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+# =========================================================================== #
+# === Epigenetik
+#
+# Epi tag. Epigenetics Tag. Epitag. Epigenetik tag. Epi tag.
+# Epigen tag. Epigenome tag.
+# =========================================================================== #
+
+- Loss of methylation of centromeric regions due to mutations in DNMT3A can contribute to ... ? <one>chromosomal instability</one>, <two>including nondisjunctions</two>. 
+- Can <one>drugs</one> such as cocaine alter the epigenome of brain cells? Yes.
+- Does <one>chronic stress</one> <two>alter the epigenome</two>? Yes. It was shown that mice exposed to stress hormones over a period of four weeks became more anxious. This was reflected via epigenetic marking of a gene that is known to be connected to post-traumatic stress in humans.
+- Is the <one>Dnmt1 DNA methyltransferase</one> (also called maintenance methyltransferase) more efficient than the DNA methyltransferase Dnmt3a? Yes.
+- <one>RNA-directed DNA methylation</one> refers to the fact that the enzymes that methylate DNA are directed to their sites of action by small RNAs, interacting with the RNAi protein ... ? <one>AGO4</one>.
+- Has <one>DNA methylation</one> been more widely studied than <two>histone modification</two>? <one>Yes</one>.
+- Name a cytosine analog that cannot be methylated. A: <one>5-aza-cytidine</one>.
+- Die Desaminierung von 5-methyl-Cytosine erzeugt ... ? <one>Thymin</one>.
+- The major conduit for epigenome-environment interactions is ... ? <one>RNA</one>.
+- <one>Wer</one> hat den Begriff <two>Epigenetik</two> ursprünglich geprägt? <one>Conrad Hal Waddington</one>, im Jahr 1942. URL: https://de.wikipedia.org/wiki/Conrad_Hal_Waddington
+- Can the same lysine in a "Histone N-terminus", be both acetylated and methylated at the same time? No - these (epigenetic) modifications are typically <one>mutually exclusive</one>.
+- Name an <one>epigenetic drug</one>. A: <one>Azacitidine</one>. URL: https://en.wikipedia.org/wiki/Azacitidine
+- Name <one>two categories</one> of DNA methyltransferases. A: (1) Maintenance Methyltransferases (2) <one>de-novo methyltransferases</one>
+- A <one>tudor domain</one> can read which particular epigenetic modification? It can read "arginine methylation".
+- The <one>Polycomb-group proteins</one> can silence which genes? They can silence <one>Hox genes</one>.
+- <one>DNA-methylation in plants</one> <two>occurs at which sequence</two>? <one>C-p-N-p-G</one>.
+- Which molecule creates the <one>H3K27me3</one> epigenetic mark? <one>PRC2</one>. URL: https://www.ncbi.nlm.nih.gov/pubmed/18931660
+- Define <one>genomic imprinting</one>. A: In <one>genomic imprinting</one>, certain autosomal genes have unusual inheritance patterns.
+- Bei den Histonen: wo finden wir die <one>histone fold</one>? Eher <one>C-Terminal</one>.
+- <one>Which person</one> coined the term <two>Epigenesis</two>? <one>Aristotle</one>.
+- Does <one>CpG-methylation in Eukarya</one> interfere with base pairing? No - the methyl-group lies outside in the major groove of the DNA double helix.
+- How would we, in general, call all changes possible through epigenetics? <one>Alterations</one>.
+- What means <one>chromatin remodeling</one>? The changing of nuleosome positions.
+- Die Anheftung eines Ubiquitinbausteins an Histon H2B ist das Signal für die Methylierung von ... ? Histon H3.
+- In Epigenetics: was heisst <one>HMTase</one>? <one>Histone methyltransferase</one>.
+- Give an example for an <one>epigenetic drug</one>. A: <one>Azacitidine</one>.
+- Which <one>epigenetic modification of the histones</one> does not affect their charge? <one>Methylation</one>.
+- What does the <one>XIC locus</one> produce? It expresses XIST, which spreads over the entire Xi-chromosome.
