Integration of RNA Biology for Next-Generation Scientists

Risultati finali

Final impact assessment report on CEITEC MU scientific excellence

CEITEC´s Strategy and R&D Support Office set the baseline for the 3 main KPIs related to the scientific excellence of the project outputs (publications of involved researchers from CEITEC MU in T10, publications realized in cooperation between Twinning partners, publications in Q1 where the first author is a PhD student from CEITEC MU whose supervisor belongs to the Twinning research team). The baseline will be compared in the final assessment report (M36). We will also add to the report KPIs that will count the specific project activities (outgoing ESR secondments, outward researchers secondments, inward researchers secondments).

Dissemination and Communication Plan

Comprehensive plan for the dissemination and communication activities

A list of desirable skills based on self-reflection within postdoc peer groups

Document that contains self-reflect of career-related topics and a list of desirable skills to tackle various career paths. This document will be produced by postdocs involved in project who will meet during Career Café Live (T3.3.) and Postdoc retreats (T3.5.). It will be disseminated through the project website and publicly available.

Mid-term impact assessment report on CEITEC MU excellence

CEITEC´s Strategy and R&D Support Office set the baseline for the 3 main KPIs related to the scientific excellence of the project outputs (publications of involved researchers from CEITEC MU in T10, publications realized in cooperation between Twinning partners, publications in Q1 where the first author is a PhD student from CEITEC MU whose supervisor belongs to the Twinning research team). The baseline will be compared in the mid-assessment report (M18).We will also add to the report KPIs that will count the specific project activities (outgoing ESR secondments, outward researchers secondments, inward researchers secondments).

A list of desirable skills based on self-reflection within ESRs groups

Project website and social media sites

Launched project website for the INTEGRNA

Podcast Interviews with the alumni

We will have in total 12 virtual career cafés. 6 alumni will be asked to participate in the podcast where they elaborate on specific career topics. The podcasts are planned to be released twice per year (M6, M12, M18, M24, M30, and M36). CEITEC MU will be in charge of 2 of those podcasts, while each partner will provide 1.

Pubblicazioni

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

Autori: Eva Klimentova, Jakub Polacek, Petr Simecek, Panagiotis Alexiou
Pubblicato in: Frontiers in Genetics, Numero 11, 2020, ISSN 1664-8021
Editore: Frontiers Media
DOI: 10.3389/fgene.2020.568546

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

Autori: Veronika Rajecka, Tomas Skalicky, Stepanka Vanacova
Pubblicato in: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Numero 1862/3, 2019, Pagina/e 343-355, ISSN 1874-9399
Editore: Elsevier BV
DOI: 10.1016/j.bbagrm.2018.12.001

Telomerase RNAs in land plants

Autori: 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
Pubblicato in: Nucleic Acids Research, Numero 47/18, 2019, Pagina/e 9842-9856, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkz695

S. HITS-CLIP Analysis of Human ALKBH8 Reveals Interactions with Fully Processed Substrate tRNAs and with Specific Noncoding RNAs

Autori: Cavallin, I.; Bartosovic, M.; Skalicky, T.; Rengaraj, P.; Demko, M.; Schmidt-Dengler, M. C.; Drino, A.; Helm, M.; Vanacova
Pubblicato in: RNA, Numero RNA 2022, 2022, ISSN 1355-8382
Editore: Cold Spring Harbor Laboratory Press
DOI: 10.1261/rna.079421.122

CDK11 is required for transcription of replication-dependent histone genes

Autori: Pavla Gajdušková, Igor Ruiz de los Mozos, Michal Rájecký, Milan Hluchý, Jernej Ule, Dalibor Blazek
Pubblicato in: Nature Structural & Molecular Biology, Numero 27/5, 2020, Pagina/e 500-510, ISSN 1545-9993
Editore: Nature Publishing Group
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

Autori: Petra Školáková, Zahra Badri, Silvie Foldynová-Trantírková, Jan Ryneš, Jiří Šponer, Miloslava Fojtová, Jiří Fajkus, Radek Marek, Michaela Vorlíčková, Jean-Louis Mergny, Lukáš Trantírek
Pubblicato in: Biochimica et Biophysica Acta (BBA) - General Subjects, Numero 1864/9, 2020, Pagina/e 129651, ISSN 0304-4165
Editore: Elsevier BV
DOI: 10.1016/j.bbagen.2020.129651

