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Koralewska N, Corradi E, Milewski MC, Masante L, Szczepanska A, Kierzek R, Figlerowicz M, Baudet ML, Kurzynska-Kokorniak A. Short 2'-O-methyl/LNA oligomers as highly-selective inhibitors of miRNA production in vitro and in vivo. Nucleic Acids Res 2024:gkae284. [PMID: 38676942 DOI: 10.1093/nar/gkae284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024] Open
Abstract
MicroRNAs (miRNAs) that share identical or near-identical sequences constitute miRNA families and are predicted to act redundantly. Yet recent evidence suggests that members of the same miRNA family with high sequence similarity might have different roles and that this functional divergence might be rooted in their precursors' sequence. Current knock-down strategies such as antisense oligonucleotides (ASOs) or miRNA sponges cannot distinguish between identical or near identical miRNAs originating from different precursors to allow exploring unique functions of these miRNAs. We here develop a novel strategy based on short 2'-OMe/LNA-modified oligonucleotides to selectively target specific precursor molecules and ablate the production of individual members of miRNA families in vitro and in vivo. Leveraging the highly conserved Xenopus miR-181a family as proof-of-concept, we demonstrate that 2'-OMe/LNA-ASOs targeting the apical region of pre-miRNAs achieve precursor-selective inhibition of mature miRNA-5p production. Furthermore, we extend the applicability of our approach to the human miR-16 family, illustrating its universality in targeting precursors generating identical miRNAs. Overall, our strategy enables efficient manipulation of miRNA expression, offering a powerful tool to dissect the functions of identical or highly similar miRNAs derived from different precursors within miRNA families.
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Affiliation(s)
- Natalia Koralewska
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Eloina Corradi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Marek C Milewski
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Linda Masante
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Agnieszka Szczepanska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Ryszard Kierzek
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Marek Figlerowicz
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Marie-Laure Baudet
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Anna Kurzynska-Kokorniak
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
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2
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Majewska AM, Dietrich MA, Budzko L, Adamek M, Figlerowicz M, Ciereszko A. Secreted novel AID/APOBEC-like deaminase 1 (SNAD1) - a new important player in fish immunology. Front Immunol 2024; 15:1340273. [PMID: 38601149 PMCID: PMC11004436 DOI: 10.3389/fimmu.2024.1340273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/12/2024] [Indexed: 04/12/2024] Open
Abstract
The AID/APOBECs are a group of zinc-dependent cytidine deaminases that catalyse the deamination of bases in nucleic acids, resulting in a cytidine to uridine transition. Secreted novel AID/APOBEC-like deaminases (SNADs), characterized by the presence of a signal peptide are unique among all of intracellular classical AID/APOBECs, which are the central part of antibody diversity and antiviral defense. To date, there is no available knowledge on SNADs including protein characterization, biochemical characteristics and catalytic activity. We used various in silico approaches to define the phylogeny of SNADs, their common structural features, and their potential structural variations in fish species. Our analysis provides strong evidence of the universal presence of SNAD1 proteins/transcripts in fish, in which expression commences after hatching and is highest in anatomical organs linked to the immune system. Moreover, we searched published fish data and identified previously, "uncharacterized proteins" and transcripts as SNAD1 sequences. Our review into immunological research suggests SNAD1 role in immune response to infection or immunization, and interactions with the intestinal microbiota. We also noted SNAD1 association with temperature acclimation, environmental pollution and sex-based expression differences, with females showing higher level. To validate in silico predictions we performed expression studies of several SNAD1 gene variants in carp, which revealed distinct patterns of responses under different conditions. Dual sensitivity to environmental and pathogenic stress highlights its importance in the fish and potentially enhancing thermotolerance and immune defense. Revealing the biological roles of SNADs represents an exciting new area of research related to the role of DNA and/or RNA editing in fish biology.
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Affiliation(s)
- Anna M. Majewska
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Mariola A. Dietrich
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Lucyna Budzko
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Mikołaj Adamek
- Fish Disease Research Unit, Institute for Parasitology, University of Veterinary Medicine, Hannover, Germany
| | - Marek Figlerowicz
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Andrzej Ciereszko
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
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3
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Budzko L, Hoffa-Sobiech K, Jackowiak P, Figlerowicz M. Engineered deaminases as a key component of DNA and RNA editing tools. Mol Ther Nucleic Acids 2023; 34:102062. [PMID: 38028200 PMCID: PMC10661471 DOI: 10.1016/j.omtn.2023.102062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Over recent years, zinc-dependent deaminases have attracted increasing interest as key components of nucleic acid editing tools that can generate point mutations at specific sites in either DNA or RNA by combining a targeting module (such as a catalytically impaired CRISPR-Cas component) and an effector module (most often a deaminase). Deaminase-based molecular tools are already being utilized in a wide spectrum of therapeutic and research applications; however, their medical and biotechnological potential seems to be much greater. Recent reports indicate that the further development of nucleic acid editing systems depends largely on our ability to engineer the substrate specificity and catalytic activity of the editors themselves. In this review, we summarize the current trends and achievements in deaminase engineering. The presented data indicate that the potential of these enzymes has not yet been fully revealed or understood. Several examples show that even relatively minor changes in the structure of deaminases can give them completely new and unique properties.
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Affiliation(s)
- Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Karolina Hoffa-Sobiech
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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4
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Zmienko A, Wojciechowski P, Figlerowicz M. Editorial: Resolving the complexity of plant genomes and transcriptomes with long reads, volume II. Front Plant Sci 2023; 14:1326500. [PMID: 38034551 PMCID: PMC10687628 DOI: 10.3389/fpls.2023.1326500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023]
Affiliation(s)
- Agnieszka Zmienko
- Institute of Bioorganic Chemistry of Polish Academy of Sciences, Poznan, Poland
- Faculty of Computing and Telecommunications, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Paweł Wojciechowski
- Institute of Bioorganic Chemistry of Polish Academy of Sciences, Poznan, Poland
- Faculty of Computing and Telecommunications, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry of Polish Academy of Sciences, Poznan, Poland
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Iżycka N, Zaborowski MP, Ciecierski Ł, Jaz K, Szubert S, Miedziarek C, Rezler M, Piątek-Bajan K, Synakiewicz A, Jankowska A, Figlerowicz M, Sterzyńska K, Nowak-Markwitz E. Cancer Stem Cell Markers-Clinical Relevance and Prognostic Value in High-Grade Serous Ovarian Cancer (HGSOC) Based on The Cancer Genome Atlas Analysis. Int J Mol Sci 2023; 24:12746. [PMID: 37628927 PMCID: PMC10454196 DOI: 10.3390/ijms241612746] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/05/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Cancer stem cells (CSCs) may contribute to an increased risk of recurrence in ovarian cancer (OC). Further research is needed to identify associations between CSC markers and OC patients' clinical outcomes with greater certainty. If they prove to be correct, in the future, the CSC markers can be used to help predict survival and indicate new therapeutic targets. This study aimed to determine the CSC markers at mRNA and protein levels and their association with clinical presentation, outcome, and risk of recurrence in HGSOC (High-Grade Serous Ovarian Cancer). TCGA (The Cancer Genome Atlas) database with 558 ovarian cancer tumor samples was used for the evaluation of 13 CSC markers (ALDH1A1, CD44, EPCAM, KIT, LGR5, NES, NOTCH3, POU5F1, PROM1, PTTG1, ROR1, SOX9, and THY1). Data on mRNA and protein levels assessed by microarray and mass spectrometry were retrieved from TCGA. Models to predict chemotherapy response and survival were built using multiple variables, including epidemiological data, expression levels, and machine learning methodology. ALDH1A1 and LGR5 mRNA expressions indicated a higher platinum sensitivity (p = 3.50 × 10-3; p = 0.01, respectively). POU5F1 mRNA expression marked platinum-resistant tumors (p = 9.43 × 10-3). CD44 and EPCAM mRNA expression correlated with longer overall survival (OS) (p = 0.043; p = 0.039, respectively). THY1 mRNA and protein levels were associated with worse OS (p = 0.019; p = 0.015, respectively). Disease-free survival (DFS) was positively affected by EPCAM (p = 0.004), LGR5 (p = 0.018), and CD44 (p = 0.012). In the multivariate model based on CSC marker expression, the high-risk group had 9.1 months longer median overall survival than the low-risk group (p < 0.001). ALDH1A1, CD44, EPCAM, LGR5, POU5F1, and THY1 levels in OC may be used as prognostic factors for the primary outcome and help predict the treatment response.
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Affiliation(s)
- Natalia Iżycka
- Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznan University of Medical Sciences, Polna 33 St., 60-535 Poznan, Poland (S.S.)
| | - Mikołaj Piotr Zaborowski
- Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznan University of Medical Sciences, Polna 33 St., 60-535 Poznan, Poland (S.S.)
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland (M.F.)
| | - Łukasz Ciecierski
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland (M.F.)
| | - Kamila Jaz
- Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznan University of Medical Sciences, Polna 33 St., 60-535 Poznan, Poland (S.S.)
| | - Sebastian Szubert
- Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznan University of Medical Sciences, Polna 33 St., 60-535 Poznan, Poland (S.S.)
| | - Cezary Miedziarek
- Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznan University of Medical Sciences, Polna 33 St., 60-535 Poznan, Poland (S.S.)
| | - Marta Rezler
- Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznan University of Medical Sciences, Polna 33 St., 60-535 Poznan, Poland (S.S.)
| | - Kinga Piątek-Bajan
- Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznan University of Medical Sciences, Polna 33 St., 60-535 Poznan, Poland (S.S.)
| | - Aneta Synakiewicz
- Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznan University of Medical Sciences, Polna 33 St., 60-535 Poznan, Poland (S.S.)
| | - Anna Jankowska
- Department of Cell Biology, Poznan University of Medical Sciences, Rokietnicka 5D St., 60-806 Poznan, Poland;
| | - Marek Figlerowicz
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland (M.F.)
| | - Karolina Sterzyńska
- Department of Histology and Embryology, Poznan University of Medical Sciences, Swiecickiego 6 St., 61-781 Poznan, Poland
| | - Ewa Nowak-Markwitz
- Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznan University of Medical Sciences, Polna 33 St., 60-535 Poznan, Poland (S.S.)
