Genetics Notes week 9
Genetics Notes week 9 Bios 206
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This 7 page Class Notes was uploaded by Becca Sehnert on Friday March 11, 2016. The Class Notes belongs to Bios 206 at University of Nebraska Lincoln taught by Dr. Christensen in Fall 2016. Since its upload, it has received 10 views. For similar materials see Genetics in Biological Sciences at University of Nebraska Lincoln.
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Date Created: 03/11/16
BIOS 206 WEEK 9 MONDAY! Chap 17 Regulation of gene expression in eukaryotes More complex in eukaryotes o DNA associated with histones and other proteins o Most mRNA must be spliced, capped, and polyadenylated prior to transport from nucleus o Transcription and translation are spatially distinct o Movement of RNA into cytoplasm after transcription o RNA stability o Modulation of mRNA translation as well as protein processing, modification, and degradation Euk DNA is combined with histone and non-histone proteins to form chromatin o Chrom structure is continuously rearranged so transcription active genes are cycled to edge of chrom territories o Transcription factor(ies) are nuclear sites that have most of the active RNA polymerase and transcription regulatory molecules Histone acetylation, catalyzed by histone acetyltransferases (HATs) is associated with increased transcription Histones can be modified by phosphorylation and methylation o DNA methylation associated with decreased gene expression o Occurs mostly on cytosine of CpG doublets in DNA o Methylation often silences genes Transcription regulation requires binding of many regulatory factors to specific DNA sequences (cis-acting sequences –on same chrom as gene it regulates) o Promoters –sequences that serve as recognition sites for transcription Have 1+ core elements that bind to specific initiation proteins Initiator (inr) TATA box TFIIB recognition element (BRE) Downstream promoter elements (DPE) Motif ten elements (MTE) o Enhancers –modular and contain several short DNA sequences increasing transcription rates (located on either side) o Silencers –cis-acting elemeents that repress the level of transcription initiation Transcription factors have 2 functional domains o DNA-binding domain Bind to specific DNA sequences Helix-turn-helix (HTH) Zinc finger Basic leucine zipper (bZIP) o Trans-activating domain Activates/represses transcription by binding to other transcription factors or RNA polymerase Transcription of GAL genes in yeast Upstream activator sequences UAS DNA sensitive region o In vitro with DNAse hypersensitivity o Experiment done outside of cell Gal80p attaches to Gal 4p What phenotype would you expect a gal80- null mutant to have? a. Inducible expression of GAL1 and GAL10; able to grow on galactose b. Constitutive expression of GAL1 and GAL10; unable to grow on galactose c. Constitutive expression of GAL1 and GAL10; able to grow on galactose d. Repressed expression of GAL1 and GAL10; unable to grow on galactose e. Repressed expression of GAL1 and GAL10; able to grow on galactose Gal80 is a repressor, and it stops transcription of RNApolymerase. Gal4 connects to UAS and turns expression of gene on and will be transcribed no matter what. Phenotype of Gal4 mutant –cell death if galactose is the only thing available. Cant do transcription. WEDNESDAY Posttransctriptional gene regulation occurs at all steps from RNA processing to protein modification Removal of introns and splicing together of exons Addition of a cap and poly-A tail mRNA stability Translation (HIF1 and HIf1 (protein) made all the time unless molecular oxygen around, then its degraded. Why? If it doesn’t have oxygen, it wants a fast response. Protein is always there if it needs to be. This is a regulatory circuit, input and outputs. Post- translational degradation –fast response) Alternative splicing can generate different iso-forms of mRNA o (Proteins differ -1 part same, second part different. Get spliced differently in thyroid and neuron cells.) Number of proteins that cell and make (its proteome) is greater than the number of genes its genome 2 MORE POINTS ON SLIDE AND PIC o (Beedle won nobel prize for “one gene, one enzyme” –he was wrong) Aprox. 2/3 of human genes undergo alternative splicing Humans produce several Dscam gene in Drosophila. 38,016 genes possible. (can splice any of XX genes. Expressed in nerve cells and each neuron is unique. Alternative splicing is modular.) Sex lethal (Sxl) transformer (tra) and doublesex (dsx) genes are part of hierarchy of gene regulation for sex determination in Drosophila o (When sex lethal protein there, splices in certain way. Nonsense (splice variant) mutation to transcription of wrong sex proteins) Sxl gene acts as switch that selects pathway of sexual development by controlling splicing of the dsx transcript in a female-specific fashion o (Tra controls dsx protein. When it isn’t there, makes different protein, specific to males. 2 different transcription factors cuz binds to different sequence.) o (Female puts certain protein in egg. When they cant do it, they develop as males and dosage compensation kills them (too many X expressed). Daughterless) (NVM about dosage compensation) Drosophila XX fertilized egg has constitutive mutant for sex-lethal. What phenotype do you predict? a. Fly will develop as a male b. Fly will develop as female c. Fly will be female, but no male offspring d. Fly will be female, but no female offspring e. Fly will have no mother Drosophila XY fertilized egg has constitutive mutant for sex-lethal. What phenotype do you predict? a. Fly will develop as a male b. Fly will develop as female c. Fly will be female, but no male offspring d. Fly will be female, but no female offspring e. Fly will have no mother RNA silencing controls gene expression in several ways Short RNA olecules regulate gene expression in cytoplasm both by repressing translation and triggering mRNA degradation