5.2 RNA polymerases and transcription factors
4 min read•august 16, 2024
RNA polymerases and transcription factors are key players in gene expression. These molecular machines work together to read DNA and create RNA, the first step in making proteins. Understanding their roles is crucial for grasping how cells control which genes are active.
This topic dives into the different types of RNA polymerases in various organisms and how they function. It also explores transcription factors, proteins that help regulate gene activity by binding to specific DNA sequences. Together, they form a complex system for fine-tuning gene expression.
RNA Polymerases: Structure vs Function
Eukaryotic RNA Polymerases
Top images from around the web for Eukaryotic RNA Polymerases
RNA Polymerase | Biology for Majors I View original
Is this image relevant?
Eukaryotic Transcription Gene Regulation | Biology for Non-Majors I View original
Is this image relevant?
Internal Structures of Eukaryotic Cells | Boundless Microbiology View original
Is this image relevant?
RNA Polymerase | Biology for Majors I View original
Is this image relevant?
Eukaryotic Transcription Gene Regulation | Biology for Non-Majors I View original
Is this image relevant?
1 of 3
Top images from around the web for Eukaryotic RNA Polymerases
RNA Polymerase | Biology for Majors I View original
Is this image relevant?
Eukaryotic Transcription Gene Regulation | Biology for Non-Majors I View original
Is this image relevant?
Internal Structures of Eukaryotic Cells | Boundless Microbiology View original
Is this image relevant?
RNA Polymerase | Biology for Majors I View original
Is this image relevant?
Eukaryotic Transcription Gene Regulation | Biology for Non-Majors I View original
Is this image relevant?
1 of 3
- Eukaryotic cells possess three distinct RNA polymerases (RNA pol I, II, and III) each transcribing specific RNA molecules
- RNA pol I transcribes ribosomal RNA (rRNA) genes for ribosome formation and protein synthesis
- RNA pol II transcribes protein-coding genes into messenger RNA (mRNA) and some small nuclear RNAs (snRNAs)
- RNA pol III transcribes transfer RNA (tRNA) genes, 5S rRNA, and other small RNAs for various cellular processes
- All three RNA polymerases share a conserved core structure but differ in subunit composition and regulatory mechanisms
- Catalytic core consists of β and β' subunits (prokaryotes) or homologs (eukaryotes) forming the active site for RNA synthesis
- Subunit composition varies among RNA polymerases
- RNA pol I (14 subunits)
- RNA pol II (12 subunits)
- RNA pol III (17 subunits)
Prokaryotic vs Eukaryotic RNA Polymerases
- Prokaryotic cells contain a single RNA polymerase transcribing all RNA types
- Key difference in transcriptional complexity between prokaryotes and eukaryotes
- Prokaryotes single RNA polymerase handles all transcription tasks
- Eukaryotes use specialized RNA polymerases for different RNA types
- Structural similarities between prokaryotic and eukaryotic RNA polymerases
- Conserved core structure across all domains of life
- Similar catalytic mechanism for RNA synthesis
RNA Polymerase Function and Regulation
- RNA polymerases catalyze the synthesis of RNA using DNA as a template
- Transcription process involves initiation, elongation, and termination phases
- Regulatory mechanisms differ among RNA polymerases
- RNA pol I regulated by upstream binding factor (UBF) and selectivity factor 1 (SL1)
- RNA pol II regulated by various general and specific transcription factors
- RNA pol III regulated by TFIIIA, TFIIIB, and TFIIIC
- Post-translational modifications of RNA polymerase subunits ( of C-terminal domain in RNA pol II)
Transcription Factors: Regulating Gene Expression
General Transcription Factors
- General transcription factors (GTFs) essential for
- Form part of the (PIC) at promoter regions
- Key GTFs include TFIIA, TFIIB, , TFIIE, TFIIF, and TFIIH
- TFIID contains TATA-binding protein (TBP) recognizing TATA box
- GTFs function in sequential assembly of PIC
- TFIID binds TATA box
- TFIIB bridges TFIID and
- TFIIF aids RNA polymerase II recruitment
- TFIIE and TFIIH facilitate DNA melting and promoter clearance