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Stolarek I, Zenczak M, Handschuh L, Juras A, Marcinkowska-Swojak M, Spinek A, Dębski A, Matla M, Kóčka-Krenz H, Piontek J, Figlerowicz M. Genetic history of East-Central Europe in the first millennium CE. Genome Biol 2023; 24:173. [PMID: 37488661 PMCID: PMC10364380 DOI: 10.1186/s13059-023-03013-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND The appearance of Slavs in East-Central Europe has been the subject of an over 200-year debate driven by two conflicting hypotheses. The first assumes that Slavs came to the territory of contemporary Poland no earlier than the sixth century CE; the second postulates that they already inhabited this region in the Iron Age (IA). Testing either hypothesis is not trivial given that cremation of the dead was the prevailing custom in Central Europe from the late Bronze Age until the Middle Ages (MA). RESULTS To address this problem, we determined the genetic makeup of representatives of the IA Wielbark- and MA Slav-associated cultures from the territory of present-day Poland. The study involved 474 individuals buried in 27 cemeteries. For 197 of them, genome-wide data were obtained. We found close genetic affinities between the IA Wielbark culture-associated individuals and contemporary to them and older northern European populations. Further, we observed that the IA individuals had genetic components which were indispensable to model the MA population. CONCLUSIONS The collected data suggest that the Wielbark culture-associated IA population was formed by immigrants from the north who entered the region of contemporary Poland most likely at the beginning of the first millennium CE and mixed with autochthons. The presented results are in line with the hypothesis that assumes the genetic continuation between IA and MA periods in East-Central Europe.
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Affiliation(s)
- Ireneusz Stolarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Michal Zenczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Luiza Handschuh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | | | - Anna Spinek
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Artur Dębski
- Department of Archaeology, Collegium Historicum, Adam Mickiewicz University, Poznan, Poland
| | - Marzena Matla
- Department of History, Collegium Historicum, Adam Mickiewicz University, Poznan, Poland
| | - Hanna Kóčka-Krenz
- Department of Archaeology, Collegium Historicum, Adam Mickiewicz University, Poznan, Poland
| | - Janusz Piontek
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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7
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Ciecierski L, Stolarek I, Figlerowicz M. Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics. Nucleic Acids Res 2023:7175335. [PMID: 37216609 DOI: 10.1093/nar/gkad428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/26/2023] [Accepted: 05/12/2023] [Indexed: 05/24/2023] Open
Abstract
Archeogenomics is a rapidly growing interdisciplinary research field driven by the development of techniques that enable the acquisition and analysis of ancient DNA (aDNA). Recent advances in aDNA studies have contributed significantly to increasing our understanding of the natural history of humans. One of the most significant challenges facing archeogenomics is the integration of highly heterogeneous genomic, archeological, and anthropological data and their comprehensive analysis, considering changes that occur in time and space. Only this complex approach can explain the relationship between past populations in the context of migration or cultural development. To address these challenges, we developed a Human AGEs web server. It focuses on creating comprehensive spatiotemporal visualizations of genomic, archeogenomic, and archeological information, which can be provided by the user or loaded from a graph database. The interactive map application at the center of Human AGEs can display multiple layers of data in various forms, such as bubble charts, pie charts, heatmaps, or tag clouds. These visualizations can be modified using various clustering, filtering, and styling options, and the map state can be exported to a high-resolution image or saved as a session file for later use. Human AGEs, along with their tutorial, are accessible at https://archeogenomics.eu/.
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Affiliation(s)
- Lukasz Ciecierski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Ireneusz Stolarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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8
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Samelak-Czajka A, Wojciechowski P, Marszalek-Zenczak M, Figlerowicz M, Zmienko A. Differences in the intraspecies copy number variation of Arabidopsis thaliana conserved and nonconserved miRNA genes. Funct Integr Genomics 2023; 23:120. [PMID: 37036577 PMCID: PMC10085913 DOI: 10.1007/s10142-023-01043-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 04/11/2023]
Abstract
MicroRNAs (miRNAs) regulate gene expression by RNA interference mechanism. In plants, miRNA genes (MIRs) which are grouped into conserved families, i.e. they are present among the different plant taxa, are involved in the regulation of many developmental and physiological processes. The roles of the nonconserved MIRs-which are MIRs restricted to one plant family, genus, or even species-are less recognized; however, many of them participate in the responses to biotic and abiotic stresses. Both over- and underproduction of miRNAs may influence various biological processes. Consequently, maintaining intracellular miRNA homeostasis seems to be crucial for the organism. Deletions and duplications in the genomic sequence may alter gene dosage and/or activity. We evaluated the extent of copy number variations (CNVs) among Arabidopsis thaliana (Arabidopsis) MIRs in over 1000 natural accessions, using population-based analysis of the short-read sequencing data. We showed that the conserved MIRs were unlikely to display CNVs and their deletions were extremely rare, whereas nonconserved MIRs presented moderate variation. Transposon-derived MIRs displayed exceptionally high diversity. Conversely, MIRs involved in the epigenetic control of transposons reactivated during development were mostly invariable. MIR overlap with the protein-coding genes also limited their variability. At the expression level, a higher rate of nonvariable, nonconserved miRNAs was detectable in Col-0 leaves, inflorescence, and siliques compared to nonconserved variable miRNAs, although the expression of both groups was much lower than that of the conserved MIRs. Our data indicate that CNV rate of Arabidopsis MIRs is related with their age, function, and genomic localization.
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Affiliation(s)
- Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
- Institute of Computing Science, Faculty of Computing and Telecommunications, Poznan University of Technology, 60-965, Poznan, Poland
| | | | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
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9
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Marszalek-Zenczak M, Satyr A, Wojciechowski P, Zenczak M, Sobieszczanska P, Brzezinski K, Iefimenko T, Figlerowicz M, Zmienko A. Analysis of Arabidopsis non-reference accessions reveals high diversity of metabolic gene clusters and discovers new candidate cluster members. Front Plant Sci 2023; 14:1104303. [PMID: 36778696 PMCID: PMC9909608 DOI: 10.3389/fpls.2023.1104303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Metabolic gene clusters (MGCs) are groups of genes involved in a common biosynthetic pathway. They are frequently formed in dynamic chromosomal regions, which may lead to intraspecies variation and cause phenotypic diversity. We examined copy number variations (CNVs) in four Arabidopsis thaliana MGCs in over one thousand accessions with experimental and bioinformatic approaches. Tirucalladienol and marneral gene clusters showed little variation, and the latter was fixed in the population. Thalianol and especially arabidiol/baruol gene clusters displayed substantial diversity. The compact version of the thalianol gene cluster was predominant and more conserved than the noncontiguous version. In the arabidiol/baruol cluster, we found a large genomic insertion containing divergent duplicates of the CYP705A2 and BARS1 genes. The BARS1 paralog, which we named BARS2, encoded a novel oxidosqualene synthase. The expression of the entire arabidiol/baruol gene cluster was altered in the accessions with the duplication. Moreover, they presented different root growth dynamics and were associated with warmer climates compared to the reference-like accessions. In the entire genome, paired genes encoding terpene synthases and cytochrome P450 oxidases were more variable than their nonpaired counterparts. Our study highlights the role of dynamically evolving MGCs in plant adaptation and phenotypic diversity.
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Affiliation(s)
| | - Anastasiia Satyr
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Faculty of Computing and Telecommunications, Poznan University of Technology, Poznan, Poland
| | - Michal Zenczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Tetiana Iefimenko
- Department of Biology, National University of Kyiv-Mohyla Academy, Kyiv, Ukraine
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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Abstract
In recent years, it has become clear that gut microbiota plays a major role in the human body, both in health and disease. Because of that, the gut microbiome and its impact on human well-being are getting wider and wider attention. Studies focused on the liver are not an exception. However, the majority of the analyses are concentrated on the bacterial part of the gut microbiota, while the fungi living in the human intestines are often omitted or underappreciated. This review is focused on the gut mycobiome as an important factor that should be taken into consideration regarding liver homeostasis and its perturbations. We have collected the findings in this field and we discuss their importance. We aim to emphasize the fungal compositional changes related to liver diseases and, by that, provide novel insights into the directions of liver research and gut microbiota as a therapeutic target for liver diseases.
