exam 2 developmental
Transcription Factors - Proteins that bind to enhancer or promoter regions and interact to activate or repress the transcription of a particular gene. Most bind to specific DNA sequences. Grouped together in families based on similarities in their DNA-binding domains.
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Transcriptional activators are a type of transcription factor.
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DNA-binding domain – recognizes a particular DNA sequence in the enhancer.
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Trans-activating domain or transcription activation domain – can activate or suppress the transcription of the gene whose promoter or enhancer it has bound; usually enables the transcription factor to interact with proteins involved in binding RNA polymerase II or with enzymes that modify histones.
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Protein-protein interaction domain – allows the transcription factor’s activity to be modulated by transcriptional co-regulators/co-activators or other transcription factors.
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Pioneer Transcription Factors (aka bookmarking transcription factors) – penetrate repressed chromatin and bind to their enhancer DNA sequences. They are important in recruiting other transcription factors and histone modification enzymes as well as controlling DNA methylation. They are critical in establishing cell lineages.
Activated oocyte - the fertilization reactions necessary to initiate development have been completed.
Somatic Cell Nuclear Transfer (SCNT) - Involves taking the nucleus from a somatic cell (like larval frog fibroblasts or gut cells) and transferring it into an enucleated egg.
“Yamanaka factors” - A set of four transcription factors implicated in maintaining inner cell mass (ICM) cells in an immature state. Pioneer transcription factors Sox2, Oct3/4, and Klf4 proteins are examples.
Gene regulatory networks (GRN) - The set of interconnections among genes specifying cell types.
Alternative pre-mRNA splicing - The splicing of pre-mRNA precursors into separate messages for different proteins by using different combinations of potential exons. It results in the production of a wide variety of proteins from the same gene.
Splice sites of the intron - “Consensus sequences” at the 5’ and 3’ ends of the introns that mark the beginning and end of the intronic region.
Spliceosomes - Complexes made up of small nuclear RNAs (snRNA) and proteins (splicing factors) that assemble at a splice site or to adjacent areas and mediate the splicing of pre-mRNA.
microRNAs (miRNA) - Naturally occurring antisense mRNA made to one of its own messages. They are RNAs of approx. 22 nucleotides made from longer precursors.
RNA interference (RNAi) - Process by which miRNAs inhibit expression of specific genes by degrading their mRNAs.
RISC (RNA-Induced Silencing Complex) - A complex involved in RNA interference that can block translation initiation by preventing the binding of initiation factors or ribosomes OR induce cleavage of the target transcript by recruiting enzymes.
Posttranslational Gene Regulation - Modifications that proteins may need to undergo to become active, such as removal of inhibitory sections (proteins with precursors), requiring a signal for destination, assembling with other proteins, or binding an ion or covalent addition of a phosphate or acetate group.
Morphogenesis - The organization of cells into multicellular arrangements such as tissues or organs.
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Epithelial Cells - A type of cell arrangement involved in morphogenesis.
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Mesenchymal Cells - A type of cell arrangement involved in morphogenesis.
Antigens - A foreign substance which induces an immune response in the body, especially the production of antibodies.
Whole Mount In Situ Hybridization - A technique where the entire embryo (or a part thereof) can be stained for specific mRNAs. It introduces a complementary sequence (probe) to the target mRNA that enables visualization. The probe is an antisense RNA labeled with digoxigenin.
Reverse transcriptase - An enzyme used in amplifying cDNA (representing mRNA) to produce cDNA from mRNA.
Polymerase Chain Reaction (PCR) - A method used to amplify cDNA, representing the specific mRNA expressed in the tissue/cells.
Forward Genetics - An approach where an organism is exposed to an agent that causes random mutations, and the resulting phenotypes are screened for ones that affect development = genetics mutagenesis screens.
Reverse Genetics - An approach where one knows the gene that they want to manipulate, making it possible to knock down or knock out the expression of that gene using methods like RNAi or a morpholino.
Gene “knock-down” - Reducing the expression of a specific gene. This can be achieved using RNA interference (RNAi) or a morpholino.
