Bio 125: Development of Multicellular Systems
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Questions and Answers

What does differential gene expression promote?

  • Cell size
  • Cell diversity (correct)
  • Cell motility
  • Chromosomal rearrangement

    • What are gene regulatory elements (GREs)?

    GREs are short sequences of 5-7 base pairs that provide information to turn genes on or off by interacting with transcription factors (TFs).

    Histone modifications can regulate DNA accessibility.

    True

    ______ are specialized proteins that interact with gene regulatory elements to control gene transcription.

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

    Match the following histone modifications with their effects:

    <p>Acetylation = Loosens histone for euchromatin formation Methylation = Can increase or decrease transcription of genes Ubiquitination = Regulates DNA accessibility Phosphorylation = Introduces structural changes in histone tails</p> Signup and view all the answers

    What is the zygote capable of?

    <p>Developing into a complete organism</p> Signup and view all the answers

    What is the role of maternal genes in the cytoplasm of the egg?

    <p>Maternal genes control embryonic development until the embryo's genome is activated.</p> Signup and view all the answers

    During the cleavage phase, the cell cycle skips the growth phases (G1 and G2).

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

    Early embryonic cleavage leads to the formation of ______.

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

    What is the main difference between holoblastic and meroblastic cleavage?

    <p>Holoblastic cleavage occurs in eggs with a large amount of yolk.</p> Signup and view all the answers

    What is the role of master regulators in gene expression?

    <p>Regulate multiple genes in differentiated cells</p> Signup and view all the answers

    Enhancers and silencers can control gene expression even if they are far away from the gene promoter.

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

    What is the purpose of insulators in gene regulation?

    <p>Form boundaries to prevent inappropriate enhancer-promoter interactions</p> Signup and view all the answers

    Chromosome Conformation Capture (3C) allows the identification and quantification of DNA sequences that are __________ interacting.

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

    Match the following germ layers with their respective functions:

    <p>Ectoderm = Origin of epidermis and nervous system Mesoderm = Origin of muscle, bones, and blood Endoderm = Origin of internal organs</p> Signup and view all the answers

    What is the main concept discussed regarding the fate of transplanted cells?

    <p>Cells adapt to new location and can change fate based on the timing of transplantation.</p> Signup and view all the answers

    What is the impact of position and time on the fate of cells?

    <p>Cells can change their fate based on location and timing of transplantation.</p> Signup and view all the answers

    Inducers are secreted cues that trigger fate decisions in responding cells.

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

    ___________ are diffusible chemical substances that are responsible for driving morphogenesis.

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

    Match the following embryonic regions with their organizer properties:

    <p>Floor Plate of the central nervous system = Induces neural tissue and generates a second body axis Zone of polarising Activity (ZPA) of limb bud = Progenitor of the vertebrate limb MS organiser = Precise dorsoventral patterning</p> Signup and view all the answers

    What does the term 'hh path, wg pathway' refer to in the context of the gene components in Drosophila?

    <p>It refers to the components of the Hedgehog and Wingless pathways, indicating that several genes encoding components of the same pathways exhibit specific phenotypes.</p> Signup and view all the answers

    Which signaling protein in Drosophila encodes a protein that doesn't share homology with other fly proteins?

    <p>Hedgehog (hh)</p> Signup and view all the answers

    In Drosophila, when Wingless (Wg) activity is reduced, more Shaven Baby transcription factors (svb TFs) can be expressed, resulting in 'harrier' larvae.

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

    Decapentapelgic (Dpp) encodes a signaling protein with homology to the ________ family.

    <p>TGF-Beta</p> Signup and view all the answers

    What are the main types of cell communication mentioned in the content?

    <p>Paracrine signaling</p> Signup and view all the answers

    Competence is the ability of cells to respond to an inducEve signal, while the cells responding are known as ________.

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

    The TGF-b superfamily includes 33 ligands like Transforming Growth Factor-bs (TGF-bs) and Bone Morphogenetic Proteins (BMPs).

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

    What is the main signal transducer for receptors in the TGFb/BMP pathway?

