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Nemeth

Institute for Biochemistry, Genetics and Microbiology
Biochemistry III - House of the Ribosome
PD Dr. Attila Nemeth
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Research

My goal is to understand genome regulation in a comprehensive way by exploring nuclear organization and genome function at the level of chromatin domain dynamics using the combination of conventional and novel experimental approaches. In order to deepen our understanding about the dynamics of functional nuclear architecture during fundamental physiological processes such as cellular senescence, differentiation and cell growth, the model systems that we primarily investigate are the human and mouse nucleolus

 

Nucleolar control of genome organization

A central feature of the eukaryotic cell nucleus is its morphological and functional heterogeneity generated by the presence of distinct nuclear compartments, which are generally composed by proteinaceous nuclear bodies and nucleoprotein structures, called chromatin domains. These are dynamic structures which specifically interact with each other within and between chromosome territories depending on the cell’s physiological state (e.g., differentiation, cell cycle, cellular age etc.). Our laboratory investigates the epigenetic regulation of chromatin domains in their natural, three-dimensional appearance in the mammalian interphase nucleus, which represents the highest level of structural order of the epigenome. In addition, we have established a novel single-molecule method called epi-combing to analyze DNA modification patterns of ribosomal DNA and satellite repeat arrays on large, megabase-sized DNA fibres

The organisation of interphase chromosomes in and around the largest nuclear compartment, the nucleolus, has been initially explored in our recent study. Currently we explore the dynamics and regulatory mechanisms of genome organization and nuclear architecture in a nucleolus-centered fashion in different model organisms and biological processes.

 

Nads

Distribution of nucleolus-associated chromosomal domains (NADs) together with satellite repeats along human chromosomes. Note that the nucleolar organizer regions (NORs) on the p-arms of the five acrocentric chromosomes (13, 14, 15, 21 and 22) contain clusters of ribosomal DNA repeats and represent the core of the nucleolar genome. NADs are labeled with red, NORs with light red, satellite repeats with deep blue, centromeres with yellow and chromosomes with light blue.

Team

Attila Nemeth

 
curriculum vitae
   

Current mentees

Dillinger, Stefan MSc/PhD student
Fladerer, Sebastian MSc student
   
   

Former mentees

Zillner, Karina MSc/PhD student
Porfenenko, Mikhail MSc student
Filarsky, Katharina MSc student
Rachow, Kathrin MSc student
Thies, Carina BSc student
Kuttenberger, Verena BSc student
Fink, Katharina BSc student
   

 

Attila Nemeth - Short CV

 

 
since 2012 Reader (Akademischer Oberrat, Privatdozent) - University of Regensburg (Germany), Dept. of Biochemistry III
2006 – 2012 Lecturer (Akademischer Rat) - University of Regensburg (Germany), Dept. of Biochemistry III; Habilitation in Biochemistry
2007 – 2008 Visiting Scientist - LMU Munich (Germany), Dept. of Human Genetics
2002 – 2006 Postdoc - LMU Munich (Germany), Dept. of Molecular Biology
1997 – 2002 PhD in Oncology - Semmelweis University (Budapest, Hungary) / DKFZ (Heidelberg, Germany)

 

 

 

 

Publications

PubMed Publicaton list

SCIENTIFIC ARTICLES INDEXED BY PUBMED

 

20) Hamdane N., Stefanovsky V., Tremblay M.G., Németh A., Paquet E., Lessard F., Sanij E., Hannan R.D. and Moss T. (2014) Conditional inactivation of Upstream Binding Factor reveals its epigenetic functions and the existence of a somatic nucleolar precursor body. PLoS Genet 10, accepted manuscript

 

19) Dillinger S.*, Villar-Garea A.*, Deutzmann R., Németh A. (2014). Analysis of histone post-translational modifications from nucleolus-associated chromatin by mass spectrometry. Methods Mol Biol, 1094, 277-93

 