+- What does the special <one>Histone Variant H3.3</one> do? This variant replaces H3 and differs at position 31 and a few residues on helix 2 that enable deposition outside of replication. Variant H3.3 is deposited at particular loci, including active rDNA arrays. While the major H3 is incorporated strictly during DNA replication, amino acid changes toward H3.3 allow replication-independent ("RI") deposition. In contrast to replication-coupled ("RC") deposition, RI deposition does not require the N-terminal tail! H3.3 is the exclusive substrate for RI deposition, and its counterpart is the only substrate retained in yeast. RI substitution of H3.3 provides a mechanism for the immediate activation of genes that are silenced by histone modification.
+- Das Phänomen "Position-effect variegation" (PEV) wurde bei Drosophila erstmals von "Hermann Muller" beschrieben. In welchem Jahr? <one>1938</one>.
+- Give an example for an <one>epigenetic mosaic</one>. A: <one>PEV</one>.
+- How does <one>DNA methylation</one> suppress gene expression? The methyl group of 5-methylcytosine sits within the major groove of the DNA.
+- How is a <one>paramutation</one> defined? An interaction between two alleles that leads to a heritable change in expression of one of the alleles.
+- The <one>affinity enrichment of methylated region</one> makes use of ...? It employs antibodies that are specific for methylcytosines.
+- How many (in %) of the human genes have <one>CpG Islands</one>? About <one>60%</one> of all human genes have CpG-Islands.
+- Give an example of a true, <one>genetic mosaic</one>. A: The <one>coat colour of some cats</one>.
+- Unterscheide zwischen <one>epigenetic change</one> und "somatic epitype". A: Der epigenetic change ist vererbbar (heritable), somatic epitype ist nicht vererbbar. Im englischen heisst dies schön: "somatic epitype is when the change in information status is not heritable"
+- <one>PEV</one> can happen in mammals as well? Yes - for example in the <one>Agouti mouse</one>.
+- Wo genau findet man die <one>Mig1-Site</one>? Zwischen <one>UAS</one> und GAL1.
+- Wie wirkt sich eine <one>Histon-Acetylierung</one> an Lysinen, wie zum Beispiel <two>H3K9Ac</two>, aus? Die Hauptwirkung der Acetylgruppe ist <one>die Neutralisierung der positiven Ladung des Lysins</one>.
+- In <one>mammals</one>: where does X chromosome inactivation start? It starts at the <one>XIC</one> (<two>X-Inactivation Center</two>).
+- Warum können wir die Substanz <one>5-Azacytidine</one> bei manchen epigenetischen Experimenten einsetzen? Da es 1 Stickstoffatom hat, das nicht methyliert werden kann.
+- When a <one>lysine</one> in a histone is acetylated, how will the "terminal NH3 group" look like? <one>-NH-C=O-CH₃</one>.
+- In der <one>Epigenetik</one>: was heisst <two>SUV39H1</two>, vor allem das <three>SUV</three>? <one>Suppressor of position effect variegation</one>.
+- Nenne zwei Methoden, wie wir <one>DNA-Methylierung</one> kartieren können. A: (1) Immunpräzipitation (2) <one>Bisulfitsequenziermethode<one>
+- Molekulare Ursache des <one>Rett-Syndroms</one>? Eine <one>Mutation</one> im <two>MeCP2 Gen</two> auf dem X-Chromosom.
+- Is <one>Heterochromatin</one> a defensive measure? Yes, it can be, when it <one>silences foreign transposons</one>.
+- Who first coined the specific term "epigenetics"? "Conrad Waddington". URL: https://en.wikipedia.org/wiki/Conrad_Hal_Waddington
+- In der Epigenetik, was heisst "KMT" und "KDM"? (1) "KMT" heisst "lysine methyltransferase". (2) "KDM" heisst "lysine demethylases".
+- Is "histone phosphorylation" linked to the "condensation of chromatin"? Yes. URL: https://en.wikipedia.org/wiki/Histone#Serine/threonine/tyrosine_phosphorylation
+- Zellulär betrachtet, wo finden wir die "XIST-RNA"? Nur "im Nucleus".