Phenomena are known as RNA-induced Dicer (Evolved as anti-viral response. Cells detect double strand RNA, and exploit it and DNA that transcribed it. Dicer chops it up. miRNA genes cleave them into precursor loop and into RITS that silence transcription. Some made on purpose, some made from viruses) RNAi technology being developed as phamacuetical agent Any disease cuased by overexpression of specific gene or normal expression of abnormal gene product could be attacked by therabpeutic RNAi RNAi holds promis for molecular medicine, ie to disrupt viral gene expression Genomic DNA is stable: however, some gene regulation by DNA rearrangement exists DNA (gene) amplification (when cell wants to make lots of one protein. IE in Drosophila protein to make egg shell hard.) (Tumor cells treated with competitive inhibitor. Makes more enzymes to fight against cancer cells. Methotrixate) DNA rearrangements during developmental regulation o Creation of new gene from gene fragments o Switch in expression of gnees due to recombination o Loss of DNA sequences in somatic cells B cells produce immunoglobins (antibodies) that bind to antigens o DNA rearrangements contribute to diversity of variable region o Human light-chain assembly o (Joined by somatic recombination, within same chromosome. Make gene with novel junction between 2 and 3. Alternative splicing happens and end product is variable due to where spliced. This is done to fight (antibodies) bacteria and the one that helps is selected for. Can be bad with frameshift mutation and lots of mutations here.) FRIDAY Special Topics I: Epigenetics Genotype and phenotype didn’t always correspond Epigenome means above the genome DNA is not the only code o DNA = Genetic o Regulate epigenetics, so still at center o Nucleosome structure affects how DNA transcribed. Chromatin = Epigenetics Intro Epigenetic traig is stable, mitotically and meiotically heritable phenotype that results from changes in gene expression without alterations in DNA sequence Epigenetics is the study of this The Epigenome is a description of genome that includes DNA and all epigenetic stages Code regulates o Developmental programs o Parent-of-origin imprinting o Transposable element activity o Centromere structure and function Explains phenotypic variation o Transient responses to environmental cues o Heritable responses to environmental cues ON gene expression o Alter expression (up or down) Initiator Maintainers PICTURE o Independent of DNA sequence changes o Altered chromatin organization o Mitotically and/or meiotically heritable o Stable, but potentially revertsible Modifier proteins Methylation Major epigenetic mechanism is the reversible methylation of DNA Methylation is associated In eukaryotes with silent genes If you deaminate the 5-methylcytosine, it becomes thymine. This is a GT pairing, not a GC. Recognize this and take out the error. CpG islands adjacent to expressed genes are unmethylated and available for transcription Genes near methylated CpG islands are transcriptionally silenced Most methylated DNA is found in reptetitive DNA of heterochromatin including centromere X chromosomes in mammalian females are inactivated by converting them to heterochromatin (dosage compensation). This inactivated X must be inactivated in meiosis to pass on to progeny. Histone modification Amino acids in N-terminal region of histones can be covalently modified by acetylation, methylation, and phosphorylation K stands for lysine. Can acetylation by adding carboxcylic acid. R stands for Q stands for glutamine Chemical modification of histones alters structure of chromatin Acetylation by histone acetyltransferase (HAT) opens chrom structure, making genes available for transcription Removal of acetyl groups by histone deacetylase (HDAC) closes configuration, silencing genes by making them unavailable Complex patterns of histon modifications that change chromatin organization and gene expression is called the histone code. Active –losely packed, methylation low Which of the following does NOT accurately complete this statement: An epigenetic trait ____. A. Cannot be passed from mother cell to daughter cell by mitosis B. Cannot be passed to next gen by meiosis C. Is change in DNA sequence D. Causes changes in genetic expression E. All are accurate Epigenetics and imprinting Imprinted genes show expression of only the maternal allele or paternal allele (Mendel would have hated this, poor guy) Differential methylation of CpG-rich regions in male vs. female gametes produces this effect Prader willis symptoms Methylated and imprinted genes remain transcriptionally silent Many imprinted genes direct aspects of growth during prenatal development o In mice, genes on X chrom are expressed in placenta, but genes on paternal X chrom are silenced. Pattern of imprinting must be reprogrammed every generation During gamete formation, imprints are erased and reset o Reprogrammed differently in different sexes If a gene is imprinted, there is probably some reason behind it that is beneficial External or internal factors disturb epigenetic pattern of imprinting or expression of imprinted genes can have serious phenotypic effects Epigenetics and Cancer Hypomethylation is property of all cancers examined to date o Hypomethylation reactivates genes, leading to unrestricted transcription of many genes including oncogenes o Some hypermethylation occurs, inactivating genes, including tumor-suppressor genes Also genetic mutations HAT and HDAC are linked to development of cancer o Reactivated stem cells can cause cancer And the environment Famine in Netherlands had children with increased risk of obesity, diabetes, and coronary heart disease F2 generation had abnormal patterns of weight gain and growth Similar in mice Can be passed down by father Reduced protein diet fed to rats during pregnancy results in permanent changes in expression of progengy and further down
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