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

    Match the ligands with their receptor tyrosine kinases pathway components:

    <p>Growth Factor ligands (GFs) = Bind to Receptor Tyrosine Kinases (RTKs) GRB2 = Recruited to the phosphorylated receptors Sos = Activated by GRB2 and promotes GDP to GTP exchange on RAS MEK = Phosphorylated by RAS ERK = Phosphorylated by MEK and promotes translocation into the nucleus</p> Signup and view all the answers

    What are some techniques used in biology for manipulating protein activity with light?

    <p>Light-induced dimerization</p> Signup and view all the answers

    Von Baer's first law suggests that specialized characteristics appear earlier in the embryo than general characteristics.

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

    What is the main function of Hox genes in animals?

    <p>controlling expression of many other downstream factors</p> Signup and view all the answers

    Von Baer proposed that the embryo of a given species deviates more and more from the adult stages of __________ animals.

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

    Match the following Hox gene segments with their corresponding organ development in vertebrates:

    <p>Hox 3 = Thymus, thyroid Hox 9,10,11 = Reproductive tracts Hox 5 = Lungs Hox 6 = Pancreas Hoxb13 = Prostate</p> Signup and view all the answers

    What controls actomyosin contraction in cell protrusions?

    <p>Rho-family GTPase</p> Signup and view all the answers

    Cell shape can be predicted solely based on the genes a cell expresses.

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

    What are the two factors that contribute to cell shape emergence?

    <p>Autonomous/intrinsic genes and Non-autonomous/extrinsic interactions with the environment.</p> Signup and view all the answers

    Cell-ECM junction includes ________ family, allowing forces between cells.

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

    Match the following cell shaping mechanisms with their descriptions:

    <p>Folding tissues = Key in shaping epithelial tissues, generates border fold lines between tissues Segregating tissues = Involves segregation of cells into separate tissue types, essential for differentiation</p> Signup and view all the answers

    What is the purpose of the pluripotency assay involving fibroblasts cells?

    <p>To induce pluripotency in fibroblast cells</p> Signup and view all the answers

    Which transcription factors are included in the Yamanaka cocktail for inducing pluripotency?

    <p>Sox2</p> Signup and view all the answers

    Pluripotency factors drive transition, leading to a decrease in self-renewal and developmental plasticity.

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

    _______ and unpacking chromatin are used to achieve changes in gene expression during development.

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

    Match the following components with their roles in epigenetic regulation:

    <p>Histone De-/Methylation = Modification of histones to regulate gene expression Chromatin remodelers = Enzymes restructure chromatin to change DNA accessibility DNA Methylation = Epigenetic modification where methyl groups are added to DNA</p> Signup and view all the answers

    What is the name of the cytokine that, when added to culture medium, maintains ES cell pluripotency?

    <p>Leukaemia inhibitory factor (LIF)</p> Signup and view all the answers

    What are the major germ layers in the developmental process?

    <p>Ectoderm, Mesoderm, Endoderm</p> Signup and view all the answers

    Pluripotent stem cells can differentiate spontaneously without specific culture conditions.

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

    Stem cells can ______ and divide, generating stem cell + progeny cell.

    <p>self-renew</p> Signup and view all the answers

    What important cellular component determines stem cell polarity?

    <p>Microtubule spindle</p> Signup and view all the answers

    Study Notes

    Development of Multicellular Systems

    From Egg to Early Embryo

    • The size of an egg does not determine the complexity of creating a new embryo.
    • The fertilized egg (zygote) is a totipotent stem cell, capable of developing into a complete organism and differentiating into any cell or tissue.
    • Development relies on surrounding follicle cells.
    • The egg contains:
      • DNA: haploid (n) → diploid (2n) during fertilization
      • Yolk: provides food and energy for the embryo
      • Cytoplasm (ooplasm): contains mRNAs and proteins, important for early development events

    Maternal Control of Development

    • Maternal genes in the cytoplasm control embryonic development until the embryo's genome is activated.
    • Maternal phase: early development depends on maternal gene contribution, duration varies among organisms.
    • Embryos developing inside (viviparity) have less yolk, while those developing outside (oviparity) have more yolk due to environmental factors.