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

Autori: Petra Procházková Schrumpfová, Miloslava Fojtová, Jiří Fajkus
Pubblicato in: Cells, Numero 8/1, 2019, Pagina/e 58, ISSN 2073-4409
Editore: MDPI
DOI: 10.3390/cells8010058

FoxO1-GAB1 Axis Regulates Homing Capacity and Tonic AKT Activity in Chronic Lymphocytic Leukemia

Autori: Seda, V.; Vojackova, E.; Ondrisova, L.; Kostalova, L.; Sharma, S.; Loja, T.; Pavlasova, G. M.; Zicha, D.; Peskova, M. K.; Krivanek, J.; Liskova, K.; Kren, L.; Benes, V.; Litzmanova, K. M.; Borsky, M.; Oppelt, J.; Verner, J.; Pospisilova, S.; Brychtova, Y.; Panovska, A.; Tan, Z.; Zhang, S.; Doubek, M.; Cerna, K. A.; Mayer, J.; Mraz, M
Pubblicato in: BLOOD, 2021, ISSN 0006-4971
Editore: American Society of Hematology
DOI: 10.1182/blood.2020008101

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

Autori: Gabriela Lochmanová, Ivana Ihnatová, Hana Kuchaříková, Sylva Brabencová, Dagmar Zachová, Jiří Fajkus, Zbyněk Zdráhal, Miloslava Fojtová
Pubblicato in: International Journal of Molecular Sciences, Numero 20/20, 2019, Pagina/e 5093, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms20205093

Functional Characterization of SMG7 Paralogs in Arabidopsis thaliana

Autori: Claudio Capitao, Neha Shukla, Aneta Wandrolova, Ortrun Mittelsten Scheid, Karel Riha
Pubblicato in: Frontiers in Plant Science, Numero 9, 2018, ISSN 1664-462X
Editore: Frontiers Media S. A.
DOI: 10.3389/fpls.2018.01602

Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy

Autori: Sona Valuchova, Pavlina Mikulkova, Jana Pecinkova, Jana Klimova, Michal Krumnikl, Petr Bainar, Stefan Heckmann, Pavel Tomancak, Karel Riha
Pubblicato in: eLife, Numero 9, 2020, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.52546

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

Autori: Na Cai, Monika Fňašková, Klára Konečná, Miloslava Fojtová, Jiří Fajkus, Eve Coomber, Stephen Watt, Nicole Soranzo, Marek Preiss, Ivan Rektor
Pubblicato in: Frontiers in Genetics, Numero 11, 2020, ISSN 1664-8021
Editore: Frontiers Media
DOI: 10.3389/fgene.2020.00087

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

Autori: Dagmar Zigáčková, Štěpánka Vaňáčová
Pubblicato in: Philosophical Transactions of the Royal Society B: Biological Sciences, Numero 373/1762, 2018, Pagina/e 20180171, ISSN 0962-8436
Editore: Royal Society of London
DOI: 10.1098/rstb.2018.0171

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

Autori: 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
Pubblicato in: EMBO reports, Numero 20/9, 2019, ISSN 1469-221X
Editore: Nature Publishing Group
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

Autori: Šárka Schořová, Jiří Fajkus, Lenka Záveská Drábková, David Honys, Petra Procházková Schrumpfová
Pubblicato in: The Plant Journal, Numero 98/2, 2019, Pagina/e 195-212, ISSN 0960-7412
Editore: Blackwell Publishing Inc.
DOI: 10.1111/tpj.14306

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

Autori: 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
Pubblicato in: Nature Communications, Numero 11/1, 2020, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-020-15435-1

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

Autori: Ketty Sinigaglia, Dagmara Wiatrek, Anzer Khan, David Michalik, Nagraj Sambrani, Jiří Sedmík, Dragana Vukić, Mary A. O'Connell, Liam P. Keegan
Pubblicato in: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Numero 1862/3, 2019, Pagina/e 356-369, ISSN 1874-9399
Editore: Elsevier BV
DOI: 10.1016/j.bbagrm.2018.10.011

Molecular characterization of Chlamydomonas reinhardtii telomeres and telomerase mutants

Autori: 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
Pubblicato in: Life Science Alliance, Numero 2/3, 2019, Pagina/e e201900315, ISSN 2575-1077
Editore: Life Science Alliance LLC
DOI: 10.26508/lsa.201900315

Hormone-Regulated Expansins: Expression, Localization, and Cell Wall Biomechanics in Arabidopsis Root Growth

