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Integration of RNA Biology for Next-Generation Scientists

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Publications

PENGUINN: Precise Exploration of Nuclear G-Quadruplexes Using Interpretable Neural Networks

Author(s): Eva Klimentova, Jakub Polacek, Petr Simecek, Panagiotis Alexiou
Published in: Frontiers in Genetics, Issue 11, 2020, ISSN 1664-8021
DOI: 10.3389/fgene.2020.568546

The role of RNA adenosine demethylases in the control of gene expression

Author(s): Veronika Rajecka, Tomas Skalicky, Stepanka Vanacova
Published in: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Issue 1862/3, 2019, Page(s) 343-355, ISSN 1874-9399
DOI: 10.1016/j.bbagrm.2018.12.001

Telomerase RNAs in land plants

Author(s): Petr Fajkus, Vratislav Peška, Michal Závodník, Miloslava Fojtová, Jana Fulnečková, Šimon Dobias, Agata Kilar, Martina Dvořáčková, Dagmar Zachová, Ivona Nečasová, Jason Sims, Eva Sýkorová, Jiří Fajkus
Published in: Nucleic Acids Research, Issue 47/18, 2019, Page(s) 9842-9856, ISSN 0305-1048
DOI: 10.1093/nar/gkz695

CDK11 is required for transcription of replication-dependent histone genes

Author(s): Pavla Gajdušková, Igor Ruiz de los Mozos, Michal Rájecký, Milan Hluchý, Jernej Ule, Dalibor Blazek
Published in: Nature Structural & Molecular Biology, Issue 27/5, 2020, Page(s) 500-510, ISSN 1545-9993
DOI: 10.1038/s41594-020-0406-8

Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA

Author(s): Petra Školáková, Zahra Badri, Silvie Foldynová-Trantírková, Jan Ryneš, Jiří Šponer, Miloslava Fojtová, Jiří Fajkus, Radek Marek, Michaela Vorlíčková, Jean-Louis Mergny, Lukáš Trantírek
Published in: Biochimica et Biophysica Acta (BBA) - General Subjects, Issue 1864/9, 2020, Page(s) 129651, ISSN 0304-4165
DOI: 10.1016/j.bbagen.2020.129651

Telomeres in Plants and Humans: Not So Different, Not So Similar

Author(s): Petra Procházková Schrumpfová, Miloslava Fojtová, Jiří Fajkus
Published in: Cells, Issue 8/1, 2019, Page(s) 58, ISSN 2073-4409
DOI: 10.3390/cells8010058

Different Modes of Action of Genetic and Chemical Downregulation of Histone Deacetylases with Respect to Plant Development and Histone Modifications

Author(s): Gabriela Lochmanová, Ivana Ihnatová, Hana Kuchaříková, Sylva Brabencová, Dagmar Zachová, Jiří Fajkus, Zbyněk Zdráhal, Miloslava Fojtová
Published in: International Journal of Molecular Sciences, Issue 20/20, 2019, Page(s) 5093, ISSN 1422-0067
DOI: 10.3390/ijms20205093

Functional Characterization of SMG7 Paralogs in Arabidopsis thaliana

Author(s): Claudio Capitao, Neha Shukla, Aneta Wandrolova, Ortrun Mittelsten Scheid, Karel Riha
Published in: Frontiers in Plant Science, Issue 9, 2018, ISSN 1664-462X
DOI: 10.3389/fpls.2018.01602

Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy

Author(s): Sona Valuchova, Pavlina Mikulkova, Jana Pecinkova, Jana Klimova, Michal Krumnikl, Petr Bainar, Stefan Heckmann, Pavel Tomancak, Karel Riha
Published in: eLife, Issue 9, 2020, ISSN 2050-084X
DOI: 10.7554/elife.52546

No Evidence of Persistence or Inheritance of Mitochondrial DNA Copy Number in Holocaust Survivors and Their Descendants

Author(s): Na Cai, Monika Fňašková, Klára Konečná, Miloslava Fojtová, Jiří Fajkus, Eve Coomber, Stephen Watt, Nicole Soranzo, Marek Preiss, Ivan Rektor
Published in: Frontiers in Genetics, Issue 11, 2020, ISSN 1664-8021
DOI: 10.3389/fgene.2020.00087

The role of 3′ end uridylation in RNA metabolism and cellular physiology

Author(s): Dagmar Zigáčková, Štěpánka Vaňáčová
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, Issue 373/1762, 2018, Page(s) 20180171, ISSN 0962-8436
DOI: 10.1098/rstb.2018.0171

CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes

Author(s): Anil Paul Chirackal Manavalan, Kveta Pilarova, Michael Kluge, Koen Bartholomeeusen, Michal Rajecky, Jan Oppelt, Prashant Khirsariya, Kamil Paruch, Lumir Krejci, Caroline C Friedel, Dalibor Blazek
Published in: EMBO reports, Issue 20/9, 2019, ISSN 1469-221X
DOI: 10.15252/embr.201847592

The plant Pontin and Reptin homologues, Ruv BL 1 and Ruv BL 2a, colocalize with TERT and TRB proteins in vivo , and participate in telomerase biogenesis

Author(s): Šárka Schořová, Jiří Fajkus, Lenka Záveská Drábková, David Honys, Petra Procházková Schrumpfová
Published in: The Plant Journal, Issue 98/2, 2019, Page(s) 195-212, ISSN 0960-7412
DOI: 10.1111/tpj.14306

Adar RNA editing-dependent and -independent effects are required for brain and innate immune functions in Drosophila

Author(s): Patricia Deng, Anzer Khan, Dionna Jacobson, Nagraj Sambrani, Leeanne McGurk, Xianghua Li, Aswathy Jayasree, Jan Hejatko, Galit Shohat-Ophir, Mary A. O’Connell, Jin Billy Li, Liam P. Keegan
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
DOI: 10.1038/s41467-020-15435-1

ADAR RNA editing in innate immune response phasing, in circadian clocks and in sleep

Author(s): Ketty Sinigaglia, Dagmara Wiatrek, Anzer Khan, David Michalik, Nagraj Sambrani, Jiří Sedmík, Dragana Vukić, Mary A. O'Connell, Liam P. Keegan
Published in: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Issue 1862/3, 2019, Page(s) 356-369, ISSN 1874-9399
DOI: 10.1016/j.bbagrm.2018.10.011

Molecular characterization of Chlamydomonas reinhardtii telomeres and telomerase mutants

Author(s): Stephan Eberhard, Sona Valuchova, Julie Ravat, Jaroslav Fulneček, Pascale Jolivet, Sandrine Bujaldon, Stéphane D Lemaire, Francis-André Wollman, Maria Teresa Teixeira, Karel Riha, Zhou Xu
Published in: Life Science Alliance, Issue 2/3, 2019, Page(s) e201900315, ISSN 2575-1077
DOI: 10.26508/lsa.201900315

The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity

Author(s): Fionna E. Loughlin, Peter J. Lukavsky, Tamara Kazeeva, Stefan Reber, Eva-Maria Hock, Martino Colombo, Christine Von Schroetter, Phillip Pauli, Antoine Cléry, Oliver Mühlemann, Magdalini Polymenidou, Marc-David Ruepp, Frédéric H.-T. Allain
Published in: Molecular Cell, Issue 73/3, 2019, Page(s) 490-504.e6, ISSN 1097-2765
DOI: 10.1016/j.molcel.2018.11.012

Cancer-Associated Substitutions in RNA Recognition Motifs of PUF60 and U2AF65 Reveal Residues Required for Correct Folding and 3′ Splice-Site Selection

Author(s): Jana Kralovicova, Ivana Borovska, Monika Kubickova, Peter J. Lukavsky, Igor Vorechovsky
Published in: Cancers, Issue 12/7, 2020, Page(s) 1865, ISSN 2072-6694
DOI: 10.3390/cancers12071865

Holocaust history is not reflected in telomere homeostasis in survivors and their offspring

Author(s): Klára Konečná, Martin Lyčka, Lucie Nohelová, Monika Petráková, Monika Fňašková, Eva Koriťáková, Pavla Polanská Sováková, Sylva Brabencová, Marek Preiss, Ivan Rektor, Jiří Fajkus, Miloslava Fojtová
Published in: Journal of Psychiatric Research, Issue 117, 2019, Page(s) 7-14, ISSN 0022-3956
DOI: 10.1016/j.jpsychires.2019.06.018

RNA methylation in nuclear pre-mRNA processing

Author(s): Helena Covelo-Molares, Marek Bartosovic, Stepanka Vanacova
Published in: Wiley Interdisciplinary Reviews: RNA, Issue 9/6, 2018, Page(s) e1489, ISSN 1757-7004
DOI: 10.1002/wrna.1489

Activation of innate immunity by mitochondrial dsRNA in mouse cells lacking p53 protein