    Mid-Blastula Transition

    • Zygotic gene transcription starts, slowing down the cell cycle.
    • Asynchrony in cell division and increased cell mobility occur.
    • This is controlled by the removal of maternally loaded inhibitors against exponentially increasing DNA amount.

    Cleavage Phase

    • The zygote undergoes repeated divisions to produce more blastomeres without an increase in embryo size.
    • Cell cycle: process of cell replication, skipped G1 and G2 phases in cleavage phase to rapidly divide.
    • Cyclins are translated from maternal mRNAs in ooplasm.

    Spacial Organization of Early Cleavage

    • Some eggs have clear polarity, with an animal-vegetal axis.
    • Cleavage patterns differ between species, depending on spindle (microtubules) orientation.
    • Mammalian embryos exhibit a rotational cleavage pattern.

    Regulation of Cellular Differentiation

    • All organisms start as a single cell, dividing to form a mass of cells, generating differences through symmetry breaking.
    • Theories of symmetry breaking:
      • Nuclear determinants are differentially distributed among cells.
      • Asymmetric cell division distributes determinants unevenly.
    • PAR proteins regulate cellular differentiation, establishing differences between poles of the embryo.

    From One to Many: Differential Gene Expression

    • Cells acquire different functions through differential gene expression.
    • Genomic equivalence: all cells share the same DNA, but cells acquire different phenotypes via differential expression.
    • Evidence for genomic equivalence:
      • Lens regeneration in salamanders
      • Cloning of amphibians and mammals

    Mechanism of Differential Gene Expression

    • Gene expression can be regulated at every step, including transcription, RNA processing, transport, and translation.
    • Gene regulatory elements (GREs) and transcription factors (TFs) interact to control gene transcription.
    • DNA accessibility is regulated by chromatin conformation, which is modified by epigenetic modifications.

    Epigenetic Modifications

    • Chromatin conformation is regulated by epigenetic modifications, such as histone modifications and DNA methylation.
    • Histone modifications:
      • Acetylation: loosens histone, making DNA accessible.
      • Methylation: can increase or decrease transcription.
    • DNA methylation:
      • Adds methyl groups to cytosine, regulating gene expression.
      • CpG islands: enriched in the vicinity of genes, regulating gene expression.

    Inheritance to the Next Generation

    • Epigenetic modifications are faithfully copied during cell division and inherited to the next generation.
    • Provides cellular memory, allowing cells to "know" their status.

    Waddington's Landscape

    • Metaphor for development and the importance of epigenetics.
    • Inclined surface represents a series of choices a cell makes, becoming more committed to its fate.

    Determining the Cell Epigenome

    • Epigenome: the collection of all epigenetic modifications on the DNA in a single cell.
    • Identifying a cell by its epigenome involves:
      1. Tissue dissociation
      2. Single-cell separation
      3. Single-cell encapsulation### Transpose-Accessible Chromatin (ATAC-seq) and Chromatin Immunoprecipitation Sequencing (ChIP-seq)
    • ATAC-seq:
      • Determines chromatin accessibility in the genome
      • Uses hyperactive transposase (Tn5) to insert oligonucleotides of known sequence
      • PCR amplification and sequencing
      • Usage of known sequences to determine chromatin organization
      • High frequency of inserted transposons indicates open chromatin
    • ChIP-seq:
      • Determines exact epigenetic modifications
      • Chromatin is fragmented, and antibodies recognizing specific epigenetic modifications bind
      • PCR amplification and sequencing
      • Used to study chromatin state and accessibility during development and in different tissues

    Study of Chromatin Accessibility in the Mouse

    • 1000 ChIP-seq assays and 132 ATAC-seq assays across 72 distinct tissue-stages
    • Study shows how chromatin state and accessibility change during development and in different tissues

    Differential Gene Expression: GREs and Promoters

    • Gene Regulatory Elements (GREs):
      • Are encoded in the genome and turn genes on and off
      • Include enhancers and silencers
      • Can be located near or far from the promoter
      • Interact with specialized proteins: transcription factors (TFs)
    • Promoters:
      • Are encoded in the genome and turn genes on and off
      • Located near the gene transcription start site
      • Where the transcription machinery assembles
      • TFs help RNA Polymerase to engage with the promoter and start transcription

