GEN 3022 1st Edition Lecture 23Outline of Last Lecture I. 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 acetylationThese 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.b. ATP-dependent chromatin remodelingc. Insulatorsd. Histone codeVI. Gene expression in bacteria/eukaryotesVII. Mutations of the lac operona. Three mutation possibilitiesb. Most likely mutationOutline of Current LectureI. Overview of Epigeneticsa. Epigeneticsb. Epigenetic inheritance c. Epigenetic regulationII. Cis and trans epigenetic changesa. Cis epigenetic changesb. Trans epigenetic changesIII. Epigenetics and developmenta. Process of developmentb. Epigenetic regulationIV. Genomic imprintinga. Igf2 gene and methylationb. CTC-binding factorV. Development of specific cell typesa. Embryonic developmentb. Polycomb group (PcG)c. Inhibition of transcriptionVI. Regulation of RNA processinga. Alternative splicingb. Alpha-tropomyosinc. Splicing factorsVII. mRNA stabilitya. regulation of stabilityb. factors that affect stabilityi. length of polyA tailii. destabilizing elementsc. RNA interferencei. miRNAii. double stranded RNAs Current LectureI. Overview of Epigeneticsa. Epigenetics: study of mechanisms that lead to changes in gene expression that can be passed from cell to cell. Reversible and do not involve a change in the sequence of DNA.b. Epigenetic inheritance: involves epigenetic changes that are passed from parent to offspring. Example: genomic imprinting from chapter 5. c. Epigenetic regulation: examples of epigenetic regulation include DNA methylation, chromatin remodeling, covalent histone modification, and localization of histone variants.II. Cis and trans epigenetic changes: cis is maintained at a specific site whereas trans are maintained by diffusible factors (transcription factors). This means that cis changes only affect one copy of a gene and trans changes affect both copies. The mode can be determined using cell fusion experiments.a. Cis epigenetic changes: maintained during cell division. b. Trans epigenetic changes: both copies of the gene are affected, which is also maintained during cell division.III. Epigenetics and development: epigenetic gene regulation may occur as a programmed developmental change or be caused by environmental agents.a. Process of development: development refers to a series of genetically programmed changes that occur to form a mature adult from an embryo.b. Epigenetic regulation: many changes that occur during development are due to epigenetic regulation. Examples of this include genomic imprinting, X-chromosome inactivation, and formation of specific cell types and tissues.IV. Genomic imprinting: form of gene regulation in which an offspring expresses the copy of a gene from one parent but not both. a. Igf2 gene and methylation: this example shows that the Igf2 gene is only inherited from the father and the mother’s copy of the gene is silenced. This is due to de novo methylation of sperm in the male (no methylation of the egg). The methylation occurs at both the imprinting control region (ICR) and the differentially methylated region (DMR). b. CTC-binding factor: methylation inhibits the binding of CTC-binding factor, which allows the Igf2 gene to be stimulated by a nearby enhancer. CTC-binding factor binds to the unmethylated region and inhibits transcription by forming a loop. V. Development of specific cell typesa. Embryonic development: epigenetic changes occur during embryonic development. These changes are remembered during cell divisions. b. Polycomb group (PcG): important regulators involved in gene expression.c. Inhibition of transcription: binding of PRC2 to a PRE (polycomb response element) leads to methylation of lysine on histone H3 (which leads to geneinhibition). PRC1 is then recruited to the gene and inhibits transcription through chromatin compaction, covalent modification of histones, and direct interaction with a transcription factor. VI. Regulation of RNA processing: common in eukaryotes for gene expression to be regulated at the RNA level due to post-transcriptional modifications.a. Alternative splicing: pre-mRNA can be spliced in more than one way to produce different polypeptides due to different amino acid sequences. Oftentimes these polypeptides have similar functions. b. Alpha-tropomyosin: protein that functions in the regulation of cell contraction and is found in smooth and striated muscle a well as some non-muscle cells. Different versions of this protein contract muscles in different ways. This is due toalternative splicing. c. Splicing factors: proteins that determine where a sequence is spliced. Example is SR proteins which have a domain rich in serine and arginine at their C-terminal end. This region is involved in protein-protein recognition while their N-terminal end is an RNA-binding domain. Splicing factors modulate the ability of spliceosomes to recognize or choose the splice sites. This can occur by inhibiting or enhancing the ability of a spliceosome to recognize a splice site. VII. mRNA stability: varies considerably in eukaryotic mRNAa. regulation of stability: regulated so that its half-life is lengthened or shortened, which affects the mRNA concentration and gene expression.b. factors that affect stabilityi. length of polyA tail: average length of newly made mRNA polyA tail is 200 nucleotides. polyA binding protein binds to tail and increases stability. This tail is shortened by exonucleases and eventually polyA binding protein can no longer bind to the tail. Once this occurs, the mRNA is rapidly degraded by exo and endonucleases.ii. destabilizing elements: found in mRNAs with short half lives. These can be found anywhere in mRNA but mostly occur at the 3’ end between the stop codon and polyA tail.c. RNA interference: double stranded RNA can silence the expression of certain genes.i. miRNA: micro RNAs are encoded by genes in eukaryotes. They do not encode a protein and give rise to small RNA