MicroRNA and Gene Regulation in C.elegans

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Questions and Answers

What is the primary function of the lin-4 gene in relation to lin-14 mRNA?

It enhances the transcription of lin-14 mRNA.

It produces microRNAs that inhibit lin-14 mRNA. (correct)

It encodes proteins that stabilize lin-14 mRNA.

It acts as a translational activator for lin-14.

Which structure is characteristic of microRNAs?

Single-stranded RNA molecules

Circular RNA forms

Hairpin loop structures (correct)

Linear RNA sequences

What is the role of the RISC complex in the RNA interference mechanism?

It degrades dsDNA.

It activates transcription of target genes.

It separates dsRNA and aligns with target mRNA. (correct)

It synthesizes new mRNA.

Which technique is used to identify when and where a gene is expressed in an embryo?

In situ hybridization Signup and view all the answers

What does the process of chromatin immunoprecipitation-sequencing (ChIP-Seq) primarily investigate?

The binding sites of transcription factors and modified nucleosomes. Signup and view all the answers

What gene functionality can be tested using the CRISPR/Cas9 system?

Gene knockdown and editing Signup and view all the answers

In the context of RNA interference, what is the significance of the 3’UTR of lin-14 mRNA?

It contains the binding site for lin-4 microRNAs. Signup and view all the answers

Which of the following systems allows the tracking of gene function through targeted gene expression in specific tissues?

GAL4-UAS system Signup and view all the answers

What is the main outcome of asymmetric cell division during development?

Different cell fates due to varying gene expression Signup and view all the answers

Which method is primarily used to map cell fates during development?

Single-cell RNA sequencing Signup and view all the answers

Which specification method focuses on the intrinsic properties of cells?

Autonomous specification Signup and view all the answers

What role do morphogen gradients play in cell development?

They facilitate the differentiation of neighboring cells. Signup and view all the answers

What does epigenetic control influence in terms of gene expression?

It affects the accessibility of DNA for transcription. Signup and view all the answers

Which experiment demonstrated the autonomous specification of muscle cells?

Conklin's tunicate blastomeres study Signup and view all the answers

What distinguishes a cell that is differentiated from one that is only specified?

Differentiated cells have stopped dividing and taken on unique functions. Signup and view all the answers

How does post-translational control affect protein expression?

It modifies proteins after they have been synthesized. Signup and view all the answers

What is the basis of conditional specification in embryonic development?

Cell fate depends on its position in the embryo Signup and view all the answers

Which of the following is NOT an inducing signal for conditional specification?

Nutrient availability Signup and view all the answers

In Driesch’s experiments with sea urchin embryos, what was concluded about blastomeres?

They have a greater potential to adopt any cell fate than expected. Signup and view all the answers

What role do morphogen gradients play in syncytial specification in Drosophila?

They specify segment identities through opposing transcription factors. Signup and view all the answers

How does syncytial specification differ from conditional specification?

Syncytial specification involves gradients of morphogens rather than cell position. Signup and view all the answers

During syncytial development, what occurs prior to cellularization?

Nuclei divide without cytoplasmic cleavage Signup and view all the answers

What technique can be used to map the fates of individual cells during development?

Single-cell RNA sequencing Signup and view all the answers

What defines cell identity as determined during development?

The genes that are expressed at any given time Signup and view all the answers

What is the role of histone modification in transcription regulation?

It prevents access to the promoter, blocking transcription. Signup and view all the answers

Which type of silencer is associated with neural restrictive functions?

NRSE: neural restrictive silencer factor Signup and view all the answers

How does DNA methylation block transcription?

Through the binding of methyl CpG-binding protein 2 (MeCP2). Signup and view all the answers

What are the consequences of loss of MeCP2 in females?

Symptoms characteristic of Rett’s syndrome. Signup and view all the answers

Which of the following best describes the term 'enhancer' in gene expression?

A regulatory element that increases the likelihood of transcription. Signup and view all the answers

In what way do specific reporters like GFP and lacZ serve a role in research?

They provide a means to visualize the expression of specific genes. Signup and view all the answers

What consequence does epigenetic modification have on nucleosome and chromatin structure?

It modulates access to specific genes, influencing transcription. Signup and view all the answers

What characteristic is NOT associated with Rett's syndrome?

Enhanced cognitive abilities Signup and view all the answers

What role do transcription factors play in gene expression?

They modulate transcription by binding to RNA pol II. Signup and view all the answers

What is the primary role of the Dscam gene in Drosophila?

It produces a membrane adhesion protein. Signup and view all the answers

Which of the following statements about pre-mRNA processing is accurate?

It allows for the production of multiple protein isoforms from a single gene. Signup and view all the answers

How does Rpl38 deficiency affect vertebrate development?

It hinders translation of specific Hox genes. Signup and view all the answers

What mechanism do microRNAs primarily use to regulate gene expression?

They promote the degradation of mRNA. Signup and view all the answers

What is the significance of enhancer binding by transcription factors?

They coordinate expression of multiple genes. Signup and view all the answers

Which factor is directly involved in the localization of mRNA in the Drosophila egg?

Nanos mRNA Signup and view all the answers

What is one consequence of alternative splicing in genes like Dscam?

Generates a diverse array of splice isoforms. Signup and view all the answers

How do anchor proteins contribute to mRNA localization in Drosophila?

They trap cytoplasmic mRNA at specific locations. Signup and view all the answers

What is the primary function of histone-modifying enzymes recruited by transcription factors?

