from the DNA in the nucleus to the protein-making machinery in the cytoplasm. This process is a foundational step of the central dogma of molecular biology, describing the flow of genetic information from DNA to RNA to protein.
Beyond mRNA, RNA polymerase II also produces other non-coding RNA molecules with significant regulatory roles. These include small nuclear RNA (snRNA) and microRNA (miRNA). Small nuclear RNAs are involved in RNA splicing, a process that removes non-coding regions, called introns, from pre-mRNA molecules to create mature mRNA. MicroRNAs are small RNA molecules that regulate gene expression by influencing mRNA stability and translation, controlling cellular processes like cell differentiation and responses to stress.
The ability of RNA polymerase II to transcribe these diverse RNA types highlights its broad influence over cellular function. It determines which genes are turned “on” or “off” and to what extent. The accurate and controlled production of these RNA molecules by Pol II directly impacts cell proliferation, metabolic enzyme expression, signaling pathways, and cell fate decisions. Its multifaceted role makes it a highly regulated enzyme, with its activity finely tuned to meet the specific needs of the cell at any given moment.
The Process of Transcription: How RNA Polymerase II Works
Transcription by RNA polymerase II is a multi-step process that includes initiation, elongation, and termination.
Initiation
The process begins with initiation, where RNA polymerase II does not directly recognize specific DNA sequences. Instead, it relies on a collection of proteins called general transcription factors (GTFs) to correctly position itself at the promoter region of a gene, which is the DNA sequence signaling the start of a gene. The GTFs assemble with Pol II at the promoter to form a pre-initiation complex. One of these GTFs, TFIIH, unwinds the DNA double helix at the transcription start site, creating an open complex where the DNA strands are separated. TFIIH also phosphorylates the C-terminal domain (CTD) of the largest subunit of RNA polymerase II, a modification that helps initiate transcription and recruit enzymes for RNA processing.
Elongation
Following initiation, the enzyme enters the elongation phase. RNA polymerase II moves along the DNA template strand, reading the genetic code and synthesizing a new RNA strand in the 5′ to 3′ direction. During this movement, the enzyme unwinds the DNA helix in front of it and re-winds it behind, maintaining a transcription bubble of unwound DNA. As Pol II elongates the RNA chain, further phosphorylation of its CTD occurs, which helps recruit factors involved in RNA processing and elongation.
Eukaryotic DNA is tightly packaged around histone proteins to form structures called nucleosomes. To transcribe through these nucleosomes, RNA polymerase II requires assistance from a protein complex called FACT. FACT temporarily removes histone proteins from the nucleosome ahead of the polymerase, loosening the DNA so Pol II can pass, and then reassembles the nucleosome behind it.
Termination
The final phase is termination, where RNA polymerase II releases the newly synthesized RNA transcript and detaches from the DNA template. Unlike RNA polymerase I and III, RNA polymerase II does not have specific signals that directly terminate its transcription. For protein-coding genes, termination is often linked to the processing of the nascent mRNA. A poly(A) signal in the emerging RNA, followed by a GU-rich sequence downstream, signals the end of the transcript.
Once these sequences are transcribed, protein complexes bind to them, leading to the cleavage of the pre-mRNA transcript. An exonuclease then degrades the remaining RNA still associated with RNA polymerase II from its 5′ end. When this exonuclease “catches up” to the polymerase, it aids in dislodging Pol II from the DNA template, concluding that round of transcription. The CTD of RNA polymerase II is then dephosphorylated, allowing the enzyme to be recycled and participate in another round of transcription.
Distinguishing RNA Polymerase II from Other RNA Polymerases
Eukaryotic cells possess multiple types of RNA polymerases, each specialized for transcribing different classes of RNA molecules. In eukaryotes, there are three main nuclear RNA polymerases: RNA polymerase I (Pol I), RNA polymerase II (Pol II), and RNA polymerase III (Pol III).
RNA polymerase I is primarily responsible for synthesizing ribosomal RNA (rRNA), with the exception of the 5S rRNA subunit. Ribosomal RNA molecules are fundamental components of ribosomes, the cellular machinery responsible for protein synthesis. Pol I is located in the nucleolus, a specialized region within the nucleus where ribosome assembly occurs.
RNA polymerase III transcribes transfer RNA (tRNA) and the 5S rRNA subunit. Transfer RNA molecules are responsible for carrying specific amino acids to the ribosome during protein synthesis, ensuring the correct sequence of amino acids is incorporated into a growing protein chain. Pol III also synthesizes other small non-coding RNAs.
RNA polymerase II stands out due to its specific role in transcribing all protein-coding genes into messenger RNA (mRNA) precursors, as well as most small nuclear RNA (snRNA) and microRNA (miRNA). This unique function positions Pol II as the primary enzyme controlling the expression of genes that lead to protein production. The distinct roles of these three polymerases highlight the intricate organization of gene expression in eukaryotic cells, where different molecular machines are dedicated to producing the diverse RNA molecules required for various cellular functions.
The Significance of RNA Polymerase II
RNA polymerase II’s accurate and regulated activity is fundamental for cellular function, organismal development, and overall health. As the enzyme responsible for transcribing all protein-coding genes, it controls the production of virtually every protein in a cell. These proteins perform a vast array of functions, from catalyzing metabolic reactions and transporting molecules to providing structural support and responding to external stimuli. Without the proper functioning of RNA polymerase II, cells would be unable to produce the necessary proteins to carry out their specialized roles, disrupting the intricate balance required for life.
The regulation of gene expression, largely orchestrated by RNA polymerase II, is the basis for cellular differentiation, allowing a single fertilized egg to develop into a complex organism with diverse cell types, each with unique functions. The enzyme’s activity is finely tuned to ensure that genes are expressed at the correct time, in the right amount, and in the appropriate location within the organism. This precise control is important for normal development and a cell’s ability to adapt to changing environmental conditions.
Dysregulation of RNA polymerase II activity can lead to various cellular problems and is implicated in numerous diseases. For instance, aberrant gene expression, often linked to issues with Pol II function, is a hallmark of many cancers. Modulators that influence RNA polymerase II activity are therefore a focus of research for developing new therapeutic strategies. Its fundamental role in the flow of genetic information from DNA to functional proteins underscores its importance as a central player in the maintenance of life and health.