Autori: Samalova, M.; Melnikava, A.; Elsayad, K.; Peaucelle, A.; Gahurova, E.; Gumulec, J.; Spyroglou, I.; Zemlyanskaya, E. V.; Ubogoeva, E. V.; Balkova, D.; Demko, M.; Blavet, N.; Alexiou, P.; Benes, V.; Mouille, G.; Hejatko, J.
Pubblicato in: Plant Physiology, 2023, ISSN 0032-0889
Editore: American Society of Plant Biologists
DOI: 10.1093/plphys/kiad228

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

Autori: 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
Pubblicato in: Molecular Cell, Numero 73/3, 2019, Pagina/e 490-504.e6, ISSN 1097-2765
Editore: Cell Press
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

Autori: Jana Kralovicova, Ivana Borovska, Monika Kubickova, Peter J. Lukavsky, Igor Vorechovsky
Pubblicato in: Cancers, Numero 12/7, 2020, Pagina/e 1865, ISSN 2072-6694
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers12071865

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

Autori: 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
Pubblicato in: Journal of Psychiatric Research, Numero 117, 2019, Pagina/e 7-14, ISSN 0022-3956
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.jpsychires.2019.06.018

RNA methylation in nuclear pre-mRNA processing

Autori: Helena Covelo-Molares, Marek Bartosovic, Stepanka Vanacova
Pubblicato in: Wiley Interdisciplinary Reviews: RNA, Numero 9/6, 2018, Pagina/e e1489, ISSN 1757-7004
Editore: John Wiley and Sons Inc.
DOI: 10.1002/wrna.1489

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

Autori: Dagmara M. Wiatrek, Maria E. Candela, Jiří Sedmík, Jan Oppelt, Liam P. Keegan, Mary A. O'Connell
Pubblicato in: RNA, Numero 25/6, 2019, Pagina/e 713-726, ISSN 1355-8382
Editore: Cold Spring Harbor Laboratory Press
DOI: 10.1261/rna.069625.118

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

Autori: Peter Javorka, Vivek K. Raxwal, Jan Najvarek, Karel Riha
Pubblicato in: Plant Direct, Numero 3/6, 2019, Pagina/e e00146, ISSN 2475-4455
Editore: Wiley & American Society of Plant Biologists and Society for Experimental Biology
DOI: 10.1002/pld3.146

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

Autori: 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
Pubblicato in: The Plant Journal, 2019, ISSN 0960-7412
Editore: Blackwell Publishing Inc.
DOI: 10.1111/tpj.14304

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

Autori: Martina Dvořáčková, Berta Raposo, Petr Matula, Joerg Fuchs, Veit Schubert, Vratislav Peška, Bénédicte Desvoyes, Crisanto Gutierrez, Jiří Fajkus
Pubblicato in: Journal of Cell Science, Numero 131/2, 2018, Pagina/e jcs202416, ISSN 0021-9533
Editore: The Company of Biologists Ltd.
DOI: 10.1242/jcs.202416

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

Autori: Vivek K. Raxwal, Craig G. Simpson, Jiradet Gloggnitzer, Juan Carlos Entinze, Wenbin Guo, Runxuan Zhang, John W.S. Brown, Karel Riha
Pubblicato in: The Plant Cell, Numero 32/9, 2020, Pagina/e 2725-2741, ISSN 1040-4651
Editore: American Society of Plant Biologists
DOI: 10.1105/tpc.20.00244

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

Autori: Petra Procházková Schrumpfová, Jiří Fajkus
Pubblicato in: Biomolecules, Numero 10/10, 2020, Pagina/e 1425, ISSN 2218-273X
Editore: MDPI
DOI: 10.3390/biom10101425

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

Autori: 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
Pubblicato in: The American Journal of Human Genetics, Numero 106/4, 2020, Pagina/e 467-483, ISSN 0002-9297
Editore: University of Chicago Press
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

Autori: 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
Pubblicato in: Journal of Medical Genetics, 2020, Pagina/e jmedgenet-2020-107048, ISSN 0022-2593
Editore: British Medical Association
DOI: 10.1136/jmedgenet-2020-107048

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

Autori: Pavla Polanská Sováková, Alžbeta Magdolenová, Klára Konečná, Veronika Rájecká, Jiří Fajkus, Miloslava Fojtová
Pubblicato in: Plant Molecular Biology, Numero 98/1-2, 2018, Pagina/e 81-99, ISSN 0167-4412
Editore: Kluwer Academic Publishers
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

