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RNA in Cell Signalling - Week 1
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RNA in Cell Signalling - Week 1

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@ModernPortland

Questions and Answers

What is the primary role of ribosomal RNA (rRNA) in the cell?

  • Major structural component of the ribosome (correct)
  • Guiding chemical modification of RNA
  • Translating mRNA signals into proteins
  • Interacting with small nuclear RNA

    • Less than 2% of the RNA transcribed from the human genome is non-coding.

    True

    What class of non-coding RNA is involved in the modification of pre-mRNA?

    Small nuclear RNA (snRNA)

    The largest class of small non-coding RNA is __________.

    <p>Piwi interacting RNA (piRNA)</p> Signup and view all the answers

    Match the non-coding RNA with its function:

    <p>Ribosomal RNA (rRNA) = Major structural component of ribosome Transfer RNA (tRNA) = Involved in translation of mRNA Small nuclear RNA (snRNA) = Pre-mRNA modification Small Nucleolar RNA (snoRNA) = Guides chemical modification of RNA</p> Signup and view all the answers

    What percentage of the human genome is transcribed into RNA?

    <p>75%</p> Signup and view all the answers

    Transfer RNA (tRNA) is solely responsible for coding proteins.

    <p>False</p> Signup and view all the answers

    What are the two classes of small nuclear RNA?

    <p>smRNA and lsmRNA</p> Signup and view all the answers

    What type of gene knockdown is typically associated with shRNA transfection?

    <p>Stable gene knockdown</p> Signup and view all the answers

    SiRNA is typically used for long-term gene expression changes.

    <p>False</p> Signup and view all the answers

    What is a key requirement for a successful overexpression system in higher eukaryotes?

    <p>A suitable cell line and a suitable vector</p> Signup and view all the answers

    Adenovirus vectors are well suited for _____ due to their ability to transduce both dividing and non-dividing cells.

    <p>oncolytic therapy</p> Signup and view all the answers

    Match the following vector types with their descriptions:

    <p>Adenovirus vectors = Carry up to 8.5 Kbs of heterologous DNA Retroviral vectors = RNA viruses that replicate via a dsDNA intermediate Vaccinia vectors = Replicates in the cytoplasm of the host cell Plasmid-based expression vectors = Common tool for gene cloning and expression</p> Signup and view all the answers

    What is the primary function of short interfering RNA (siRNA)?

    <p>Cleaving RNAs derived from viruses and repeat sequences</p> Signup and view all the answers

    Micro RNA (microRNA) is involved in translational repression or cleavage of target mRNAs.

    <p>True</p> Signup and view all the answers

    What is the purpose of providing a homologous repair template in gene editing?

    <p>To facilitate precise mutations and knock-ins</p> Signup and view all the answers

    Indel refers to the combination of insertion and deletion of bases in an organism's genome.

    <p>True</p> Signup and view all the answers

    What are the most common group of non-coding RNAs (ncRNAs) that are over 200 bases in length?

    <p>Long non-coding RNA (LncRNA)</p> Signup and view all the answers

    LncRNAs can act as either ___________ or ___________ transcriptional regulatory elements.

    <p>cis, trans</p> Signup and view all the answers

    What are the two main mechanisms of RNA interference?

    <p>Short interfering RNA (siRNA) and short hairpin RNA (shRNA)</p> Signup and view all the answers

    CRISPR/Cas9 technology relies on __________ to create site-specific genomic modifications.

    <p>site-specific nucleases</p> Signup and view all the answers

    Match the following non-coding RNAs with their primary functions:

    <p>siRNA = Cleaving RNAs from viruses microRNA = Translational repression of target mRNAs exRNA = Cell-cell communication scaRNA = Regulates spliceosome RNAs</p> Signup and view all the answers

    Match the following terms to their definitions:

    <p>Gene knockdown = A technique that reduces gene expression significantly RNA interference = Method involving the degradation of target mRNA Homology directed repair = Process that uses a repair template for precise modifications Nuclease-deficient Cas9 = Cas9 variant fused with effector domains for specific localization</p> Signup and view all the answers

    Which long non-coding RNA is associated with the deactivation of X chromosome function?

    <p>Xist</p> Signup and view all the answers

    Loss of regulation of LncRNAs has not been linked to human cancers.

    <p>False</p> Signup and view all the answers

    Which type of RNA is produced during RNA interference?

    <p>Anti-sense RNA</p> Signup and view all the answers

    Nuclease-deficient Cas9 is used to introduce double-stranded breaks in DNA.

    <p>False</p> Signup and view all the answers

    What example of LncRNA has been noted for its role in cancer metastasis?

    <p>HOTAIR</p> Signup and view all the answers

    Extracellular RNA (exRNA) is believed to be involved in ___________ and ___________ regulation.

    <p>cell-cell communication, cell</p> Signup and view all the answers

    What is the result of using two sgRNAs with mutated Cas9?

    <p>It introduces a staggered double-stranded break.</p> Signup and view all the answers

    The formation of a __________ is crucial for the degradation of target mRNA during RNA interference.