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Affiliation(s)
- Natalia Szóstak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Philips
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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11
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Stolarek I, Samelak-Czajka A, Figlerowicz M, Jackowiak P. Dimensionality reduction by UMAP for visualizing and aiding in classification of imaging flow cytometry data. iScience 2022; 25:105142. [PMID: 36193047 PMCID: PMC9526149 DOI: 10.1016/j.isci.2022.105142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/29/2022] [Accepted: 09/09/2022] [Indexed: 11/27/2022] Open
Abstract
Recent advances in imaging flow cytometry (IFC) have revolutionized high-throughput multiparameter analyses at single-cell resolution. Although enabling the discovery of population heterogeneities and the detection of rare events, IFC generates hyperdimensional datasets that demand innovative analytical approaches. Current methods work in a supervised manner, utilize only limited information content, or require large annotated reference datasets. Dimensionality reduction algorithms, including uniform manifold approximation and projection (UMAP), have been successfully applied to analyze the large number of parameters generated in various high-throughput techniques. Here, we apply a workflow incorporating UMAP to analyze different IFC datasets. We demonstrate that it out-competes other popular dimensionality reduction methods in speed and accuracy. Moreover, it enables fast visualization, clustering, and tagging of unannotated objects in large-scale experiments. We anticipate that our workflow will be a robust method to address complex IFC datasets, either alone or as an upstream addition to the deep learning approaches. UMAP dimensionality reduction provides fast and accurate method of IFC data analysis UMAP yields improved object clustering and tagging of the multispectral IFC data PCA decomposition allows multispectral signals merging for direct image embedding
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Affiliation(s)
- Ireneusz Stolarek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Anna Samelak-Czajka
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
- Corresponding author
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12
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Morawiec E, Miklasińska-Majdanik M, Bratosiewicz-Wąsik J, Wojtyczka RD, Swolana D, Stolarek I, Czerwiński M, Skubis-Sikora A, Samul M, Polak A, Kruszniewska-Rajs C, Pudełko A, Figlerowicz M, Bednarska-Czerwińska A, Wąsik TJ. From Alpha to Delta-Genetic Epidemiology of SARS-CoV-2 (hCoV-19) in Southern Poland. Pathogens 2022; 11:pathogens11070780. [PMID: 35890025 PMCID: PMC9316897 DOI: 10.3390/pathogens11070780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
In Poland, the first case of SARS-CoV-2 infection was confirmed in March 2020. Since then, many circulating virus lineages fueled rapid pandemic waves which inflicted a severe burden on the Polish healthcare system. Some of these lineages were associated with increased transmissibility and immune escape. Mutations in the viral spike protein, which is responsible for host cell recognition and serves as the primary target for neutralizing antibodies, are of particular importance. We investigated the molecular epidemiology of the SARS-CoV-2 clades circulating in Southern Poland from February 2021 to August 2021. The 921 whole-genome sequences were used for variant identification, spike mutation, and phylogenetic analyses. The Pango B.1.1.7 was the dominant variant (n = 730, 89.68%) from March 2021 to July 2021. In July 2021, the B.1.1.7 was displaced by the B.1.617.2 lineage with 66.66% in July 2021 and 92.3% in August 2021 frequencies, respectively. Moreover, our results were compared with the sequencing available on the GISAID platform for other regions of Poland, the Czech Republic, and Slovakia. The analysis showed that the dominant variant in the analyzed period was B.1.1.7 in all countries and Southern Poland (Silesia). Interestingly, B.1.1.7 was replaced by B.1.617.2 earlier in Southern Poland than in the rest of the country. Moreover, in the Czech Republic and Slovakia, AY lineages were predominant at that time, contrary to the Silesia region.
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Affiliation(s)
- Emilia Morawiec
- Department of Microbiology, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800 Zabrze, Poland;
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800 Zabrze, Poland
| | - Maria Miklasińska-Majdanik
- Department of Microbiology and Virology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (M.M.-M.); (R.D.W.); (D.S.)
| | - Jolanta Bratosiewicz-Wąsik
- Department of Biopharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland;
| | - Robert D. Wojtyczka
- Department of Microbiology and Virology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (M.M.-M.); (R.D.W.); (D.S.)
| | - Denis Swolana
- Department of Microbiology and Virology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (M.M.-M.); (R.D.W.); (D.S.)
| | - Ireneusz Stolarek
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznań, Poland; (I.S.); (M.F.)
| | - Michał Czerwiński
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
- American Medical Clinic, 40-851 Katowice, Poland
| | - Aleksandra Skubis-Sikora
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
- Department of Cytophysiology, Chair of Histology and Embryology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, 40-055 Katowice, Poland
| | - Magdalena Samul
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
| | - Agnieszka Polak
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
| | - Celina Kruszniewska-Rajs
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland
| | - Adam Pudełko
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
- Department of Clinical Chemistry and Laboratory Diagnostics, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland
| | - Marek Figlerowicz
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznań, Poland; (I.S.); (M.F.)
| | - Anna Bednarska-Czerwińska
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
- American Medical Clinic, 40-851 Katowice, Poland
- Department of Gynecology and Obstetrics, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800 Zabrze, Poland
| | - Tomasz J. Wąsik
- Department of Microbiology and Virology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (M.M.-M.); (R.D.W.); (D.S.)
- Correspondence: ; Tel.: +48-32-364-1621
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13
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Ehrlich H, Luczak M, Ziganshin R, Mikšík I, Wysokowski M, Simon P, Baranowska‐Bosiacka I, Kupnicka P, Ereskovsky A, Galli R, Dyshlovoy S, Fischer J, Tabachnick KR, Petrenko I, Jesionowski T, Lubkowska A, Figlerowicz M, Ivanenko VN, Summers AP. Arrested in Glass: Actin within Sophisticated Architectures of Biosilica in Sponges. Adv Sci (Weinh) 2022; 9:e2105059. [PMID: 35156333 PMCID: PMC9009123 DOI: 10.1002/advs.202105059] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Actin is a fundamental member of an ancient superfamily of structural intracellular proteins and plays a crucial role in cytoskeleton dynamics, ciliogenesis, phagocytosis, and force generation in both prokaryotes and eukaryotes. It is shown that actin has another function in metazoans: patterning biosilica deposition, a role that has spanned over 500 million years. Species of glass sponges (Hexactinellida) and demosponges (Demospongiae), representatives of the first metazoans, with a broad diversity of skeletal structures with hierarchical architecture unchanged since the late Precambrian, are studied. By etching their skeletons, organic templates dominated by individual F-actin filaments, including branched fibers and the longest, thickest actin fiber bundles ever reported, are isolated. It is proposed that these actin-rich filaments are not the primary site of biosilicification, but this highly sophisticated and multi-scale form of biomineralization in metazoans is ptterned.
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Affiliation(s)
- Hermann Ehrlich
- Institute of Electronic and Sensor MaterialsTU Bergakademie FreibergFreiberg09599Germany
- Center for Advanced TechnologyAdam Mickiewicz UniversityPoznan61614Poland
| | - Magdalena Luczak
- Institute of Bioorganic ChemistryPolish Academy of SciencesPoznan61704Poland
| | - Rustam Ziganshin
- Institute of Bioorganic ChemistryRussian Academy of SciencesMoscow142290Russian Federation
| | - Ivan Mikšík
- Institute of PhysiologyThe Czech Academy of SciencesPrague142 20Czech Republic
| | - Marcin Wysokowski
- Institute of Electronic and Sensor MaterialsTU Bergakademie FreibergFreiberg09599Germany
- Faculty of Chemical TechnologyInstitute of Chemical Technology and EngineeringPoznan University of TechnologyPoznan60965Poland
| | - Paul Simon
- Max Planck Institute for Chemical Physics of SolidsDresden01187Germany
| | - Irena Baranowska‐Bosiacka
- Department of Biochemistry and Medical ChemistryPomeranian Medical University in SzczecinSzczecin70111Poland
| | - Patrycja Kupnicka
- Department of Biochemistry and Medical ChemistryPomeranian Medical University in SzczecinSzczecin70111Poland
| | - Alexander Ereskovsky
- Institut Méditerranéen de Biodiversité et d'Ecologie (IMBE)CNRSIRDAix Marseille UniversitéMarseille13003France
- Biological FacultySt. Petersburg State UniversitySt. Petersburg199034Russian Federation
- Koltzov Institute of Developmental Biology of Russian Academy of SciencesMoscow119334Russian Federation
| | - Roberta Galli
- Clinical Sensoring and MonitoringDepartment of Anesthesiology and Intensive Care MedicineTU DresdenDresden01307Germany
| | - Sergey Dyshlovoy
- Laboratory of Experimental OncologyUniversity Medical Center Hamburg‐EppendorfHamburg20251Germany
- Laboratory of PharmacologyA.V. Zhirmunsky National Scientific Center of Marine BiologyFar Eastern BranchRussian Academy of SciencesVladivostok690041Russian Federation
| | - Jonas Fischer
- Institute of Electronic and Sensor MaterialsTU Bergakademie FreibergFreiberg09599Germany
| | | | - Iaroslav Petrenko
- Institute of Electronic and Sensor MaterialsTU Bergakademie FreibergFreiberg09599Germany
| | - Teofil Jesionowski
- Faculty of Chemical TechnologyInstitute of Chemical Technology and EngineeringPoznan University of TechnologyPoznan60965Poland
| | - Anna Lubkowska
- Department of Functional Diagnostics and Physical MedicineFaculty of Health SciencesPomeranian Medical University in SzczecinSzczecin71210Poland
| | - Marek Figlerowicz
- Institute of Bioorganic ChemistryPolish Academy of SciencesPoznan61704Poland
| | - Viatcheslav N. Ivanenko
- Department of Invertebrate ZoologyBiological FacultyLomonosov Moscow State UniversityMoscow119991Russian Federation
| | - Adam P. Summers
- Department of BiologyFriday Harbor LabsUniversity of WashingtonFriday HarborWA98195USA
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Ruszkowski M, Strugala A, Indyka P, Tresset G, Figlerowicz M, Urbanowicz A. Cryo-EM reconstructions of BMV-derived virus-like particles reveal assembly defects in the icosahedral lattice structure. Nanoscale 2022; 14:3224-3233. [PMID: 35156989 DOI: 10.1039/d1nr05650f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The increasing interest in virus-like particles (VLPs) has been reflected by the growing number of studies on their assembly and application. However, the formation of complete VLPs is a complex phenomenon, making it difficult to rationally design VLPs with desired features de novo. In this paper, we describe VLPs assembled in vitro from the recombinant capsid protein of brome mosaic virus (BMV). The analysis of VLPs was performed by Cryo-EM reconstructions and allowed us to visualize a few classes of VLPs, giving insight into the VLP self-assembly process. Apart from the mature icosahedral VLP practically identical with native virions, we describe putative VLP intermediates displaying non-icosahedral arrangements of capsomers, proposed to occur before the final disorder-order transition stage of icosahedral VLP assembly. Some of the described VLP classes show a lack of protein shell continuity, possibly resulting from too strong interaction with the cargo (in this case tRNA) with the capsid protein. We believe that our results are a useful prerequisite for the rational design of VLPs in the future and lead the way to the effective production of modified VLPs.
