Ludwig, A. K. (2017)
The Guardians of the Epigenome - Regulation and Role of Nucleotide Modifications.
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung
Kurzbeschreibung (Abstract)
While from a genetic perspective all cells of an organism are identical, they vary greatly in type and function. Major determinants of cellular diversity are epigenetic alterations, including post-synthetic modifications of nucleic acids. In DNA, the best-studied chemical modification is the methylation of cytosine at carbon C5. 5-methylcytosine (5mC) plays a central role in the regulation of gene expression and has been implicated in a variety of biological processes and diseases. While initially considered as a relatively stable epigenetic mark, a family of proteins named Ten eleven translocation (Tet), were recently shown to catalyze the conversion of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in an iterative oxidation reaction. These oxidized derivatives have been shown to modulate gene expression and control cellular metabolism. Hence, to avert the formation of aberrant, pathogenic DNA modifications, Tet activity must be precisely regulated. Here, we analyzed the potential of methyl-CpG binding domain (MBD) proteins to control Tet dioxygenase activity in vitro and in vivo. We demonstrate that prior binding of Mecp2 and Mbd2 to DNA protects 5mC from Tet1 mediated oxidation in a concentration dependent manner. The mechanism is based on competitive, sequence unspecific binding to DNA and correlates with nucleic acid coverage and retention time of MBD proteins on DNA. Accordingly, we find increased levels of the Tet oxidation product 5hmC at pericentric heterochromatin in neurons of Mecp2 deficient mice with concomitant reactivation of highly methylated major satellite DNA repeats. Moreover, we find increased expression and retrotransposition of endogenous and engineered long interspersed nuclear elements (LINE1) as potential consequence of unconfined Tet1 activity in human cells. Similar to DNA, RNA contains a variety of post-synthetic modifications that extend their chemical information and properties. One out of < 100 noncanonical ribonucleobases is C5-methylated cytosine, which is present in various types of RNA, including ribosomal RNA (rRNA). Recent studies have shown that Tet proteins do not exclusively hydroxylate methylcytosine in DNA, but also act on 5mC in single-stranded ribonucleic acids. Since modification of rRNA potentially requires the localization of Tet proteins to the nucleolus, the place of rRNA synthesis and ribosome assembly, it is important to understand the general principles of protein targeting to this subnuclear compartment. Therefore, we determined the molecular requirements that are necessary and sufficient for the localization and accumulation of peptides and proteins inside nucleoli of living cells. Our data indicate that peptide units composed of consecutive, positively charged arginines with an isoelectric point ≥ 12.6 meet the chemical conditions for nucleolar localization. Consistent with this, we mapped an arginine-rich region within the low complexity insert of Tet2, which accumulated in nucleoli upon deletion of its regulatory N-terminal domain. Using a pH sensitive dye, we revealed that the nucleolus is relatively acidic. Accordingly, we show that arginine-rich peptides, which carry a net positive charge under these electrochemical conditions, interact with negatively charged RNA in vitro. This interaction in turn, is consistent with the conservation of this nucleolar targeting principle from insects to man. Finally we developed a detailed protocol for the visualization of nucleoli in living cells using fluorescently tagged cell-penetrating peptides (CPP), which allows precise nucleolar localization analysis of various proteins, such as Tet. In summary, our data contribute to understanding the regulation of Tet activity outside and (Tet) protein localization inside of nucleoli.
