14.1 Transcription initiation, elongation, and termination
3 min read•july 22, 2024
RNA transcription is the process of copying genetic information from DNA to RNA. It's a crucial step in , allowing cells to produce proteins and regulate their functions.
The transcription process involves three main stages: , , and . Each stage requires specific enzymes and factors, working together to ensure accurate and efficient RNA production from the DNA template.
Transcription Process
Role of RNA polymerase in transcription
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- is the key enzyme that synthesizes RNA from a DNA template consists of multiple subunits working together to perform transcription (core enzyme and sigma factor in prokaryotes, multiple subunits in eukaryotes)
- During initiation, RNA polymerase binds to the region of the gene, separates the double-stranded DNA to expose the template strand, and positions itself at the
- In elongation, RNA polymerase moves along the template strand in the 3' to 5' direction, catalyzes the formation of phosphodiester bonds between ribonucleotides, and synthesizes the RNA strand complementary to the template DNA strand
- Upon termination, RNA polymerase encounters a , releases the newly synthesized RNA strand, and dissociates from the DNA template
Transcription initiation: prokaryotes vs eukaryotes
- Prokaryotic transcription initiation involves RNA polymerase directly binding to the promoter region containing conserved sequences like -10 (Pribnow box) and -35 elements, with the sigma factor () aiding in promoter recognition and binding without the need for extensive transcription factor assembly
- Eukaryotic transcription initiation requires the assembly of like TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH at the promoter in a specific order, with TFIID recognizing and binding to the , followed by the recruitment of other GTFs and RNA polymerase II to form the , and additional regulatory can modulate gene expression
Promoters and transcription factors
- Promoter regions are located upstream of the transcription start site, contain specific DNA sequences recognized by transcription factors and RNA polymerase, act as binding sites for the transcriptional machinery, and regulate the initiation of transcription and gene expression
- Transcription factors are proteins that bind to specific DNA sequences in the promoter or enhancer regions, can act as activators or repressors of gene expression, with activators promoting the recruitment and assembly of the transcriptional machinery and repressors preventing or reducing the binding of RNA polymerase or activators, and modulate gene expression in response to cellular signals (hormones) or developmental cues (embryonic patterning)
Steps of transcription elongation and termination
- Elongation:
- RNA polymerase escapes the promoter and enters the elongation phase
- Nucleoside triphosphates (NTPs) are added to the growing RNA strand
- RNA polymerase maintains a transcription bubble, separating the DNA strands
- The nascent RNA strand forms a short DNA-RNA hybrid with the template strand
- RNA polymerase moves along the template strand, synthesizing RNA in the 5' to 3' direction
- Termination:
- Occurs when RNA polymerase encounters a termination signal
- In prokaryotes:
- Rho-dependent termination involves the Rho protein binding to the nascent RNA and causing dissociation
- Rho-independent termination occurs at specific sequences that form a stem-loop structure, causing RNA polymerase to stall and dissociate
- In eukaryotes:
- Termination is coupled with of the 3' end of the RNA
- Cleavage and polyadenylation specificity factor (CPSF) and cleavage stimulation factor (CstF) recognize specific sequences and cleave the RNA
- Poly(A) polymerase adds a poly(A) tail to the 3' end of the cleaved RNA
Key Terms to Review (18)
Capping: Capping is a vital process in RNA biology where a modified guanine nucleotide is added to the 5' end of a newly synthesized mRNA molecule. This cap structure plays several key roles, including protecting the RNA from degradation, facilitating its export from the nucleus, and enhancing its translation efficiency by aiding ribosome binding. The capping process is an essential step that occurs post-transcriptionally, ensuring that the mRNA is mature and ready for protein synthesis.
Elongation: Elongation is the process by which a polymer, such as DNA or RNA, is synthesized through the addition of nucleotide units, resulting in the lengthening of the nucleic acid chain. This term is crucial as it represents a key phase in both the replication of DNA and the synthesis of RNA and proteins, involving the sequential addition of nucleotides or amino acids during these vital biological processes.
Enhancers: Enhancers are regulatory DNA sequences that can significantly increase the transcription of specific genes, playing a crucial role in gene expression. These sequences can be located far from the promoter they regulate and interact with transcription factors to facilitate the assembly of the transcription machinery, ultimately influencing the initiation phase of transcription.
Gene expression: Gene expression is the process by which information from a gene is used to synthesize a functional gene product, typically proteins, which ultimately influence the phenotype of an organism. This process involves several key steps including transcription of DNA into messenger RNA (mRNA) and translation of mRNA into proteins, influenced by various signaling pathways and cellular mechanisms.