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Affiliation(s)
- Milosz Ruszkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Aleksander Strugala
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Paulina Indyka
- Jagiellonian University, Solaris National Synchrotron Radiation Centre, Czerwone Maki 98, 30-392 Cracow, Poland
- Jagiellonian University, Malopolska Centre of Biotechnology (MCB), 30-387 Cracow, Poland
| | - Guillaume Tresset
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Anna Urbanowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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15
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Zmienko A, Wojciechowski P, Figlerowicz M. Editorial: Resolving the Complexity of Plant Genomes and Transcriptomes With Long Reads. Front Plant Sci 2022; 12:832257. [PMID: 35126441 PMCID: PMC8813858 DOI: 10.3389/fpls.2021.832257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Agnieszka Zmienko
- Institute of Bioorganic Chemistry of Polish Academy of Sciences, Poznan, Poland
| | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry of Polish Academy of Sciences, Poznan, Poland
- Faculty of Computing and Telecommunications, Institute of Computing Science, Poznan University of Technology Poznan, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry of Polish Academy of Sciences, Poznan, Poland
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16
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Nowis K, Jackowiak P, Figlerowicz M, Philips A. At-C-RNA database, a one-stop source for information on circRNAs in Arabidopsis thaliana in a unified format. Database (Oxford) 2021; 2021:6425494. [PMID: 34788390 PMCID: PMC8594480 DOI: 10.1093/database/baab074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 11/29/2022]
Abstract
Circular RNAs (circRNAs) are a large class of noncoding RNAs with functions that, in most
cases, remain unknown. Recent genome-wide analysis of circRNAs using RNA-Seq has revealed
that circRNAs are abundant and some of them conserved in plants. Furthermore, it has been
shown that the expression of circRNAs in plants is regulated in a tissue-specific manner.
Arabidopsis thaliana circular RNA database is a new resource designed
to integrate and standardize the data available for circRNAs in a model plant A.
thaliana, which is currently the best-characterized plant in terms of circRNAs.
The resource integrates all applicable publicly available RNA-seq datasets. These datasets
were subjected to extensive reanalysis and curation, yielding results in a unified format.
Moreover, all data were normalized according to our optimized approach developed for
circRNA identification in plants. As a result, the database accommodates circRNAs
identified across organs and seedlings of wild-type A. thaliana and its
single-gene knockout mutants for genes related to splicing. The database provides free
access to unified data and search functionalities, thus enabling comparative analyses of
A. thaliana circRNAs between organs, variants and studies for the first
time. Database URLhttps://plantcircrna.ibch.poznan.pl/
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Affiliation(s)
- Katarzyna Nowis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego str. 12/14, Poznan 61-704, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego str. 12/14, Poznan 61-704, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego str. 12/14, Poznan 61-704, Poland
| | - Anna Philips
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego str. 12/14, Poznan 61-704, Poland
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17
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Grzegorzewska AE, Mostowska A, Świderska MK, Marcinkowski W, Stolarek I, Figlerowicz M, Jagodziński PP. Polymorphism rs368234815 of interferon lambda 4 gene and spontaneous clearance of hepatitis C virus in haemodialysis patients: a case-control study. BMC Infect Dis 2021; 21:102. [PMID: 33482747 PMCID: PMC7821534 DOI: 10.1186/s12879-021-05777-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/07/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In non-uremic subjects, IFNL4 rs368234815 predicts HCV clearance. We investigated whether rs368234815 is associated with spontaneous HCV clearance in haemodialysis patients and whether it is a stronger predictor of HCV resolution than the IFNL polymorphisms already associated with HCV clearance in dialysis subjects. We also evaluated an association of rs368234815 with patients` survival and alterations in transcription factor binding sites (TFBS) caused by IFNL polymorphisms. METHODS Among 161 haemodialysis patients with positive anti-HCV antibodies, 68 (42.2%) spontaneously resolved HCV infection, whereas 93 remained HCV RNA positive. Patients were tested for near IFNL3 rs12980275, IFNL3 rs4803217, IFNL4 rs12979860, IFNL4 rs368234815, and near IFNL4 rs8099917. IFNL4 rs368234815 polymorphism (TT/TT, ΔG/TT, ΔG/ΔG) was genotyped by restriction fragment length polymorphism analysis; other IFNL polymorphisms - by high resolution melting curve analysis. We used the Kaplan-Meier method with the log-rank test for survival analysis. In silico analysis included the use of ENCODE TFBS ChIP-seq data, HOCOMOCO, JASPAR CORE, and CIS-BP databases, and FIMO software. RESULTS The probability (OR, 95%CI, P) of spontaneous HCV clearance for rs368234815 TT/TT patients was higher than for the ΔG allele carriers (2.63, 1.38-5.04, 0.003). This probability for other major homozygotes varied between 2.80, 1.45-5.43, 0.002 for rs12980275 and 2.44, 1.27-4.69, 0.007 for rs12979860. In the additive model, rs368234815 TT/TT was the strongest predictor of HCV clearance (6.38, 1.69-24.2, 0.003). Survival analysis suggested an association of the ΔG allele with mortality due to neoplasms (log-rank P = 0.005). The rs368234815 ∆G allele caused TFBS removal for PLAGL1. CONCLUSIONS In haemodialysis patients, the association of rs368234815 with the spontaneous HCV clearance is better than that documented for other IFNL3/IFNL4 polymorphisms only in the additive mode of inheritance. However, identifying the homozygosity in the variant ∆G allele of rs368234815 means a more potent prediction of persistent HCV infection in haemodialysis subjects that we observe in the case of the variant homozygosity of other tested IFNL3/IFNL4 polymorphisms. Removal of PLAGL1 TFBS in subjects harbouring the rs368234815 ∆G allele may contribute to cancer susceptibility. The association of rs368234815 with cancer-related mortality needs further studies in HCV-exposed subjects.
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Affiliation(s)
- Alicja E. Grzegorzewska
- Department of Nephrology, Transplantology and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355 Poznań, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Święcickiego 6, 60-781 Poznań, Poland
| | - Monika K. Świderska
- Department of Nephrology, Transplantology and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355 Poznań, Poland
| | | | - Ireneusz Stolarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Paweł P. Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Święcickiego 6, 60-781 Poznań, Poland
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18
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Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni JC, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T. LifeTime and improving European healthcare through cell-based interceptive medicine. Nature 2020; 587:377-386. [PMID: 32894860 PMCID: PMC7656507 DOI: 10.1038/s41586-020-2715-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/25/2020] [Indexed: 01/14/2023]
Abstract
Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution. This mission will be implemented through the development, integration and application of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during the progression from health to disease. The analysis of large molecular and clinical datasets will identify molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. The timely detection and interception of disease embedded in an ethical and patient-centred vision will be achieved through interactions across academia, hospitals, patient associations, health data management systems and industry. The application of this strategy to key medical challenges in cancer, neurological and neuropsychiatric disorders, and infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade.
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Affiliation(s)
- Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Charité-Universitätsmedizin, Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany.
| | - Geneviève Almouzni
- Institut Curie, CNRS, PSL Research University, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le cancer, Paris, France.
| | - Stanislaw A Gorski
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
| | - Stein Aerts
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Michela G Bertero
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Annelien L Bredenoord
- Department of Medical Humanities, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | - Susanna Chiocca
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Bart De Strooper
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
- UK Dementia Research Institute at UCL, University College London, London, UK
| | - Angelika Eggert
- Berlin Institute of Health (BIH), Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Norbert Hubner
- Charité-Universitätsmedizin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Grietje Krabbe
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marc A Marti-Renom
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Mihai G Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Dörthe Nickel
- Institut Curie, PSL Research University, Paris, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, Montpellier, France
| | | | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Stefano Piccolo
- Department of Molecular Medicine, University of Padua School of Medicine, Padua, Italy
- IFOM, The FIRC Institute of Molecular Oncology, Padua, Italy
| | - Inês Pinheiro
- Institut Curie, CNRS, PSL Research University, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le cancer, Paris, France
| | - Ana Pombo
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt University of Berlin, Berlin, Germany
| | - Christian Popp
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Wolf Reik
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Sergio Roman-Roman
- Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Joachim L Schultze
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Giuseppe Testa
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
- Human Technopole, Milan, Italy
| | - Dimitris Thanos
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München - German Research Center for Environmental Health, Munich, Germany
- Faculty of Biology, Ludwig-Maximilians Universität, Munich, Germany
| | - Alfonso Valencia
- ICREA, Barcelona, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Céline Vallot
- Department of Translational Research, Institut Curie, PSL Research University, Paris, France
- CNRS UMR3244, Institut Curie, PSL University, Paris, France
| | - Alexander van Oudenaarden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Marie Vidal
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Thierry Voet
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
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19
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Philips A, Nowis K, Stelmaszczuk M, Jackowiak P, Podkowiński J, Handschuh L, Figlerowicz M. Expression Landscape of circRNAs in Arabidopsis thaliana Seedlings and Adult Tissues. Front Plant Sci 2020; 11:576581. [PMID: 33014000 PMCID: PMC7511659 DOI: 10.3389/fpls.2020.576581] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/25/2020] [Indexed: 05/27/2023]
Abstract
RNA-seq is currently the only method that can provide a comprehensive landscape of circular RNA (circRNAs) in the whole organism and its particular organs. Recent years have brought an increasing number of RNA-seq-based reports on plant circRNAs. Notably, the picture they revealed is questionable and depends on the applied circRNA identification and quantification techniques. In consequence, little is known about the biogenesis and functions of circRNAs in plants. In this work, we tested two experimental and six bioinformatics procedures of circRNA analysis to determine the optimal approach for studying the profiles of circRNAs in Arabidopsis thaliana. Then using the optimized strategy, we determined the accumulation of circular and corresponding linear transcripts in plant seedlings and organs. We observed that only a small fraction of circRNAs was reproducibly generated. Among them, two groups of circRNAs were discovered: ubiquitous and organ-specific. The highest number of circRNAs with significantly increased accumulation in comparison to other organs/seedlings was found in roots. The circRNAs in seedlings, leaves and flowers originated mainly from genes involved in photosynthesis and the response to stimulus. The levels of circular and linear transcripts were not correlated. Although RNase R treatment enriches the analyzed RNA samples in circular transcripts, it may also have a negative impact on the stability of some of the circRNAs. We also showed that the normalization of NGS data by the library size is not proper for circRNAs quantification. Alternatively, we proposed four other normalization types whose accuracy was confirmed by ddPCR. Moreover, we provided a comprehensive characterization of circRNAs in A. thaliana organs and in seedlings. Our analyses revealed that plant circRNAs are formed in both stochastic and controlled processes. The latter are less frequent and likely engage circRNA-specific mechanisms. Only a few circRNAs were organ-specific. The lack of correlation between the accumulation of linear and circular transcripts indicated that their biogenesis depends on different mechanisms.