To modify histones and influence chromatin structure. Signup and view all the answers

Study Notes

C.elegans

lin-4 gene encodes microRNAs
lin-4 microRNA is complementary to the 3’UTR of lin-14 mRNA
lin-4 microRNA inhibits gene expression by triggering degradation of lin-14 mRNA

Lin-14

Transcription factor required during the first larval phase
Lin-14 is not needed afterward
Binding of small RNAs (microRNAs) to repetitive sequences in the 3’UTR of lin-14 mRNA triggers degradation of transcripts

MicroRNAs

“Hairpin-loop” structures trigger a protective mechanism - RNA interference
RNA interference inhibits transcription and translation of genes
Target sequence recognition depends on the strength of miRNA complementarity

Drosha

Drosha is the enzyme that makes individual pre-miRNA hairpins.

RISC Complex

RISC: RNA-induced silencing complex
RISC separates dsDNA strands and aligns with the 3’UTR of the target mRNA
Cleaves the mRNA or blocks translation

Basic Tools of Developmental Genetics

In Situ Hybridization

Used to determine when and where genes are expressed in an embryo
Example: Localizing odd-skipped gene expression in Drosophila by in situ hybridization
RNA probe against odd-skipped mRNA is designed and used for hybridization and immunodetection

Chromatin Immunoprecipitation-Sequencing (ChIP-Seq)

Determines where transcription factors bind and the location of modified nucleosomes

CRISPR/Cas9

Used to test gene function by introducing gene edits

GAL4-UAS System

Used to test gene function by controlling gene expression in a specific tissue or cell type.

Cre-Lox System

Allows for the deletion or recombination of specific DNA sequences in a tissue-specific manner

Specifying Cell Identity

Cell Fate Specification

Autonomous: cell fate is determined by intrinsic factors within the cell itself
Conditional: cell fate depends on interactions with neighboring cells or the environment
Syncytial: cell fate is determined by gradients of signaling molecules within a common cytoplasm

Single-Cell RNA Sequencing

Used to map cell fates by determining which genes are expressed at any given time
Helps to define cell identity

GFP and lacZ Reporters

GFP reporter fused to retina-specific gene in zebrafish
lacZ reporter fused to neuron-specific L1 gene in mouse

Differentiation

Cell stops dividing and develops specialized structural elements and functional properties

Autonomous Specficiation

Conklin described autonomous specification of muscle cells in tunicate blastomeres
Removal of B4.1 blastomere results in a larva with no tail muscles
Whittaker found that Macho mRNA segregates asymmetrically in the cytoplasm to drive tail muscle development

Conditional Specification

Driesch’s experiments: conditional specification in sea urchin embryos
Blastomeres have greater potential for cell fates than expected during normal development
Cell-cell interactions are critical for normal development

Syncytial Specification

Syncytial blastoderm in Drosophila
Morphogen gradients specify syncytial cell fates
Opposing gradients of Bicoid and Caudal transcription factors specify segment identities
Autonomous: Transcription factors are differentially expressed after cellularization
Conditional: Position relative to neighboring nuclei determines cell fate

Epigenetic Modifications

Modulate access to genes and influence transcription
Nucleosomes and chromatin structure play a role in epigenetic regulation

Histone Modifications

Histone methylation can prevent access to promoters and block transcription
Histone acetylation exposes DNA to RNA polymerase II and transcription factors, activating transcription

DNA Methylation

DNA methylation blocks transcription by preventing the binding of transcription factors
Loss of MeCP2 (methyl CpG-binding protein 2) leads to Rett’s syndrome in females. Symptoms: loss of language, difficulty walking, repetitive hand movements.

Transcription Factors

Transcription factors regulate gene transcription by binding to specific DNA sequences
Transcription factors in a given family share DNA-binding domains
Yamanaka factors can induce pluripotent stem cells from differentiated skin cells

Pre-mRNA Processing: Alternative Splicing

Differential pre-mRNA processing can produce a wide variety of proteins from the same gene
Splicing: cut, rearrange, and ligate exons together
Protein isoforms can play similar roles in different cells or contrasting roles in the same cell
Dscam gene in Drosophila contains 115 exons and can generate 38,016 splice isoforms
Dscam encodes a membrane adhesion protein essential for self-avoidance between dendrites from the same neuron
Mutations in the Dscam homologue can contribute to the neurological defects associated with Down syndrome.

mRNA Translation: Ribosomal Selectivity and Cytoplasmic Localization

Mouse: selective activation of translation of specific mRNAs
Drosophila egg: mRNA localization in the cytoplasm
Nanos mRNA diffuses and is trapped by anchor proteins at the posterior pole
Hsp83 mRNA is degraded everywhere except at the posterior pole, where it is protected by protein complexes
Bicoid and Oscar mRNAs are actively transported by motor proteins to the posterior and anterior poles, respectively
Rpl38 deficiency: cannot translate subset of Hox genes to specify vertebrae → deformed skeleton

MicroRNA Regulation of mRNA Transcription and Translation

MicroRNAs (miRNAs) regulate gene expression by binding to target mRNAs
MicroRNAs can either block translation or trigger mRNA degradation
The strength of the complementarity between the miRNA and its target mRNA determines the regulatory outcome
MicroRNAs play crucial roles in various biological processes, including development, differentiation, and disease.

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Description

This quiz explores the role of microRNAs, specifically the lin-4 gene, in gene regulation during the development of C.elegans. Learn how microRNAs interact with mRNA and their significance in RNA interference and developmental genetics.