General transcription factors (GTFs): General transcription factors (GTFs) are essential proteins that help initiate the process of transcription by assisting RNA polymerase in binding to specific promoter regions of DNA. These factors are critical for the formation of a functional transcription complex, which is required to kickstart the synthesis of RNA from a DNA template. GTFs ensure that transcription occurs accurately and efficiently by interacting with other components of the transcription machinery.
Initiation: Initiation refers to the process that marks the beginning of a biological mechanism, such as DNA replication, transcription, or translation. This crucial step involves the assembly of necessary components, such as proteins and nucleic acids, to kickstart the synthesis of new strands of DNA, RNA, or proteins. Each type of initiation is finely tuned to ensure accurate and efficient processing of genetic information.
Messenger RNA (mRNA): Messenger RNA (mRNA) is a type of RNA that carries genetic information from DNA to the ribosome, where proteins are synthesized. It plays a crucial role in the process of transcription, where the DNA sequence is copied into an RNA format, and serves as the template for translation, the process by which proteins are made based on the genetic code. mRNA is essential for gene expression and the flow of genetic information within a cell.
Non-coding RNA: Non-coding RNA (ncRNA) refers to a type of RNA that does not translate into proteins but plays crucial roles in regulating gene expression and maintaining cellular functions. These molecules are essential for various biological processes, including transcription regulation, RNA processing, and chromatin remodeling, linking them closely to the dynamics of transcription initiation, elongation, and termination.
Polyadenylation: Polyadenylation is the process of adding a tail of adenine nucleotides to the 3' end of a pre-mRNA molecule, which is crucial for the stability, transport, and translation of mRNA. This modification occurs after transcription and is a key step in RNA processing that enhances the lifespan of mRNA in the cytoplasm, thus facilitating protein synthesis.
Preinitiation complex (PIC): The preinitiation complex (PIC) is a large assembly of proteins that forms on the promoter region of DNA, crucial for the initiation of transcription. This complex includes RNA polymerase II, general transcription factors, and various regulatory proteins that help position the RNA polymerase at the start site of transcription. The formation of the PIC is essential for accurately starting the transcription process, as it lays the groundwork for both elongation and termination phases.
Promoter: A promoter is a specific DNA sequence located upstream of a gene that serves as the binding site for RNA polymerase and other transcription factors to initiate transcription. Promoters are crucial for controlling the expression of genes, influencing when and how much a gene is expressed in both prokaryotic and eukaryotic cells.
Rho factor: Rho factor is a protein involved in the termination of transcription in prokaryotic cells. It functions as a helicase that unwinds RNA from the DNA template, facilitating the release of the newly synthesized RNA molecule from the RNA polymerase complex. This process is crucial for ensuring that transcription stops at the correct location, allowing cells to regulate gene expression efficiently.
RNA polymerase: RNA polymerase is an essential enzyme responsible for synthesizing RNA from a DNA template during the process of transcription. This enzyme plays a critical role in the expression of genes, converting the genetic code into functional RNA molecules that carry out various functions in the cell.
TATA Box: The TATA box is a DNA sequence found in the promoter region of genes in eukaryotic organisms, typically consisting of the nucleotide sequence TATAAA. It plays a critical role in the initiation of transcription by serving as a binding site for transcription factors and RNA polymerase II, which are essential for the accurate start of gene expression.
Termination: Termination is the final step in the processes of DNA replication, transcription, and translation where synthesis of nucleic acids or proteins ceases. This critical event ensures that the genetic information is accurately passed on during replication, that RNA synthesis concludes at specific sites, and that protein assembly is completed properly, contributing to cellular function and regulation.
Termination signal: A termination signal is a specific sequence of nucleotides in DNA that indicates the end of transcription, prompting RNA polymerase to stop synthesizing RNA. This signal plays a crucial role in ensuring that RNA is produced to the correct length and that the synthesis process is properly regulated, impacting gene expression and cellular function.
Transcription Factors: Transcription factors are proteins that regulate the transcription of specific genes by binding to nearby DNA. They play a critical role in controlling gene expression, influencing cellular processes such as growth, differentiation, and response to environmental signals. Their function is essential in both prokaryotic and eukaryotic cells, and they interact with the nuclear envelope and various RNA polymerases during the transcription process.
Transcription start site: The transcription start site (TSS) is the location on a DNA strand where transcription begins, marking the point at which RNA polymerase binds and starts synthesizing RNA. This site is crucial in gene expression as it determines the start of the messenger RNA (mRNA) and influences the regulation of transcription initiation, elongation, and termination processes.