15.3 Eukaryotic Transcription
4 min read•june 14, 2024
Eukaryotic transcription is a complex process that turns DNA into RNA. It involves three main steps: initiation, , and . Each step requires specific proteins and enzymes to work together, ensuring accurate gene expression.
plays a crucial role in transcribing protein-coding genes. It works with general transcription factors to start transcription, then continues adding nucleotides to form . The process ends with the addition of a poly(A) tail, preparing the RNA for further processing.
Eukaryotic Transcription
Steps of eukaryotic transcription
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- Initiation
- assembles at the region
- such as , , , , , and bind to the along with RNA polymerase II
- , a subunit of TFIID, recognizes and binds to the sequence (typically TATAAA) located 25-30 base pairs upstream of the transcription start site
- Transcription factor IIB (TFIIB) binds to TBP and recruits RNA polymerase II to the promoter
- Transcription factors IIE (TFIIE) and IIH (TFIIH) join the complex to complete PIC formation
- TFIIH, which possesses activity, unwinds the DNA template strand to expose the transcription start site and enable RNA polymerase II to initiate transcription
- The unwound region forms a , allowing RNA polymerase II to access the template strand
- assembles at the region
- Elongation
- RNA polymerase II synthesizes the pre-mRNA molecule in the 5' to 3' direction by adding nucleotides complementary to the DNA template strand
- Elongation factors such as and help maintain the stability and processivity of RNA polymerase II during transcription elongation
- RNA polymerase II continues to synthesize the pre-mRNA until it reaches a termination signal
- Termination
- recognizes the polyadenylation signal sequence (typically AAUAAA) near the 3' end of the pre-mRNA
- binds to the GU-rich sequence located 20-40 nucleotides downstream of the polyadenylation signal
- The pre-mRNA is cleaved by the cleavage complex at a site 10-35 nucleotides downstream of the polyadenylation signal
- adds a poly(A) tail consisting of 200-250 adenine residues to the 3' end of the cleaved pre-mRNA
- RNA polymerase II and the associated transcription factors dissociate from the DNA template, marking the end of transcription
Function of RNA polymerase II
- Catalyzes the synthesis of pre-mRNA molecules from protein-coding genes by forming phosphodiester bonds between ribonucleotides
- Maintains the correct reading frame during transcription elongation to ensure accurate base pairing with the DNA template strand
- Interacts with various GTFs, , , and elongation factors to regulate the efficiency and fidelity of transcription
- Plays a crucial role in gene expression by producing pre-mRNA molecules that undergo further processing to yield mature mRNA for translation
Roles of RNA polymerases I, II, III
- transcribes genes in the nucleolus
- Synthesizes the 28S, 18S, and 5.8S rRNA components of the large and small ribosomal subunits
- rRNAs are essential for ribosome assembly and function in protein synthesis
- RNA polymerase II transcribes protein-coding genes in the nucleoplasm
- Produces pre-mRNA molecules that are processed into mature mRNA for translation
- Also transcribes some involved in and that regulate gene expression post-transcriptionally
- transcribes various small non-coding RNA genes in the nucleoplasm
- Synthesizes that deliver amino acids to ribosomes during protein synthesis
- Transcribes the 5S rRNA component of the large ribosomal subunit
- Produces other small such as (involved in splicing) and (a component of the signal recognition particle)
Transcription factors in gene regulation
- General transcription factors (GTFs) are required for the assembly of the pre-initiation complex (PIC) at the promoter region
- GTFs such as TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH ensure accurate positioning of RNA polymerase II and facilitate transcription initiation
- GTFs interact with the core promoter elements (TATA box, initiator, and downstream promoter element) to recruit RNA polymerase II
- Activators enhance the rate of transcription initiation
- Bind to specific DNA sequences called located upstream, downstream, or within introns of the regulated gene
- Interact with co-activators (CBP/p300) and the mediator complex to recruit and stabilize the PIC at the promoter
- Examples of activators include , , and
- Repressors reduce the rate of transcription initiation
- Bind to specific DNA sequences called located upstream, downstream, or within introns of the regulated gene
- Interact with co-repressors (Sin3, NCoR) to inhibit the assembly or stability of the PIC
- Examples of repressors include , , and
- Chromatin remodeling factors alter the accessibility of DNA to transcription factors and RNA polymerase II