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Affiliation(s)
- Anna Philips
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna Nowis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Michal Stelmaszczuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Jan Podkowiński
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Luiza Handschuh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
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20
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Perrigue PM, Rakoczy M, Pawlicka KP, Belter A, Giel-Pietraszuk M, Naskręt-Barciszewska M, Barciszewski J, Figlerowicz M. Cancer Stem Cell-Inducing Media Activates Senescence Reprogramming in Fibroblasts. Cancers (Basel) 2020; 12:cancers12071745. [PMID: 32629974 PMCID: PMC7409320 DOI: 10.3390/cancers12071745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 06/26/2020] [Indexed: 01/05/2023] Open
Abstract
Cellular senescence is a tumor-suppressive mechanism blocking cell proliferation in response to stress. However, recent evidence suggests that senescent tumor cells can re-enter the cell cycle to become cancer stem cells, leading to relapse after cancer chemotherapy treatment. Understanding how the senescence reprogramming process is a precursor to cancer stem cell formation is of great medical importance. To study the interplay between senescence, stemness, and cancer, we applied a stem cell medium (SCM) to human embryonic fibroblasts (MRC5 and WI-38) and cancer cell lines (A549 and 293T). MRC5 and WI-38 cells treated with SCM showed symptoms of oxidative stress and became senescent. Transcriptome analysis over a time course of SCM-induced senescence, revealed a developmental process overlapping with the upregulation of genes for growth arrest and the senescence-associated secretory phenotype (SASP). We demonstrate that histone demethylases jumonji domain-containing protein D3 (Jmjd3) and ubiquitously transcribed tetratricopeptide repeat, X chromosome (Utx), which operate by remodeling chromatin structure, are implicated in the senescence reprogramming process to block stem cell formation in fibroblasts. In contrast, A549 and 293T cells cultured in SCM were converted to cancer stem cells that displayed the phenotype of senescence uncoupled from growth arrest. The direct overexpression of DNA methyltransferases (Dnmt1 and Dnmt3A), ten-eleven translocation methylcytosine dioxygenases (Tet1 and Tet3), Jmjd3, and Utx proteins could activate senescence-associated beta-galactosidase (SA-β-gal) activity in 293T cells, suggesting that epigenetic alteration and chromatin remodeling factors trigger the senescence response. Overall, our study suggests that chromatin machinery controlling senescence reprogramming is significant in cancer stem cell formation.
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Affiliation(s)
- Patrick M. Perrigue
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, Poland; (M.R.); (K.P.P.); (A.B.); (M.G.-P.); (M.N.-B.); (J.B.); (M.F.)
- Correspondence: ; Tel.: +48-61-852-85-03
| | - Magdalena Rakoczy
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, Poland; (M.R.); (K.P.P.); (A.B.); (M.G.-P.); (M.N.-B.); (J.B.); (M.F.)
| | - Kamila P. Pawlicka
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, Poland; (M.R.); (K.P.P.); (A.B.); (M.G.-P.); (M.N.-B.); (J.B.); (M.F.)
| | - Agnieszka Belter
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, Poland; (M.R.); (K.P.P.); (A.B.); (M.G.-P.); (M.N.-B.); (J.B.); (M.F.)
| | - Małgorzata Giel-Pietraszuk
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, Poland; (M.R.); (K.P.P.); (A.B.); (M.G.-P.); (M.N.-B.); (J.B.); (M.F.)
| | - Mirosława Naskręt-Barciszewska
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, Poland; (M.R.); (K.P.P.); (A.B.); (M.G.-P.); (M.N.-B.); (J.B.); (M.F.)
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, Poland; (M.R.); (K.P.P.); (A.B.); (M.G.-P.); (M.N.-B.); (J.B.); (M.F.)
- NanoBioMed Center, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, Poland; (M.R.); (K.P.P.); (A.B.); (M.G.-P.); (M.N.-B.); (J.B.); (M.F.)
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21
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Philips A, Stolarek I, Handschuh L, Nowis K, Juras A, Trzciński D, Nowaczewska W, Wrzesińska A, Potempa J, Figlerowicz M. Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia. BMC Genomics 2020; 21:402. [PMID: 32539695 PMCID: PMC7296668 DOI: 10.1186/s12864-020-06810-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/08/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Recent advances in the next-generation sequencing (NGS) allowed the metagenomic analyses of DNA from many different environments and sources, including thousands of years old skeletal remains. It has been shown that most of the DNA extracted from ancient samples is microbial. There are several reports demonstrating that the considerable fraction of extracted DNA belonged to the bacteria accompanying the studied individuals before their death. RESULTS In this study we scanned 344 microbiomes from 1000- and 2000- year-old human teeth. The datasets originated from our previous studies on human ancient DNA (aDNA) and on microbial DNA accompanying human remains. We previously noticed that in many samples infection-related species have been identified, among them Tannerella forsythia, one of the most prevalent oral human pathogens. Samples containing sufficient amount of T. forsythia aDNA for a complete genome assembly were selected for thorough analyses. We confirmed that the T. forsythia-containing samples have higher amounts of the periodontitis-associated species than the control samples. Despites, other pathogens-derived aDNA was found in the tested samples it was too fragmented and damaged to allow any reasonable reconstruction of these bacteria genomes. The anthropological examination of ancient skulls from which the T. forsythia-containing samples were obtained revealed the pathogenic alveolar bone loss in tooth areas characteristic for advanced periodontitis. Finally, we analyzed the genetic material of ancient T. forsythia strains. As a result, we assembled four ancient T. forsythia genomes - one 2000- and three 1000- year-old. Their comparison with contemporary T. forsythia genomes revealed a lower genetic diversity within the four ancient strains than within contemporary strains. We also investigated the genes of T. forsythia virulence factors and found that several of them (KLIKK protease and bspA genes) differ significantly between ancient and modern bacteria. CONCLUSIONS In summary, we showed that NGS screening of the ancient human microbiome is a valid approach for the identification of disease-associated microbes. Following this protocol, we provided a new set of information on the emergence, evolution and virulence factors of T. forsythia, the member of the oral dysbiotic microbiome.
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Affiliation(s)
- Anna Philips
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Ireneusz Stolarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Luiza Handschuh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Katarzyna Nowis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
| | - Dawid Trzciński
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
| | - Wioletta Nowaczewska
- Department of Human Biology, Faculty of Biological Sciences, Wroclaw University, 50-138, Wroclaw, Poland
| | - Anna Wrzesińska
- Anthropological Laboratory, Museum of the First Piasts at Lednica, 62-261, Lednogora, Poland
| | - Jan Potempa
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland.,Department of Oral Immunity and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, 40202, USA
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland. .,Institute of Computing Science, Poznan University of Technology, 60-965, Poznan, Poland.
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22
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Zmienko A, Marszalek-Zenczak M, Wojciechowski P, Samelak-Czajka A, Luczak M, Kozlowski P, Karlowski WM, Figlerowicz M. AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome. Plant Cell 2020; 32:1797-1819. [PMID: 32265262 PMCID: PMC7268809 DOI: 10.1105/tpc.19.00640] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 03/09/2020] [Accepted: 03/30/2020] [Indexed: 05/13/2023]
Abstract
Copy number variations (CNVs) greatly contribute to intraspecies genetic polymorphism and phenotypic diversity. Recent analyses of sequencing data for >1000 Arabidopsis (Arabidopsis thaliana) accessions focused on small variations and did not include CNVs. Here, we performed genome-wide analysis and identified large indels (50 to 499 bp) and CNVs (500 bp and larger) in these accessions. The CNVs fully overlap with 18.3% of protein-coding genes, with enrichment for evolutionarily young genes and genes involved in stress and defense. By combining analysis of both genes and transposable elements (TEs) affected by CNVs, we revealed that the variation statuses of genes and TEs are tightly linked and jointly contribute to the unequal distribution of these elements in the genome. We also determined the gene copy numbers in a set of 1060 accessions and experimentally validated the accuracy of our predictions by multiplex ligation-dependent probe amplification assays. We then successfully used the CNVs as markers to analyze population structure and migration patterns. Finally, we examined the impact of gene dosage variation triggered by a CNV spanning the SEC10 gene on SEC10 expression at both the transcript and protein levels. The catalog of CNVs, CNV-overlapping genes, and their genotypes in a top model dicot will stimulate the exploration of the genetic basis of phenotypic variation.
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Affiliation(s)
- Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
| | | | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Luczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
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23
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Pokornowska M, Milewski MC, Ciechanowska K, Szczepańska A, Wojnicka M, Radogostowicz Z, Figlerowicz M, Kurzynska-Kokorniak A. The RNA-RNA base pairing potential of human Dicer and Ago2 proteins. Cell Mol Life Sci 2019; 77:3231-3244. [PMID: 31655860 PMCID: PMC7391396 DOI: 10.1007/s00018-019-03344-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/24/2019] [Accepted: 10/14/2019] [Indexed: 12/22/2022]
Abstract
The ribonuclease Dicer produces microRNAs (miRNAs) and small interfering RNAs that are handed over to Ago proteins to control gene expression by targeting complementary sequences within transcripts. Interestingly, a growing number of reports have demonstrated that the activity of Dicer may extend beyond the biogenesis of small regulatory RNAs. Among them, a report from our latest studies revealed that human Dicer facilitates base pairing of complementary sequences present in two nucleic acids, thus acting as a nucleic acid annealer. Accordingly, in this manuscript, we address how RNA structure influences the annealing activity of human Dicer. We show that Dicer supports hybridization between a small RNA and a complementary sequence of a longer RNA in vitro, even when both complementary sequences are trapped within secondary structures. Moreover, we show that under applied conditions, human Ago2, a core component of RNA-induced silencing complex, displays very limited annealing activity. Based on the available data from new-generation sequencing experiments regarding the RNA pool bound to Dicer in vivo, we show that multiple Dicer-binding sites within mRNAs also contain miRNA targets. Subsequently, we demonstrate in vitro that Dicer but not Ago2 can anneal miRNA to its target present within mRNA. We hypothesize that not all miRNA duplexes are handed over to Ago proteins. Instead, miRNA-Dicer complexes could target specific sequences within transcripts and either compete or cooperate for binding sites with miRNA-Ago complexes. Thus, not only Ago but also Dicer might be directly involved in the posttranscriptional control of gene expression.
