Petr Svoboda

Summary

Affiliation: Institute of Molecular Genetics
Country: Czech Republic

Publications

  1. ncbi request reprint Transgenic RNAi reveals essential function for CTCF in H19 gene imprinting
    Andrew M Fedoriw
    Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
    Science 303:238-40. 2004
  2. ncbi request reprint miRNA, piRNA, siRNA -- Kleine Wiener Ribonukleinsäuren
    Helge Grosshans
    Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
    Bioessays 29:940-3. 2007
  3. ncbi request reprint RNA silencing in mammalian oocytes and early embryos
    Petr Svoboda
    Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
    Curr Top Microbiol Immunol 320:225-56. 2008
  4. doi request reprint Preparation of dsRNA for microinjection experiments in mouse
    Petr Svoboda
    Institute of Molecular Genetics, Academy of Sciences of Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
    Cold Spring Harb Protoc 2009:pdb.prot5131. 2009
  5. ncbi request reprint Clearance of Parental Products
    Petr Svoboda
    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20, Prague 4, Czech Republic
    Adv Exp Med Biol 953:489-535. 2017
  6. doi request reprint Sculpting the Transcriptome During the Oocyte-to-Embryo Transition in Mouse
    Petr Svoboda
    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic Electronic address
    Curr Top Dev Biol 113:305-49. 2015
  7. doi request reprint A toolbox for miRNA analysis
    Petr Svoboda
    Institute of Molecular Genetics of the AS CR, v v i, Videnska 1083, 142 20 Prague 4, Czech Republic Electronic address
    FEBS Lett 589:1694-701. 2015
  8. doi request reprint Renaissance of mammalian endogenous RNAi
    Petr Svoboda
    Institute of Molecular Genetics of the AS CR, v v i, Videnska 1083, 142 20 Prague 4, Czech Republic Electronic address
    FEBS Lett 588:2550-6. 2014
  9. doi request reprint Choosing the sequence of dsRNA for RNAi in mouse
    Petr Svoboda
    Institute of Molecular Genetics, Academy of Sciences of Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
    Cold Spring Harb Protoc 2009:pdb.ip63. 2009
  10. doi request reprint Cloning and sequencing an inverted repeat
    Petr Svoboda
    Institute of Molecular Genetics, Academy of Sciences of Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
    Cold Spring Harb Protoc 2009:pdb.ip64. 2009

