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U of M GCD 3022 - DNA methylation
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GEN 3022 1st Edition Lecture 22Outline of Last Lecture I. Introductiona. Eukaryotes and gene regulationb. Necessity of gene regulationII. Transcriptional Factorsa. General Transcription factorsb. Regulatory Transcription factorsi. Control elementsii. Activators and repressorsiii. Enhancers and silencersc. Combinatorial controli. Common factors that contribute to combinatorial controld. Structural features of regulatory transcription factorsi. Domains ii. Motifse. Variation in regulatory transcription factor functionsi. Three main functions f. Steroid receptorsi. Action of steroid hormonesThese 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.ii. Response of the cell to steroid hormones1. Glucocorticoids2. Gonadocorticoidsg. CREB proteini. Mechanismii. cAMP response element (CRE)III. Chromatin remodeling and histonesa. Purposeb. Structure of chromatini. Closed conformationii. Open conformationiii. Nucleosomesc. ATP-dependent chromatin remodelingd. Histonesi. 5 histone genesii. Humane histone genesiii. Specialized chromatine. Histone codei. Modification of histones in mammalsii. Protein recognition and bindingIV. DNA methylationa. DNA methylation in eukaryotesb. CpG islandsi. Housekeeping genesii. Tissue-specific genesc. HeritabilityV. Insulatorsa. Purposeb. MechanismOutline of Current LectureI. DNA methylationa. Maintenance of methylationb. Unmethylated CpG islandsc. Housekeeping genesII. Regions of the lac operona. Disruption of -10 and -35 sequencesb. Lac repressor binding sitec. Product of lacIIII. Functions of the lac operona. Inducer of the lac operonb. Production of mRNA transcriptsIV. Transcription factorsa. Inducible systemb. Molecules that induce transcriptionc. Modulation of regulatory transcription factorsd. DNA binding sitesV. DNA modulationa. Histone acetylationb. ATP-dependent chromatin remodelingc. Insulatorsd. Histone codeVI. Gene expression in bacteria/eukaryotesVII. Mutations of the lac operona. Three mutation possibilitiesb. Most likely mutationCurrent LectureI. DNA methylationa. Maintenance of methylation: maintenance methylation refers to DNA methylation patterns that are maintained during replication of somatic cells. b. Unmethylated CpG islands: generally, when CpG islands are unmethylated, it means that chromatin in the promoter region is open, allowing access of transcription factors and RNA polymerase.c. Housekeeping genes: housekeeping genes are constitutively expressed.II. Regions of the lac operon: the regions of the lac operon are lacI, lacO, lacP, lacZ, lacA, and lacYa. Disruption of -10 and -35 sequences: most likely due to a mutation in lacP because -10 and -35 are promoter sequences.b. Lac repressor binding site: in the absence of lactose, the lac repressor is bound tothe lacO site.III. Functions of the lac operona. LacI function: the most convincing evidence that the product of lacI can work in trans is a merozygote with only one functional lacI gene is able to regulate both copies of the lac operon. b. Inducer of the lac operon: allolactose is considered the inducer of the lac operonc. Production of mRNA transcripts: transcription of the lac operon results in the production of only one mRNA transcript.IV. Transcription factorsa. Inducible system: in an inducible system there is a repressor protein that is bound to DNA in the absence of any other factor.b. Molecules that induce transcription: two molecules that work to induce transcription are a repressor and an inducer. An example would be the lac operon repressor and its inducer, allolactose. c. Modulation of regulatory transcription factors: regulatory transcription factors can be modulated by the binding of small effector molecules (inducer, inhibitor), protein-protein interactions, and covalent modifications. d. DNA binding sites: DNA sites that bind regulatory transcription factors are cis acting. V. DNA modulationa. Histone acetylation: histone acetylation can loosen chromatin packing because it decreases the positive charge on the R group of lysine, which weakens the bond between DNA and the histone proteins.b. ATP-dependent chromatin remodeling complexes: these complexes are responsible for the change in location of nucleosomes, eviction of nucleosomes from DNA, and replacement of standard histones with histone variants. c. Insulators: insulators function by defining the boundaries in chromatin and limiting the extent of chromatin changes that occur (ex: acetylation). They can also block activity of enhancers.d. Histone code: the pattern of histones that are recognized by specific proteins. These proteins bind to the DNA to regulate transcription through chromatin remodeling. VI. Gene expression in bacteria/eukaryotes: the four levels of gene expression that are regulated in bacteria/eukaryotes are transcription, RNA processing, translation, and post-translational modifications.VII. Mutations of the lac operon: a strain of E. coli produces B-galactosidase when lactose is present and does not produce it when lactose is not present. This is the wild-type phenotype. The mutant phenotype does not produce B-galactosidase regardless of the presence of lactose. Both the mutant and the merozygote must be considered for this scenario.a. Four mutation possibilities: the mutation could occur at any region of the lac operon (except lacO). A mutation in lacP would result in no expression of the operon under any circumstances because the promoter could not bind to the operon. A mutation in lacZ would result in no production of B-galactosidase. A mutation in lacI would result in no recognition of allolactose, which would mean that the repressor is always bound to the operator. A mutation in lacY would result in no production of permease, and thus no import of lactose into the cell. b. Most likely mutation: the most likely mutation is the mutation of the lacI region because it would result in the repressor always being bound to the operator. This mutation would function in trans instead of


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U of M GCD 3022 - DNA methylation

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