DevelopmentW2010.Lecture4notes - Development BIO 120 Winter...

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Development BIO 120 Winter 2010 Jeremy Lee Eva Murdock Patrick Yuh Lecture 4 Epigenetic Regulation; Cell-cell and Cell-ECM Interactions I. Epigenetic Regulation: DNA Packaging and Chromatin Modification a. Chromatin Structure 1. Chromosomes are comprised of DNA plus proteins; together this is called chromatin . (Fig. #1) 2. DNA is tightly wound two times around histone protein octamers to form a nucleosome (Fig. #1, #2). 3. Nucleosomes form in clusters of six, called solenoids , with each nucleosome in a solenoid anchored to a histone H1 molecule. 4. Solenoids are coiled together forming thickened loops (Fig. #3) 5. The solenoid loops are thought to be associated with, and attached to, an organizing scaffold, which is composed of non-histone protein, primarily an enzyme, topoisomerase II . Loops are thought to be attached to the scaffold via specialized DNA sequences, called scaffold attachment regions (SARs.) 6. The scaffold itself, with the associated loops of packed solenoids, spirals tightly to form the highly condensed chromosome. b. Histone Modifications and Transcriptional Regulation 1. Core of nucleosome composed of a histone octamer, composed of 2 subunits each of H2A, H2B, H3, and H4 (Figs. #2, #4, #5) 2. Tails of histones can be modified by acetylation, methylation, phosphorylation, sumoylation (SUMO = small ubiquitin-related modifier proteins), and ubiquitination. (Figs. #5, #6, #7.) 3. Modifications of histones catalyzed by specific histone modifying enzymes (Figs. #6, #7 #8.) Examples: Histone acetyltransferases (HATs): add acetyl groups to lysines Histone deacetylases (HDACs): remove acetyl groups from lysines Histone methyltransferases (HMTs): add methyl groups to lysines or arginines Histone demethylases (e.g. LSD1): remove methyl groups Histone kinases (e.g. H3K): Add phosphate groups to serines Histone phosphatases: Remove phosphate groups 3. Histone modification and transcriptional regulation i. Histone modifications affect packaging of DNA; may act directly by changing conformation of histone or by acting as "marks" that recruit other factors that modify nucleosomes and DNA packaging with histones. ii. Packaging of DNA affects access of transcription factors and associated proteins to promoter elements and enhancer sequences and therefore may affect which genes are "available" for transcription. Transcription of a whole group of genes may be affected by local histone modifications.
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iii. Specific histone modifications are commonly associated with specific effects. For example, acetylation is commonly associated with increased access to transcription factors and is, therefore, generally (though not always) associated with increased transcription (Fig. #8) iv. Modification effect may depend on which amino acid is modified. This is the case with methylation for example (Fig. #8) II. The process of morphogenesis
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DevelopmentW2010.Lecture4notes - Development BIO 120 Winter...

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