    Differential Gene Expression: Transcription Factors

    • 6-8% of proteins are estimated to work as TFs, regulating gene expression through DNA binding
    • Motifs:
      • Most TFs regulate transcription by binding to this defined sequence
      • Are short and degenerate
      • Specific nucleotides at specific positions
    • TFs act in a combinatorial way:
      • By collaborating or competing with other TFs, common target genes can be regulated
      • A relatively small number of proteins generates a large diversity of cell types
      • 1 enhancer can contain several different motifs
      • 1 TF has one motif
      • Different combinations of TFs are present in different cells

    Mechanism of Enhancer Action

    • Enhancers and silencers can be located far away from the promoter they control
    • Example: Sonic hedgehog (Shh) promoter
      • Signaling molecule for patterning vertebrate limb depends on an enhancer located 1Mb away
      • Within the enhancer, there are different motifs
      • Point mutations in this enhancer can cause limb defects

    Topologically Associated Domains (TADs)

    • Enhancers and promoters come to close physical proximity via loop formation
    • This leads to the formation of protein complexes that can regulate RNA Polymerase activity
    • Genome might be organized in loops and logically associated domains
    • TADs:
      • Are interacting genomic regions
      • DNA sequences physically interact more with each other than with sequences outside of the TAD
      • Identification of TADs via Chromosome Conformation Capture (3C)

    Chromosome Conformation Capture (3C)

    • 3C allows the identification and quantification of DNA sequences that are physically interacting
    • Steps:
      1. Formaldehyde treatment: introduces bonds that cross-link protein-DNA interactions
      2. If two loci interact, they will be "frozen" in this conformation
      3. Restriction enzyme treatment: bonded Protein-DNA interactions stay intact
      4. Ligation: in highly diluted DNA
      5. Reverse cross-linking: releases formaldehyde-mediated bonds
      6. Amplification and sequencing: of DNA fragments
      • Loci that are far from each other are ligated together
      • The probability of this happening depends on proximity in the 3D space and frequency of interaction
      • By analyzing hybrid molecules, the quantification of the degree of physical interaction is possible

    Insulators

    • Form boundaries in 3C diagrams
    • Sequences are CCCTC rich
    • These consensus sequences are bound by CCCTC-binding factor (CTCF)
    • Prevent inappropriate enhancer-promoter interactions
    • Mutations cause developmental phenotypes
    • Chromosomal rearrangements that disrupt these boundaries
    • New enhancer-promoter interactions

    Transcriptional Hubs

    • Are multiple enhancers and promoters that are co-expressed
    • Performed loops: primed and ready to respond to a specific signal
    • Signal makes one or more TFs available
    • Leads to conformational change
    • Allows immediate transcription of all the genes within the loop

    Laboratory Experiments

    • In vivo enhancer activity assay
    • Detection and localization of mRNAs: in situ hybridization
    • Single-cell transcriptomics
      • Technique examines the gene expression level of individual cells by simultaneously measuring the mRNA concentration of many genes
      • Helpful if you want to know "all the activity" in the cell

    Spatial Patterning of Tissues and Embryos

    • Difference between cells and organs/organisms
    • Cells are organized into tissues/organs
    • Biological function usually emerges in the scale of tissues/organs, not at the individual cell level
    • How cells are organized over large scales drives morphological and evolutionary diversity

    Organizing Differentiation in Space and Time

    • Body axes
      • Animal-vegetal axis: forms future anteroposterior body axis
      • Dorsoventral axis: is orthogonal to the animal-vegetal axis
    • Embryo positioning
      • Gastrulation: dynamic organization of the embryo into three germ layers
      • Ectodermal, mesodermal, and endodermal germ layers
    • Evidence that differentiation is regulated in space and time
      • Observation: fate mapping and lineage tracing
      • Manipulation: "cut & paste" experiments
      • Impact of position and time on fate
        • Cells normally select a fate appropriate for their location in the embryo
        • Cells are specified if they execute a normal fate when isolated
        • Cells can adapt to a new fate appropriate for the location if moved before determination
        • Fate of late-stage donors is determined