- such as and add acetyl groups to lysine residues on histone tails, reducing chromatin compaction and increasing DNA accessibility
- remove acetyl groups from histone tails, promoting chromatin condensation and reducing DNA accessibility
- ATP-dependent chromatin remodeling complexes (, ) use energy from ATP hydrolysis to slide or evict nucleosomes, exposing DNA regions for transcription factor binding
Transcription and RNA processing
- The encompasses the region of DNA that is transcribed into a single RNA molecule, including the coding sequence and regulatory regions
- Co-transcriptional RNA processing occurs as the pre-mRNA is being synthesized:
- : Addition of a 7-methylguanosine cap to the 5' end of the pre-mRNA
- Splicing: Removal of introns and joining of exons to form the mature mRNA
- Polyadenylation: Addition of a poly(A) tail to the 3' end of the pre-mRNA
- These processes are coordinated with transcription to ensure efficient and accurate production of mature mRNA molecules
Key Terms to Review (58)
7SL RNA: 7SL RNA is a small RNA molecule that plays a crucial role in the process of eukaryotic transcription, specifically as a component of the signal recognition particle (SRP). This RNA helps direct the ribosome to the endoplasmic reticulum during protein synthesis, ensuring that proteins destined for secretion or membrane localization are properly synthesized. Its structure and function highlight the importance of non-coding RNAs in cellular processes.
Activators: Activators are proteins that bind to specific DNA sequences, enhancing the transcription of genes by promoting the recruitment of RNA polymerase and other necessary transcription factors. They play a crucial role in the regulation of gene expression in eukaryotic cells, working alongside enhancers and other regulatory elements to fine-tune the levels of transcription based on cellular signals and environmental conditions.
CAAT box: The CAAT box is a conserved nucleotide sequence found in the promoter region of eukaryotic genes. It plays a crucial role in the binding of transcription factors, enhancing gene expression efficiency.
Capping: Capping is the process of adding a modified guanine nucleotide to the 5' end of a newly synthesized eukaryotic mRNA molecule. This cap structure plays a crucial role in stabilizing the mRNA, facilitating its export from the nucleus, and enhancing its translation efficiency. The cap protects the mRNA from degradation and serves as a recognition signal for ribosomes during protein synthesis.
Chromatin structure: Chromatin structure refers to the organization and packaging of DNA within the nucleus of eukaryotic cells, where DNA is wrapped around histone proteins, forming nucleosomes. This intricate arrangement plays a crucial role in regulating gene expression and ensuring that genetic material is properly managed during processes like transcription and replication. The dynamic nature of chromatin structure allows for both compact packing of DNA and accessibility for transcriptional machinery, influencing how genes are turned on or off.
Cleavage and polyadenylation specificity factor (CPSF): CPSF is a multi-subunit protein complex that plays a crucial role in the post-transcriptional modification of eukaryotic mRNA by recognizing the polyadenylation signal and facilitating the cleavage of pre-mRNA at the correct site. This process is essential for generating mature mRNA molecules, which are critical for proper gene expression and regulation.
Cleavage stimulatory factor (CstF): Cleavage stimulatory factor (CstF) is a multi-protein complex that plays a critical role in the process of mRNA cleavage and polyadenylation during eukaryotic transcription. CstF is essential for the proper cleavage of pre-mRNA at the polyadenylation site, ensuring the stability and maturation of the resulting mRNA molecules. By facilitating the addition of a poly(A) tail, CstF helps to enhance mRNA stability, nuclear export, and translation efficiency.
CREB: CREB, or cAMP response element-binding protein, is a cellular transcription factor that plays a critical role in regulating gene expression in response to various signals, particularly those involving cyclic AMP (cAMP). It acts as a mediator of cellular responses to hormones and other signaling molecules, influencing processes such as metabolism, growth, and memory formation.
ELL: ELL stands for Enhancer Locus Location, a critical aspect of eukaryotic transcription that refers to the position of enhancer elements in relation to the genes they regulate. Enhancers are short regions of DNA that can significantly boost the transcription of specific genes, acting from a distance to control gene expression. Understanding ELL is crucial for grasping how enhancers interact with transcription factors and the transcriptional machinery during the process of gene expression.
