Main Ideas - The human genome is substantially regulated by epigenetic alterations that do not affect nucleotide sequence."- These epigenetic changes are most commonly caused by histone modifications, DNA methylation, and long non-coding RNAs (lncRNAs)"- DNA methylation usually occurs at CpG dinucleotides and causes gene silencing"- CpG islands in promoters are often unmethylayed and thus remain active"- DNA methylation patterns are heritable because of the palindromic nature of the CpG dinucleotide, and thus are transmitted thru generations"- Most of the human genome appears to be transcribed as lncRNAs"- Long ncRNAs are commonly involved in allelic inactivation (imprinting and X chromosome inactivation)"- The inactivation of 1 X chromosome in females is the best studied ex. of epigenetic regulation by lncRNAs"- The Xist lncRNA is responsible for inactivating one of the X chromosomes"- The TsiX long, antisense ncRNA is responsible for keeping one of the X chromosomes active Learning Objectives 1) Define epigenetic inheritance 2) Discuss the molecular mechanisms that lead to epigenetic alterations 3) Discuss epigenetic reprogramming in embryogeneis 4) Discuss X chromosome inactivation 1) Define epigenetic inheritance - Lamarck was right, too!: changes in the envi-->adaptive change-->retained in a much shorter period of time"- Epigenetic inheritance= The heritable and reversible modifications that affect gene expression (transcriptionn) and genome stability w/o changing the nucleotide sequence."- Changes in chromatin structure and accessibilty "- Cellular 'memory,' est. and erased by enzymes."- much more frequent that genetic events = nucleotide changes"- can be inherited cell to cell and generation to generation"- Epigen. changes can occur during mitosis and or meiosis"- Can be stable (X inactivation) or dynamic (induced by envi changes, chem exposure, stress)"- Functions of Epigentic Marking A. Cell differentiation: why a liver cell is diff. than a tongue cell, why genes are active or inactive in a certain cell, express diff. groups of genes in each cell type"B. Maintenance of genome structure: facilitate DNA repair and mark centromeres and telomeres for during replication and recombination"C. Repression of repetitive elements and invasive DNA: compact the DNA to prevent txn of it/prevent their expression"D. Dosage compensation: so there's a dosage equivalent between males XY and females XX in all somatic cells"E. Genomic/parental imprinting: exclusive repression of only 1 parental allele-->pheno diffs between 2 genetically 'identical' individs. Imprints are set in the germline, but erased in the embryo's own primordial germ cells. 2) Discuss the molecular mechanisms that lead to epigenetic alterations - All of the below processes work together to est. global and local chromatin states-->determine gene expression"- The modifications of histones and DNA methylation occur in concert"- The epigenome (epigenetic status) helps determine the way that the genome is expressed in diff.cell types and developmental stages. An aberrant epigenome contributes to cancer and other diseases and syndromes. - Histone modifications - Histones are tightly packaging the DNA, but the tails can be accessed by enzymes-->can affect how readily genes are expressed"- Histone mods are req. for epigenetic inheritance"- Histone mods can mark active and repressive chromatin---> rapid changes in gene expression"- Can affect transcriptional activity"- Histone acetylation: neutralizes the + charge on histones-->weakens their interactions w/DNA-->opens up chromatin-->allows more txn"- HDAC= histone deacetylase"- HAT= histone acetyltransferase - Histone methylation: creates a docking site for proteins that have specific methyl-histone binding domains-->can recruit other proteins that modify chrom to compact or open it up, add mods or erase mods - DNA methylation - How it occurs: addition of methyl to 5-position of cytosine= 5-methylcytosine (5MeC, 5mC, m^5C) via 1 of 3 major human methyltransferases - DNMT1 (DNA methylatransferase 1): maintains the existing methylation patterns following DNA replication during cell division. Affinity for hemi-methylated DNA."- DNMT3A and DNMT3B: de novo methylation= targets previously unmethylated CpGs. Highly expressed in the embryo during implantation= est. new methylation patterns"- Where it occurs: mostly on C's followed by a G= the CpG (CG) dinucleotide - methylation of CpGs or methylation of CpG islands-->gene silencing"- most (70/80%) are methylated except clusters of CpGs in active genes= CpG islands. "- CpG islands are located near promoters of actively transcribed housekeeping genes and tumor suppressor genes-->thus keeps these genes actively transcribed."- methylated CpG islands occur in large, repitive sequences, near transposons, and in intergenic (between genes) regions"- During development"- Can be inherited and reversed"= why it's an epigenetic mark"- Inherited because: CpG is a palindrome when double-stranded= its the same in both directions. So if there is an CpG island, it will be copied onto the daughter strand--this methylation of it is then maintained by DNMT1 because it preferentially methylates hemimethylated DNA."- Leads to chromatin compaction and gene silencing"- Long non-coding RNAs (lncRNAs)=RNAs that have funcs other than being coded into a protein - Mediate allelic silencing"- X chromosome inactivation (ex. calico cats)"- Maternal and paternal imprinting"- Mechanisms:"- Tethered to the site of txn and tag the allele of origin for epigenetic marking (X chrom). Seems to "coat" the X chrom."- Interfere w/binding of proteins like RNA pol II so txn is blocked 3) Discuss epigenetic reprogramming in embryogeneis - Fertilized ovum= zygote is totipotent= has the developmental potential to become a whole organism. Zygote divides-->embryo-->potential of all the cells becomes more limited"- epigenetic mods during development determine this cell differentiation and cell fates by limiting the developmental potential of individual cells and their progeny cells"- Epigentic programming takes place in 2 key pts during development across the genome:"- in the early embryo: a wave of reprogramming, global demethylation and then de novo methylation. Imprinting marks are protected though."- in primordial germ cells (PGCs): tissue specific and imprinting marks are erased. Offspring developing its own germ cells. 4) Discuss X chromosome inactivation - A
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