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Affiliation(s)
- Maria Pokornowska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marek C Milewski
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Kinga Ciechanowska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Agnieszka Szczepańska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marta Wojnicka
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Ziemowit Radogostowicz
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marek Figlerowicz
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, 60-965, Poznan, Poland
| | - Anna Kurzynska-Kokorniak
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
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24
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Machałowski T, Wysokowski M, Tsurkan MV, Galli R, Schimpf C, Rafaja D, Brendler E, Viehweger C, Żółtowska-Aksamitowska S, Petrenko I, Czaczyk K, Kraft M, Bertau M, Bechmann N, Guan K, Bornstein SR, Voronkina A, Fursov A, Bejger M, Biniek-Antosiak K, Rypniewski W, Figlerowicz M, Pokrovsky O, Jesionowski T, Ehrlich H. Spider Chitin: An Ultrafast Microwave-Assisted Method for Chitin Isolation from Caribena versicolor Spider Molt Cuticle. Molecules 2019; 24:E3736. [PMID: 31623238 PMCID: PMC6833065 DOI: 10.3390/molecules24203736] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/07/2019] [Accepted: 10/14/2019] [Indexed: 01/07/2023] Open
Abstract
Chitin, as a fundamental polysaccharide in invertebrate skeletons, continues to be actively investigated, especially with respect to new sources and the development of effective methods for its extraction. Recent attention has been focused on marine crustaceans and sponges; however, the potential of spiders (order Araneae) as an alternative source of tubular chitin has been overlooked. In this work, we focused our attention on chitin from up to 12 cm-large Theraphosidae spiders, popularly known as tarantulas or bird-eating spiders. These organisms "lose" large quantities of cuticles during their molting cycle. Here, we present for the first time a highly effective method for the isolation of chitin from Caribena versicolor spider molt cuticle, as well as its identification and characterization using modern analytical methods. We suggest that the tube-like molt cuticle of this spider can serve as a naturally prefabricated and renewable source of tubular chitin with high potential for application in technology and biomedicine.
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Affiliation(s)
- Tomasz Machałowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, 60965 Poznan, Poland.
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Marcin Wysokowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, 60965 Poznan, Poland.
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Mikhail V Tsurkan
- Leibniz Institute of Polymer Research Dresden, Dresden 01069, Germany.
| | - Roberta Galli
- Clinical Sensoring and Monitoring, Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine, TU Dresden, 01307 Dresden, Germany.
| | - Christian Schimpf
- Institute of Materials Science, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - David Rafaja
- Institute of Materials Science, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Erica Brendler
- Institute of Analytical Chemistry, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Christine Viehweger
- Institute of Analytical Chemistry, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Sonia Żółtowska-Aksamitowska
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, 60965 Poznan, Poland.
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Iaroslav Petrenko
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Katarzyna Czaczyk
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 60637 Poznan, Poland.
| | - Michael Kraft
- Institute of Chemical Technology, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Martin Bertau
- Institute of Chemical Technology, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Nicole Bechmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany.
| | - Kaomei Guan
- Institute of Pharmacology and Toxicology, TU Dresden, 01307 Dresden, Germany.
| | - Stefan R Bornstein
- Center for Regenerative Therapies Dresden, TU Dresden, 01307 Dresden, Germany.
- Department of Medicine III, University Hospital Carl Gustav Carus Dresden, TU Dresden, 01307 Dresden, Germany.
| | - Alona Voronkina
- Department of Pharmacy, National Pirogov Memorial Medical University, 21018 Vinnytsia, Ukraine.
| | - Andriy Fursov
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61704 Poznan, Poland.
| | | | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61704 Poznan, Poland.
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61704 Poznan, Poland.
| | - Oleg Pokrovsky
- Geoscience and Environment Toulouse, UMR 5563 CNRS, 31400 Toulouse, France.
- BIO-GEO-CLIM Laboratory, Tomsk State University, Lenina St. 36, 634050 Tomsk, Russia.
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, 60965 Poznan, Poland.
| | - Hermann Ehrlich
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany.
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Koralewska N, Ciechanowska K, Pokornowska M, Figlerowicz M, Kurzyńska-Kokorniak A. Human ribonuclease Dicer – structure and functions. Postepy Biochem 2019; 65:173-182. [PMID: 31643164 DOI: 10.18388/pb.2019_267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/14/2019] [Indexed: 11/10/2022]
Abstract
Endoribonuclease III Dicer plays a crucial role in the biogenesis of small regulatory RNAs, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, this is not the only role that Dicer plays in cells. For example, it has been shown that Dicer is involved in processing of diverse classes of RNA, including tRNA and snoRNA, cleavage of repeat-element-derived RNAs, and maintenance of genome integrity. Dicer has also been found to participate in the chromosome fragmentation during apoptosis or in the inflammatory processes. Moreover, a recent discovery of Dicer-binding passive sites in mRNAs and long non-coding RNAs, and its putative nucleic acid chaperone activity, has pointed out a novel regulatory role of the enzyme. Here we focus on human Dicer and review its structure and function including recent findings on miRNA-independent roles and their impact on cell biology.
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Machałowski T, Wysokowski M, Żółtowska-Aksamitowska S, Bechmann N, Binnewerg B, Schubert M, Guan K, Bornstein SR, Czaczyk K, Pokrovsky O, Kraft M, Bertau M, Schimpf C, Rafaja D, Tsurkan M, Galli R, Meissner H, Petrenko I, Fursov A, Voronkina A, Figlerowicz M, Joseph Y, Jesionowski T, Ehrlich H. Spider Chitin. The biomimetic potential and applications of Caribena versicolor tubular chitin. Carbohydr Polym 2019; 226:115301. [PMID: 31582063 DOI: 10.1016/j.carbpol.2019.115301] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/15/2019] [Accepted: 09/05/2019] [Indexed: 12/31/2022]
Abstract
Diverse fields of modern technology and biomedicine can benefit from the application of ready-to-use chitin-based scaffolds. In this work we show for the first time the applicability of tubular and porous chitin from Caribena versicolor spiders as a scaffold for the development of an effective CuO/Cu(OH)2 catalyst for the reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AM), and as a scaffold for the tissue engineering of selected cells. The formation of CuO/Cu(OH)2 phases on and within the chitinous tubes leads to a hybrid material with excellent catalytic performance with respect to the reduction of p-nitrophenol. On the other hand, experimental results provide for the first time strong evidence for the biocompatibility of spider chitin with different cell types, a human progenitor cell line (hPheo1), as well as cardiomyocytes differentiated from induced pluripotent stem cells (iPSC-CMs) that were cultured on a tube-like scaffold.
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Affiliation(s)
- Tomasz Machałowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Poznan 60965, Poland
| | - Marcin Wysokowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Poznan 60965, Poland; Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, Freiberg 09599, Germany
| | - Sonia Żółtowska-Aksamitowska
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Poznan 60965, Poland; Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, Freiberg 09599, Germany
| | - Nicole Bechmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, TU Dresden, Dresden 01307, Germany
| | - Björn Binnewerg
- Institute of Pharmacology and Toxicology, TU Dresden, Dresden 01307, Germany
| | - Mario Schubert
- Institute of Pharmacology and Toxicology, TU Dresden, Dresden 01307, Germany
| | - Kaomei Guan
- Institute of Pharmacology and Toxicology, TU Dresden, Dresden 01307, Germany
| | - Stefan R Bornstein
- Department of Medicine III, University Hospital Carl Gustav Carus Dresden, TU Dresden, Dresden 01307, Germany
| | - Katarzyna Czaczyk
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Poznan 60637, Poland
| | - Oleg Pokrovsky
- Geoscience and Environment Toulouse, UMR 5563 CNRS, Toulouse 31400, France; BIO-GEO-CLIM Laboratory, Tomsk State University, Tomsk, Russia
| | - Michael Kraft
- Institute of Chemical Technology, TU Bergakademie Freiberg, Freiberg 09599, Germany
| | - Martin Bertau
- Institute of Chemical Technology, TU Bergakademie Freiberg, Freiberg 09599, Germany
| | - Christian Schimpf
- Institute of Materials Science, TU Bergakademie Freiberg, Freiberg 09599, Germany
| | - David Rafaja
- Institute of Materials Science, TU Bergakademie Freiberg, Freiberg 09599, Germany
| | - Mikhail Tsurkan
- Leibnitz Institute of Polymer Research Dresden, Dresden 01069, Germany
| | - Roberta Galli
- Clinical Sensoring and Monitoring, Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine, TU Dresden, Dresden 01307, Germany
| | - Heike Meissner
- Department of Prosthetic Dentistry, Faculty of Medicine, TU Dresden, Dresden 01307, Germany
| | - Iaroslav Petrenko
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, Freiberg 09599, Germany
| | - Andriy Fursov
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, Freiberg 09599, Germany
| | - Alona Voronkina
- Department of Pharmacy, National Pirogov Memorial Medical University, Vinnytsia 21018, Ukraine
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61704, Poland
| | - Yvonne Joseph
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, Freiberg 09599, Germany
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Poznan 60965, Poland.
| | - Hermann Ehrlich
- Institute of Electronics and Sensor Materials, TU Bergakademie Freiberg, Freiberg 09599, Germany.