+- In der Epigenetik, was kann das "Mig1-Protein"? Es kann die Aktivierung der Gal-Gene verhindern.
+- When does the Barr body decondense? During the "S phase".
+- Beim Histon-Code, welche Aminosäuren werden acetyliert? Nur "Lysin-Reste".
+- Name a technique that can be used to do a genome-wide analysis of methylation. A: "Microarray-based methods".
+- Name a protein that can bind to the "H3K4me3 mark". A: The "NURF protein". URL: https://en.wikipedia.org/wiki/H3K4me3
+- Wie können wir den Methylierungsstatus eines Gens analysieren? Durch "Restriktionsverdau mit Enzymen", die methylierte DNA schneiden können (oder eben nicht).
+- Bromodomain and Chromodomain recognize what, respectively? (1) Bromodomain  recognize acetylated lysine. (2) Chromodomain recognize methylated lysines.
+- Was erhalten wir wenn wir 5-Methylcytosin deaminieren? Wir erhalten "Thymin".
+- Unmethylated CpGs are usually associated with ...? With the promoters of "active housekeeping genes".
+- Can you give an example for "epigenetics in Candida albicans"? An epigenetic switch underlies the transition between white and opaque cells - two states that are heritable for many generations.
+- In mammals in general, what percentage of the CG dinucleotides are methylated? 70-80% - save for CpG islands near gene promoters.
+- Name one factor that may inhibit the spreading process of PEV-Heterochromatin. A: An "active promoter" may inhibit spreading.
+- Which enzyme would you use for "cutting linker DNA"? Micrococcal Nuclease.
+- Welche Zellen produzieren besonders viel MECP2? Die "Nervenzellen".
+- Wie lange ist das "X-inactivation center" (von-bis)? 100.000 - 500.000 bp
+- Gib ein Beispiel für "transgenerationale Epigenetik". A: Wenn Mäuse bestimmten Gerüchen ausgesetzt werden, reagieren ihre Nachkommen auf die gleichen Gerüche, obwohl sie sie zuvor nicht kannten.
+- Does "DNA Methylation" occur in Bacteria? Yes.
+- Some genes on the inactivated X-chromosome escape repression and are actively transcribed from both X chromosomes. Name 1 characteristic of most of these genes! A: They possess functional Homologs on the Y chromosome and therefore dosage compensation is achieved, by keeping both genes active.
+- In DNA methylation of humans, what 2 classes of DNA methylase can we distinguish? (1) "de-novo methylases" (2) "maintenance-methylases"
+- MeCP2 can recruit with Histone deacetylase? It can recruit the "Sin3A histone deacetylase".
+- In mammals, which three conserved enzymes are important for methylation of Cytosine at position 5? (1) DNA methyltransferase 1 aka "DNMT1" (2) DNMT3A (3) DNMT3B
+- In general, which enzymes recognize CpG islands? Methyltransferase enzymes.
+- What is the "Epigenome"? This is the complete set of chromatin modifications possessed by an individual organism.
+- In sperm chromatin, what replaces the histones? Polyamines such as "spermidine".
+- MeCP2 can recruit which complex? It can recruit the "Sin3A histone deacetylase complex".
+- Nenne 5 Veränderungen an Histon-Proteinen mit Hilfe eines Mnemonic. A: "AMPUS", so wie in Campus. (1) Acetylierung (2) Methylierung (3) Phosphorylierung (4) Ubiquitinierung (5) Sumoylierung
+- Gender of C. elegans XO and XX? XO are males, XX are hermaphrodites.
+- Compare the two restriction enzymes "HpaII" and "MspI". A: Both recognize the sequence "CCGG". HpaII cuts only when the DNA is unmethylated, whereas MspI is the stronger cutter - it cuts always. In other words, methylation partially protects against HpaII digestions.
+- How can we "reverse methylation"? We make use of "azacitidine".
+- Name an "epigenetic disease". A: The Angelman Syndrome.
+- Which gene is critical for "human X chromosome inactivation"? The Xist gene.
+- Was können wir über Gene sagen, die über Imprinting reguliert werden? Sie sind oft in Cluster angeordnet.
