Podcast
Questions and Answers
What is the function of miRNAs?
What is the function of miRNAs?
What is the precursor of miRNA called?
What is the precursor of miRNA called?
What is the function of the microprocessor complex in miRNA biogenesis?
What is the function of the microprocessor complex in miRNA biogenesis?
What is the role of Exportin 5 in miRNA biogenesis?
What is the role of Exportin 5 in miRNA biogenesis?
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What is the function of Dicer in miRNA biogenesis?
What is the function of Dicer in miRNA biogenesis?
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What is the function of the RNA-induced silencing complex (RISC)?
What is the function of the RNA-induced silencing complex (RISC)?
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What is the consequence of miRNA dysregulation?
What is the consequence of miRNA dysregulation?
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What is the function of microRNAs?
What is the function of microRNAs?
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What is the precursor of miRNA called?
What is the precursor of miRNA called?
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What is the name of the complex that catalyzes the production of pre-miRNA from pri-miRNA in the nucleus?
What is the name of the complex that catalyzes the production of pre-miRNA from pri-miRNA in the nucleus?
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What is the role of Exportin 5 (XPO5) in the biogenesis of miRNA?
What is the role of Exportin 5 (XPO5) in the biogenesis of miRNA?
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What is the name of the enzyme that cleaves the loop from the hairpin structure, producing a short double-stranded RNA with two overhangs at both 3' termini, which contains the future mature miRNA?
What is the name of the enzyme that cleaves the loop from the hairpin structure, producing a short double-stranded RNA with two overhangs at both 3' termini, which contains the future mature miRNA?
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What is the name of the complex onto which the mature miRNA is loaded, which inhibits translation or degrades the target mRNA?
What is the name of the complex onto which the mature miRNA is loaded, which inhibits translation or degrades the target mRNA?
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What is the name of the RNA polymerase that transcribes miRNA genes?
What is the name of the RNA polymerase that transcribes miRNA genes?
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What is the primary level at which gene expression is regulated?
What is the primary level at which gene expression is regulated?
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What determines whether a gene is transcribed?
What determines whether a gene is transcribed?
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What are enhancers and what is their function?
What are enhancers and what is their function?
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What are the common structural motifs found in DNA-binding proteins?
What are the common structural motifs found in DNA-binding proteins?
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What is promoter proximal pausing?
What is promoter proximal pausing?
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What are negative elongation factors and what is their role in transcription?
What are negative elongation factors and what is their role in transcription?
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What are positive transcription elongation factors (PTEF-b) and how are they activated?
What are positive transcription elongation factors (PTEF-b) and how are they activated?
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Why is regulation by promoter proximal pausing important for genes involved in development and response to stimuli?
Why is regulation by promoter proximal pausing important for genes involved in development and response to stimuli?
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Which of the following is a structural motif found in DNA-binding proteins?
Which of the following is a structural motif found in DNA-binding proteins?
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What is the role of enhancers in gene expression?
What is the role of enhancers in gene expression?
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What is promoter proximal pausing?
What is promoter proximal pausing?
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Which of the following is a transcription factor that requires a ligand to become activated?
Which of the following is a transcription factor that requires a ligand to become activated?
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What is the function of positive transcription elongation factors (PTEF-b)?
What is the function of positive transcription elongation factors (PTEF-b)?
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What is the role of heterodimers in transcription factor regulation?
What is the role of heterodimers in transcription factor regulation?
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What is the importance of regulation by promoter proximal pausing?
What is the importance of regulation by promoter proximal pausing?
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What is the role of specific transcription factors in gene expression?
What is the role of specific transcription factors in gene expression?