Specific Transcription Factors
- Bind to enhancer or silencer regions to activate or repress gene expression
- Respond to various cellular signals (hormones, growth factors, stress)
- Contain DNA-binding domains recognizing specific DNA sequences
- Zinc finger domain (Sp1 transcription factor)
- Helix-turn-helix domain (Homeodomain proteins)
- Leucine zipper domain (c-Fos and c-Jun proteins)
- Possess activation or repression domains interacting with other regulatory proteins
- Combinatorial control achieved through multiple transcription factor interactions
- Post-translational modifications alter activity, localization, or DNA-binding affinity
- Phosphorylation (CREB protein in response to cAMP signaling)
- (p53 protein in response to DNA damage)
RNA Polymerase and Transcription Factors: Interaction
Pre-Initiation Complex Assembly
- Sequential binding of general transcription factors and RNA polymerase to core promoter
- TFIID (containing TBP) recognizes and binds TATA box, initiating PIC formation
- TFIIB bridges TFIID and RNA polymerase II, positioning polymerase at transcription start site
- TFIIF associates with RNA polymerase II, aiding recruitment to promoter
- TFIIE and TFIIH facilitate DNA melting and promoter clearance
- Mediator complex bridges specific transcription factors at and general transcription machinery
Transcription Factor-Mediated Regulation
- Activator proteins enhance transcription initiation or reinitiation
- Interaction with PIC components (VP16 protein of Herpes Simplex Virus)
- Recruitment of chromatin remodeling complexes (SWI/SNF complex)
- Repressor proteins inhibit transcription
- Competition with activators for binding sites (NF-κB and IκB proteins)
- Recruitment of histone deacetylases (HDAC) to promote chromatin compaction
- Direct interaction between transcription factors and RNA polymerase subunits
- Modulation of polymerase activity or processivity during elongation
- Example σ factors in bacteria directing RNA polymerase to specific promoters
Promoter and Enhancer Regions: Significance in Transcription
Promoter Structure and Function
- Promoters DNA sequences upstream of transcription start site
- Binding sites for RNA polymerase and general transcription factors
- Core promoter elements guide PIC assembly
- TATA box (-25 to -30 bp upstream of start site)
- Initiator (Inr) (overlaps transcription start site)
- Downstream Promoter Element (DPE) (+28 to +32 bp downstream of start site)
- Proximal promoter elements within few hundred base pairs of start site
- Contain binding sites for specific transcription factors
- Fine-tune gene expression (GC box, CCAAT box)
Enhancers and Long-Range Regulation
- Distal regulatory elements located upstream, downstream, or within introns
- Contain clusters of binding sites for multiple transcription factors
- Act over long distances through DNA looping or chromatin remodeling
- Modular nature allows complex spatiotemporal regulation of gene expression
- Developmental regulation (β-globin locus control region)
- Tissue-specific expression (liver-specific albumin enhancer)
- Super-enhancers large clusters driving high-level expression of critical genes
- Associated with key developmental and disease-related genes (c-Myc in cancer)
- Insulators block enhancer action on promoters
- Maintain specificity of enhancer-promoter interactions
- CTCF protein binds insulators and mediates chromatin looping
Key Terms to Review (25)
5' cap addition: 5' cap addition is a crucial modification that occurs at the 5' end of eukaryotic mRNA molecules during the processing of pre-mRNA. This structure, consisting of a modified guanine nucleotide, serves several important functions such as enhancing mRNA stability, facilitating ribosome binding during translation, and assisting in mRNA export from the nucleus to the cytoplasm.
Acetylation: Acetylation is a biochemical process where an acetyl group (–COCH₃) is added to a molecule, often modifying proteins or DNA and influencing their function. This modification plays a critical role in gene expression, protein stability, and cellular regulation by affecting the interaction between molecules and their targets.