18) Németh A. (2014). Methyl-combing—single molecule analysis of DNA modifications on stretched DNA fibers. Methods Mol Biol, 1094, 233-41

 

17) Diermeier S., Németh A., Rehli M., Grummt I., Längst G. (2013) Chromatin-specific regulation of mammalian rDNA transcription by clustered TTF-I binding sites. PLoS Genet 9, e1003786

 

16) Zillner K., Filarsky M., Rachow K., Weinberger M., Längst G.#, Németh A.# (2013) Large-scale organization of ribosomal DNA chromatin is regulated by Tip5. Nucleic Acids Res 41, 5251-62.

 

15) Németh A.#, Perez-Fernandez J., Merkl P., Hamperl S., Gerber J., Griesenbeck J., Tschochner H.# (2013). RNA polymerase I termination: where is the end? BBA - Gene Regulatory Mechanisms 1829, 306-17. Review.

 

14) Hochstatter J., Hölzel M., Rohrmoser M., Schermelleh L., Leonhardt H., Keough R., Gonda T.J., Imhof A., Eick D., Längst G.#, Németh A.# (2012). Myb-binding protein 1a (Mybbp1a) regulates levels and processing of pre-ribosomal RNA. J Biol Chem 287, 24365-77.

 

13) Reiter A.*, Hamperl S.*, Seitz H., Merkl P., Perez-Fernandez J., Williams L., Gerber J., Németh A., Léger I., Gadal O., Milkereit P., Griesenbeck J., Tschochner H. (2012). The Reb1-homolog Ydr026c/Nsi1 is required for efficient RNA polymerase I termination in yeast. EMBO J 31, 3480-93.

 

12) Zillner K., Németh A. (2012). Single molecule, genome-scale analyses of DNA modifications: exposing the epigenome with next generation technologies. Epigenomics 4, 403-14. Review.

 

11) Felle M., Joppien S., Németh A., Diermeier S., Thalhammer V., Dobner T., Kremmer E., Kappler R., Längst G. (2011). The USP7/Dnmt1 complex stimulates the DNA methylation activity of Dnmt1 and regulates the stability of UHRF1. Nucleic Acids Res 39, 8355-65.

 

10) Németh A.#, Längst G.# (2011). Genome organization in and around the nucleolus. Trends Genet 27, 149-56. Review.

 

9) Németh A., Conesa A., Santoyo-Lopez J., Medina I., Montaner D., Péterfia B., Solovei I., Cremer T., Dopazo J., Längst G. (2010). Initial genomics of the human nucleolus. PLoS Genet 6, e1000889.

Highlighted in Nature (2010 Apr 1;464(7289):652.) and Nature Reviews Genetics (2010 May 1;11(5):314.), and selected for the „PLoS Collection: Epigenetics 2010

 

8) Németh A., Längst G. (2008). Chromatin organization of active ribosomal RNA genes. Epigenetics 3, 243-5.

 

7) Németh A., Guibert S., Tiwari V.K., Ohlsson R., Längst G. (2008). Epigenetic regulation of TTF-I mediated promoter-terminator interactions of rRNA genes. EMBO J 27, 1255-65.

 

6) Espada J., Ballestar E., Santoro R., Fraga M. F., Villar-Garea A., Németh A., Lopez-Serra L., Ropero S., Aranda A., Orozco H., Moreno V., Juarranz A., Stockert J. C., Längst G., Grummt I., Bickmore W., Esteller M. (2007). Epigenetic disruption of ribosomal RNA genes and nucleolar architecture in DNA methyltransferase 1 (Dnmt1) deficient cells. Nucleic Acids Res 35, 2191-8.

 

5) Németh A., Strohner R., Grummt I., Längst G. (2004). The chromatin remodeling complex NoRC and TTF-I cooperate in the regulation of the mammalian rRNA genes in vivo. Nucleic Acids Res 32, 4091-4099.