Elongation: Elongation refers to the stage in transcription and translation where nucleotides or amino acids are sequentially added to a growing RNA or polypeptide chain, respectively. During this process, RNA polymerase or ribosomes catalyze the addition of these building blocks, allowing for the synthesis of RNA in transcription and proteins in translation. Elongation is crucial for gene expression and is characterized by specific mechanisms that ensure accuracy and efficiency.
Elongin: Elongin is a multi-protein complex that plays a critical role in the elongation phase of transcription in eukaryotic cells. It is involved in the recruitment of RNA polymerase II to promote efficient transcription elongation by stabilizing the transcription machinery as RNA synthesis progresses. This complex helps to facilitate the proper processing of RNA molecules and ensures that genes are expressed accurately.
Enhancers: Enhancers are regulatory DNA sequences that can significantly increase the transcription of specific genes. They function by providing binding sites for transcription factors, which are proteins that help initiate the process of transcription, ultimately influencing how genes respond to various signals in the cell. Enhancers can be located far away from the genes they regulate and are crucial for the precise control of gene expression, especially in eukaryotic organisms.
FACT: A FACT (Facilitates Chromatin Transcription) complex is a protein complex that reorganizes nucleosomes to make DNA more accessible for transcription. It plays a critical role in maintaining chromatin structure during the transcription process.
GC-rich boxes: GC-rich boxes are DNA sequences with a high frequency of guanine (G) and cytosine (C) nucleotides. They play a crucial role in the regulation of gene transcription in eukaryotic cells.
Gcn5: Gcn5 is a histone acetyltransferase (HAT) that plays a crucial role in the regulation of gene expression in eukaryotic cells. It is part of the Gcn5/PCAF family and is known for modifying histones, particularly by adding acetyl groups to lysine residues, which leads to an open chromatin structure that facilitates transcription. This modification is essential for the recruitment of transcription factors and RNA polymerase II to promoters, thereby enhancing transcriptional activity.
General transcription factors (GTFs): General transcription factors (GTFs) are essential protein complexes that help initiate the process of transcription in eukaryotic cells by facilitating the binding of RNA polymerase to the promoter region of a gene. They are critical for the formation of the transcription initiation complex, which is necessary for the accurate and efficient transcription of genes into messenger RNA (mRNA). GTFs interact with DNA sequences, other transcription factors, and RNA polymerase II, making them crucial players in gene expression regulation.
Helicase: Helicase is an essential enzyme that unwinds the double-stranded DNA helix during processes such as DNA replication and transcription. By breaking the hydrogen bonds between the base pairs, helicase creates two single-stranded templates that are crucial for the synthesis of new DNA or RNA strands. Its activity is critical for allowing other enzymes, like DNA polymerase or RNA polymerase, to access the genetic information stored in the DNA.
Histone acetyltransferases (HATs): Histone acetyltransferases (HATs) are enzymes that catalyze the addition of acetyl groups to specific lysine residues on histone proteins, which leads to an open chromatin structure and promotes gene transcription. This process is a key mechanism of epigenetic regulation, as the acetylation of histones alters their interaction with DNA, allowing transcription factors and RNA polymerase to access the DNA for transcription.
Histone deacetylases (HDACs): Histone deacetylases (HDACs) are a group of enzymes that remove acetyl groups from the lysine residues on histone proteins, leading to a more compact and transcriptionally inactive chromatin structure. This process is critical for regulating gene expression in eukaryotic cells by influencing chromatin remodeling and accessibility, thereby playing a significant role in the overall control of transcription.
ISWI: ISWI refers to a family of ATP-dependent chromatin remodeling complexes that are essential for regulating gene expression in eukaryotic cells. These complexes use the energy from ATP hydrolysis to reposition, eject, or restructure nucleosomes, thus influencing the accessibility of DNA to transcription factors and other regulatory proteins. ISWI complexes play a crucial role in maintaining chromatin structure and facilitating appropriate gene expression during various cellular processes.
MeCP2: MeCP2, or methyl CpG binding protein 2, is a protein that plays a crucial role in regulating gene expression in eukaryotic cells by binding to methylated DNA. This protein is essential for the development and functioning of the nervous system, and its mutations are linked to severe neurological disorders, particularly Rett syndrome. The connection between MeCP2 and both transcription regulation and nervous system disorders highlights its importance in cellular function and overall health.