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Wiatr K, Piasecki P, Marczak Ł, Wojciechowski P, Kurkowiak M, Płoski R, Rydzanicz M, Handschuh L, Jungverdorben J, Brüstle O, Figlerowicz M, Figiel M. Altered Levels of Proteins and Phosphoproteins, in the Absence of Early Causative Transcriptional Changes, Shape the Molecular Pathogenesis in the Brain of Young Presymptomatic Ki91 SCA3/MJD Mouse. Mol Neurobiol 2019; 56:8168-8202. [PMID: 31201651 PMCID: PMC6834541 DOI: 10.1007/s12035-019-01643-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/10/2019] [Indexed: 12/19/2022]
Abstract
Spinocerebellar ataxia type 3 (SCA3/MJD) is a polyQ neurodegenerative disease where the presymptomatic phase of pathogenesis is unknown. Therefore, we investigated the molecular network of transcriptomic and proteomic triggers in young presymptomatic SCA3/MJD brain from Ki91 knock-in mouse. We found that transcriptional dysregulations resulting from mutant ataxin-3 are not occurring in young Ki91 mice, while old Ki91 mice and also postmitotic patient SCA3 neurons demonstrate the late transcriptomic changes. Unlike the lack of early mRNA changes, we have identified numerous early changes of total proteins and phosphoproteins in 2-month-old Ki91 mouse cortex and cerebellum. We discovered the network of processes in presymptomatic SCA3 with three main groups of disturbed processes comprising altered proteins: (I) modulation of protein levels and DNA damage (Pabpc1, Ddb1, Nedd8), (II) formation of neuronal cellular structures (Tubb3, Nefh, p-Tau), and (III) neuronal function affected by processes following perturbed cytoskeletal formation (Mt-Co3, Stx1b, p-Syn1). Phosphoproteins downregulate in the young Ki91 mouse brain and their phosphosites are associated with kinases that interact with ATXN3 such as casein kinase, Camk2, and kinases controlled by another Atxn3 interactor p21 such as Gsk3, Pka, and Cdk kinases. We conclude that the onset of SCA3 pathology occurs without altered transcript level and is characterized by changed levels of proteins responsible for termination of translation, DNA damage, spliceosome, and protein phosphorylation. This disturbs global cellular processes such as cytoskeleton and transport of vesicles and mitochondria along axons causing energy deficit and neurodegeneration also manifesting in an altered level of transcripts at later ages.
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Affiliation(s)
- Kalina Wiatr
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Piotr Piasecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Łukasz Marczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Paweł Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland.,Institute of Computing Science, Poznan University of Technology, Poznań, Poland
| | - Małgorzata Kurkowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Luiza Handschuh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Johannes Jungverdorben
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn School of Medicine & University Hospital Bonn, 53127, Bonn, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn School of Medicine & University Hospital Bonn, 53127, Bonn, Germany
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Maciej Figiel
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland.
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28
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Grzegorzewska AE, Mostowska A, Świderska M, Marcinkowski W, Stolarek I, Figlerowicz M, Jagodziński PP. FP679IFNL4 rs368234815 POLYMORPHISM AND SPONTANEOUS CLEARANCE OF HEPATITIS C VIRUS IN HEMODIALYSIS PATIENTS. Nephrol Dial Transplant 2019. [DOI: 10.1093/ndt/gfz106.fp679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Świtońska K, Szlachcic WJ, Handschuh L, Wojciechowski P, Marczak Ł, Stelmaszczuk M, Figlerowicz M, Figiel M. Identification of Altered Developmental Pathways in Human Juvenile HD iPSC With 71Q and 109Q Using Transcriptome Profiling. Front Cell Neurosci 2019; 12:528. [PMID: 30713489 PMCID: PMC6345698 DOI: 10.3389/fncel.2018.00528] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/19/2018] [Indexed: 12/29/2022] Open
Abstract
In Huntington disease (HD) subtle symptoms in patients may occur years or even decades prior to diagnosis. HD changes at a molecular level may begin as early as in cells that are non-lineage committed such as stem cells or HD patients induced pluripotent stem cells (iPSCs) offering opportunity to enhance the understanding of the HD pathogenesis. In addition, juvenile HD non-linage committed cells were previously not directly investigated in detail by RNA-seq. In the present manuscript, we define the early HD and juvenile HD transcriptional alterations using 6 human HD iPS cell lines from two patients, one with 71 CAGs and one with 109 CAG repeats. We identified 107 (6 HD lines), 198 (3 HD71Q lines) and 217 (3 HD109Q lines) significantly dysregulated mRNAs in each comparison group. The analyses showed that many of dysregulated transcripts in HD109Q iPSC lines are involved in DNA damage response and apoptosis, such as CCND1, CDKN1A, TP53, BAX, TNFRSF10B, TNFRSF10C, TNFRSF10D, DDB2, PLCB1, PRKCQ, HSH2D, ZMAT3, PLK2, and RPS27L. Most of them were identified as downregulated and their proteins are direct interactors with TP53. HTT probably alters the level of several TP53 interactors influencing apoptosis. This may lead to accumulation of an excessive number of progenitor cells and potential disruption of cell differentiation and production of mature neurons. In addition, HTT effects on cell polarization also demonstrated in the analysis may result in a generation of incorrect progenitors. Bioinformatics analysis of transcripts dysregulated in HD71Q iPSC lines showed that several of them act as transcription regulators during the early multicellular stages of development, such as ZFP57, PIWIL2, HIST1H3C, and HIST1H2BB. Significant upregulation of most of these transcripts may lead to a global increase in expression level of genes involved in pathways critical for embryogenesis and early neural development. In addition, MS analysis revealed altered levels of TP53 and ZFP30 proteins reflecting the functional significance of dysregulated mRNA levels of these proteins which were associated with apoptosis and DNA binding. Our finding very well corresponds to the fact that mutation in the HTT gene may cause precocious neurogenesis and identifies pathways likely disrupted during development.
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Affiliation(s)
- Karolina Świtońska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | | | - Luiza Handschuh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Paweł Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.,Institute of Computing Science, Poznan University of Technology, Poznań, Poland
| | - Łukasz Marczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Michał Stelmaszczuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Maciej Figiel
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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Szczepaniak A, Książkiewicz M, Podkowiński J, Czyż KB, Figlerowicz M, Naganowska B. Legume Cytosolic and Plastid Acetyl-Coenzyme-A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications. Genes (Basel) 2018; 9:genes9110563. [PMID: 30469317 PMCID: PMC6265850 DOI: 10.3390/genes9110563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 01/01/2023] Open
Abstract
Acetyl-coenzyme A carboxylase (ACCase, E.C.6.4.1.2) catalyzes acetyl-coenzyme A carboxylation to malonyl coenzyme A. Plants possess two distinct ACCases differing by cellular compartment and function. Plastid ACCase contributes to de novo fatty acid synthesis, whereas cytosolic enzyme to the synthesis of very long chain fatty acids, phytoalexins, flavonoids, and anthocyanins. The narrow leafed lupin (Lupinus angustifolius L.) represents legumes, a plant family which evolved by whole-genome duplications (WGDs). The study aimed on the contribution of these WGDs to the multiplication of ACCase genes and their further evolutionary patterns. The molecular approach involved bacterial artificial chromosome (BAC) library screening, fluorescent in situ hybridization, linkage mapping, and BAC sequencing. In silico analysis encompassed sequence annotation, comparative mapping, selection pressure calculation, phylogenetic inference, and gene expression profiling. Among sequenced legumes, the highest number of ACCase genes was identified in lupin and soybean. The most abundant plastid ACCase subunit genes were accB. ACCase genes in legumes evolved by WGDs, evidenced by shared synteny and Bayesian phylogenetic inference. Transcriptional activity of almost all copies was confirmed. Gene duplicates were conserved by strong purifying selection, however, positive selection occurred in Arachis (accB2) and Lupinus (accC) lineages, putatively predating the WGD event(s). Early duplicated accA and accB genes underwent transcriptional sub-functionalization.
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Affiliation(s)
- Anna Szczepaniak
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
| | - Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
| | - Jan Podkowiński
- Department of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland.
| | - Katarzyna B Czyż
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
| | - Marek Figlerowicz
- Department of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland.
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
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Grzegorzewska AE, Niepolski L, Świderska MK, Mostowska A, Stolarek I, Warchoł W, Figlerowicz M, Jagodziński PP. ENHO, RXRA, and LXRA polymorphisms and dyslipidaemia, related comorbidities and survival in haemodialysis patients. BMC Med Genet 2018; 19:194. [PMID: 30413149 PMCID: PMC6234788 DOI: 10.1186/s12881-018-0708-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/23/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND The energy homeostasis-associated gene (ENHO), retinoid X receptor alpha gene (RXRA), and liver X receptor alpha gene (LXRA) are involved in adipogenic/lipogenic regulation. We investigated whether single-nucleotide polymorphisms in these genes (ENHO rs2281997, rs72735260; RXRA rs749759, rs10776909, rs10881578; LXRA rs2279238, rs7120118, rs11039155) are associated with dyslipidaemia, related comorbidities and survival of haemodialysis (HD) patients also tested for T-helper (Th) cell interleukin genes (IL). METHODS The study was carried out in 873 HD patients. Dyslipidaemia was diagnosed by the recommendations of the Kidney Disease Outcomes Quality Initiative (K/DOQI) guidelines (2003); atherogenic dyslipidaemia was referred to if the TG/HDL cholesterol ratio was equal to or higher than 3.8. Genotyping of ENHO SNPs, LXRA SNPs, and IL12A rs568408 was carried out using HRM analysis. RXRA SNPs, IL12B rs3212227, and IL18 rs360719 were genotyped using PCR-RFLP analysis. The circulating adropin concentration was determined in 126 patients by enzyme-linked immunosorbent assay. Survival probability was analysed using the Kaplan-Meier method in 440 patients followed through 7.5 years. RESULTS Dyslipidaemia by K/DOQI was diagnosed in 459 patients (91% revealed hyper-LDL- cholesterolaemia), atherogenic dyslipidaemia was diagnosed in 454 patients, and 231 patients were free of dyslipidaemia by both criteria. The variant allele (T) of ENHO rs2281997 was associated with the hyper-LDL cholesterolaemic pattern of dyslipidaemia by K/DOQI. The frequency of atherogenic dyslipidaemia was lower in T-allele bearers than in CC-genotype patients. The rs2281997 T allele was associated with lower cardiovascular mortality in HD patients showing atherogenic dyslipidaemia. ENHO, RXRA, and LXRA showed epistatic interactions in dyslipidaemia. Circulating adropin was lower in atherogenic dyslipidaemia than in non-atherogenic conditions. RXRA rs10776909 was associated with myocardial infarction. Bearers of LXRA rs2279238, rs7120118 or rs11039155 minor alleles showed higher mortality. ENHO SNP positions fell within the same DNase 1 hypersensitivity site expressed in the Th1 cell line. Epistatic interactions occurred between rs2281997 and Th1 IL SNPs (rs360719, rs568408). CONCLUSIONS Atherogenic dyslipidaemia occurs in HD patients in whom ENHO encodes less adropin. ENHO, RXRA, and LXRA SNPs, separately or jointly, are associated with dyslipidaemia, myocardial infarction, and survival in HD patients. Differences in the availability of transcription binding sites may contribute to these associations.