Collaborators

Detail Information

Publications38

  1. ncbi request reprint Transgenic RNAi reveals essential function for CTCF in H19 gene imprinting
    Andrew M Fedoriw
    Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
    Science 303:238-40. 2004
    ..Our results suggest that CTCF protects the H19 DMD from de novo methylation during oocyte growth and is required for normal preimplantation development...
  2. ncbi request reprint miRNA, piRNA, siRNA -- Kleine Wiener Ribonukleinsäuren
    Helge Grosshans
    Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
    Bioessays 29:940-3. 2007
  3. ncbi request reprint RNA silencing in mammalian oocytes and early embryos
    Petr Svoboda
    Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
    Curr Top Microbiol Immunol 320:225-56. 2008
    ..This review will discuss possible roles of RNA silencing pathways in mouse oocytes and early embryos as well as the use of RNA silencing for experimental inhibition of gene expression in this model system...
  4. doi request reprint Preparation of dsRNA for microinjection experiments in mouse
    Petr Svoboda
    Institute of Molecular Genetics, Academy of Sciences of Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
    Cold Spring Harb Protoc 2009:pdb.prot5131. 2009
    ..We usually include RNase T1 treatment of the annealed RNA prior to the purification step in order to remove unannealed single-stranded RNA (ssRNA), which can interfere with the quantification of dsRNA in a nondenaturing agarose gel...
  5. ncbi request reprint Clearance of Parental Products
    Petr Svoboda
    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20, Prague 4, Czech Republic
    Adv Exp Med Biol 953:489-535. 2017
    ....
  6. doi request reprint Sculpting the Transcriptome During the Oocyte-to-Embryo Transition in Mouse
    Petr Svoboda
    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic Electronic address
    Curr Top Dev Biol 113:305-49. 2015
    ....
  7. doi request reprint A toolbox for miRNA analysis
    Petr Svoboda
    Institute of Molecular Genetics of the AS CR, v v i, Videnska 1083, 142 20 Prague 4, Czech Republic Electronic address
    FEBS Lett 589:1694-701. 2015
    ..Accordingly, this review provides an elementary roadmap to navigate among available tools for miRNA analysis. The most common problems and errors observed in miRNA research are also discussed. ..
  8. doi request reprint Renaissance of mammalian endogenous RNAi
    Petr Svoboda
    Institute of Molecular Genetics of the AS CR, v v i, Videnska 1083, 142 20 Prague 4, Czech Republic Electronic address
    FEBS Lett 588:2550-6. 2014
    ..Here, I will provide an up-to-date review of the mammalian endogenous RNAi pathway with a focus on its defensive role and overlaps with miRNA and piRNA pathways. ..
  9. doi request reprint Choosing the sequence of dsRNA for RNAi in mouse
    Petr Svoboda
    Institute of Molecular Genetics, Academy of Sciences of Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
    Cold Spring Harb Protoc 2009:pdb.ip63. 2009
    ..RNA interference (RNAi) is a suitable method for sequence-specific post-transcriptional gene silencing for a number of model systems. Here, we describe selection of the target sequence for efficient RNAi knockdown in mouse...
  10. doi request reprint Cloning and sequencing an inverted repeat
    Petr Svoboda
    Institute of Molecular Genetics, Academy of Sciences of Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
    Cold Spring Harb Protoc 2009:pdb.ip64. 2009
    ..Although we have successfully sequenced IRs using both strategies, we suggest using the latter to sequence transgenic constructs...
  11. doi request reprint Cloning a transgene for transgenic RNAi in mouse oocytes
    Petr Svoboda
    Institute of Molecular Genetics, Academy of Sciences of Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
    Cold Spring Harb Protoc 2009:pdb.prot5134. 2009
    ..Subsequently, the IR is cloned, inserted into the transgenic cassette, and characterized by sequencing. Finally, the transgene is released from the cassette, purified, and provided to the transgenic facility...
  12. doi request reprint RNAi experiments in mouse oocytes and early embryos
    Petr Svoboda
    Institute of Molecular Genetics, Academy of Sciences of Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
    Cold Spring Harb Protoc 2009:pdb.top56. 2009
    ....
  13. pmc The role of miRNAs and endogenous siRNAs in maternal-to-zygotic reprogramming and the establishment of pluripotency
    Petr Svoboda
    Institute of Molecular Genetics AS CR, Praha, Czech Republic
    EMBO Rep 11:590-7. 2010
    ....
  14. pmc Why mouse oocytes and early embryos ignore miRNAs?