MicroRNAs (miRNAs): MicroRNAs (miRNAs) are small, non-coding RNA molecules, typically 21-25 nucleotides long, that play a crucial role in regulating gene expression in eukaryotic cells. They function by binding to complementary sequences on target messenger RNAs (mRNAs), leading to mRNA degradation or inhibition of translation. This regulatory mechanism is essential for maintaining cellular processes such as development, differentiation, and response to environmental changes.
NF-κB: NF-κB (Nuclear Factor kappa-light-chain-enhancer of activated B cells) is a protein complex that plays a crucial role in regulating immune response, cell survival, and inflammation. This transcription factor is activated in response to various stimuli, including cytokines and stress signals, and is essential for mediating the cellular response to these signals by controlling the expression of specific genes.
Octamer boxes: Octamer boxes are DNA sequence elements found in the promoter region of genes. They play a crucial role in the regulation of gene transcription by binding specific transcription factors called octamer-binding proteins.
P300/CBP: p300/CBP refers to two closely related transcriptional co-activators, p300 and CREB-binding protein (CBP), which play essential roles in the regulation of gene expression in eukaryotic cells. These proteins are involved in various cellular processes by facilitating the assembly of transcriptional machinery and modifying chromatin structure, thus enhancing the transcription of specific genes in response to various signals.
Poly(A) polymerase: Poly(A) polymerase is an enzyme responsible for adding a polyadenylate (poly(A)) tail to the 3' end of eukaryotic mRNA molecules during transcription. This modification is crucial for mRNA stability, export from the nucleus, and efficient translation. By facilitating these processes, Poly(A) polymerase plays a significant role in gene expression regulation.
Pre-initiation complex (PIC): The pre-initiation complex (PIC) is a crucial assembly of transcription factors and RNA polymerase II that forms at the promoter region of a gene before the initiation of transcription in eukaryotic cells. This multi-protein complex ensures proper positioning of RNA polymerase II and is essential for accurately starting transcription. The formation of the PIC is a highly regulated process, involving various proteins that help the RNA polymerase recognize the promoter and begin synthesizing RNA.
Pre-mRNA: Pre-mRNA is the initial transcript synthesized from a DNA template during the process of transcription in eukaryotic cells. It contains both exons, which are coding regions, and introns, which are non-coding sequences that need to be removed before the mRNA can be translated into protein.
Promoter: A promoter is a specific DNA sequence where RNA polymerase binds to initiate transcription of a gene. It contains essential regulatory elements that control the expression of adjacent genes.
Promoter: A promoter is a specific DNA sequence located upstream of a gene that serves as a binding site for RNA polymerase and transcription factors, initiating the process of transcription. It plays a crucial role in determining when and how much a gene is expressed, influencing various biological processes and cellular functions.
Repressors: Repressors are proteins that bind to specific DNA sequences and inhibit gene transcription by blocking the binding of RNA polymerase to the promoter or by interfering with the formation of the transcriptional machinery. They play a crucial role in regulating gene expression in eukaryotic cells, ensuring that genes are only expressed when needed, which is essential for cellular function and differentiation.
REST: REST, or REgulatory SEquencing of Transcription, refers to a mechanism in eukaryotic transcription that ensures precise regulation of gene expression. It involves various factors and processes that influence how and when genes are transcribed into messenger RNA, thus playing a crucial role in cellular function and development. REST helps maintain the balance between gene activation and repression, ensuring that the right genes are expressed at the right times.
Ribosomal RNA (rRNA): Ribosomal RNA (rRNA) is a type of non-coding RNA that plays a crucial role in protein synthesis by serving as a fundamental component of ribosomes. Ribosomes are the cellular machinery that translate messenger RNA (mRNA) into proteins, and rRNA provides the structural framework and catalytic activity needed for this process. In eukaryotic cells, rRNA is produced in the nucleolus and then combined with ribosomal proteins to form the large and small subunits of the ribosome, which are essential for translation.
RNA polymerase I: RNA polymerase I is an essential enzyme in eukaryotic cells responsible for synthesizing ribosomal RNA (rRNA), which is a critical component of ribosomes. It primarily transcribes the genes encoding rRNA in the nucleolus, playing a significant role in the formation of ribosomal subunits necessary for protein synthesis, linking it to broader cellular functions.