Author(s): Dagmara M. Wiatrek, Maria E. Candela, Jiří Sedmík, Jan Oppelt, Liam P. Keegan, Mary A. O'Connell
Published in: RNA, Issue 25/6, 2019, Page(s) 713-726, ISSN 1355-8382
DOI: 10.1261/rna.069625.118

artMAP: A user-friendly tool for mapping ethyl methanesulfonate-induced mutations in Arabidopsis

Author(s): Peter Javorka, Vivek K. Raxwal, Jan Najvarek, Karel Riha
Published in: Plant Direct, Issue 3/6, 2019, Page(s) e00146, ISSN 2475-4455
DOI: 10.1002/pld3.146

Roles of RAD 51 and RTEL 1 in telomere and rDNA stability in Physcomitrella patens

Author(s): Ivana Goffová, Radka Vágnerová, Vratislav Peška, Michal Franek, Kateřina Havlová, Marcela Holá, Dagmar Zachová, Miloslava Fojtová, Andrew Cuming, Yasuko Kamisugi, Karel J. Angelis, Jiří Fajkus
Published in: The Plant Journal, 2019, ISSN 0960-7412
DOI: 10.1111/tpj.14304

Replication of ribosomal DNA in Arabidopsis occurs both inside and outside the nucleolus during S phase progression

Author(s): Martina Dvořáčková, Berta Raposo, Petr Matula, Joerg Fuchs, Veit Schubert, Vratislav Peška, Bénédicte Desvoyes, Crisanto Gutierrez, Jiří Fajkus
Published in: Journal of Cell Science, Issue 131/2, 2018, Page(s) jcs202416, ISSN 0021-9533
DOI: 10.1242/jcs.202416

Nonsense-Mediated RNA Decay Factor UPF1 Is Critical for Posttranscriptional and Translational Gene Regulation in Arabidopsis

Author(s): Vivek K. Raxwal, Craig G. Simpson, Jiradet Gloggnitzer, Juan Carlos Entinze, Wenbin Guo, Runxuan Zhang, John W.S. Brown, Karel Riha
Published in: The Plant Cell, Issue 32/9, 2020, Page(s) 2725-2741, ISSN 1040-4651
DOI: 10.1105/tpc.20.00244

Composition and Function of Telomerase—A Polymerase Associated with the Origin of Eukaryotes

Author(s): Petra Procházková Schrumpfová, Jiří Fajkus
Published in: Biomolecules, Issue 10/10, 2020, Page(s) 1425, ISSN 2218-273X
DOI: 10.3390/biom10101425

Bi-allelic ADARB1 Variants Associated with Microcephaly, Intellectual Disability, and Seizures

Author(s): Tiong Yang Tan, Jiří Sedmík, Mark P. Fitzgerald, Rivka Sukenik Halevy, Liam P. Keegan, Ingo Helbig, Lina Basel-Salmon, Lior Cohen, Rachel Straussberg, Wendy K. Chung, Mayada Helal, Reza Maroofian, Henry Houlden, Jane Juusola, Simon Sadedin, Lynn Pais, Katherine B. Howell, Susan M. White, John Christodoulou, Mary A. O’Connell
Published in: The American Journal of Human Genetics, Issue 106/4, 2020, Page(s) 467-483, ISSN 0002-9297
DOI: 10.1016/j.ajhg.2020.02.015

Biallelic variants in ADARB1 , encoding a dsRNA-specific adenosine deaminase, cause a severe developmental and epileptic encephalopathy

Author(s): Reza Maroofian, Jiří Sedmík, Neda Mazaheri, Marcello Scala, Maha S Zaki, Liam P Keegan, Reza Azizimalamiri, Mahmoud Issa, Gholamreza Shariati, Alireza Sedaghat, Christian Beetz, Peter Bauer, Hamid Galehdari, Mary A O’Connell, Henry Houlden
Published in: Journal of Medical Genetics, 2020, Page(s) jmedgenet-2020-107048, ISSN 0022-2593
DOI: 10.1136/jmedgenet-2020-107048

Telomere elongation upon transfer to callus culture reflects the reprogramming of telomere stability control in Arabidopsis

Author(s): Pavla Polanská Sováková, Alžbeta Magdolenová, Klára Konečná, Veronika Rájecká, Jiří Fajkus, Miloslava Fojtová
Published in: Plant Molecular Biology, Issue 98/1-2, 2018, Page(s) 81-99, ISSN 0167-4412
DOI: 10.1007/s11103-018-0765-2

Human-like telomeres in Zostera marina reveal a mode of transition from the plant to the human telomeric sequences

