Research topics
In diploid mammalian cells, some 6x109 base pairs of DNA fold as a nucleo-protein complex (i.e. chromatin) into higher-order arrays so as to fit in a nucleus measuring only 10 µm. The nucleus also contains machineries for transcription of genes and processing of RNA products, and for precise DNA replication, repair and recombination. Nuclear interior is therefore functionally highly compartmentalized, and the recent evidence points strongly to structure-related regulation of nuclear functions - however, the mechanisms forming the 3D-structure of the nucleus are still mostly obscure. We therefore employ a multi-disciplinary approach in order to study nuclear functions in relation to the higher-order nuclear structures, e.g. nuclear bodies, the nucleolus, and the nucleoskeleton. Our research concentrates on:
The relationship between nuclear compartmentalization and regulation of gene expression.
Structure, dynamics, and function of the nucleoskeleton, which might direct nuclear compartmentalization.
Functions of nuclear myosin I, actin and actin-binding proteins in transcription and gene expression.
Development of new microscopy methods for ultrastructural studies.
Current grant support
Grant Agency of the Academy of Sciences of the Czech Republic (grant: The role of PML in cellular senescence, No. IAA500390501)
Academy of Sciences of the Czech Republic (grant: New nanoparticles for ultrastructural diagnostics, No. KAN200520704)
Grant Agency of the Czech Republic (grant: Function of nuclear myosin in gene expression, No. GA204/07/1592, and grant: Molecular biology of differentiating cell, No. 204/09/H084)
Ministry of Education, Youth and Sports of the Czech Republic (grant: Center of Functional Organization of the Cell, No.: LC 545; grant: Flurescence Microscopy in Biological and Medical Research, No. LC06063; grant: Structure and irregularities of the nucleoskeleton: identification and diagnostic, No.: 2B06063)
Ministry of Industry and Trade of the Czech Republic (grant: Development of a kit for detection of mutations in structural proteins of a cell, No. FR-TI3/588)
FEI (grant: Ultrastructural investigation of vinculin functions in the cell nucleus - Stipendium)
Most important recent papers
(2004-present; names of the lab members underlined)Philimonenko AA, Jackson DA, Hodny Z, Janacek J, Cook PR, Hozak P. Dynamics of DNA replication: an ultrastructural study. J Struct Biol 148(3): 279-89, 2004. (Pubmed) (DOI)
Hofmann WA, Stojiljkovic L, Fuchsova B, Vargas GM, Mavrommatis E, Philimonenko V, Kysela K, Goodrich JA, Lessard JL, Hope TJ, Hozak P, de Lanerolle P. Actin is part of pre-initiation complexes and is necessary for transcription by RNA polymerase II. Nat Cell Biol 6(11): 1094-101, 2004. (Pubmed) (DOI)
Kysela K, Philimonenko AA, Philimonenko VV, Janacek J, Kahle M, Hozak P. Nuclear distribution of actin and myosin I depends on transcriptional activity of the cell. Histochem Cell Biol 124(5): 347-58, 2005. (Pubmed) (DOI)
Philimonenko AA, Hodny Z, Jackson DA, Hozak P. The microarchitecture of DNA replication domains. Histochem Cell Biol 125(1-2): 103-17, 2006. (Pubmed) (DOI)
Kahle M, Pridalova J, Spacek M, Dzijak R, Hozak P. Nuclear myosin is ubiquitously expressed and evolutionary conserved in vertebrates. Histochem Cell Biol 127(2): 139-48, 2007. (Pubmed) (DOI)
Novakova Z, Man P, Novak P, Hozak P, Hodny Z. Separation of nuclear protein complexes by blue native polyacrylamide gel electrophoresis. Electrophoresis 27(7): 1277-87, 2006. (Pubmed) (DOI)
Vlasakova J, Novakova Z, Rossmeislova L, Kahle M, Hozak P, Hodny Z. Histone deacetylase inhibitors suppress IFNalpha-induced up-regulation of promyelocytic leukemia protein. Blood 109(4): 1373-80, 2007. (Pubmed) (DOI)
Janderova-Rossmeislova L, Novakova Z, Vlasakova J, Philimonenko V, Hozak P, Hodny Z. PML protein association with specific nucleolar structures differs in normal, tumor and senescent human cells. J Struct Biol 159(1): 56-70, 2007. (Pubmed) (DOI)
Fulka H, St John JC, Fulka J, Hozak P. Chromatin in early mammalian embryos: achieving the pluripotent state. Differentiation 76(1): 3-14, 2008. (Pubmed) (DOI)
Stradalova V, Gaplovska-Kysela K, Hozak P. Ultrastructural and nuclear antigen preservation after high-pressure freezing/freeze-substitution and low-temperature LR White embedding of HeLa cells. Histochem Cell Biol 130(5): 1047-52, 2008. (Pubmed) (DOI)
Ogushi S, Palmieri C, Fulka H, Saitou M, Miyano T, Fulka J Jr. The maternal nucleolus is essential for early embryonic development in mammals. Science 319(5863): 613-6, 2008. (Pubmed) (DOI)
Dingova H, Fukalova J, Maninova M, Philimonenko VV, Hozak P. Ultrastructural localization of actin and actin-binding proteins in the nucleus. Histochem Cell Biol 131(3): 425-34, 2009. (Pubmed) (DOI)
Novakova Z, Hubackova S, Kosar M, Janderova-Rossmeislova L, Dobrovolna J, Vasicova P, Vancurova M, Horejsi Z, Hozak P, Bartek J, Hodny Z. Cytokine expression and signaling in drug-induced cellular senescence. Oncogene 29(2): 273-84, 2010. (Pubmed) (DOI)
Sobol M, Nebesarova J, Hozak P. A method for preserving ultrastructural properties of mitotic cells for subsequent immunogold labeling using low-temperature embedding in LR White resin. Histochem Cell Biol 135(1): 103-10, 2011. (Pubmed) (DOI)
Sobol M, Philimonenko VV, Hozak P. Comparison of methods of high-pressure freezing and automated freeze-substitution of suspension cells combined with LR White embedding. Histochem Cell Biol 134(6): 631-41, 2010. (Pubmed) (DOI)
Philimonenko AA, Janacek J, Snyers L, Almeder M, Berger W, Schmidt W, Schofer C, Hozak P, Weipoltshammer K. Chromosomal dynamics of cell cycle regulator gene p21 during transcriptional activation. J Struct Biol 173(2): 382-90, 2011. (Pubmed) (DOI)
Philimonenko VV, Janacek J, Harata M, Hozak P. Transcription-dependent rearrangements of actin and nuclear myosin I in the nucleolus. Histochem Cell Biol 134(3): 243-9, 2010. (Pubmed) (DOI)
Reviews
Castano E, Philimonenko VV, Kahle M, Fukalova J, Kalendova A, Yildirim S, Dzijak R, Dingova-Krasna H, Hozak P. Actin complexes in the cell nucleus: new stones in an old field. Histochem Cell Biol 133(6): 607-26, 2010. (Pubmed) (DOI)
Teaching, lectures, public presentations
Acquisition and Processing of the Image in Microscopy - (link)
Transmission elektron microscopy in life science - (link)
PhD Educative project GA ČR "Molecular biology of a differentiating cell" - (link)
Microscopy immunodetection in biomedicine - (link)