RNA polymerase II: RNA polymerase II is a crucial enzyme in eukaryotic cells responsible for synthesizing messenger RNA (mRNA) from DNA during the transcription process. It plays a key role in gene expression by converting genetic information encoded in DNA into RNA, which can then be translated into proteins. This enzyme also facilitates the processing of pre-mRNA, including capping and polyadenylation, which are vital for mRNA stability and translation efficiency.
RNA polymerase III: RNA polymerase III is a multi-subunit enzyme responsible for synthesizing various types of RNA, including tRNA, 5S rRNA, and other small non-coding RNAs in eukaryotic cells. This enzyme plays a crucial role in transcription, which is the first step of gene expression, and is essential for producing the RNA molecules that are necessary for protein synthesis and various cellular processes.
RNAs: RNAs (ribonucleic acids) are essential molecules in the process of converting genetic information from DNA into proteins. They play diverse roles such as coding, decoding, regulation, and expression of genes.
Silencers: Silencers are regulatory DNA sequences that inhibit the transcription of specific genes in eukaryotic cells. They function by binding to repressor proteins, which then interact with the transcription machinery to prevent gene expression, thereby playing a crucial role in the precise control of gene regulation. This inhibition can be critical for cellular differentiation and response to environmental signals.
Small nuclear: Small nuclear RNA (snRNA) molecules are a component of the spliceosome, which is responsible for splicing pre-mRNA in eukaryotic cells. They play a critical role in the processing and modification of RNA transcripts during gene expression.
Small nuclear RNAs (snRNAs): Small nuclear RNAs (snRNAs) are a class of non-coding RNA molecules found in the nucleus of eukaryotic cells that play a critical role in the processing of pre-messenger RNA (pre-mRNA). They are essential components of the spliceosome, the molecular machine responsible for removing introns from pre-mRNA and facilitating the joining of exons, thus enabling the proper expression of genes. snRNAs are integral to the post-transcriptional modification processes that ultimately contribute to gene regulation and protein diversity.
Sp1: Sp1 is a transcription factor that binds to specific DNA sequences, playing a crucial role in the regulation of gene expression in eukaryotic cells. It is part of the Sp/KLF family of transcription factors and is known for its ability to activate or repress a variety of genes by interacting with their promoters, thus influencing cellular processes like growth, differentiation, and apoptosis.
Splicing: Splicing is the process by which introns are removed and exons are joined together in a pre-mRNA molecule to produce a mature mRNA transcript. This mechanism is crucial for gene expression in eukaryotic cells, as it ensures that only the coding sequences are translated into proteins. Proper splicing is essential for generating functional proteins and contributes to the diversity of proteins that can be produced from a single gene through alternative splicing.
SWI/SNF: SWI/SNF is a multi-subunit protein complex that functions as an ATP-dependent chromatin remodeling factor, playing a critical role in regulating gene expression by altering chromatin structure. By moving, evicting, or restructuring nucleosomes, SWI/SNF facilitates access to DNA for transcription factors and other regulatory proteins, influencing both transcription initiation and epigenetic modifications.
TATA box: The TATA box is a DNA sequence found in the promoter region of many genes in eukaryotes, essential for the initiation of transcription. It serves as a binding site for transcription factors and RNA polymerase II, playing a critical role in the regulation of gene expression by facilitating the formation of the transcription initiation complex.
TATA-binding protein (TBP): The TATA-binding protein (TBP) is a crucial component of the transcription machinery in eukaryotic cells, responsible for recognizing and binding to the TATA box within the promoter region of genes. By binding to the TATA box, TBP initiates the assembly of the transcription pre-initiation complex, enabling RNA polymerase II to begin transcription. TBP's role is vital in regulating gene expression and ensuring accurate transcription initiation.
Termination: Termination refers to the final step in the processes of transcription and translation, signaling the end of RNA synthesis in transcription and the completion of polypeptide synthesis in translation. It is a crucial event that ensures the accurate production of RNA and proteins, maintaining cellular functions. This process involves specific sequences and factors that recognize when to halt synthesis, ensuring that only the required genetic information is produced and that proteins are properly folded and functional.
