BIO 344 1st Edition Lecture 10 Outline of Last Lecture I. Chromatin and Gene Expressiona. NucleosomeII. Histonea. Structureb. Negative supercoilingIII. Chromatina. Transcription regulationOutline of Current Lecture I. Remodeling ComplexesII. Histone codea. Reading and writing the codeIII. ActivationIV. RepressionV. Dynamica. PropogationVI. Stress induced epigenetic control of behaviora. Bdnfb. Exons and promotersThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.VII. DNA methylationCurrent LectureRemodeling Complexes—three methods- Sliding, remodeling (H2AZ- variant of H2), and evictiono All ATP users- Acetylation weakens affinity to activate but does not remove histones—must remodel the chromatin- Methylation repressesHistone Code- Different histone modifications are recognized by proteins in the cell to activate or repress based on modifications to cause different outcomes in expression- Heterochromatin are typically marked with H3o H3K9me gene silencing H3, K=lysine, 9= residue, me= methylo H3K9ac gene expression Ac= acetylo 9 residue of lysine is mutually exclusive Can be either acetylated or methylated, but can not be both at the same time- Protein complexes are readers and writers for the histone codeo Readers recognize different residues Bromodomains recognize acetylated lysine Chromodomains, PHD, tudor domains recognize methylated lysine- Ex: PHD has hydrophobic region to recognize/bind the trimethyl group on lysine and is recruited when the histone is methylatedActivation- Transcription factor, like GCN4 can recruit a coactivator, like GCN5 (a HAT)o If nucleosome is nearby, it will get a transferred acetyl group to weaken its affinity for DNA- Kinase can phosphorylate H3S10o Recognized by TFIID and recruited Recruitment is established by the modification pathwayo TFIID can be recruited even if there isn’t a TATA boxRepression- Histone methyl transferase (HMT) o repress or silence transcription- histone demthylases (HDM)o reverse methylationDynamics of histone remodeling- activation or repression with acetylation or methylationo as well as the reverse of each- chromatin marks can spreado reader and writer can propagate a mark—propagate repression or activationo ex: propagation of activation- GCN5 bound to GCN4 (HAT), nearby histones will be acetylated, adjacent HATs and nucleosomes will continue to be acetylated propagating the acetylation down the DNAStress Induced epigenetic control of behavior- Brain derived neurotrophic growth factor (Bdnf)o Persistant downregulation leads to hippocampus atrophyo Bdnf induces antidepressant activityo Lack of Bdnf leads to impaired antidepressant activity This is induced by stressors and since it causes a modification of genes, it can be passed on Ex: pregnant women who lived during a period of starvation (stressor) have modified genes that allow them to survive in such conditions (i.e. efficient usage and storage of nutrients). This can be passed to the child. Even if the child is living under normal conditions (access to food) they will have a more efficient usage and storage of nutrients, more than they should, causing diabetes or obesity.o Bdnf is controlled by multiple promoters Exon 8 (E VIII) codes for Bdnf P1, P2, P3, P4, P5 promoters can control other noncoding exons- E VIII can be regulated with these five different promoters- Ex: Could splice in a way for promoter 1 to allow E1 to be bound toE VIII Chronic defeat stress leads to persistant epigenetic marks in chromatin- See slides for mouse experiment and result graph- Results—correlation of Bdnf to chromatin: o promoter 4 drives the responseo Bdnf repression is caused by increase in histone methylationo chronic stress leads to increase H3-K27 dimethylation (a repressive mark at P3m P4)o the mark lasts 4 weeks after removal of the stress (persisting) technique used: Chromatin immunoprecipitation (CHIP)- see slides for steps of technique- amplify with PCRo epigenetics are reversible dynamic between repressive and active state, as mentioned beforeDNA methylation- different from histone methylation- DNMT, dMTase, SAM- Happens on CG residueso CpG= phosphate between C and G adjacent C and G, not base paired Usually clustered in “islands” of CpGo Dinucleotide palindrome, so both strands get methylatedo Propagates—inherited cell to cell with cell divisionso CpG islands cluser in promoter regions Active promoters are nonmethylatedo DNA methylation propagation blocks gene expression by blocking activator binding to
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