CSB328 Exam Study Notes

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University of Toronto St. George
Cell and Systems Biology
Stephanie Lepage

CSB328 EXAM REVIEW DIFFERENTIAL GENE EXPRESSION Nuclear equivalence Every cell is genetically equivalent - Weismann o Nuclear determinants are progressively lost as somatic cells divide Cells are different because determinants in the nuclei were asymmetrically divided o Determinants dictate what cells differentiate into o Implies the nuclei of differentiated cells are NOT equivalent Nuclear determinants were chromosomes Every cell in the body has the same number of chromosomes - Driesch o Demonstrates the concept of regulative development Cells communicate with each other to generate one single larva o Each nucleus has all the determinants to drive complete development o Implies the nuclei are equivalent - Spemann o Blastula stage nucleus is able to drive complete development o Suggests nuclear determinants are not lost as cells divide o Implies the blastula stage nuclei are equivalent - Somatic nuclear transfer o Demonstrates that the nuclei of fully differentiated cells still retain all the necessary information to drive complete development o Implies fully differentiated cells are equivalent Poke unfertilized host egg with glass needle Mitotic spindles and chromosomes will spill out Transfer nuclei from undifferentiated cells into host egg Differential gene expression How are different cell types made? - Transcription o Every nucleus is genetically equivalent, but not every nucleus has the same potential to drive complete development Implies the nuclei lose potency as development proceeds o Histone modification Histone acetyltransferase Adds acetyl groups to histone tails Destabilize nucleosomes (uncondensed) Loose packing of DNA Allow transcription Histone deacetylase Removes acetyl groups from histone tails Stabilize nucleosomes (condensed) Tight packing of DNA No transcription Histone methyltransferase (depends on position of methylation) Adds methyl groups to histone tails Stabilize nucleosomes Tight packing of DNA Low transcription Destabilize nucleosomes Loose packing of DNA High transcription o DNA modification DNA methyltransferase Add methyl group to CG rich region of DNA Prevent transcription factors from binding to the enhancer region Prevent transcription Modifying nucleosomes through methylated DNA MeCP2 + Histone deacetylase o MeCP2 recognizes methylated cytosine of DNA o Recruits histone deacetylase o Stabilize nucleosome (condensed) o Promote tight packing of DNA o No transcription MeCP2 + Histone methyltransferase o MeCP2 recognizes methylated cytosine of DNA o Recruits histone methyltransferase o Stabilize nucleosome (condensed) o Promote tight packing of DNA o No transcription DNA methylation pattern changes during development Allows genes to be expressed at the right time and place o For example, globin genes are important for red blood cells 6 weeks -globin Required for embryonic development 12 weeks -globin Required for fetal development DNA methylation patterns are inheritable Dnmt3 (de novo methyltransferase) methylates unmethylated cytosine on DNA Dnmt1 (perpetuating methyltransferase) copies new methylation pattern to the next generation o Adds methyl groups on the newly synthesized DNA strand during cell division (cDNA) o Importance of CG rich region The DNA methylation pattern is maintained in each cell division o Cell types can remain in a differentiated state even though they undergo cell division o Enhancer modularity Multiple enhancers allow a gene to be expressed or to not being expressed in specific tissues Each enhancer has its own specific set of transcription factors For example, crystallin of lens and somatostatin of pancreas Both genes require a transcription factor called Pax6 Pax6 recognizes the enhancer region of two separate genes, but it is the specific combination of transcription factors that leads to differential gene expression - RNA processing o RNA selection Many mRNA are transcribed in every cell, but only a subset are processed (spliced) and enter the cytoplasm to be further translated into functional proteins o Alternative splicing Generates different proteins depending on which introns are spliced out and which exons are kept in For example, tryptomyosin of muscles Generate slightly different tryptomyosin proteins that are specialized for one particular cell type- Translation o Subcellular RNA localization Diffusion and local anchoring Anchored proteins are selectively translated in one localized region of the cell Asymmetric cell division into one side of the cell Localized protection General degradation of transcript in regions where you dont want the protein to be translated Active transport along cytoskeleton Motor proteins will travel differentially along microtubules to certain regions of the cell MUSCLE DEVELOPMENT - Axial mesoderm (chordamesoderm) notochord - Paraxial mesoderm somites sclerotome (cartilage), myotome (skeletal muscle), dermatome (dermis, skeletal muscle) - Intermediate mesoderm kidney, gonads - Lateral plate mesoderm blood, body cavity, extraembryonic tissue - Somitogenesis Division of the paraxial mesoderm into somites (segments) o Somites form progressively at regular intervals from A (R) P (C) on each side of the neural tube or notochord o Different organisms produce different numbers of somites - Notch signaling pathway influences periodicity and location of boundary formation o Delta ligand binds to Notch receptor o Protease cleaves Notch receptor cytoplasmic domain o Cytop
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