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Questions and Answers
Which gene is considered a pair-rule gene involved in Drosophila development?
Which gene is considered a pair-rule gene involved in Drosophila development?
What is the role of Giant in the regulation of the Even Skipped gene?
What is the role of Giant in the regulation of the Even Skipped gene?
What method is used to identify the DNA sequences that transcription factors like Giant bind to?
What method is used to identify the DNA sequences that transcription factors like Giant bind to?
What is a crucial step in the ChIP-seq process for identifying bound DNA sequences?
What is a crucial step in the ChIP-seq process for identifying bound DNA sequences?
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Which component is NOT typically associated with the regulation of gene expression in Drosophila development?
Which component is NOT typically associated with the regulation of gene expression in Drosophila development?
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What is the primary function of the Bicoid (Bcd) protein in the early Drosophila embryo?
What is the primary function of the Bicoid (Bcd) protein in the early Drosophila embryo?
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What is the relationship between Bcd mRNA and the bcd gene in terms of genetic requirement?
What is the relationship between Bcd mRNA and the bcd gene in terms of genetic requirement?
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How does the Bcd protein gradient affect the expression of the hb and otd genes?
How does the Bcd protein gradient affect the expression of the hb and otd genes?
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What role does the protein Hb play in the regulation of Kruppel transcription?
What role does the protein Hb play in the regulation of Kruppel transcription?
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What differentiates the Otd and hb genes in terms of interaction with Bcd protein?
What differentiates the Otd and hb genes in terms of interaction with Bcd protein?
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What is the role of Giant in the regulation of the Drosophila Eve gene?
What is the role of Giant in the regulation of the Drosophila Eve gene?
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How does alternative splicing affect gene expression?
How does alternative splicing affect gene expression?
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What mechanism allows mRNA localization to specific regions of the cytosol?
What mechanism allows mRNA localization to specific regions of the cytosol?
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Which factor is necessary for the female fate in Drosophila regarding the Sxl gene?
Which factor is necessary for the female fate in Drosophila regarding the Sxl gene?
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What is a primary function of Dicer in RNA interference?
What is a primary function of Dicer in RNA interference?
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Which of the following describes the role of RISC in RNA interference?
Which of the following describes the role of RISC in RNA interference?
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How does Kruppel affect the transcription of the Eve gene?
How does Kruppel affect the transcription of the Eve gene?
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What is a key characteristic of mRNAs regarding their stability?
What is a key characteristic of mRNAs regarding their stability?
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Which event triggers the lariat formation during pre-mRNA splicing?
Which event triggers the lariat formation during pre-mRNA splicing?
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What role do egg-polarity genes have in Drosophila embryos?
What role do egg-polarity genes have in Drosophila embryos?
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What is a characteristic feature of mature eukaryotic mRNAs?
What is a characteristic feature of mature eukaryotic mRNAs?
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What helps to bind bicoid mRNA to the cytoskeleton in Drosophila eggs?
What helps to bind bicoid mRNA to the cytoskeleton in Drosophila eggs?
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In the context of transcription regulation, what role does the protein Bcd play?
In the context of transcription regulation, what role does the protein Bcd play?
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What effect does Sxl have on tra RNA splicing in Drosophila?
What effect does Sxl have on tra RNA splicing in Drosophila?
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Study Notes
Eve Regulation
- Eve is a pair-rule gene, meaning it is expressed in a striped pattern along the Drosophila embryo.
- Eve stripe 2 expression relies on a specific regulatory sequence.
- The Eve gene is regulated through combinatorial controls, a combination of activators and repressors.
- Bcd, Hb, Giant, and Kruppel regulate Eve.
- Giant, a repressor protein, represses Eve expression.
- The binding of Giant to DNA is localized to the anterior of the embryo. This localization contributes to the formation of Eve expression patterns in the embryo.
- DNA sequences that Giant binds to can be identified using Chromatin IP (ChIP) followed by DNA sequencing (Chip-seq).
- The number of sequence reads in Chip-seq indicates the frequency of protein occupancy, which relates to the affinity of the protein and its concentration.
- Giant binds multiple sites upstream of the Eve gene and within the Eve stripe 2 enhancer.
Giant Binding & Eve Expression
- Mutations in all three Giant binding sites in the Eve stripe 2 enhancer block Eve stripe 2 expression.
- This suggests that multiple binding sites contribute to the function of the repressor in regulating Eve stripe 2 expression.
