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The regulation of Ten-eleven translocation proteins (methylcytosine modifiers) by methyl-CpG binding domain proteins (methylcytosine readers)

Zhang, Peng (2016)
The regulation of Ten-eleven translocation proteins (methylcytosine modifiers) by methyl-CpG binding domain proteins (methylcytosine readers).
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung

Kurzbeschreibung (Abstract)

Cytosine modifications diversify the genome and allow cell differentiation by the action of cytosine modification readers and modifiers. The epigenetic information of 5-methylcytosine can be translated by cytosine modification readers, such as the methyl-CpG binding domain (MBD) proteins. The aberrant interactions of MBD proteins with 5-methylcytosine cause diseases like Rett syndrome and also decrease genome stability, thus, the levels of both MBD protein and its substrate 5mC must be precisely regulated. Although, 5mC can be modified by Ten-eleven translocation (Tet) protein to 5-hydroxymethylcytosine (5hmC), which affects the binding ability of MBD proteins to DNA, the interplay of MBD proteins, Tet1 proteins and their substrate is still unknown. Since post translational modifications of Mecp2, the founding member of MBD protein family have been described before, we initially focused on the effect of poly(ADP-ribosyl)ation of Mecp2 on chromatin structure and its DNA binding ability. We show that in mouse brain endogenous Mecp2 is poly(ADP-ribosyl)ated in vivo. Furthermore, we find that poly(ADP-ribosyl)ation of Mecp2 decreases its ability to cluster pericentric heterochromatin. Finally, we demonstrate that poly(ADP-ribosyl)ated Mecp2 decrease binding ability to heterochromatin DNA. To understand the regulation of Tet mediated 5mC oxidation, we focused on how Tet proteins convert 5mC to 5hmC. We developed and optimized methods to step by step detect processes involved in Tet oxidation, including Tet-DNA binding, 5mC flipping and 5mC oxidation. We show that the catalytic domain of Tet1 (Tet1CD) binds to DNA in a non-sequence specific manner. Furthermore, we were able to detect DNA base flipping induced by Tet1CD. Finally, our methods can be used to easily and sensitively detect Tet oxidation products. By using these methods, we next tested whether MBD proteins affect Tet mediated 5mC oxidation. We focused on the five best studied MBD proteins including Mbd1, Mbd2, Mbd3, Mbd4 and Mecp2. We show that Mbd1 enhances Tet1 mediated 5hmC formation by facilitating its localization to methylated DNA. Moreover, the CXXC3 domain of Mbd1 is necessary for this enhancement. Compared with Mbd1, we find that Mbd3 and Mbd4 do not affect Tet1 mediated 5mC oxidation. In contrast to Mbd1, we show that Mbd2 and Mecp2 as well as its subdomains MBD and IDTRD block Tet mediated 5hmC formation in a concentration dependent manner in vivo and in vitro. Moreover, binding of Mecp2 to DNA impairs the DNA binding ability of Tet1CD in vitro and thus, direct binding of Mecp2 to DNA is sufficient to effectively prevent Tet1 mediated 5mC oxidation. These results indicate that the binding ability of MBD proteins and Tet proteins to DNA is important for 5mC conservation and conversion, respectively. Finally, we focused on the biological consequences of MBD proteins and Tet proteins mediated 5mC conservation and conversion. In mouse cells, we find that the Tet oxidation product 5hmC is enriched in neurons of mouse model for Rett syndrome (Mecp2 knockout mice). Moreover, we find that Tet1 reactivates expression of major satellite repeats in the absence of Mecp2. In human cells, we show that Tet1 activates endogenous and ectopic long interspersed nuclear elements 1 expression and transposition and this activation can be repressed by Mbd2 and Mecp2 as well as its subdomains MBD and IDTRD. These results indicate that the fine balance between methylcytosine readers” and “erasers/writers” regulates transcriptional noise and genome stability.

Typ des Eintrags: Dissertation
Erschienen: 2016
Autor(en): Zhang, Peng
Art des Eintrags: Erstveröffentlichung
Titel: The regulation of Ten-eleven translocation proteins (methylcytosine modifiers) by methyl-CpG binding domain proteins (methylcytosine readers)
Sprache: Englisch
Referenten: Cardoso, Prof. Dr. M. Cristina ; Süß, Prof. Dr. Beatrix
Publikationsjahr: 16 September 2016
Ort: Darmstadt
Datum der mündlichen Prüfung: 16 September 2016
URL / URN: http://tuprints.ulb.tu-darmstadt.de/5696
Kurzbeschreibung (Abstract):

