Transcriptome Analyses in Cancer Research
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Transcriptome Analyses in Cancer Research

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Questions and Answers

What is the primary modification that occurs first during RNA processing of eukaryotic pre-mRNAs?

  • RNA Polyadenylation
  • RNA Capping (correct)
  • Intron Removal
  • RNA Splicing

    • What does transcriptome analysis provide for a particular cell type?

  • A cellular metabolic profile
  • A signature of cell type (correct)
  • An immunological response profile
  • A detailed genetic sequence

    • Which enzyme complex performs RNA splicing in eukaryotic cells?

  • Ribosome
  • RNA Polymerase
  • Nuclease
  • Spliceosome (correct)

    • What phenomenon allows different protein forms to be produced from the same gene?

    <p>Alternative RNA Splicing</p> Signup and view all the answers

    What is the relationship between transcription elongation and RNA processing in eukaryotes?

    <p>Transcription elongation is tightly coupled to RNA processing.</p> Signup and view all the answers

    How does transcriptome analysis contribute to understanding disease states such as cancer?

    <p>By identifying altered cellular transcripts</p> Signup and view all the answers

    Which of the following is NOT a function of RNA processing in eukaryotic cells?

    <p>DNA Replication</p> Signup and view all the answers

    What does the term 'signature' refer to in the context of transcriptome analyses?

    <p>The characteristic expression profile of transcripts</p> Signup and view all the answers

    What is the primary function of RNA splicing in eukaryotic cells?

    <p>To separate coding exons from non-coding introns</p> Signup and view all the answers

    What is alternative splicing primarily responsible for?

    <p>Increasing the number of proteins that can be produced from a single gene</p> Signup and view all the answers

    What role do exon junction complexes (EJCs) play in RNA splicing?

    <p>They serve as markers for correctly spliced RNA</p> Signup and view all the answers

    In Drosophila, what determines the sex of an individual based on splicing?

    <p>The X:A ratio of chromosomes</p> Signup and view all the answers

    What is the role of the gene 'Sex-lethal' in Drosophila splicing regulation?

    <p>It acts as a splicing repressor</p> Signup and view all the answers

    How does the 'Doublesex' gene function in the context of Drosophila sex determination?

    <p>It regulates sex gene expression</p> Signup and view all the answers

    What typically happens to splice products when splicing is not properly regulated?

    <p>They can be nonfunctional</p> Signup and view all the answers

    Which of these is NOT a component of the spliceosome involved in RNA splicing?

    <p>RNA polymerase</p> Signup and view all the answers

    What does the IC50 value indicate in transcriptome analyses?

    <p>The concentration of a compound required to inhibit cell proliferation by 50%</p> Signup and view all the answers

    Which of the following processes is NOT part of eukaryotic RNA processing?

    <p>Replication of RNA in the cytoplasm</p> Signup and view all the answers

    What role does the cap-binding complex (CBC) play in RNA processing?

    <p>It helps export RNA from the nucleus and is important for mRNA translation</p> Signup and view all the answers

    Which part of the biological hierarchy is involved in post-transcriptional regulation?

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

    The primary function of the modified guanine nucleotide added to the 5' end of pre-mRNA is to:

    <p>Help in RNA processing and export from the nucleus</p> Signup and view all the answers

    In the context of cell state, what does the color blue represent in the expression profile?

    <p>Low expression of genes</p> Signup and view all the answers

    Which organelle is primarily involved in mRNA translation?

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

    Which of the following statements is TRUE regarding differentiated neutrophils?

    <p>They exhibit a specific “signature” of cell state</p> Signup and view all the answers

    What is the role of the Sxl protein in Drosophila sex determination?

    <p>Represses splicing of Tra RNA</p> Signup and view all the answers

    What does the Dsx protein do in Drosophila?

    <p>Represses male gene expression</p> Signup and view all the answers

    Which factor is involved in 3’ polyadenylation?

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

    What is the typical outcome of introducing high levels of miRNA targeting Sxl RNA in Drosophila?

    <p>Creation of a male Drosophila</p> Signup and view all the answers

    What occurs after RNA is cleaved during the polyadenylation process?

    <p>Transcription terminates</p> Signup and view all the answers

    What is the function of poly-A binding proteins?

    <p>Aid in RNA stability</p> Signup and view all the answers

    Which protein is known to activate the splicing of Dsx?

    <p>Tra protein</p> Signup and view all the answers

    Which of the following accurately describes Tra RNA in male Drosophila?