    <p>RNA induced silencing complex (RISC)</p> Signup and view all the answers

    What role do LncRNAs play in relation to oncogenes and tumor suppressor genes?

    <p>They can function as both oncogenes and tumor suppressor genes</p> Signup and view all the answers

    What is a potential outcome of gene knockdown?

    <p>Temporary reduction of gene product levels</p> Signup and view all the answers

    Which technique involves the permanent deactivation of a specific gene within an organism?

    <p>Gene knockout</p> Signup and view all the answers

    Homologous recombination does not utilize the cell's own DNA repair mechanisms.

    <p>False</p> Signup and view all the answers

    What is one common method used to introduce synthetic DNA sequences into cells?

    <p>Electroporation</p> Signup and view all the answers

    As of 2009, approximately ______ genes had been knocked out of mice.

    <p>11,000</p> Signup and view all the answers

    Which of the following techniques is used to create engineered mutations directed to a specific locus?

    <p>Homologous recombination</p> Signup and view all the answers

    Site-specific nucleases can be used to achieve gene knockouts.

    <p>True</p> Signup and view all the answers

    What is the main purpose of gene knockdowns in research?

    <p>To study gene function and its role in signaling pathways.</p> Signup and view all the answers

    _______ is a technology that can be used in homologous recombination to target specific genes.

    <p>CRISPR/Cas9</p> Signup and view all the answers

    Match the following gene delivery techniques with their descriptions:

    <p>Electroporation = Using an electrical field to increase cell membrane permeability Microinjection = Directly injecting DNA into a cell Viral vectors = Using viruses to deliver genetic material into cells Liposomes = Encapsulating DNA in lipid-based carriers</p> Signup and view all the answers

    What type of RNA accounts for a large proportion of transcribed RNA within eukaryotic cells?

    <p>Non-coding RNA</p> Signup and view all the answers

    Study Notes

    RNA Overview

    • RNA plays a crucial role in the central dogma of molecular biology.
    • Over 75% of the human genome is transcribed to RNA, but less than 2% encodes proteins.
    • The remaining RNA consists of non-coding transcripts.

    Non-Coding RNA (ncRNA) Classification

    • Ribosomal RNA (rRNA): Major component of ribosomes; interacts with mRNA.
    • Transfer RNA (tRNA): Facilitates translation of mRNA into proteins.
    • Small Nuclear RNA (snRNA): Involved in pre-mRNA modification; includes smRNA and lsmRNA.
    • Small Nucleolar RNA (snoRNA): Guides modifications of other RNA molecules.
    • Piwi-interacting RNA (piRNA): Largest class of small ncRNA; involved in gene silencing in germlines.
    • Short Interfering RNA (siRNA): Silences genes by degrading RNAs from viruses and repetitive sequences.
    • Micro RNA (microRNA): Regulates gene silencing through mRNA cleavage.
    • Extracellular RNA (exRNA): Participates in cell-cell communication and regulation.
    • Small Cajal body-specific RNA (scaRNA): Regulates RNA polymerase II activities within Cajal bodies.

    Long Non-Coding RNA (LncRNA)

    • Defined as non-coding RNAs over 200 bases long, regulating gene expression and protein function.
    • Act as transcriptional regulatory elements, either enhancing or repressing transcription.
    • Example: Xist deactivates the X chromosome by interacting with polycomb-repressive complexes.
    • Changes in LncRNA regulation link to human cancers, with overexpression of HOTAIR associated with metastasis and tumorigenesis.

    Gene Manipulation Techniques

    • Gene Knockdown: Alters gene expression, reducing protein levels significantly without complete deactivation; can be temporary or permanent.
    • RNA Interference: Transient gene knockdown via anti-sense RNA production, employing siRNA or shRNA mechanisms leading to mRNA degradation.
    • CRISPR/Cas9: Allows precise genome editing by introducing specific nicks or fusions for targeted gene modification.

    Laboratory Applications

    • Investigating gene expression profiles helps understand cell signaling mechanisms.
    • Overexpression and gene knockout/knockdown methods are essential for studying signaling pathways.

    Gene Knockout Techniques

    • Permanent gene deactivation with methods like homologous recombination and site-specific nucleases.
    • Homologous recombination has successfully knocked out approximately 11,000 genes in mice, equating to half the mouse genome.

    shRNA vs siRNA

    • shRNA generally enables stable, long-term gene knockdown, while siRNA typically leads to transient gene silencing.

    Overexpression Systems

    • Employed predominantly in mammalian cells using immortalized cell lines and suitable vectors to produce protein overexpression.
    • Common vector types:
      • Adenovirus Vectors: High transgene expression in dividing and non-dividing cells, carrying up to 8.5 kb of DNA.
      • Retroviral Vectors: RNA viruses replicating via a dsDNA intermediate, including lentiviruses.
      • Vaccinia Vectors: Double-stranded DNA viruses replicating in the host cell cytoplasm.
      • Plasmid-based Vectors: Common in recombinant DNA technology for protein expression.

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