Cytosine modifications diversify the genome and allow cell differentiation by the action of cytosine modification readers and modifiers. The epigenetic information of 5-methylcytosine can be translated by cytosine modification readers, such as the methyl-CpG binding domain (MBD) proteins. The aberrant interactions of MBD proteins with 5-methylcytosine cause diseases like Rett syndrome and also decrease genome stability, thus, the levels of both MBD protein and its substrate 5mC must be precisely regulated. Although, 5mC can be modified by Ten-eleven translocation (Tet) protein to 5-hydroxymethylcytosine (5hmC), which affects the binding ability of MBD proteins to DNA, the interplay of MBD proteins, Tet1 proteins and their substrate is still unknown. Since post translational modifications of Mecp2, the founding member of MBD protein family have been described before, we initially focused on the effect of poly(ADP-ribosyl)ation of Mecp2 on chromatin structure and its DNA binding ability. We show that in mouse brain endogenous Mecp2 is poly(ADP-ribosyl)ated in vivo. Furthermore, we find that poly(ADP-ribosyl)ation of Mecp2 decreases its ability to cluster pericentric heterochromatin. Finally, we demonstrate that poly(ADP-ribosyl)ated Mecp2 decrease binding ability to heterochromatin DNA. To understand the regulation of Tet mediated 5mC oxidation, we focused on how Tet proteins convert 5mC to 5hmC. We developed and optimized methods to step by step detect processes involved in Tet oxidation, including Tet-DNA binding, 5mC flipping and 5mC oxidation. We show that the catalytic domain of Tet1 (Tet1CD) binds to DNA in a non-sequence specific manner. Furthermore, we were able to detect DNA base flipping induced by Tet1CD. Finally, our methods can be used to easily and sensitively detect Tet oxidation products. By using these methods, we next tested whether MBD proteins affect Tet mediated 5mC oxidation. We focused on the five best studied MBD proteins including Mbd1, Mbd2, Mbd3, Mbd4 and Mecp2. We show that Mbd1 enhances Tet1 mediated 5hmC formation by facilitating its localization to methylated DNA. Moreover, the CXXC3 domain of Mbd1 is necessary for this enhancement. Compared with Mbd1, we find that Mbd3 and Mbd4 do not affect Tet1 mediated 5mC oxidation. In contrast to Mbd1, we show that Mbd2 and Mecp2 as well as its subdomains MBD and IDTRD block Tet mediated 5hmC formation in a concentration dependent manner in vivo and in vitro. Moreover, binding of Mecp2 to DNA impairs the DNA binding ability of Tet1CD in vitro and thus, direct binding of Mecp2 to DNA is sufficient to effectively prevent Tet1 mediated 5mC oxidation. These results indicate that the binding ability of MBD proteins and Tet proteins to DNA is important for 5mC conservation and conversion, respectively. Finally, we focused on the biological consequences of MBD proteins and Tet proteins mediated 5mC conservation and conversion. In mouse cells, we find that the Tet oxidation product 5hmC is enriched in neurons of mouse model for Rett syndrome (Mecp2 knockout mice). Moreover, we find that Tet1 reactivates expression of major satellite repeats in the absence of Mecp2. In human cells, we show that Tet1 activates endogenous and ectopic long interspersed nuclear elements 1 expression and transposition and this activation can be repressed by Mbd2 and Mecp2 as well as its subdomains MBD and IDTRD. These results indicate that the fine balance between methylcytosine readers” and “erasers/writers” regulates transcriptional noise and genome stability.