TFIIA: TFIIA is a transcription factor that plays a vital role in the initiation of eukaryotic transcription by enhancing the binding of RNA polymerase II to the promoter region of genes. It acts as a coactivator that helps stabilize the interaction between the transcriptional machinery and DNA, facilitating the formation of a pre-initiation complex necessary for gene expression.
TFIIB: TFIIB is a general transcription factor essential for the initiation of transcription in eukaryotic cells. It plays a crucial role by interacting with RNA polymerase II and helping to recruit additional factors necessary for the formation of the transcription pre-initiation complex, which is vital for gene expression.
TFIID: TFIID is a crucial multi-subunit protein complex that plays a key role in initiating transcription by RNA polymerase II in eukaryotic cells. This complex is made up of the TATA-binding protein (TBP) and several TBP-associated factors (TAFs), which together recognize and bind to the promoter region of a gene, allowing the assembly of the transcription machinery and regulating gene expression.
TFIIE: TFIIE is a crucial transcription factor involved in the initiation of transcription by RNA polymerase II in eukaryotic cells. It plays a key role in the assembly of the transcription pre-initiation complex and is essential for the recruitment of RNA polymerase II to the promoter region of genes, influencing the overall transcription process and gene expression regulation.
TFIIF: TFIIF, or Transcription Factor II F, is a multi-subunit protein complex that plays a crucial role in eukaryotic transcription by interacting with RNA polymerase II and facilitating the formation of the pre-initiation complex at promoter regions. It is essential for the recruitment of RNA polymerase II to specific gene promoters and is involved in the regulation of transcriptional activation, making it vital for proper gene expression.
TFIIH: TFIIH is a multi-subunit protein complex that plays a critical role in the process of transcription in eukaryotic cells. It is essential for the unwinding of DNA at the transcription start site and has functions in nucleotide excision repair, linking these two vital cellular processes. The complex is composed of both ATP-dependent helicase activity, which helps in separating the DNA strands, and kinase activity, which phosphorylates the C-terminal domain of RNA polymerase II, crucial for the transition from transcription initiation to elongation.
Transcription bubble: A transcription bubble is a localized region of unwound DNA that occurs during the process of transcription, where RNA polymerase synthesizes RNA from a DNA template. This bubble forms as the enzyme separates the two strands of the double helix, allowing access to the coding region of a gene. In this way, the transcription bubble plays a crucial role in enabling the synthesis of RNA in both prokaryotic and eukaryotic organisms.
Transcription bubble.: The transcription bubble is a localized region where the DNA double helix unwinds, allowing RNA polymerase to access the template strand for RNA synthesis. It typically encompasses about 17 base pairs and moves along the DNA as transcription proceeds.
Transcription unit: A transcription unit is a segment of DNA that is transcribed into RNA, serving as the basic functional unit of transcription. It encompasses the region that includes not only the coding sequence for a gene but also the necessary regulatory elements like promoters and terminators that control when and how much RNA is produced. Understanding transcription units is crucial for grasping the complexity of gene expression in eukaryotic cells.
Transfer RNAs (tRNAs): Transfer RNAs (tRNAs) are small RNA molecules that play a crucial role in the process of translation by bringing amino acids to ribosomes during protein synthesis. Each tRNA molecule is specific to one amino acid and carries it to the ribosome, where the tRNA's anticodon pairs with the corresponding codon on the mRNA, ensuring that the correct amino acid is added to the growing polypeptide chain. This specificity and function are vital for accurately translating the genetic code into functional proteins.
U6 snRNA: U6 snRNA is a small nuclear RNA that plays a crucial role in the splicing of pre-messenger RNA (pre-mRNA) in eukaryotic cells. It is part of the spliceosome complex, where it helps catalyze the removal of introns and the joining of exons during gene expression. U6 snRNA is essential for accurate splicing and contributes to the regulation of gene expression by ensuring that only properly processed mRNAs are translated into proteins.
YY1: YY1 is a transcription factor that plays a crucial role in regulating gene expression in eukaryotic cells. It is known for its ability to bind to specific DNA sequences and influence various biological processes, including transcriptional activation and repression. YY1 is also involved in chromatin remodeling and can interact with multiple other proteins, making it a key player in the complex regulation of eukaryotic transcription.