Genetics Flipped Lesson 7.PDF

MD210 Genetics Flipped Lesson 7 – Epigenetics Epigenetics - Heritable/Enduring change in gene expression not related to variation in nucleotide sequence (A, C, T & G of nucleotide sequence don’t change but a chemical modification occurs that changes the expression of the gene sequences. Related to c...

MD210 Genetics Flipped Lesson 7 – Epigenetics Epigenetics - Heritable/Enduring change in gene expression not related to variation in nucleotide sequence (A, C, T & G of nucleotide sequence don’t change but a chemical modification occurs that changes the expression of the gene sequences. Related to chromatin confirmation.) - May be enduring in the sense of: o the life of a long lived cell o retained from mother to daughter cell (X-inactivation) o retained from parent to offspring (imprinting) - Epigenetics relate to DNA factors other than nucleotide sequence that impact on gene expression Epigenetics biochemical basis (Readability of genes based on chromatin structure. Condensation of chromatin and packaging density of DNA are regulated by chemical modifications of histones. Chemical modifications of histones influenced by DNA methylation. DNA methylation occurs in regions of DNA known as CPG islands – nucleotide sequences rich in cytosines and guanines, usually located in the promotor regions upstream of genes.) DNA Methylation - Gene “switched on” o Active (open) chromatin o Unmethylated cytokines (white circles) o Acetylated histones (Transcription machinery can get in, bind to the promotor, and transcribe the gene) - Gene “Switched off” o Silent (condensed) chromatin o Methylated cytosines (red circles) o Deacetylated histones (tight wrapping of nucleosome). Biallelic/Monoallelic Expression - Humans Are Diploid - 23 Pairs of Homologous Chromosomes (1 homolog inherited from each parent) - 2 Copies (often different alleles) of each gene - Biallelic expression – both alleles expressed - Monoallelic expression – only one of the two alleles is expressed Imprinting - Involves Monoallelic Expression - The expression of genes in a parent-of-origin-specific manner - Only the allele inherited from a specific parent (either the maternal or paternal allele) is expressed for imprinted genes - <1% of human genes are imprinted (rare) Imprinting - Imprinting is related to Methylation of Cytosines (in promoter) & histones - Modification of DNA but not nucleotide sequence change (epigenetic) - Enduring, but not permanent change (can last from cell to cell, mother to daughter, but not permanent) Genomic Imprinting (E.g. Chr 1. In the body cells will have 1 copy of each from both parents. In the germ cells the imprint pattern will be deleted. For every Ova, all chromosomes rewritten with a sex specific imprint – maternal imprint rewritten onto Ova. All paternal imprint patterns deleted in primordial germ cells – all sperm rewritten with paternal imprint. In the zygote have 2 homologs, 1 with maternal imprint and 1 with paternal imprint.) Imprinting example: IGF2 (How imprinting works to control the monoallelic expression of genes) - Insulin Like Growth Factor 2 (IGF2) (Gene involved in growth cycle) - Only the Paternal Allele is Normally Expressed for this gene - The Maternal Allele is “Imprinted” (shut down) (not transcribed and translated into protein) (In image – Homolog of Chr 11 from father, written with paternal methylation pattern on IGF2 – will be active – euchromatin – it will transcribe into mRNA and the mRNA will translated into the IGF2 protein. Maternal homolog also has IGF2 but its written with a maternal methylation pattern – its imprinted – its going to be shut down, wont be transcribed into mRNA and wont be translated into a protein. Stops too much IGF2 being produced and stops the cells from growing out of control) Clinical example - The Drapers Imprinting & Sally - Sally has an allele of Insulin Like Growth Factor 2 (IGF2) from Don – which works (paternal allele) - She has an allele of Insulin Like Growth Factor 2 from Betty that is switched off (imprinted (because was written with the maternal pattern)) Question - If Sally has a child, which allele of the IGF2 gene will work? - In any oocytes that Sally (the mother) makes, whichever version of the allele is present will be switched off (her ova will be rewritten with the maternal methylation pattern) - Imprints are erased in the Germline and re-established in gametes In the sperm all imprints are erased and rewritten with the paternal pattern, even the alleles that came from mum In the ova all imprints are erased and rewritten with the maternal pattern, even the alleles that came from dad Diseases Related to Imprinting - For imprinted genes, the inheritance of maternal and paternal alleles is required for normal development (need both a maternally imprinted homolog and a paternally imprinted homolog – some genes expressed from both) - Imprinted genes are more vulnerable to mutation – haploid expression (only have 1 copy of gene with the correct methylation pattern). (if there is a mutation in the paternal homolog – it’s the paternal homolog that’s usually expressed – wont have any functional gene – maternal homolog will still be shut down and cant be switched back on) - Dominant mutations (dominant inheritance patterns) Angelman Syndromes - Small - Profound intellectual disability - (unable to speak and with particular behaviour pattern (characterised with a happy, friendly demeanour, inappropriate laughter)) Prader-Willi Syndrome - Floppy babies (hypotonia) - Intellectual/cognitive disability (not as profound as Angelman) - Uncontrollable appetite (often leads to obesity) - Hypogonadism in males - (Skin-picking behaviour that causes scabs and scars) - Study in the UK in 2000 estimated birth incidence to