Alternatives oder übersetztes Abstract:
Alternatives AbstractSprache

Modifikationen der DNA-Base Cytosin haben eine Erweiterung des genetischen Alphabets zur Folge und regulieren mit Hilfe von Proteinen, die Cytosin und dessen Modifikationen binden beziehungsweise weiter modifizieren können, die Differenzierung der Zelle. Die epigenetische Information von 5-methylcytosin (5mC) wird von Cytosinmodifikations-Lesern, wie beispielsweise der Methyl-CpG-Bindedomäne (MBD) Proteinfamilie verarbeitet. Gestörte Interaktionen von MBD Proteinen mit 5mC haben Krankheiten, wie das Rett Syndrom zur Folge und beeinträchtigen die genomische Stabilität. Folglich muss die Menge an MBD Proteinen, sowie deren Substrat 5mC präzise reguliert werden. Obwohl bekannt ist, dass die Oxidation von 5mC zu 5-hydroxymethylcytosin (5hmC) durch Ten-eleven translocation (Tet) Proteine die DNA-Bindung der MBD Proteinen beeinflusst, weiß man erst wenig über die Interaktion von MBD Proteinen, Tet Proteinen, sowie deren Substrat 5mC. Da Mecp2, das zuerst ausführlich erforschte Mitglied der MBD Proteinfamilie, posttranslational modifiziert wird, haben wir zunächst den Effekt der poly(ADP-ribosyl)ierung von Mecp2 auf die Chromatin Struktur, sowie auf die Bindung von DNA untersucht. Wir zeigen, dass endogenes Mecp2 im Maushirn poly(ADP-ribosyl)iert wird. Des Weiteren beobachten wir, dass poly(ADP-ribosyl)ierung von Mecp2 dessen Fähigkeit zur Kondensierung von perizentrischem Heterochromatin und die Bindung an heterochromatische DNA reduziert. Um die Regulation der von Tet katalysierten 5mC Oxidation besser zu verstehen, untersuchten wir wie Tet Proteine 5mC modifizieren. Hierfür entwickelten beziehungsweise optimierten wir Methoden um die bei der Tet katalysierten 5mC Oxidation beteiligten Schritte (Bindung von Tet an DNA, 5mC-flipping und 5mC Oxidation) zu detektieren. Wir zeigen, dass die katalytische Domäne von Tet1 (Tet1CD) Sequenz-unabhängig DNA bindet. Des Weiteren zeigen wir, dass Tet1CD einen Base-flipping Mechanismus benutzt, um Zugang zu 5mC zu erhalten. Letztlich ermöglichen die von uns entwickelten Methoden die einfache und sensitive Detektion von Tet Oxidationsprodukten. Durch Anwendung der oben beschriebenen Methoden untersuchten wir weiterhin, ob MBD Proteine die von Tet katalysierte 5mC Oxidation beeinträchtigen. Hierfür legten wir den Fokus auf die fünf am besten beschriebenen MBD Proteine Mbd1, Mbd2, Mbd3, Mbd4 und Mecp2. Wir zeigen, dass Mbd1 die Ausbildung von 5hmC begünstigt, indem es die Bindung von Tet1 an methylierte DNA fördert, wofür die CXXC3 Domäne von Mbd1 unbedingt notwendig ist. Mbd3 und Mbd4 haben im Vergleich zu Mbd1 keine Auswirkungen auf die von Tet katalysierte 5mC Oxidation. Mbd2 und Mecp2, sowie die beiden Mecp2 Subdomänen MBD und IDTRD hingegen, verhindern das Entstehen von 5hmC in Abhängigkeit ihrer Konzentration in vitro als auch in vivo. Darüber hinaus beeinträchtigt die Bindung von Mecp2 an DNA die Interaktion von Tet1CD mit DNA in vitro. Folglich ist die Bindung von Mecp2 an DNA ausreichend, um die von Tet1 katalysierte 5mC Oxidation zu unterbinden. Dies zeigt, dass die Bindung von MBD und Tet Proteinen sowohl für den Schutz, als auch für die Umsetzung von 5mC entscheidend ist. Zuletzt konzentrierten wir uns auf die biologischen Konsequenzen der MBD- und Tet Protein vermittelten 5mC Konservierung und Konvertierung. Wir zeigen erhöhte Level des Tet Oxidationsprodukts 5hmC in Neuronen eines Maus-Modells für Rett Syndrom (Mecp2 knockout Mäuse). Des Weiteren beobachten wir, dass Tet1 in der Abwesenheit von Mecp2 die Expression von Major Satellite DNA in Mauszellen reaktiviert. Für humane Zellen zeigen wir, dass Tet1 die Expression und Retrotransposition von endogenen und ektopischen L1 Elementen (long interspresed nuclear elements 1) begünstigt. Dies kann wiederum durch Mbd2 und Mecp2, sowie den beiden Mecp2 Subdomänen MBD und IDTRD unterdrückt werden. Dies deutet darauf hin, dass ein feines Gleichgewicht zwischen Proteinen, die 5mC erstellen, Proteinen die 5mC binden und Proteinen die 5mC entfernen, Transkriptionslevel reguliert und darüber hinaus die genomische Stabilität gewährleistet.

Deutsch
URN: urn:nbn:de:tuda-tuprints-56961
Sachgruppe der Dewey Dezimalklassifikatin (DDC): 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
Fachbereich(e)/-gebiet(e): 10 Fachbereich Biologie
10 Fachbereich Biologie > Cell Biology and Epigenetics
Hinterlegungsdatum: 02 Okt 2016 19:55
Letzte Änderung: 02 Okt 2016 19:55
PPN:
Referenten: Cardoso, Prof. Dr. M. Cristina ; Süß, Prof. Dr. Beatrix
Datum der mündlichen Prüfung / Verteidigung / mdl. Prüfung: 16 September 2016
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