Autori: Vratislav Peska, Martin Mátl, Terezie Mandáková, Daniel Vitales, Petr Fajkus, Jiří Fajkus, Sònia Garcia
Pubblicato in: Journal of Experimental Botany, Numero 71/19, 2020, Pagina/e 5786-5793, ISSN 0022-0957
Editore: Oxford University Press
DOI: 10.1093/jxb/eraa293

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

Autori: Georgios K. Georgakilas, Andrea Grioni, Konstantinos G. Liakos, Eliska Chalupova, Fotis C. Plessas, Panagiotis Alexiou
Pubblicato in: Scientific Reports, Numero 10/1, 2020, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-020-66454-3

CDK9 activity is critical for maintaining MDM4 overexpression in tumor cells

Autori: Monika Štětková, Kateřina Growková, Petr Fojtík, Barbora Valčíková, Veronika Palušová, Amandine Verlande, Radek Jorda, Vladimír Kryštof, Václav Hejret, Panagiotis Alexiou, Vladimír Rotrekl, Stjepan Uldrijan
Pubblicato in: Cell Death & Disease, Numero 11/9, 2020, ISSN 2041-4889
Editore: Nature Publishing Group
DOI: 10.1038/s41419-020-02971-3

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

Autori: Kateřina Adamusová, Solmaz Khosravi, Satoru Fujimoto, Andreas Houben, Sachihiro Matsunaga, Jiří Fajkus, Miloslava Fojtová
Pubblicato in: The Plant Journal, Numero 102/4, 2020, Pagina/e 678-687, ISSN 0960-7412
Editore: Blackwell Publishing Inc.
DOI: 10.1111/tpj.14653

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

Autori: Vratislav Peška, Terezie Mandáková, Veronika Ihradská, Jiří Fajkus
Pubblicato in: International Journal of Molecular Sciences, Numero 20/3, 2019, Pagina/e 733, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms20030733

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

Autori: Anzer Khan, Simona Paro, Leeanne McGurk, Nagraj Sambrani, Marion C. Hogg, James Brindle, Giuseppa Pennetta, Liam P. Keegan, Mary A. O’Connell
Pubblicato in: BMC Biology, Numero 18/1, 2020, ISSN 1741-7007
Editore: BioMed Central
DOI: 10.1186/s12915-020-0747-0

The Effects of RNA Editing in Cancer Tissue at Different Stages in Carcinogenesis

Autori: Kurkowiak, M.; Arcimowicz, L.; Chrusciel, E.; Urban-Wojciuk, Z.; Papak, I.; Keegan, L.; O’Connell, M.; Kowalski, J.; Hupp, T.; Marek-Trzonkowska, N.
Pubblicato in: RNA BIOLOGY, 2021, Pagina/e 1524–1539, ISSN 1555-8584
Editore: RNA BIOLOGY
DOI: 10.1080/15476286.2021.1877024

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

Autori: 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
Pubblicato in: Leukemia, Numero 32/9, 2018, Pagina/e 2028-2031, ISSN 0887-6924
Editore: Nature Publishing Group
DOI: 10.1038/s41375-018-0211-0

Visualization of the Nucleolus Using Ethynyl Uridine

Autori: Martina Dvořáčková, Jiří Fajkus
Pubblicato in: Frontiers in Plant Science, Numero 9, 2018, ISSN 1664-462X
Editore: Frontiers Media S. A.
DOI: 10.3389/fpls.2018.00177

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

Autori: Adriana Roithová, Zuzana Feketová, Štěpánka Vaňáčová, David Staněk
Pubblicato in: Nucleic Acids Research, Numero 48/11, 2020, Pagina/e 6184-6197, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa301

G4 Structures in Control of Replication and Transcription of rRNA Genes

Autori: Kateřina Havlová, Jiří Fajkus
Pubblicato in: Frontiers in Plant Science, Numero 11, 2020, ISSN 1664-462X
Editore: Frontiers Media S. A.
DOI: 10.3389/fpls.2020.593692

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

Autori: Deepak Kumar Yadav, Dagmar Zigáčková, Maria Zlobina, Tomáš Klumpler, Christelle Beaumont, Monika Kubíčková, Štěpánka Vaňáčová, Peter J Lukavsky
Pubblicato in: Nucleic Acids Research, Numero 48/4, 2019, Pagina/e 2091-2106, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkz1163

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