+- Gib ein Beispiel für ein Histon, an das Ubiquitin angeheftet werden kann. A: Histon H2A.
+- In general, the activity of HATs correlates with? It correlates with "increased gene expression".
+- In Epigenetics, we may employ "Zebularine". Why? Zebularine is a nucleoside analog of Cytidine. It can inhibit DNA methylation. URL: https://en.wikipedia.org/wiki/Zebularine
+- In order to preserve "methylation signature", we may make use of bisulfite. But after bisulfite treatment, we have to employ which other technique? We have to use a PCR.
+- What is an "epidrug"? This is a drug that can effect "epigenomic modifications".
+- What is the effect of applying Sodium Bisulfite to DNA? Sodium Bisulfite converts unmethylated cytosine to uracil. URL: https://en.wikipedia.org/wiki/Sodium_bisulfite
+- Im menschlichen Genom sind wieviel % der Cytosine methyliert? 3-4%
+- Länge der Xist-RNA? 17.000 bases.
+- What is the "methylome"? This is the set of nucleic acid methylation modifications in an organisms genome. 
+- Name 3 different ways how to study DNA methylation. A: (1) Bisulfite sequencing (2) Methylated DNA Immunoprecipitation (MeDIP) with antibodies against methylcytosine (3) Endonucleases distinguishing between methylated and unmethylated nucleotides
+- Explain from a molecular genetics view why "royal gelly" is so powerful. A: It silences the expression of the Dnmt3 gene.
+- A. W. für "Epigenetic variation"? Epimutations.
+- In a developing fetus, damage can occur against epigenetic mechanisms, thus unrelated to DNA changes. Name 3 common causes for "direct effects" here. A: (1) tobacco smoke (2) bisphenol A (3) alcohol
+- Which Igf2-copy is inactive in the fetus? The maternal copy.
+- Aufgabe der Polycomb-Proteine? Sie schalten Gene dauerhaft ab.
+- The "Maintenance DNA Methyltransferase Dnmt1" prefers what as substrate? It prefers "hemimethylated DNA".
+- Name one common "epigenetic signal". A: CG.
+- Was ist die "fünfte Base der DNA"? Methylcytosin.
+- In the Histone Code, which Aminoacid is subject to most modifications? Lysine.
+- Which enzymes add methyl groups (CH3) onto cytosines? The DNA methyltransferases.
+- Paramutation in corn is brought about by ...? siRNAs
+- What is the best understood mechanism of "epigenetic change"? Methylation of DNA.
+- "Affinity purification" methylierter DNA können wir mit welchen zwei Systemen durchführen? Sowohl mit anti-5-meC Antibody, als auch mit dem MBD-Protein.
+- Give an example for a RNA that is "poly-adenylated" yet remains in the nucleus. A: The XIST-RNA.
+- How does the Xist-gene work in female mice? One X chromosome becomes coated with Xist RNA - the one that allows transcription from the XIC locus of that mRNA - and the other does not.
+- How is a "replicon" defined? This is any molecule of DNA that possesses its own origin of replication.
+- How can a cell disable potentially dangerous transposable elements? It can simply try to methylate them.
+- Wenn ich "sodium bisulfite" auf ssDNA loslasse, was passiert? Die Cytosine werden Uracil, aber nur wenn sie nicht methyliert vorliegen.
+- H3K3me3 is an active chromatin mark, that is associated with ... ? It is associated with "transcriptional activation".
+- 5-Azocytidine wird an Stelle von ... in DNA eingebaut? An Stelle von Cytosine.
+- Was ist das "Rett Syndrom"? Eine Form schweren Autismus.
+- Name 3 ways how we can study cytosine methylation in e. g. the human genome. A: (1) methylation-sensitive restriction enzyme mapping (2) deamination of unmethylated cytosines with sodium bisulphite (3) enrichment with targeting antibodies
+- In the human genome, we can find so called CpG islands, which are CG-dense regions. They are prevalent at transcription start sites of ... which two general class of genes? (1) housekeeping genes (2) developmental regulator genes
+- How many CpGs can we find in the human genome? About 28 million.