    Morphogens and Positional Information

    • Exploiting diffusion to pattern tissues
    • Morphogens: diffusible chemical substances that drive morphogenesis
    • Generating chemical gradients
      • Establish localized source of factor
      • Allow diffusion of factor from source
      • Chemical gradient can provide graded positional information
      • Gradients provide a mechanism to allow positioning to influence differentiation
    • Source and sink model
      • Factors deplete/destroy morphogen depletion
      • Ensures morphogen gradient
    • From morphogen gradient to domains
      • Morphogen gradient theory offers a mechanism to generate positional information
      • Animal body plans are not organized in continuous gradients
      • Embryos become subdivided into discrete regions/domains

    Evidence for Morphogen Thresholds

    • Morphogen decreases with distance from the source
    • Morphogen provides cells with positional value
    • Cells switch on specific target genes that have different morphogen activation thresholds
    • Positional information provides a mechanism to go from morphogen source to gradient to tissue pattern
    • Multiple morphogen gradients can be combined to form more complex patterns### Heidelberg Screen
    • The screen involves two approaches:
      • Knowing where to look: mutated important developmental genes result in strong defects in embryo/larvae
      • Genome-wide approach: isolated many differently patterned mutant larvae, leading to the identification of many genes that caused deletions of body regions when mutated

    Bicoid Morphogen

    • Bicoid is a maternal-effect gene: the phenotype of an embryo is not determined by its genotype, but by the genotype of its mother
    • Bicoid mutant: complete loss of anterior structures (e.g., head) and mirror-image duplication of the most posterior segments
    • Bicoid gene encodes transcription factors (TFs) that bind to DNA to regulate transcription and to mRNA to regulate translation
    • Maternal Bcd mRNA is localized to the anterior pole of the oocyte, and a single cell contains many nuclei in one cytoplasm (syncytium) during early stages

    Spatial Patterning of Tissues and Embryos

    • Morphogen gradient: a concentration-dependent gradient of a signaling molecule that induces different gene expressions in different regions of a tissue
    • Different morphogens in Drosophila:
      • Hedgehog (hh)
      • Wingless (Wg/Wnt)
      • Decapentaplegic (dpp/BMP)
    • Morphogen patterns of activation/repression occur in a concentration-dependent manner
      • Failure of expression: segment polarity and limb defect mutants are often different alleles of the same gene that fail to complement when crossed
      • Pleiotropic: a single gene produces more than one effect in several tissues

    Molecular Mechanisms of Morphogen Action

    • Morphogen expression and secretion by defined source cells
    • Extracellular signal gradients convert to patterns of gene expression
    • Wingless (Wg/Wnt) pathway:
      • Ligands: Wnt
      • Receptors: Frizzled, G-protein-coupled receptor (GPCR), and LRP
      • Signal transduction: Dishevelled
      • Transcription factors: B-catenin/Armadillo and TCF/LEF
    • Hedgehog (hh) pathway:
      • Ligands: Shh/hh
      • Receptors: Patched (multitransmembrane receptor) and Smoothened (GPCR)
      • Signal transduction: Fused
      • Transcription factors: Gli full-length (GliFL) and Gli Repressor (GliR)

    Integrand Models and Molecules

    • Competent cells receive positional information from neighboring cells that "organize" them
    • Organiser gene expression is induced in floor plate by neighboring notochord
    • Shh signaling in cilia: Smoothened receptor must enter cilium to signal
    • Receptor localization, signal transduction, and cilia are regulated by Shh signaling

    Reaction-Diffusion Systems

    • Pauses in the reaction-diffusion system generate complex patterns
    • Principles of reaction-diffusion systems:
      • Local increase in diffusible "activator" triggers peak in expression via "auto-activation"
      • Activator triggers expression of its own faster-diffusing inhibitor, which represses activator outside local peak
      • Changing geometry: spots to branch networks

    Investigation of Morphogen Activity

    • Indirect activity of morphogens: measuring the impact on final embryonic structures
    • Direct activity of morphogens: measuring the impact on expression of target genes
    • Quantitative light microscopy to measure local concentrations of morphogens

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    This quiz covers the development of multicellular systems, from eggs to early embryos, and the process of differentiation through gene expression.

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