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Nucleoar Structure

Institute of Biochemistry, Genetics and Microbiology
Biochemistry III - House of the Ribosome
Nucleolar Structure - Attila Németh
blank Sfb960 Housemarke Klein Rna-biology blank


Research

End of August 2016, the group of Attila Németh has stopped working at the University of Regensburg.  On these sides you find a synopsis of their accomplishments as well as the new contact information of Attila Németh.

The research of our group is focused on the biology of the mammalian nucleolus. On the one hand we investigate the function of the nucleolus in genome organization and establishment of nuclear architecture, on the other hand we work on the elucidation of molecular mechanisms that coordinate ribosomal gene transcription with changes in cell growth.

Nucleolar control of genome organization

Nucleolus-associated chromosomal domains (NADs) are structural and functional units of genome organization in the interphase. NADs are enriched in different gene families and certain satellite repeats, and they represent mainly a heterochromatin environment in addition to transcriptionally active ribosomal DNA.

Currently we address the following questions:
• How do nucleoli contribute to genome organization in different mammalian cell types?
• Does cellular aging alters the composition of nucleolus-associated chromatin?

Nucleolar Structure 1

Figure 1. Distribution of NADs along human chromosomes in HeLa cells. Nucleolar organizer regions are indicated with light red boxes. Confocal microscopy images on the right illustrate frequent association of centromeres with nucleoli (Németh et al., 2010).

Regulation of ribosomal RNA synthesis and processing


Regulation of ribosomal gene transcription is a key factor in controlling cell growth. Our main interest lies on the understanding of the mechanisms that regulate transcription of ribosomal RNA genes and the tightly linked processing of the pre-rRNA.

We aim to answer the following questions in our ongoing projects:
• What are the cis and trans factors that regulate higher-ordered organization of rRNA genes on active and inactive nucleolar organizer regions?
• How are the active rRNA genes spatially organized within the mammalian nucleolus?

Nucleolar Structure 2

Figure 2. Loop model of rRNA gene transcription. TTF-I binds next to the spacer promoter (SP) and the gene promoter (P) of ribosomal DNA (rDNA) and to multiple binding sites in the terminator region. Promoter-terminator interactions are mediated by TTF-I suggesting looping of active genes (Németh et al., 2008, Diermeier et al., 2014).

TEAM

Attila Nemeth

 
curriculum vitae
   

Former mentees

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

Attila Nemeth - Short CV

since 2016 Staff Scientist - IMB Mainz (Germany), Developmental Epigenomics Group

2012 - 2016

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

 

22) Filarsky M.*, Zillner K.*, Araya I.*, Villar-Garea A., Merkl R., Längst G.#, Németh A.# (2015) The extended AT-hook is a novel RNA binding motif. RNA Biol 12, 2015 Jul 9:0. [Epub ahead of print]

 

21) Zillner K., Komatsu J., Filarsky K., Kalepu R., Bensimon A., Németh A. (2015). Active human nucleolar organizer regions are interspersed with inactive rDNA repeats in normal and tumor cells. Epigenomics 7, 363-78

 

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, e1004505

 

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.

contact

Dr. Attila Nemeth

Staff Scientist
Developmental Epigenomics - Tiwari Group
Institute of Molecular Biology GmbH
Ackermannweg 4
55128 Mainz
Germany

Phone: +49 (0) 6131-39-21461
Fax: +49 (0) 6131-39-21521
Email: a.nemeth@imb.de 

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

Attila Németh

 

Nemeth Attila

a.nemeth@imb.de
+49 (0)6131-39-21461
IMB Mainz