    Petr Svoboda
    Institute of Molecular Genetics AS CR, Prague, Czech Republic
    RNA Biol 7:559-63. 2010
    ..Here, I discuss how and why mouse oocytes and early embryos ignore the regulatory power of miRNAs, adding another surprising feature to the field of small RNAs...
  15. ncbi request reprint Off-targeting and other non-specific effects of RNAi experiments in mammalian cells
    Petr Svoboda
    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
    Curr Opin Mol Ther 9:248-57. 2007
    ..The causes of non-specific effects and possible approaches to minimize them are discussed in this review...
  16. doi request reprint A retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes
    Matyas Flemr
    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
    Cell 155:807-16. 2013
    ..The alternative Dicer isoform, whose phylogenetic origin demonstrates evolutionary plasticity of RNA-silencing pathways, is the main determinant of endogenous RNAi activity in the mouse female germline. ..
  17. pmc Shortcomings of short hairpin RNA-based transgenic RNA interference in mouse oocytes
    Lenka Sarnova
    Department of Epigenetic Regulations, Institute of Molecular Genetics of the AS CR, Videnska 1083, CZ 14220 Prague 4, Czech Republic
    J Negat Results Biomed 9:8. 2010
    ..Transgenic RNAi in mouse oocytes based on a shRNA offers several potential advantages, including simple cloning of the transgenic vector and an ability to use the same targeting construct in any cell type...
  18. pmc dsRNA expression in the mouse elicits RNAi in oocytes and low adenosine deamination in somatic cells
    Jana Nejepinska
    Institute of Molecular Genetics AS CR, Videnska 1083, 14220 Prague 4, Czech Republic
    Nucleic Acids Res 40:399-413. 2012
    ..RNA editing neither prevented the cytoplasmic localization nor processing into siRNAs. Thus, a long dsRNA structure is well tolerated in mammalian cells and is mainly causing a robust RNAi response in oocytes...
  19. doi request reprint Control of the interferon response in RNAi experiments
    Jana Nejepinska
    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
    Methods Mol Biol 820:133-61. 2012
    ..The aim of this text is to provide theoretical and practical information for scientists who want to control interferon response and other adverse effects in their RNAi experiments...
  20. doi request reprint Production and application of long dsRNA in mammalian cells
    Katerina Chalupníková
    Institute of Molecular Genetics AS CR, Prague, Czech Republic
    Methods Mol Biol 942:291-314. 2013
    ..We present an overview of currently available vectors for dsRNA expression and provide the latest update on oocyte-specific transgenic RNAi approaches...
  21. ncbi request reprint The activity of inducible nitric oxide synthase in rejected skin xenografts is selectively inhibited by a factor produced by grafted cells
    Vladimir Holan
    Institute of Molecular Genetics, Academy of Sciences, Prague, Czech Republic
    Xenotransplantation 12:227-34. 2005
    ..However, whether NO plays a role in rejection of skin xenografts has not been documented...
  22. doi request reprint Lin28a is dormant, functional, and dispensable during mouse oocyte-to-embryo transition
    Matyas Flemr
    Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
    Biol Reprod 90:131. 2014
    ..Our data imply dual repression of Let-7 during OET in the mouse model, the selective suppression of Let-7 biogenesis by Lin28 homologs superimposed on previously reported global suppression of miRNA activity. ..
  23. doi request reprint Transgenic RNAi in mouse oocytes: the first decade
    Radek Malik
    Institute of Molecular Genetics AS CR, Videnska 1083, Prague, Czech Republic
    Anim Reprod Sci 134:64-8. 2012
    ..This review provides an overview and discusses benefits and drawbacks encountered by us and our colleagues while working with the oocytes-specific transgenic RNAi system...
  24. pmc Deep sequencing reveals complex spurious transcription from transiently transfected plasmids
    Jana Nejepinska
    Institute of Molecular Genetics AS CR, Prague, Czech Republic
    PLoS ONE 7:e43283. 2012
    ..The unexpected complexity of expression from transiently transfected plasmids underscores the importance of appropriate experimental controls...
  25. doi request reprint Ribonucleoprotein localization in mouse oocytes
    Matyas Flemr
    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
    Methods 53:136-41. 2011
    ..Application of these techniques to whole-mount fixed oocytes and early embryos can provide information about RNP composition and localization with three-dimensional resolution...