be in the region of 1:22,000, previous estimates have estimated a birth incidence between 1:10,000 and 1:25,000. - Uncertainty is due to the fact that PWS may still go undiagnosed - Note: Ascertainment & the reported incidence of illness (often vary significantly from what they actually are) Angelman, Prader Willi and Imprinting - Both associated with a de novo deletion on long arm of Chr 15 (15q11-q13) - Both usually for identical sets of genes but…(depends on which homolog it involves) - Deletion from paternal Chr 15 = Prader Willi - Deletion from maternal Chr 15 = Angelman How does that work? Another way it can happen – Uniparental Disomy (UPD) - UPD occurs when 2 copies of a Chr come from the same parent - Therefore both will have either maternal or paternal pattern of methylation (missing the expression of either 1 set of genes involved in Prader Willi syndrome or the other set involved in Angelman) Mechanisms of UPD (Trisomy rescue – zygote that has 3 copies of the same chromosome, the paternal copy is removed to make it a normal disomy zygote instead of the extra maternal copy being removed. Gamete complementation – one germ cell missing a copy of a chromosome, the other can compliment it by having a duplicate of a copy. Monosomy rescue – if there’s one chromosome missing because 1 germ cell didn’t have a chromosome, the other chromosome can duplicate itself so that there are two homologs from the same parent. Monosomy rescue – if 1 of the copies are faulty it can be excluded and can get duplication through the functional copy but it will have the same methylation pattern.) X-Inactivation (another epigenetic phenomenon) - The random transcriptional silencing of all but one X chromosome in females (X chromosome is very big, contains a lot of genes compared to Y chromosome – gene dosing. 2 copies of X chromosome in female that are both active there will be a lot of genes expressed to a much higher extent in females than males. X-inactivation means 1 X chromosome in each cell is transcriptionally silent) - Heritable from mother cell to all daughter cells in an individual (once X inactivation happens in one cell, all of the daughter cells of that cell have the same copy of that X inactivated.) - Not heritable from parent to child Human Embryonic Development X inactivation happens around time of late blastocyst formation when differentiation of layers starts X Inactivation - Early in Embryonic Development (totipotent cells) both X chromosomes are active - With differentiation to pluripotent cells random X inactivation (late blastocyst stage) - Inactivated X condensed on periphery of nucleus (Barr body (aka sex chromatin)) X Chromosome Inactivation - Random inactivation of paternal or maternal X - The inactivation is retained through all subsequent mitosis – all daughter cells - But not retained across generations - XIST gene in the X inactivation centre (Xic) produces Xist RNA transcript that covers the X chromosome to be inactivated (Xi). - Subsequent DNA methylation (epigenetic) then makes this silencing permanent in all daughter cells. Skewed X-inactivation - Ratio of inactivated maternal X to paternal X should be equal (random), but is uneven (skewed) in 10-15% of women - Preferential inactivation of the “abnormal” X in heterozygotes is the reason why there is such variability in the expression of X-linked disorders. - If the diseased X-linked allele does not cause selection, the extent of the primary stochastic skewing can influence the severity of the disease. - Skewed X-inactivation common in cases of severe X mutation or structural anomaly Rett Syndrome - X-linked dominant disorder - Usually caused by mutations in MECP2 gene (X Chr) - Affects young girls from 6-18 mo o Brain/cognitive function impaired o Hand coordination lost (hand-wringing) o Seizures and breathing problems - Substantial phenotypic variability - May be influenced by Skewed X-inactivation - Skewing >80% is rare o Asymptomatic/less severe carriers Duchenne Muscular Dystrophy - X-linked DMD – dystrophin (Xp21.2) - Muscle fibre weakness that presents in childhood - Difficulty walking and rising (Gower manoeuvre) - Wheelchair by teens - Respiratory weakness - Mild cognitive impairment - Cardiomyopathy (ventricular remodelling) - Heterozygous female carriers: - Mild cardiomyopathy, increased CK and muscle weakness but don’t present with DMD Those who do may have skewed X-inactivation Things to Remember 1. Epigenetics relate to DNA factors other than nucleotide sequence that impact on gene expression (primarily methylation of CpG dinucleotides) 2. Imprinting involves monoallelic expression of genes in a parent-of-origin specific manner. Imprinted genes are shut down. All imprints are erased in the germ line and renewed in the gametes. 3. For imprinted genes, the inheritance of maternal and paternal alleles is required for normal development. Imprinted genes are more vulnerable to mutation – haploid expression (dominant mutations) 4. Angelman and Prader Willi are 2 syndromes related to imprinting of Chr 15 5. X-inactivation is the random transcriptional silencing of all but one X chromosome in females 6. Skewed X-inactivation occurs in 10-15% of women. Preferential inactivation of the “abnormal” X in heterozygotes is the reason why there is such variability in the expression of X-linked disorders. Question With regards to X chromosome inactivation, which of the following is NOT true A. The inactivated X chromosome forms a Barr body B. Either the maternal or paternal X chromosome is inactivated at random in each pluripotent cell C. The XIST gene is transcribed from the X-inactivation centre on the X-chromosome that will be active D. Subsequent DNA methylation is what makes X-inactivation permanent in all daughter cells