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Morpholino Antisense Oligonucleotides (morpholino (MO)) - A 25 nucleotide sequence, antisense to the start site or splice junction of a target gene, commonly used in frogs and fish to "knock-down" gene expression. Start site MOs bind mRNA and prevent translation, while splice site MOs bind pre-mRNA and prevent proper splicing.
Gene “knock-out” - Targeted removal or inactivation of a specific gene within an organism's genome. This can be done through methods like homologous recombination and CRISPR-Cas9.
Conditional targeted knockouts - A method to knock out a gene in a specific tissue or at a specific time.
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Cre-loxP recombination system - A site-specific recombinase technology that uses homologous recombination to place two cre-recombinase recognition sites (loxP sequences) flanking important exons of a gene ("floxed" gene). When Cre recombinase is expressed, it excises the DNA between the loxP sites, leading to a gene knockout. Cre expression can be controlled temporally and spatially using tissue-specific or inducible promoters.
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CreER recombinases - Tamoxifen-inducible Cre recombinases that translocate into the nucleus and mediate site-specific recombination when tamoxifen binds to them.
CRISPR/Cas9 GENOME EDITING - A gene editing system based on a natural prokaryotic defense mechanism against viruses. CRISPR (clustered regularly interspaced short palindromic repeats) in DNA is transcribed into guide RNAs (gRNAs or sgRNAs) that recognize specific viral DNA segments. The gRNA also binds to an endonuclease called Cas9 (CRISPR associated enzyme 9), which catalyzes a double-strand break in the foreign DNA. This system can be harnessed to target specific genes for editing by designing a gRNA complementary to the target sequence.
Differential Cell Affinity - Each type of cell has a different set of proteins at its surface, and some of these differences are responsible for forming the structure of tissues and organs during development.
Differential Adhesion Hypothesis - A model by Malcolm Steinberg (1964) to explain patterns of cell sorting based on thermodynamic principles, suggesting that cells rearrange themselves into the most thermodynamically stable pattern, and this sorting occurs because cell types differ in the strength of their adhesions.
Cadherins - Calcium-dependent adhesion molecules critical for establishing and maintaining intercellular connections and crucial to the spatial segregation of cell types and the organization of animal form. They are transmembrane proteins that interact with other cadherins on adjacent cells (homophilic or heterophilic binding) and are anchored into the cell by a complex of proteins called catenins. Cadherins + catenins form classic adherens junctions.
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E-cadherin (epithelial cadherin) - A cadherin expressed on all early mammalian embryonic cells, later restricted to epithelial tissues.
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P-cadherin (placental cadherin) - A cadherin that helps the placenta stick to the uterus.
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N-cadherin (neural cadherin) - A cadherin highly expressed on the cells of the developing CNS.
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R-cadherin - A cadherin critical in retina formation.
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Protocadherins - Cadherins that lack connections to the cytoskeleton (actin) through catenins and are important in keeping migrating epithelial cells together.
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Homophilic binding - Binding of the same type of cadherin on another cell.
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Heterophilic binding - Binding of different cadherins on adjacent cells.
Extracellular matrix (ECM) - The cell’s environment, an insoluble network of macromolecules secreted by cells, including collagen, proteoglycans, and glycoproteins like fibronectin and laminin. It is involved in cell adhesion, migration, and the formation of epithelial sheets and tubes and can provide cues for directional cell movement and differentiation.
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Collagen - The main structural protein in the extracellular matrix, abundant in connective tissues.
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Proteoglycans - Large extracellular proteins with glycosaminoglycan (GAG) polysaccharide side chains that can present paracrine factors in high concentration to their receptors.
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Glycoproteins - Proteins which contain oligosaccharide chains (glycans) covalently attached to amino acid side-chains.
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Fibronectin - A glycoprotein that creates order in the ECM, forms fibrils, acts as an intermediary adhesive molecule, and provides attachment for integrins, paving the “roads” for cell migration.
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Laminin - A glycoprotein on which epithelial cells “sit,” assembling the ECM, promoting cell adhesion and growth, and encouraging cell migration.