+- How many human genes, in percent, have CpG-Islands? About 60%. 
+- Name a protein that can recruit Dnmt1. A: The SRA Protein Np95 (Uhrf1).
+- Name 3 general erasers in Epigenetics. A: (1) Phosphatases (2) Deacetylases (3) Demethylases
+- Durchmesser eines Nucleosomes? 30nm.
+- What are "Readers" in Epigenetics? Readers are detector proteins that specifically recognize and bind to modified histone tails.
+- Nenne das erste Protein in dem eine Chromodomäne gefunden wurde. A: Drosophila melanogaster Polycomb (Pc).
+- Name 6 "classic epigenetic phenomens". A: (1) PEV "position effect variegation" in Drosophila (2) Dosage compensation such as in X-inactivation in mammals (3) Mating type switching in yeast (4) Heterochromatin formation (5) Imprinting (6) Polycomb and Trithorax Group proteins (differentiation, cell identity)
+- Wann wurde "Position effect variegation" in Drosophila erstmals beschrieben? 1941.
+- What does "DNase I" do? It cleaves DNA moleulces and degrades them into their constituent nucleotides.
+- What is "Bisulfite sequencing"? The use of bisulfite treatment of DNA to determine its "pattern of methylation".
+- W. h. "Dnmt" in der Epigenetik? DNA-Methyltransferase.
+- What was the first discovered epigenetic mark? DNA methylation.
+- Name the six steps used in RRBS ("Reduced representation bisulfite sequencing"). A: (1) Enzyme Digestion (2) Library Preparation (3) Size Selection (4) Bisulfite Conversion (5) PCR Amplification (6) Sequencing
+- When was the "Maintenance DNA Methyltransferase Dnmt1" purified? 1983.
+- Nenne eine Erweiterung der "sodium bisulfite" Methodik. A: RRBS: Reduced representation bisulfite sequencing. Sie erlaubt es uns "genome-wide methylation profiles" zu erstellen.
+- Welche 3 Teilschritte kann man bei der Konversion von C nach U mittels sodium bisulfite unterscheiden? (1) Sulfonation (2) Hydrolytic deamination (3) alkali-desulphonation
+- Woran bindet das Protein HP1? Es bindet an methyliertes Histone H3.
+- Name one CG-binding protein that organises genome structure at CG islands. A: Cfp1
+- Give one example for a E(var) mutation. A: SWI/SNF complex.
+- In der Epigenetik, was heisst "CIMP"? "CpG island methylator phenotype".
+- Im menschlichen Genom findet man zahlenmässig, anhand der Basenpaare, häufiger SINES oder LINES? LINES (21%) - sie sind länger.
+- Can licking be considered "epigenetic"? Yes, by rats. Increased licking by rat mothers altered the offspring epigenome at a glucocorticoid receptor (GR) gene promoter in the hippocampus. These offspring showed differences in DNA methylation.
+- What are Su(var) genes? Genes that, when mutated, reduce the spread of heterochromatin. The wild-type products of these genes are required for spreading.
+- Was ist der "Position Effekt"? Gene, welche in der Nähe des Heterochromatins liegen, können durch Ausbreitung des Heterochromatins abgeschaltet werden.
+- W. h. "XIST"? XIC inactivation X-chromosome Xi specific transcript.
+- Nenne 2 Modelle zur Funktionsweise genetischer Imprints. A: (1) Insulator Model (2) ncRNA Model
+- In Mammals, how many genes are produced either by paternal or maternal gene (in %)? 1%.
+- What are the XIST molecules doing? About 300 of them cover the X chromosome.
+- Name a very important, genetically important, feature about chromatin structure. A: It can be inherited.
+- In the Histone code, where do methyl groups, acetyl groups and phosphate groups end up? (1) Methyl groups are added to either lysine or arginine (2) acetyl groups to lysine residues (3) phosphate groups to serine residues
+- What does RepA do? It introduces chromatin modifications into the XIST promoter that lead to transcriptional activation.
+- Where can we find H3K9me2 und H3K9me3? In promoter regions.