Chromatin immunoprecipitation (ChIP): Chromatin immunoprecipitation (ChIP) is a laboratory technique used to investigate the interaction between proteins and DNA within the chromatin structure. This method enables researchers to identify specific binding sites of transcription factors and RNA polymerases on DNA, providing insights into gene regulation and the mechanisms of transcription. By cross-linking proteins to DNA and subsequently isolating the protein-DNA complexes, ChIP reveals how various proteins influence gene expression and chromatin dynamics.
Core enzyme: A core enzyme is the essential component of RNA polymerase that is responsible for the synthesis of RNA during transcription. This enzyme binds to DNA and catalyzes the formation of RNA strands by incorporating ribonucleotides in a sequence determined by the DNA template. The core enzyme works in conjunction with various transcription factors to initiate and regulate the transcription process effectively.
Enhancers: Enhancers are regulatory DNA sequences that increase the likelihood of transcription of a particular gene by providing binding sites for transcription factors. They can function independently of their target gene's promoter and can act over large distances, influencing gene expression by looping the DNA to bring the enhancer into proximity with the promoter region.
MRNA processing: mRNA processing is the series of modifications that pre-messenger RNA undergoes to become mature messenger RNA, ready for translation. This process includes capping, polyadenylation, and splicing, which are essential for the stability, transport, and translation of mRNA in eukaryotic cells. Each modification plays a crucial role in ensuring that mRNA can be efficiently translated into proteins.
Phosphorylation: Phosphorylation is a biochemical process where a phosphate group is added to a molecule, typically a protein, which can alter the function and activity of that molecule. This process plays a crucial role in regulating various cellular activities, including gene expression, metabolism, and signal transduction pathways.
Pre-initiation complex: The pre-initiation complex (PIC) is a crucial assembly of proteins that forms at the promoter region of a gene, preparing it for transcription by RNA polymerase. This complex is essential for accurate and regulated transcription initiation, as it recruits RNA polymerase along with various transcription factors to the DNA template, ensuring that the transcription machinery is correctly positioned to start synthesizing RNA.
Promoter recognition: Promoter recognition refers to the process by which RNA polymerases identify and bind to specific DNA sequences known as promoters, initiating the transcription of genes. This is a critical first step in gene expression, as it determines where transcription will begin and which genes will be expressed. The accurate identification of promoters is facilitated by transcription factors that help recruit RNA polymerase to the correct site on the DNA.
Reporter assays: Reporter assays are experimental techniques used to measure the activity of specific regulatory elements in gene expression by linking them to a reporter gene that produces a measurable signal. These assays are particularly useful in understanding the effects of enhancers, silencers, and transcription factors on transcriptional regulation, revealing how genes can be controlled at the molecular level.
Rna polymerase holoenzyme: RNA polymerase holoenzyme is a multi-subunit enzyme complex that is essential for the transcription of DNA into RNA. It includes the core RNA polymerase enzyme and a sigma factor, which helps the complex recognize and bind to specific promoter regions on the DNA template, initiating the transcription process. This combination of subunits allows for precise regulation and initiation of gene expression in response to various cellular signals.
RNA polymerase I: RNA polymerase I is a multi-subunit enzyme responsible for synthesizing ribosomal RNA (rRNA) in eukaryotic cells. This enzyme plays a crucial role in the transcription process, specifically in the production of the rRNA components that form the structural and functional core of ribosomes, which are essential for protein synthesis.
RNA polymerase II: RNA polymerase II is an enzyme responsible for synthesizing messenger RNA (mRNA) in eukaryotic cells, playing a critical role in the transcription process. It transcribes protein-coding genes and is essential for the expression of genes regulated by various factors, including enhancers and silencers. Its interaction with transcription factors also helps facilitate precise control over gene expression.