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Study Notes
Biogenesis of MicroRNA
- Double-stranded RNA inhibits gene expression via RNA interference (RNAi)
- RNAi is conserved in all eukaryotes and regulates endogenous genes, transposon silencing, and pathogen defense in plants
- MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression by binding to mRNA and inhibiting translation or degrading the target mRNA
- miRNAs are involved in various biological processes, including development, differentiation, and immune response, and their dysregulation is implicated in diseases such as cancer and neurological disorders
- miRNAs are encoded by endogenous genes and transcribed by RNA polymerase II
- miRNA genes are regulated by transcription factors and enhancers and are sensitive to chromatin status
- miRNA precursors are long RNAs called pri-miRNA that contain a self-complementary region that forms a hairpin structure
- The microprocessor complex, including Drosha and DGCR8, catalyzes the production of pre-miRNA from pri-miRNA in the nucleus
- Pre-miRNA is exported from the nucleus into the cytoplasm by Exportin 5 (XPO5)
- In the cytoplasm, Dicer cleaves the loop from the hairpin structure, producing a short double-stranded RNA with two overhangs at both 3' termini, which contains the future mature miRNA
- Dicer recognizes the base of pre-miRNA and its loop, allowing for correct positioning within the catalytic site
- The mature miRNA is loaded onto the RNA-induced silencing complex (RISC), which inhibits translation or degrades the target mRNA
Biogenesis of MicroRNA
- Double-stranded RNA inhibits gene expression via RNA interference (RNAi)
- RNAi is conserved in all eukaryotes and regulates endogenous genes, transposon silencing, and pathogen defense in plants
- MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression by binding to mRNA and inhibiting translation or degrading the target mRNA
- miRNAs are involved in various biological processes, including development, differentiation, and immune response, and their dysregulation is implicated in diseases such as cancer and neurological disorders
- miRNAs are encoded by endogenous genes and transcribed by RNA polymerase II
- miRNA genes are regulated by transcription factors and enhancers and are sensitive to chromatin status
- miRNA precursors are long RNAs called pri-miRNA that contain a self-complementary region that forms a hairpin structure
- The microprocessor complex, including Drosha and DGCR8, catalyzes the production of pre-miRNA from pri-miRNA in the nucleus
- Pre-miRNA is exported from the nucleus into the cytoplasm by Exportin 5 (XPO5)
- In the cytoplasm, Dicer cleaves the loop from the hairpin structure, producing a short double-stranded RNA with two overhangs at both 3' termini, which contains the future mature miRNA
- Dicer recognizes the base of pre-miRNA and its loop, allowing for correct positioning within the catalytic site
- The mature miRNA is loaded onto the RNA-induced silencing complex (RISC), which inhibits translation or degrades the target mRNA
Regulation of Gene Expression: Transcription Factors and Enhancers
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Gene expression is regulated primarily at the level of transcription initiation.
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Transcription initiation depends on the accessibility of the gene within open chromatin and the presence of specific gene regulatory sequences and regulatory proteins that recruit RNA polymerase.
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The accessibility of the gene within open chromatin is a prerequisite for transcription initiation.
-
The presence of specific gene regulatory sequences and the availability of regulatory proteins that recruit RNA polymerase determine whether a gene is transcribed.
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Enhancers are modular elements located more distal to the transcription start site and contain binding sites for specific transcription factors.
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Enhancers determine the efficiency and specificity of transcription initiation, controlling the activity of a promoter from various locations, independently of their orientation.
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Specific transcription factors are proteins that recognize and bind precise nucleotide sequences to regulate the activity of genes and determine where and when a gene is transcribed.
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Transcription factors function in a combinatorial, cooperative, and synergistic manner to regulate gene expression.
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Enhancers stimulate the transcription of genes and their activity can be measured using a synthetic gene with a reporter gene.
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Helix-turn-helix, zinc fingers, leucine zipper, and helix-loop-helix are common structural motifs found in DNA-binding proteins.
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Heterodimers increase the number of functional TFs and opportunities for combinatorial control of gene expression.
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The estrogen receptor is a transcription factor that requires a ligand to become activated and its activation leads to the transcription of target genes.Understanding Promoter Proximal Pausing in Transcription
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Promoter proximal pausing is a regulatory mechanism that occurs after RNA polymerase II recruitment at the promoter.
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RNA polymerase II is phosphorylated during promoter clearance, and transcription proceeds until a block occurs when the transcript reaches the 20-40 nucleotides long mark.
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Negative elongation factors bind to RNA polymerase II and prevent it from proceeding.
-
Positive transcription elongation factors (PTEF-b) can reactivate RNA polymerase II through phosphorylation.
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PTEF-b is located in the nucleus, close to the promoter and needs to be released and activated by transcription factors (TFs) to reactivate stalled RNA polymerase II.
-
TFs can either contact PTEF-b directly or through a mediator to promote the release of inhibitory complexes and activate PTEF-b.