Typ des Eintrags: | Dissertation | ||||
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Erschienen: | 2017 | ||||
Autor(en): | Ludwig, A. K. | ||||
Art des Eintrags: | Erstveröffentlichung | ||||
Titel: | The Guardians of the Epigenome - Regulation and Role of Nucleotide Modifications | ||||
Sprache: | Englisch | ||||
Referenten: | Cardoso, Prof. Dr. M. Cristina ; Süß, Prof. Dr. Beatrix | ||||
Publikationsjahr: | 16 März 2017 | ||||
Ort: | Darmstadt | ||||
Datum der mündlichen Prüfung: | 11 Mai 2017 | ||||
URL / URN: | http://tuprints.ulb.tu-darmstadt.de/6244 | ||||
Kurzbeschreibung (Abstract): | While from a genetic perspective all cells of an organism are identical, they vary greatly in type and function. Major determinants of cellular diversity are epigenetic alterations, including post-synthetic modifications of nucleic acids. In DNA, the best-studied chemical modification is the methylation of cytosine at carbon C5. 5-methylcytosine (5mC) plays a central role in the regulation of gene expression and has been implicated in a variety of biological processes and diseases. While initially considered as a relatively stable epigenetic mark, a family of proteins named Ten eleven translocation (Tet), were recently shown to catalyze the conversion of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in an iterative oxidation reaction. These oxidized derivatives have been shown to modulate gene expression and control cellular metabolism. Hence, to avert the formation of aberrant, pathogenic DNA modifications, Tet activity must be precisely regulated. Here, we analyzed the potential of methyl-CpG binding domain (MBD) proteins to control Tet dioxygenase activity in vitro and in vivo. We demonstrate that prior binding of Mecp2 and Mbd2 to DNA protects 5mC from Tet1 mediated oxidation in a concentration dependent manner. The mechanism is based on competitive, sequence unspecific binding to DNA and correlates with nucleic acid coverage and retention time of MBD proteins on DNA. Accordingly, we find increased levels of the Tet oxidation product 5hmC at pericentric heterochromatin in neurons of Mecp2 deficient mice with concomitant reactivation of highly methylated major satellite DNA repeats. Moreover, we find increased expression and retrotransposition of endogenous and engineered long interspersed nuclear elements (LINE1) as potential consequence of unconfined Tet1 activity in human cells. Similar to DNA, RNA contains a variety of post-synthetic modifications that extend their chemical information and properties. One out of < 100 noncanonical ribonucleobases is C5-methylated cytosine, which is present in various types of RNA, including ribosomal RNA (rRNA). Recent studies have shown that Tet proteins do not exclusively hydroxylate methylcytosine in DNA, but also act on 5mC in single-stranded ribonucleic acids. Since modification of rRNA potentially requires the localization of Tet proteins to the nucleolus, the place of rRNA synthesis and ribosome assembly, it is important to understand the general principles of protein targeting to this subnuclear compartment. Therefore, we determined the molecular requirements that are necessary and sufficient for the localization and accumulation of peptides and proteins inside nucleoli of living cells. Our data indicate that peptide units composed of consecutive, positively charged arginines with an isoelectric point ≥ 12.6 meet the chemical conditions for nucleolar localization. Consistent with this, we mapped an arginine-rich region within the low complexity insert of Tet2, which accumulated in nucleoli upon deletion of its regulatory N-terminal domain. Using a pH sensitive dye, we revealed that the nucleolus is relatively acidic. Accordingly, we show that arginine-rich peptides, which carry a net positive charge under these electrochemical conditions, interact with negatively charged RNA in vitro. This interaction in turn, is consistent with the conservation of this nucleolar targeting principle from insects to man. Finally we developed a detailed protocol for the visualization of nucleoli in living cells using fluorescently tagged cell-penetrating peptides (CPP), which allows precise nucleolar localization analysis of various proteins, such as Tet. In summary, our data contribute to understanding the regulation of Tet activity outside and (Tet) protein localization inside of nucleoli. |
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URN: | urn:nbn:de:tuda-tuprints-62449 | ||||
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 |
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Hinterlegungsdatum: | 28 Mai 2017 19:55 | ||||
Letzte Änderung: | 28 Mai 2017 19:55 | ||||
PPN: | |||||
Referenten: | Cardoso, Prof. Dr. M. Cristina ; Süß, Prof. Dr. Beatrix | ||||
Datum der mündlichen Prüfung / Verteidigung / mdl. Prüfung: | 11 Mai 2017 | ||||
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