  26. pmc P-body loss is concomitant with formation of a messenger RNA storage domain in mouse oocytes
    Matyas Flemr
    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
    Biol Reprod 82:1008-17. 2010
    ..We propose that the cortex of growing oocytes serves as an mRNA storage compartment, which contains a novel type of RNA granule related to P-bodies...
  27. pmc Reporters transiently transfected into mammalian cells are highly sensitive to translational repression induced by dsRNA expression
    Jana Nejepinska
    Institute of Molecular Genetics of the ASCR, v v i, Prague, Czech Republic
    PLoS ONE 9:e87517. 2014
    ..Thus, dsRNA expression represents a hidden danger in transient transfection experiments and must be taken into account during interpretation of experimental results...
  28. pmc Nuclear LSm8 affects number of cytoplasmic processing bodies via controlling cellular distribution of Like-Sm proteins
    Ivan Novotny
    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
    Mol Biol Cell 23:3776-85. 2012
    ....
  29. doi request reprint Fluorescence-based high-throughput screening of dicer cleavage activity
    Katerina Podolska
    1Institute of Molecular Genetics of the ASCR, v v i, Prague 4, Czech Republic
    J Biomol Screen 19:417-26. 2014
    ..As a proof of principle, a small library of bioactive compounds was analyzed, demonstrating potential of the assay. ..
  30. doi request reprint Targeting genes in living mammals by RNA interference
    Katerina Podolska
    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska, Prague, Czech Republic
    Brief Funct Genomics 10:238-47. 2011
    ....
  31. pmc Impaired noradrenaline-induced lipolysis in white fat of aP2-Ucp1 transgenic mice is associated with changes in G-protein levels
    Pavel Flachs
    Department of Adipose Tissue Biology and Center for Integrated Genomics, Institute of Physiology, Academy of Sciences of the Czech Republic, Vídenská 1803, 142 20 Prague, Czech Republic
    Biochem J 364:369-76. 2002
    ..They also demonstrate changes at the G-protein level that tend to overcome the reduction of lipolysis when ATP level in adipocytes is low. Therefore, respiratory uncoupling may exert a broad effect on hormonal signalling in adipocytes...
  32. pmc RNAi: mammalian oocytes do it without RNA-dependent RNA polymerase
    Paula Stein
    Department of Biology, University of Pennsylvania, 415 South University Avenue, Philadelphia, PA 19104 6018, USA
    RNA 9:187-92. 2003
    ..These results indicate that an RdRp is not involved in dsRNA-mediated mRNA degradation in mammalian oocytes, and possibly in mammals in general, and therefore that only homologous sequences to the dsRNA are targeted for degradation...
  33. ncbi request reprint Transgenic RNAi in mouse oocytes: a simple and fast approach to study gene function
    Paula Stein
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 6018, USA
    Dev Biol 256:187-93. 2003
    ..This approach provides a powerful method to study the functions of any oocyte-synthesized gene during oocyte development and early embryogenesis...
  34. pmc Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells
    Daniela Schmitter
    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4002 Basel, Switzerland
    Nucleic Acids Res 34:4801-15. 2006
    ..Taken together, our data suggest that, independent of the effect on translation, miRNAs affect levels of a few hundred mRNAs in HEK293 cells...
  35. pmc Maternal BRG1 regulates zygotic genome activation in the mouse
    Scott J Bultman
    Department of Genetics and the Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    Genes Dev 20:1744-54. 2006
    ..Depletion of maternal BRG1 did not affect global levels of histone acetylation, whereas dimethyl-H3K4 levels were reduced. These data provide a framework for understanding the mechanism of ZGA...
  36. ncbi request reprint Abundant transcripts from retrotransposons are unstable in fully grown mouse oocytes
    Mareike Puschendorf
    Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
    Biochem Biophys Res Commun 347:36-43. 2006
    ....
  37. pmc Lack of homologous sequence-specific DNA methylation in response to stable dsRNA expression in mouse oocytes
    Petr Svoboda
    Friedrich Miescher Institute for Biomedical Research, PO Box 2543, 4002 Basel, Switzerland
    Nucleic Acids Res 32:3601-6. 2004
    ..These data demonstrate that dsRNA does not directly induce DNA methylation in the trans form of this sequence in these mammalian cells...
  38. ncbi request reprint RNAi and expression of retrotransposons MuERV-L and IAP in preimplantation mouse embryos
    Petr Svoboda
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 6018, USA
    Dev Biol 269:276-85. 2004
    ....