Author(s): Vratislav Peska, Martin Mátl, Terezie Mandáková, Daniel Vitales, Petr Fajkus, Jiří Fajkus, Sònia Garcia
Published in: Journal of Experimental Botany, Issue 71/19, 2020, Page(s) 5786-5793, ISSN 0022-0957
DOI: 10.1093/jxb/eraa293

Multi-branch Convolutional Neural Network for Identification of Small Non-coding RNA genomic loci

Author(s): Georgios K. Georgakilas, Andrea Grioni, Konstantinos G. Liakos, Eliska Chalupova, Fotis C. Plessas, Panagiotis Alexiou
Published in: Scientific Reports, Issue 10/1, 2020, ISSN 2045-2322
DOI: 10.1038/s41598-020-66454-3

CDK9 activity is critical for maintaining MDM4 overexpression in tumor cells

Author(s): Monika Štětková, Kateřina Growková, Petr Fojtík, Barbora Valčíková, Veronika Palušová, Amandine Verlande, Radek Jorda, Vladimír Kryštof, Václav Hejret, Panagiotis Alexiou, Vladimír Rotrekl, Stjepan Uldrijan
Published in: Cell Death & Disease, Issue 11/9, 2020, ISSN 2041-4889
DOI: 10.1038/s41419-020-02971-3

Two combinatorial patterns of telomere histone marks in plants with canonical and non‐canonical telomere repeats

Author(s): Kateřina Adamusová, Solmaz Khosravi, Satoru Fujimoto, Andreas Houben, Sachihiro Matsunaga, Jiří Fajkus, Miloslava Fojtová
Published in: The Plant Journal, Issue 102/4, 2020, Page(s) 678-687, ISSN 0960-7412
DOI: 10.1111/tpj.14653

Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum

Author(s): Vratislav Peška, Terezie Mandáková, Veronika Ihradská, Jiří Fajkus
Published in: International Journal of Molecular Sciences, Issue 20/3, 2019, Page(s) 733, ISSN 1422-0067
DOI: 10.3390/ijms20030733

Membrane and synaptic defects leading to neurodegeneration in Adar mutant Drosophila are rescued by increased autophagy

Author(s): Anzer Khan, Simona Paro, Leeanne McGurk, Nagraj Sambrani, Marion C. Hogg, James Brindle, Giuseppa Pennetta, Liam P. Keegan, Mary A. O’Connell
Published in: BMC Biology, Issue 18/1, 2020, ISSN 1741-7007
DOI: 10.1186/s12915-020-0747-0

Rituximab primarily targets an intra-clonal BCR signaling proficient CLL subpopulation characterized by high CD20 levels

Author(s): Gabriela Pavlasova, Marek Borsky, Veronika Svobodova, Jan Oppelt, Katerina Cerna, Jitka Novotna, Vaclav Seda, Miloslava Fojtova, Jiri Fajkus, Yvona Brychtova, Michael Doubek, Sarka Pospisilova, Jiri Mayer, Marek Mraz
Published in: Leukemia, Issue 32/9, 2018, Page(s) 2028-2031, ISSN 0887-6924
DOI: 10.1038/s41375-018-0211-0

Visualization of the Nucleolus Using Ethynyl Uridine

Author(s): Martina Dvořáčková, Jiří Fajkus
Published in: Frontiers in Plant Science, Issue 9, 2018, ISSN 1664-462X
DOI: 10.3389/fpls.2018.00177

DIS3L2 and LSm proteins are involved in the surveillance of Sm ring-deficient snRNAs

Author(s): Adriana Roithová, Zuzana Feketová, Štěpánka Vaňáčová, David Staněk
Published in: Nucleic Acids Research, Issue 48/11, 2020, Page(s) 6184-6197, ISSN 0305-1048
DOI: 10.1093/nar/gkaa301

G4 Structures in Control of Replication and Transcription of rRNA Genes

Author(s): Kateřina Havlová, Jiří Fajkus
Published in: Frontiers in Plant Science, Issue 11, 2020, ISSN 1664-462X
DOI: 10.3389/fpls.2020.593692

Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition

Author(s): Deepak Kumar Yadav, Dagmar Zigáčková, Maria Zlobina, Tomáš Klumpler, Christelle Beaumont, Monika Kubíčková, Štěpánka Vaňáčová, Peter J Lukavsky
Published in: Nucleic Acids Research, Issue 48/4, 2019, Page(s) 2091-2106, ISSN 0305-1048
DOI: 10.1093/nar/gkz1163