Epigenetics (1) - Introduction to Epigenetics PDF

Epigenetics An introduction Epigenetics definition ‘Epi’: On top of /Above Definition: Epigenetics is the science of how genes can be switched on or off by factors beyond the DNA sequence, such as environment. Epi-genetics – study of heritable changes in the phenotype or gene express...

Epigenetics An introduction Epigenetics definition ‘Epi’: On top of /Above Definition: Epigenetics is the science of how genes can be switched on or off by factors beyond the DNA sequence, such as environment. Epi-genetics – study of heritable changes in the phenotype or gene expression caused by mechanisms other than changes in the underlying DNA sequence. Epi-genome – Genome with epigenetic modifications. History: First coined by C.H. Waddington to mean above or in addition to genetics to explain differentiation ‘Epi’ – ‘genetics’ ‘Epi’: On top of /Above Definition: Epigenetics is the science of how genes can be switched on or off by factors beyond the DNA sequence, such as environment. History: First coined by C.H. Waddington to mean above or in addition to genetics to explain differentiation. Waddington focused his genetic assimilation work on the Waddington was using genetic crossveinless trait of Drosophila. assimilation to support so-called This trait occurs with high Lamarckian inheritance, the acquisition frequency in heat-treated flies. of inherited characteristics through the After a few generations, the trait effects of the environment during an can be found in the population, organism's lifetime. without the application of heat  Questions Related to Epigenetics How do different adult stem cells know their fate? o Myoblasts can only form muscle cells o Keratinocytes only form skin cells How can identical twins have different natural hair colors? How can a single individual have two different eye colors? How can identical twin liter mates show different coat colors? Imprinting. How can one of the parental allele silenced. X- inactivation- Dosage Compensation  Packing of DNA into chromatin Each base pair (bp) in DNA – 0.34 nm long # of bp/cell – billions Each cell has - 2 m of DNA. Has to fit in nucleus 2-10 um in size Human body has 50 trillion cells – 100 trillion m of DNA. Distance between sun and earth – 150 billion m 2 m of DNA in a nucleus with a diameter of 5-10 mm Each of us has enough DNA to go from here to sun and come back more than Chromatin not only packages DNA, but also regulates DNA accessibility through 300 times. modifications in chromatin structure. Nucleosomes- The basic repeating unit of Chromatin Mechanisms of Epigenetics There are 3 known mechanisms of Epigenetics 1- DNA Methylation 2-Histone Modification 3- Non-coding RNA DNA Methylation & Histone Modifications Form the Epigenetic Code Cytosine methylation S adenosyl methionine is the universal methyl donor S adenosyl methionine is the methyl Methylation patterns in human diseases Cancer  CpG Islands  CpG island: a cluster of CpG residues often found near gene promoters (at least 200 bp and with a GC percentage that is greater than 60%)  ~29,000 CpG islands in human genome (~60% of all genes are associated with CpG islands)  Most CpG islands are unmethylated in normal cells. Progressive Alterations in DNA Methylation in Cancer Global Region-Specific + Hypomethylation Hypermethylation Normal Cancer Accumulation of lities Epigenetic Abnorma CpG Island Methylation: A Stable, Heritable and Positively Detectable Signal 1 2 3 4 5 Carcinoma Normal Epithelia Dysplasia Carcinoma in situ Metastasis CpG Island Methylation: A Stable, Heritable and Positively Detectable Signal 1 2 3 4 5 Carcinoma Normal Epithelia Dysplasia Carcinoma in situ Metastasis CpG Island Methylation: A Stable, Heritable and Positively Detectable Signal 1 2 3 4 5 Carcinoma Normal Epithelia Dysplasia Carcinoma in situ Metastasis DNA Methylation Differentiates Totipotent Embryonic Stem Cells from Unipotent Adult Stem Cells  How methylation inhibits transcription Activators bind to unmethyla ted promoters Establishment and Maintenance of Cytosine Methylation Dnmt3a/Dnmt3B (De novo)-------- Dnmt1( maintenance) Dnmt= DNA methyltransferase Bisulfite sequencing A lab method to detect methylation The use of bisulfite treatment of DNA before routine sequencing to determine the pattern of methylation. Treatment of DNA with bisulfite converts cytosine residues to uracil, This treatment leaves 5-methylcytosine residues unaffected. Thus, bisulfite treatment introduces specific changes in the DNA sequence that depend on the methylation status of individual cytosine residues,  Methylation and suicidal behavior Mitotic Arrest Deficient 1-Like Protein 1- MAD1L1 In humans, childhood abuse alters hypothalamic-pituitary-adrenal (HPA) stress responses and increases the risk of suicide. We examined epigenetic differences in a neuron-specific glucocorticoid receptor (NR3C1) promoter between postmortem hippocampus obtained from suicide victims with a history of childhood abuse and those from either suicide victims with no childhood abuse or controls. Decreased levels of NR3C1 mRNA and increased cytosine methylation of an NR3C1 promoter were found to be associated with suicide victims with a history of childhood