 

4) Németh A., Längst G. (2004). Chromatin higher order structure: opening up chromatin for transcription. Brief Funct Genomic Proteomic 2, 334-43. Review.

 

3) Strohner R., Németh A., Nightingale K.P., Grummt I., Becker P.B., Längst G. (2004). Recruitment of the nucleolar remodeling complex NoRC establishes ribosomal DNA silencing in chromatin. Mol Cell Biol 24, 1791-1798.

 

2) Várkonyi J., Kovalszky I., Németh A., Demeter J., Raposa T. (2001). Increased risk for cancer in multiple myeloma patients and their first-degree relatives. Haematologia 31, 45-50.

 

1) Strohner R.*, Németh A.*, Jansa P., Hofmann-Rohrer U., Santoro R., Längst G., Grummt I. (2001). NoRC--a novel member of mammalian ISWI-containing chromatin remodeling machines. EMBO J 20, 4892-4900.

 

* joint first authors

# joint corresponding authors

 

 

OTHER PUBLICATIONS

 

5) Németh A., Längst G. (2013). Chromatin organization and the mammalian nucleolus. In: Proteins of the Nucleolus (Springer), 119-48. Book Chapter.

 

4) Zillner K., Komatsu J., Filarsky K., Bensimon A., Németh A. (2012). Deciphering repetitive DNA methylation patterns on single DNA fibers using Epi-Combing. FEBS Journal 279, SI Supp. 1 512-3. Meeting Abstract.

 

3) Diermeier S., Németh A., Exler J., Längst G. (2012). Epigenomic characterization of the structure-function relation in chromatin. FEBS Journal 279, SI Supp. 1 480. Meeting Abstract.

 

2) Griesenbeck J., Längst G., Milkereit P., Németh A., Tschochner H. (2011). Ribosomen-Biogenese: Hierarchie oder koordiniertes Miteinander? BioSpektrum 13, 750-3.

 

1) Németh A., Rachow K., Hoffmeister H., Strohner R., Weinberger M., Längst G. (2009). NoRC regulates higher order rDNA structure. Cell Oncol 31, 146-7. Meeting Abstract.

 

 

 


CONFERENCES

 

 

16) EMBO Conference on Nuclear Structure and Dynamics

L'Isle-sur-la-Sorgue (France), 02 – 06. October 2013, poster presentation

“Molecular mapping of nucleolus-associated chromatin dynamics during cellular aging”

 

15) 5th TRR81 PhD Minisymposia

MPI Bad Nauheim (Germany), 14. February 2013, invited speaker

“Exploring chromosomal domains by functional genomics and dynamic molecular combing”

 

14) RNA Polymerase I & III Transcription Meeting

Warrenton (Virginia, USA), 07 – 11. June 2012, selected speaker

“Single molecule analysis of human rDNA methylation in the megabase range”

 

13) 46. Herbsttreffen

Burg Hornberg, Neckarzimmern (Germany), 03 – 05. November 2011, selected speaker

“Organization of the nucleolus-associated genome and epigenome in mammalian cells”

 

12) Epigenomics of Common Diseases Conference

Wellcome Trust Conference Centre, Hinxton, Cambridge (UK), 13 – 16. September 2011, selected speaker

“Epi-combing: genome-scale single molecule analysis of epigenetic DNA marks”

 

11) EMBO Conference Series on Chromatin and Epigenetics

EMBL, Heidelberg (Germany), 01 – 05. June 2011, poster presentation

Evolutionarily conserved nucleolar localization of the gene, pre-mRNA and protein

of the key regulator of RNA polymerase I transcription

 

10) 9th EMBL Transcription Meeting

EMBL, Heidelberg (Germany), 28 – 31. August 2010, poster presentation

“NoRC regulates the higher order structure of the ribosomal DNA”

 

9) 8th International Conference on Ribosome Synthesis

Regensburg (Germany), 26 – 30. August 2009, selected speaker

“Genomics of the human nucleolus”