-
Regulation by promoter proximal pausing is important for genes involved in development and response to stimuli.
-
Examples of genes regulated by promoter proximal pausing are those encoding heat shock proteins in Drosophila and target genes of hypoxia-inducible factors (HIF).
-
Heat shock factor is activated in response to excessive heat and can unlock RNA polymerase II, promoting the release of paused RNA polymerase II and production of heat shock proteins.
-
HIFs stabilize under low oxygen conditions, bind to regulatory elements of their target genes, and promote the release of paused RNA polymerase II, allowing the production of proteins required for cell survival in hypoxic environments.
-
PTEF-b needs to be released and activated by transcription factors to reactivate stalled RNA polymerase II.
-
Regulation by promoter proximal pausing is important for genes involved in development and response to stimuli, such as heat shock proteins and HIFs target genes.
Regulation of Gene Expression: Transcription Factors and Enhancers
-
Gene expression is regulated primarily at the level of transcription initiation.
-
Transcription initiation depends on the accessibility of the gene within open chromatin and the presence of specific gene regulatory sequences and regulatory proteins that recruit RNA polymerase.
-
The accessibility of the gene within open chromatin is a prerequisite for transcription initiation.
-
The presence of specific gene regulatory sequences and the availability of regulatory proteins that recruit RNA polymerase determine whether a gene is transcribed.
-
Enhancers are modular elements located more distal to the transcription start site and contain binding sites for specific transcription factors.
-
Enhancers determine the efficiency and specificity of transcription initiation, controlling the activity of a promoter from various locations, independently of their orientation.
-
Specific transcription factors are proteins that recognize and bind precise nucleotide sequences to regulate the activity of genes and determine where and when a gene is transcribed.
-
Transcription factors function in a combinatorial, cooperative, and synergistic manner to regulate gene expression.
-
Enhancers stimulate the transcription of genes and their activity can be measured using a synthetic gene with a reporter gene.
-
Helix-turn-helix, zinc fingers, leucine zipper, and helix-loop-helix are common structural motifs found in DNA-binding proteins.
-
Heterodimers increase the number of functional TFs and opportunities for combinatorial control of gene expression.
-
The estrogen receptor is a transcription factor that requires a ligand to become activated and its activation leads to the transcription of target genes.Understanding Promoter Proximal Pausing in Transcription
-
Promoter proximal pausing is a regulatory mechanism that occurs after RNA polymerase II recruitment at the promoter.
-
RNA polymerase II is phosphorylated during promoter clearance, and transcription proceeds until a block occurs when the transcript reaches the 20-40 nucleotides long mark.
-
Negative elongation factors bind to RNA polymerase II and prevent it from proceeding.
-
Positive transcription elongation factors (PTEF-b) can reactivate RNA polymerase II through phosphorylation.
-
PTEF-b is located in the nucleus, close to the promoter and needs to be released and activated by transcription factors (TFs) to reactivate stalled RNA polymerase II.
-
TFs can either contact PTEF-b directly or through a mediator to promote the release of inhibitory complexes and activate PTEF-b.
-
Regulation by promoter proximal pausing is important for genes involved in development and response to stimuli.
-
Examples of genes regulated by promoter proximal pausing are those encoding heat shock proteins in Drosophila and target genes of hypoxia-inducible factors (HIF).
-
Heat shock factor is activated in response to excessive heat and can unlock RNA polymerase II, promoting the release of paused RNA polymerase II and production of heat shock proteins.
-
HIFs stabilize under low oxygen conditions, bind to regulatory elements of their target genes, and promote the release of paused RNA polymerase II, allowing the production of proteins required for cell survival in hypoxic environments.
-
PTEF-b needs to be released and activated by transcription factors to reactivate stalled RNA polymerase II.
-
Regulation by promoter proximal pausing is important for genes involved in development and response to stimuli, such as heat shock proteins and HIFs target genes.
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Test your knowledge on the biogenesis of microRNA with this quiz! Learn about the process of how miRNAs are produced, regulated, and function in different biological processes. From the microprocessor complex to the RNA-induced silencing complex, this quiz covers all the essential details of miRNA biogenesis. Challenge yourself and see how much you know about this important regulatory mechanism in gene expression!