Integrins - Receptor proteins (heterodimeric) that integrate the extracellular and intracellular scaffolds, allowing them to work together and signal from the outside to the inside of the cell, altering gene expression. The presence of bound integrin can prevent apoptosis, and loss of contact with the ECM can lead to anoikis ("death upon detachment").
Epithelial-Mesenchymal Transition (EMT) - An orderly series of events whereby epithelial cells are transformed into mesenchymal cells, often initiated by paracrine factors that alter gene expression, leading to downregulation of cadherins, release of attachment to laminin/integrins, secretion of enzymes to break down the basal lamina, rearrangement of the actin cytoskeleton, and secretion of new ECM.
Matrix metalloproteinases (MMPs) - Enzymes secreted during EMT to break down the basal lamina.
Induction - Tissue organization via intercellular interactions where cell behaviors like adhesion, migration, differentiation, and division are regulated by signals sent from one cell and received by another, often involving reciprocal interactions.
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Inducer - The tissue that produces a signal(s) (paracrine factor) that changes the cellular behavior of the other tissue.
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Paracrine factors - Proteins secreted by a cell or a group of cells that diffuse over short distances to alter the behavior or differentiation of adjacent cells.
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Responder - The cell or tissue being induced.
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Competence - The ability of a cell or tissue to receive and respond to a specific inductive signal, requiring both a receptor protein for the inducing factor and the ability to respond to the signal.
Instructive interaction - A type of inductive interaction where a signal from the inducing cell is necessary for initiating new gene expression in the responding cell.
Permissive interaction - A type of inductive interaction where the responding tissue has already been specified and needs only an environment that permits the expression of these traits, such as requiring an ECM to develop.
Juxtacrine interactions - Cell membrane proteins on one cell surface interact with receptor proteins on adjacent cell surfaces.
Autocrine interactions - The same cells that secrete paracrine factors also respond to them.
Morphogen - A diffusible biochemical molecule that can determine the fate of a cell by its concentration, leading to different genes being activated at high versus low levels. Morphogens can be transcription factors or paracrine factors.
Paracrine factors (ligands) - Proteins that bind to a receptor and trigger a series of enzymatic reactions within the cell, resulting in the regulation of transcription factors (changes in gene expression) or the regulation of the cytoskeleton (changes in cell shape and movement) = signal transduction cascades.
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Fibroblast Growth Factor (FGF) family - A family of paracrine factors with nearly two dozen distinct genes in vertebrates, generating hundreds of protein isoforms. FGFs bind to fibroblast growth factor receptors (FGFRs), which are receptor tyrosine kinases (RTKs), and are involved in processes like blood cell differentiation, limb growth, and casein gene activation.
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Hedgehog family - A family of paracrine factors used by the embryo to induce particular cell types and create boundaries between tissues. Vertebrates have homologues like sonic hedgehog (shh), desert hedgehog (dhh), and indian hedgehog (ihh), which act as morphogens, secreted from a cellular source, displayed in a spatial gradient, and inducing differential gene expression at different threshold concentrations. Reception of Hedgehog proteins in vertebrate cells occurs on the primary cilium.
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Wnt family - A family of cysteine-rich glycoprotein paracrine factors critical in establishing the polarity of insect and vertebrate limbs, promoting stem cell proliferation, and involved in urogenital system development, guiding mesenchymal cell migration and pathfinding axons.
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TGF-β superfamily - A superfamily of over 30 structurally related members, including the TGF-β family, Nodal and Activin families, bone morphogenetic proteins (BMPs), and the Vg1 family. TGF-β family members regulate ECM formation and cell division, while BMPs regulate cell division, apoptosis, cell migration, and differentiation and act as morphogens.
Receptor tyrosine kinases (RTKs) - Cell surface receptors that, upon binding to their ligand (e.g., FGFs), activate intracellular signaling pathways through tyrosine phosphorylation.
Primary cilium - A focal extension of the cell membrane made by microtubules that extends into the extracellular environment (approx. 1–3 μm) and functions as a highly specialized sensory organelle that interprets changes in the surrounding environment in nearly all mammalian cell types. Defects in cilia (ciliopathies) can lead to various developmental abnormalities.