Eve Expression Patterns
- Eve stripe 2 expression is regulated by a complex interplay of activators and repressors including Bcd, Hb, Giant, and Kruppel.
- Bcd and Hb must be bound to Eve’s regulatory sequence for the gene to be activated. Bcd sites have low affinity, suggesting a synergistic effect on RNA polymerase recruitment.
- Giant and Kruppel can inhibit expression of Eve by preventing Bcd and Hb binding or blocking their interaction with RNA polymerase II.
Post-Transcriptional Regulation of Gene Expression
- Post-transcriptional regulation of gene expression occurs after transcription.
- These mechanisms include alternative splicing, regulation of nuclear export, mRNA localization, miRNA, and nonsense-mediated decay.
Alternative Splicing
- Alternative splicing allows the production of different protein isoforms from the same gene.
- This involves the differential inclusion or exclusion of specific exons in the final mRNA transcript.
- This can lead to a wide range of protein isoforms and increased proteomic diversity.
- Specific regulatory sequences within the pre-mRNA determine splicing patterns.
RNA Splicing
- Splicing removes introns from pre-mRNAs.
- The spliceosome, a complex of RNA and proteins, catalyzes splicing.
- Splicing occurs through a stepwise process involving the recognition of splice sites by snRNPs (small nuclear ribonucleoproteins).
Drosophila Sex Determination
- Sex determination in Drosophila is regulated by a cascade of genes.
- The Sxl gene, which regulates the expression of the tra gene, is a key player.
- Sxlon leads to the production of a functional Tra protein, ultimately leading to female development.
- Sxloff leads to the production of a non-functional Tra protein, resulting in male development.
- Sxl inhibits the splicing of tra RNA by binding to the splice acceptor site for exon 2. This prevents the spliceosome from interacting with that splice acceptor site.
- The spliceosome then interacts with an alternative splice acceptor site, leading to the production of a functional Tra protein, leading to female development.
- In the absence of Sxl, the splicing mechanism uses the proximal splice site, leading to a non-functional Tra protein and male development.
mRNA Localization
- Sequences in the 3’ UTR of some mRNAs determine their localization within the cytosol.
- mRNAs are localized to specific regions by proteins that bind their 3’ UTRs and link them to the cytoskeleton.
- This precise localization allows for the targeted expression of proteins based on the needs of different cellular regions.
- The 3’ UTR of the bicoid mRNA contains a sequence that binds the Staufen protein, linking the mRNA to microtubules at the anterior of the egg.
- Translation of the bicoid mRNA, thus yielding the bicoid protein, occurs at the anterior of the egg.
Mature mRNA Structure
- Mature eukaryotic mRNAs have a 5’ cap and a 3’ polyA tail.
- The 3’ polyA tail interacts with proteins bound to the 5’ cap, creating a protective structure that prevents mRNA degradation.
- This structure ensures the stability and longevity of mature mRNAs.
mRNA Stability
- All mRNAs are subject to degradation.
- Specific sequences within the mRNA can influence its stability by affecting the recruitment of destabilizing or stabilizing factors.
- Some mRNAs are more stable than others, ensuring their appropriate expression levels.
Egg Polarity Genes
- Egg-polarity genes are maternally deposited transcripts that control the body axis formation in the early Drosophila embryo.
- These genes establish polarity in the egg, setting up the anterior-posterior and dorsal-ventral axes.
- These include genes such as bicoid and nanos.
Bicoid Gene
- The bicoid gene (bcd) is one such egg-polarity gene, responsible for specifying anterior structures during development.
- Its mRNA is localized to the anterior of the egg during oogenesis.
- This mRNA gradient is essential for establishing the anterior-posterior axis of the embryo.
- The Bicoid protein forms a gradient from the anterior to the middle of the egg.
- It acts as a transcription factor, promoting the expression of genes essential for anterior structures.
- The bcd gene is considered a maternal effect gene, meaning its function is required in the mother to ensure proper development of the embryo.
Target Genes of Bcd
- The bicoid protein gradient is a key regulator of target genes through its binding affinity.
- Its target genes include otd, hb (and others) which are required in the embryo – zygotic genes.
- The otd and hb genes have different numbers of Bcd binding sites and varying affinities for Bcd protein.
Gradient of Bcd Protein
- Gradient of Bcd protein determines the expression of target genes, including Hb, Giant, Otd, and Kruppel.
- Hb is repressed by Bcd, while Giant is repressed by Bcd at the anterior and activated by other transcription factors at the posterior.
- Kruppel is regulated by Hb and another transcription factor at the posterior.
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