RNA polymerase III: RNA polymerase III is an enzyme responsible for synthesizing small RNA molecules, including transfer RNA (tRNA), ribosomal RNA (5S rRNA), and other small non-coding RNAs. This enzyme plays a critical role in the transcription process, converting DNA sequences into RNA, which is essential for protein synthesis and various cellular functions. It operates within the eukaryotic nucleus and is vital for maintaining cellular homeostasis by generating the necessary RNA components for translation and ribosome assembly.
Sigma factor: A sigma factor is a protein that is essential for the initiation of transcription in prokaryotes by binding to RNA polymerase and directing it to specific promoter regions on the DNA. It plays a crucial role in recognizing the start sites of genes, thus enabling the RNA polymerase to properly initiate the synthesis of RNA from the DNA template.
Silencers: Silencers are regulatory DNA sequences that inhibit the transcription of specific genes in eukaryotic cells. They function by binding to repressor proteins that block the assembly of the transcription machinery, preventing RNA polymerase from initiating transcription and thus reducing gene expression.
TFIID: TFIID is a multi-subunit protein complex that plays a crucial role in the initiation of transcription by RNA polymerase II. It is essential for recognizing and binding to specific DNA sequences at the promoter regions of genes, thereby facilitating the recruitment of other transcription factors and RNA polymerase itself to initiate gene expression.
Transcription bubble: The transcription bubble is a localized region of unwound DNA that occurs during the process of transcription, where RNA polymerase synthesizes RNA from the DNA template. This structure forms as the double-stranded DNA separates to allow access for RNA polymerase, creating a small, transient region that enables the complementary base pairing between the template strand and the newly synthesized RNA.
Transcription complex: The transcription complex is a multi-protein assembly that facilitates the process of transcription, where DNA is converted into RNA. This complex includes RNA polymerase, transcription factors, and various other proteins that work together to initiate and regulate the transcription of specific genes, ensuring proper gene expression.
Transcription elongation: Transcription elongation is the process during gene expression in which RNA polymerase synthesizes a growing RNA strand by adding nucleotides complementary to the DNA template strand. This stage follows initiation and involves the progressive unwinding of the DNA helix, allowing RNA polymerase to traverse the DNA and extend the RNA transcript. The efficiency and fidelity of elongation are influenced by various transcription factors and the presence of RNA polymerases, which coordinate the synthesis of RNA molecules.
Transcription initiation: Transcription initiation is the first step in the process of gene expression where RNA polymerase binds to a specific region of DNA, called the promoter, to begin synthesizing RNA. This process involves several critical factors, including transcription factors that help position the RNA polymerase correctly and facilitate the unwinding of DNA strands. Successful transcription initiation is essential for accurate and efficient gene expression, as it sets the stage for the elongation and eventual production of mRNA.
Transcription termination: Transcription termination is the process by which RNA polymerase ceases transcription of a gene, resulting in the release of the newly synthesized RNA molecule. This crucial step ensures that RNA synthesis is accurately completed and occurs in response to specific signals, including sequences in the DNA template and the involvement of various transcription factors that interact with RNA polymerase.
Transcriptional activation: Transcriptional activation is the process by which specific proteins, known as transcription factors, increase the likelihood that a particular gene will be transcribed into RNA. This involves a complex interplay of regulatory elements that can enhance or inhibit gene expression, playing a crucial role in determining how genes are turned on or off in response to various signals.
Transcriptional repression: Transcriptional repression is the process by which gene expression is inhibited, preventing the transcription of specific genes into mRNA. This can occur through various mechanisms that silence gene activity, such as DNA methylation, histone modifications, and the action of repressor proteins. Understanding this process is crucial for comprehending how cells regulate gene expression and maintain cellular identity.
Ubiquitination: Ubiquitination is a cellular process that involves the attachment of ubiquitin, a small protein, to a target protein, marking it for degradation or regulating its function. This post-translational modification plays a critical role in maintaining cellular homeostasis, influencing various biological processes, and interacting with other regulatory mechanisms such as histone modifications and transcriptional control.