+- Enhancer-blocking insulators must be placed between ...? An enhancer and a promoter.
+- What exactly is "position-effect variegation"? The phenomen in which heterochromatin can spread into euchromatin and silence genes.
+- The ChIP technique allows us what effectively? It allows us to separate heterochromatin and euchromatin.
+- Give an example for a Su(var) protein. A: HP-1.
+- What does "maternal imprinting" mean? The copy of a gene derived from the mother is inactivated.
+- Why do we require "barrier insulators" in Epigenetics? Barrier insulators prevent the spreading of heterochromatin, by creating a local environment unfavourable to heterochromatin formation.
+- Was "vererbt" die Epigenetik? DNA-Methylierungsmuster.
+- Name a "chromatin remodeling complex". A: Swi/Snf.
+- Welchen Effekt hat das Protein HP-1? When it binds to epigenetic marks, like H3K9me, it can form heterochromatin.
+- Wann werden Histone synthetisiert? In der S-Phase.
+- Enzymtyp Mcm (bei DNA-Replikation wichtig)? Helikase.
+- Which proteins "read" acetylated histones (reading means = recognize and bind to)? Proteins with bromo-domains.
+- In Epigenetics, we have the SET domain which is 130 amino acids long. Why the name SET? Su(var)3-9, E(z) (enhancer of zeste) and trithorax.
+- What is "reverse modeling"? Active chromatin becomes inactive chromatin.
+- Acetylation of Lyseine Histone H4 is often preceded by ...? Phosphorylation of Serine-10 in that molecule.
+- Wie können wir experimentell XX-Mäusemänner erstellen? Wir übertragen das Sry-Gen in die Maus.
+- What is the effect when K4 becomes methylated in a Histone? It HDAC recruitment.
+- In a typical genome, where could we expect to find cytosine methylation in general? In genes that are NOT transcribed.
+- Affinity enrichment of methylated DNA was first demonstrated with ..? With the methyl-binding protein 2 (MeCP2).
+- What is the MeDIP technique? MeDIP is short for "Methylated DNA immunoprecipitation". This technique involves the immunoprecipitation of the methylated fraction of a genomic DNA sample with a monoclonal antibody against methylcytosine, followed either by hybridization of the immunprecipitated raction against the input fraction on a microarray or next-generation sequencing (MeDIP-seq).
+- Warum verwenden wir Sodium Bisulfite in der Epigenetik und wie gehen wir vor? Wir können damit methylierte Cytosine detektieren. Sodium Bisulfite konvertiert unmethylierte Cytosine zu Uracil, und danach via PCR zu Thymidine. Methylierte Cytosine hingegen sind gegenüber Bisulfite resistent und verändert sich nicht.
+- Name 3 mechanisms of dosage compensation for X-linked genes. A: (1) Inactivation (2) hyperactivation (3) hypoactivation
+- In Epigenetics, what are "readers"? These are detector proteins that specifically recognize and bind modified histone tails.
+- In Epigenetics, for histone modifications, name three "erasers". A: (1) Phosphatases (2) Deacetylases (3) Demethylases
+- Wie können wir Acetylierung an Histonen nachweisen? Mittels CHiP und Antikörpern gegen acetylierte Histone.
+- How many different histone modifications are known? 150.
+- In Epigenetics, which protein recruits Dnmt1? The SRA Protein Np95 (Uhrf1).
+- Name 5 different Histone Modifications. A: A,M,P,U,S (1) Acetylation (2) Methylation (3) Phosphorylation (4) Ubiquitination (5) Sumoylation
+- In Epigenetic, the protein Mig1 recruits what ...? Tup1.
+- In der Epigenetik, welche Aminosäuren können durch Methylgruppen modifiziert werden? (1) Lysin (2) Arginin
+- Wenn ich genomische DNA mit "sodium bisulphite" behandle, was passiert mit dieser DNA? Unmethylierte Cytosine werden in Uracil konvertiert, methylierte Cytosine sind hingegen geschützt.
+- Welches Molekül war das erste entdeckte "histone modifying enzyme"? Gcn5 Histone Acetyltransferase.