abuse. Mechanisms of Epigenetics There are 3 known mechanisms of Epigenetics 1- DNA Methylation 2-Histone Modification 3- Non-coding RNA Chromatin Structure- Two forms Silent Genes Active Genes Core Histones are highly conserved proteins They are rich in basic amino acids (three α helices connected by two loops) The N-terminal tails protrude from the core alanine - ala – A arginine - arg - R asparagine - asn – N aspartic acid - asp - D cysteine - cys – C glutamine - gln - Q glutamic acid - glu – E glycine - gly - G histidine - his – H isoleucine - ile - I leucine - leu – L lysine - lys - K methionine - met – M phenylalanine - phe - F proline - pro – P serine - ser - S threonine - thr – T tryptophan - trp - W tyrosine - tyr – Y valine - val - V Histone Modifications Acetylation Me Ac Me Methylation Ub ‘Histone Code’ Ubiquitination Su SUMO (Small Ubiquitin-like Modifier) proteins Sumoylation not used for degradation tagging. Used for P nuclear-cytocilic transport, protein stability and transcription control Phosphorylation  Acetylation of Lysines Acetylation of the lysines at the N terminus of Acetyl histones removes positive charges, thereby reducing the affinity between histones and DNA. This makes RNA polymerase and Reversable transcription factors easier to access the promoter process region. Histone acetylation enhances transcription while histone deacetylation represses transcription. Methylation of Arginines and Lysines  Arginine can be methylated to form mono-methyl, symmetrical di-methyl and asymmetrical di- methylarginine.  Lysine can be methylated to form mono-methyl, di-methyl and tri-methylysine.  Methylation of Histone H3-K27 k=lysine  H3K27me3 is distinct in that it has only one known methyltransferase: EZH2- SUZ12 EZH2. Enhancer of zeste homolog 2 EED HD AC lysine methyltransferase  EZH2 is part of the DNMT PC PRC2 complex which is EZH2 responsible for the K27 repression many genes involved in Polycomb Repressive Complex 2 ( development and cell PRC2), differentiation.  It is thus believed that H3K27me3 is critical for H3K27 is known for one thing: shutting down the repression of transcription. When H3K27 is trimethylated, it is developmental genes. tightly associated with inactive gene promoters.  H3K27me3 is also an  Chromatin modifications Mark Transcriptionally relevant sites Biological Role Methylated cytosine CpG islands Transcriptional Repression (meC) (DNA) Acetylated lysine (Kac) H3 (9,14,18,56), H4 (5,8,13,16), H2A, H2B Transcriptional Activation Phosphorylated H3 (3,10,28), H2A, H2B Transcriptional Activation serine/threonine (S/Tph) Methylated argine (Rme) H3 (17,23), H4 (3) Transcriptional Activation Methylated lysine (Kme) H3 (4,36,79) Transcriptional Activation H3 (9,27), H4 (20) Transcriptional Repression Ubiquitylated lysine H2B (123/120) Transcriptional Activation (Kub) H2A (119) Transcriptional Repression Sumoylated lysine (Ksu) H2B (6/7), H2A (126) Transcriptional Repression Acetylation and phosphorylation – help to open chromatin. Histone modifications matter Latham and Dent Nat Struct Mol Biol 2007  Structure & Epigenetics of Euchromatin versus Heterochromatin Writing – Erasing – Reading Epigenetics  DNMTs, DNA methyltransferases; HATs, histone acetyltranferases; HDACs, histone deacetylases; MBD, methyl-CpG-binding domain; TET, ten-eleven translocation; TF, transcription factor. Post-translational modifications on histone tails. Epigenetic signal writers are indicated in red, readers in green, and erasers in blue. Acetylated lysine residues are represented by green rectangles, methylated lysines by blue triangles and methylated CpGs of genomic DNA by magenta circles. (B) States of the chromatin and associated histone lncRNA and Epigenetics Detailed mechanism for DNA methylation regulation by lncRNAs in direct mode. (A). LncRNAs recruit DNMTs to genome loci; (B). LncRNAs sequester DNMTs from genome loci; (C). LncRNAs regulate expression level of DNMTs; (D). LncRNAs function as ceRNA to regulate DNMT expression level; (E). LncRNAs influence the ubiquitination of DNMT proteins to affect the degradation. (F). LncRNAs promote subcellular location of DNMT proteins. Long non-coding RNA and epigenetics H19- example/histone modifications Polycomb Repressive Complex 2 (PRC2) EZH2- lysin methyltransferase, Suppressor Up: Silencing of IGF2. Down: Silencing of E- cadherine Activator Activation of miR-200. PCAF is a histone acetyltransferase Loss of E cadherin is the hallmark of the EMT process  H19 Suppress E-cadherin to Induce EMT through Multiple Modes of Action HMGA2:High-mobility group AT- hook 2.  Rainbow and Copycat Calico cat coat color cannot be cloned!!! Not based on genetics Based on Epigenetics: Color gene is X-linked Random X-inactivation of cells in blastula all daughter cells will inherit that pattern (A)Xist RNA is expressed from the X chromosome and functions in cis to silence the X chromosome. (B) Xist coats the X chromosome locally, interacts with the chromatin through the adaptor complex YY1, (C) This recruits the repressive polycomb group complex PRC2 to deposit histone H3 lysine 27 trimethyl (H3K27me3) marks on nucleosomes. Maternal behavior causes epigenetic change in methylation in the brain of its her offspring