    <p>It is spliced but produces nonfunctional protein.</p> Signup and view all the answers

    Study Notes

    Transcriptome Analyses

    • Transcriptome analyses are used to study a large set of cellular transcripts, providing a “signature” of cell type
    • Transcriptome analyses is powerful because it can be used to understand cell state, response to extracellular stimuli, and disease states (e.g., cancer)

    Transcriptome Analyses Using Model Cell Line for AML

    • Cells at different stages of development (Primary acute myelogenous leukemia, differentiated neutrophils) can be analyzed using transcriptome analyses
    • The different stages of cells can be visualized in a heatmap, with blue representing low expression and red representing high expression

    IC50

    • IC50 refers to the concentration of a compound required to inhibit cell proliferation by 50%
    • IC50 can be used to determine the effectiveness of a drug or treatment

    Regulation of Genome Expression

    • The genome is the complete set of genetic information in an organism
    • The transcriptome is the complete set of RNAs in an organism
    • The proteome is the complete set of proteins in an organism
    • The metabolome is the complete set of metabolites in an organism
    • The interactome is the complete set of molecular interactions in an organism
    • Post-transcriptional regulation of gene expression occurs after transcription and includes RNA processing and translation
    • Post-translational regulation of gene expression occurs after translation and includes protein folding, modifications, and degradation

    RNA Processing

    • Eukaryotic RNA processing is tightly coupled to transcription:
      • Covalent modifications of RNA ends
      • Removal of intron sequences

    RNA Capping

    • RNA capping is the addition of a modified guanine nucleotide to the 5’ end of pre-mRNA
    • RNA capping involves three enzymes
    • The cap is bound by the cap-binding complex (CBC)
    • RNA capping functions include:
      • Helps in RNA processing and export from the nucleus
      • Important role in translation of mRNAs in the cytosol
      • Protects mRNA from degradation

    RNA Splicing

    • RNA splicing removes intron sequences from newly transcribed pre-mRNAs
    • Exons are coding sequences
    • Introns are non-coding sequences
    • Alternative splicing is when different cells can splice an RNA transcript differently to make different proteins from the same gene
    • ~75% of human genes produce multiple proteins, increasing the coding potential of the genome

    Spliceosome

    • The spliceosome is an enzyme complex made up of RNA and proteins that carry out RNA splicing
    • Spliceosome binds to proper splicing sites
    • Exon junction complexes (EJCs) are markers for properly spliced RNA

    Alternative Splicing Regulation: Drosophila sex determination

    • Drosophila sex determination is based on the ratio of X chromosomes (X): autosomal sets (A)
      • X:A = 0.5 Male (Default)
      • X:A = 1.0 Female
    • Three genes are involved in Drosophila sex determination:
      • Sex-lethal (Sxl): splicing repressor
      • Transformer (Tra): splicing activator
      • Doublesex (Dsx): regulates sex gene expression
    • All three genes contain regulated splice sites

    Alternative Splicing Regulation: Drosophila sex determination - Males

    • In males, the regulated splicing of Sxl, Tra, and Dsx results in nonfunctional proteins
    • Sxl proteins are required for functional Tra protein
    • Dsx protein represses female gene expression

    Alternative Splicing Regulation: Drosophila sex determination - Females

    • In females, the regulated splicing of Sxl, Tra, and Dsx results in functional proteins
    • Sxl protein represses the splicing of Sxl and Tra RNA
    • Tra protein activates the splicing of Dsx RNA
    • Dsx protein represses male gene expression

    3' Polyadenylation

    • Polyadenylation signals are encoded in the genome
    • RNA polymerase recruits protein complexes to the RNA
    • Polyadenylation involves three major protein factors:
      • Cleavage stimulation factor (CstF)
      • Cleavage and polyadenylation specificity factor (CPSF)
      • Poly-A polymerase (PAP)
      • PAP adds ~200 A nucleotides to the 3' end of RNA from ATP
      • Poly-A tail is bound by poly-A binding proteins, aiding in:
        • RNA export
        • translation
        • mRNA stability

    Polyadenylation and Termination

    • RNA is cleaved
    • Transcription terminates
    • Poly-A polymerase (PAP) adds ~200 A nucleotides to the 3' end of RNA
    • The poly-A tail is bound by poly-A binding proteins
    • Poly-A binding proteins aid in:
      • RNA export
      • translation
      • mRNA stability

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    BIO230 Lecture 5: Regulation Of Genome Expression PDF

    Description

    This quiz explores the fundamentals of transcriptome analyses, focusing on their application in understanding acute myelogenous leukemia (AML) and the significance of IC50 in drug effectiveness. Participants will learn about cell state signatures and how gene expression regulation is pivotal in cancer biology. Gain insights into heatmap visualizations and the interplay between transcriptomes and genomic data.

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