 

8) MC-GARD Higher Order Genome Architecture Meeting

Edinburgh (UK), 01 – 05. April 2009, poster presentation

“NoRC regulates higher order rDNA structure”

 

7) 8th EMBL Transcription Meeting

EMBL, Heidelberg (Germany), 23 – 27. August 2008, poster presentation

“Epigenetic regulation of TTF-I mediated promoter-terminator interactions of rRNA genes”

 

 

6) RNA Polymerase I Transcription Meeting

Regensburg (Germany), 04 – 07. October 2007, selected speaker

“Multiple TTF-I binding sites establish higher order rDNA chromatin structure”

 

5) 7th International Conference on Ribosome Synthesis

Warrenton (Virginia, USA), 16 – 20. August 2006, poster presentation

“Topology of ribosomal RNA synthesis in mouse”

 

4) EMBO Conference on Nuclear Structure and Dynamics

La Grande Motte (France), September 2005, poster presentation

“Multiple TTF-I binding sites establish higher order rDNA chromatin structure”

 

3) 6th EMBL Transcription Meeting

EMBL, Heidelberg (Germany), August 2004, poster presentation

“The chromatin remodeling complex NoRC and TTF-I cooperate in the regulation of the mammalian rRNA genes”

 

2) RNA Polymerase I & III Transcription Meeting

Asilomar (California, USA), 02 – 05. June 2004, selected speaker

“Molecular mechanisms of TTF-I – NoRC dependent ribosomal RNA gene silencing”

 

1) XXII. Congress of the Hungarian Cancer Society

Budapest (Hungary), September 1997, selected speaker

“DNA damage measurement at the TP53 locus after UV-irradiation and cisplatin treatment by competitive PCR”

‘Best Young Scientist Presentation - Promega Award’

 

 

COURSES

 

SCIENCEPLUS Workshop „Team- & Führungskompetenz in der Wissenschaft“

Regensburg (Germany) 18. May 2012

 

Fortbildungsveranstaltung für Projektleiter und Beauftragte Biologische Sicherheit (BBS)

Regensburg (Germany) 15 – 16. April 2010

 

UD-HHMI Lecture and Practical Course on Modern Technologies on Gene Expression Detection and Data Integration

Debrecen (Hungary) 16 – 27. July 2006

 

Teaching

Link zu LSF

Vst.-Nr. Veranstaltungen Semester
54062 Biochemisches Seminar vor Beginn des Semesters in Gruppen als Block  SoSe 2014
54063 Biochemisches Praktikum vor Beginn des Semesters in Gruppen als Block  SoSe 2014
54209 Progress report on RNP biogenesis and function  SoSe 2014
54211 Laufende wissenschaftliche Arbeiten der Biochemie/independent studies of biochemistry  SoSe 2014
54213 Laufende wissenschaftliche Arbeiten der Biochemie  SoSe 2014
54215 Funktionelle Zellkernarchitektur/functional architecture of the nucleus  SoSe 2014
54221 Ribosome biogenesis and regulation of transcription  SoSe 2014
54237 3D organization of the human genome  SoSe 2014

Contact

PD Dr. Attila Nemeth

Department of Biochemistry III
Biochemistry Center Regensburg
University of Regensburg
Universitaetsstr. 31
D-93053 Regensburg
GERMANY

T: +49-941-943-2846 (office)
T: +49-941-943-2809 (lab)
F: +49-941-943-2474
E: attila.nemeth@ur.de
W: http://www.ur.de/biologie-vorklinische-medizin/fakultaet/research/nemeth/index.html

  1. Fakultät für Biologie und Vorklinische Medizin
  2. Faculty Research

Nemeth-Lab

 

Nemeth191x191

Dr. Attila Nemeth
Tel: 0941-943-2846
Attila.Nemeth@ur.de
Room: VKL 1.0.10e