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Affiliation(s)
- Alicja E Grzegorzewska
- Department of Nephrology, Transplantology and Internal Diseases, Poznan University of Medical Sciences (PUMS), Poznań, Poland.
| | | | - Monika K Świderska
- Department of Nephrology, Transplantology and Internal Diseases, Poznan University of Medical Sciences (PUMS), Poznań, Poland
| | | | - Ireneusz Stolarek
- Polish Academy of Sciences, Institute of Bioorganic Chemistry, Poznań, Poland
| | | | - Marek Figlerowicz
- Polish Academy of Sciences, Institute of Bioorganic Chemistry, Poznań, Poland
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Obrępalska-Stęplowska A, Zmienko A, Wrzesińska B, Goralski M, Figlerowicz M, Zyprych-Walczak J, Siatkowski I, Pospieszny H. The Defense Response of Nicotiana benthamiana to Peanut Stunt Virus Infection in the Presence of Symptom Exacerbating Satellite RNA. Viruses 2018; 10:E449. [PMID: 30142955 PMCID: PMC6165542 DOI: 10.3390/v10090449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/02/2018] [Accepted: 08/22/2018] [Indexed: 01/22/2023] Open
Abstract
Peanut stunt virus (PSV) is a widespread disease infecting legumes. The PSV strains are classified into four subgroups and some are defined by the association of satellite RNAs (satRNAs). In the case of PSV, the presence of satRNAs alters the symptoms of disease in infected plants. In this study, we elucidated the plant response to PSV-G strain, which occurs in natural conditions without satRNA. However, it was found that it might easily acquire satRNA, which exacerbated pathogenesis in Nicotiana benthamiana. To explain the mechanisms underlying PSV infection and symptoms exacerbation caused by satRNA, we carried out transcriptome profiling of N. benthamiana challenged by PSV-G and satRNA using species-specific microarrays. Co-infection of plants with PSV-G + satRNA increased the number of identified differentially expressed genes (DEGs) compared with the number identified in PSV-G-infected plants. In both treatments, the majority of up-regulated DEGs were engaged in translation, ribosome biogenesis, RNA metabolism, and response to stimuli, while the down-regulated DEGs were required for photosynthesis. The presence of satRNA in PSV-G-infected plants caused different trends in expression of DEGs associated with phosphorylation, ATP binding, and plasma membrane.
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Affiliation(s)
- Aleksandra Obrępalska-Stęplowska
- Department of Entomology, Animal Pests and Biotechnology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka Street, 60-318 Poznań, Poland.
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704 Poznań, Poland.
- Institute of Computing Science, Faculty of Computing Science, Poznań University of Technology, 2 Piotrowo Street, 60-965 Poznań, Poland.
| | - Barbara Wrzesińska
- Department of Entomology, Animal Pests and Biotechnology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka Street, 60-318 Poznań, Poland.
| | - Michal Goralski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704 Poznań, Poland.
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704 Poznań, Poland.
- Institute of Computing Science, Faculty of Computing Science, Poznań University of Technology, 2 Piotrowo Street, 60-965 Poznań, Poland.
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, University of Life Sciences in Poznań, Wojska Polskiego 28 Street, 60-637 Poznań, Poland.
| | - Idzi Siatkowski
- Department of Mathematical and Statistical Methods, University of Life Sciences in Poznań, Wojska Polskiego 28 Street, 60-637 Poznań, Poland.
| | - Henryk Pospieszny
- Department of Virology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka Street, 60-318 Poznań, Poland.
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Handschuh L, Wojciechowski P, Kazmierczak M, Marcinkowska-Swojak M, Luczak M, Lewandowski K, Komarnicki M, Blazewicz J, Figlerowicz M, Kozlowski P. NPM1 alternative transcripts are upregulated in acute myeloid and lymphoblastic leukemia and their expression level affects patient outcome. J Transl Med 2018; 16:232. [PMID: 30126426 PMCID: PMC6102803 DOI: 10.1186/s12967-018-1608-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 08/14/2018] [Indexed: 11/29/2022] Open
Abstract
Background Expression of the NPM1 gene, encoding nucleophosmin, is upregulated in cancers. Although more than ten NPM1 transcripts are known, the reports were usually limited to one predominant transcript. In leukemia, the NPM1 expression has not been widely studied so far. In acute myeloid leukemia (AML), the mutational status of the gene seems to play a pivotal role in carcinogenesis. Therefore, the aim of the study was to quantify alternative NPM1 transcripts in two types of acute leukemia, AML and ALL (acute lymphoblastic leukemia). Methods Using droplet digital PCR, we analyzed the levels of three protein-coding NPM1 transcripts in 66 samples collected from AML and ALL patients and 16 control samples. Using RNA-seq, we detected 8 additional NPM1 transcripts, including non-coding splice variants with retained introns. For data analysis, Welch two sample t-test, Pearson’s correlation and Kaplan–Meier analysis were applied. Results The levels of the particular NPM1 transcripts were significantly different but highly correlated with each other in both leukemia and control samples. Transcript NPM1.1, encoding the longest protein (294 aa), had the highest level of accumulation and was one of the most abundant transcripts in the cell. Comparing to NPM1.1, the levels of the NPM1.2 and NPM1.3 transcripts, encoding a 265-aa and 259-aa proteins, were 30 and 3 times lower, respectively. All three NPM1 transcripts were proportionally upregulated in both types of leukemia compared to control samples. In AML, the levels of NPM1 transcripts decreased in complete remission and increased again with relapse of the disease. Low levels of NPM1.1 and NPM1.3 were associated with better prognosis. The contribution of non-coding transcripts to the total level of NPM1 gene seemed to be marginal, except for one short 5-end transcript accumulated at high levels in AML and control cells. Aberrant proportions of particular NPM1 splice variants could be linked to abnormal expression of genes encoding alternative splicing factors. Conclusions The levels of the studied NPM1 transcripts were different but highly correlated with each other. Their upregulation in AML and ALL, decrease after therapy and association with patient outcome suggests the involvement of elevated NPM1 expression in the acute leukemia pathogenesis. Electronic supplementary material The online version of this article (10.1186/s12967-018-1608-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luiza Handschuh
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Szamarzewskiego 84, 60-569, Poznan, Poland.
| | - Pawel Wojciechowski
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Maciej Kazmierczak
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Szamarzewskiego 84, 60-569, Poznan, Poland
| | - Malgorzata Marcinkowska-Swojak
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Magdalena Luczak
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Technology and Chemical Engineering, Poznan University of Technology, Poznan, Poland
| | - Krzysztof Lewandowski
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Szamarzewskiego 84, 60-569, Poznan, Poland
| | - Mieczyslaw Komarnicki
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Szamarzewskiego 84, 60-569, Poznan, Poland
| | - Jacek Blazewicz
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Marek Figlerowicz
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Piotr Kozlowski
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Technology and Chemical Engineering, Poznan University of Technology, Poznan, Poland
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Rakoczy M, Femiak I, Alejska M, Figlerowicz M, Podkowinski J. Sorghum CCoAOMT and CCoAOMT-like gene evolution, structure, expression and the role of conserved amino acids in protein activity. Mol Genet Genomics 2018; 293:1077-1089. [PMID: 29721721 PMCID: PMC6153501 DOI: 10.1007/s00438-018-1441-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/24/2018] [Indexed: 11/28/2022]
Abstract
Sorghum is a crop plant that is grown for seeds, sucrose, forage and biofuel production. In all these applications, lignin is a superfluous component that decreases the efficiency of technological processes. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) is an enzyme involved in monolignol synthesis that affects the efficiency of lignification and lignin composition. The sorghum genome harbors one CCoAOMT gene and six closely related CCoAOMT-like genes. The structures of four sorghum CCoAOMT-like enzymes suggest that these proteins might methylate caffeoyl coenzyme A and contribute to monolignol synthesis. In this study, two sorghum genes, CCoAOMT and one CCoAOMT-like, were found to be highly expressed in leaves, stems and immature seeds. The promoters of these genes possess clusters of transcription factor-binding sites specific for lignification, and this suggests that they are important for lignification. Phylogenetic analysis revealed that one sorghum CCoAOMT-like enzyme is closely related to ancestral cyanobacterial CCoAOMT-like proteins. The remaining CCoAOMT-like enzymes, including the one highly expressed in the leaves and stem, are closely related to CCoAOMT. Genes from these two groups possess different, evolutionarily conserved gene structures. The structure of the sorghum CCoAOMT-like protein from the ancestral clade was modeled and differences between enzymes from the two clades were analyzed. These results facilitate a better understanding of the evolution of genes involved in lignification, and provide valuable data for sorghum improvement through traditional breeding or molecular genetic techniques. The findings suggest that CCoAOMT-like genes might be recruited in lignification and raise questions of the frequency of such functional shifts.
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Affiliation(s)
- M Rakoczy
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - I Femiak
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - M Alejska
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - M Figlerowicz
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - J Podkowinski
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland.
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Grzegorzewska A, Frycz B, Świderska M, Niepolski L, Mostowska A, Stolarek I, Figlerowicz M, Jagodziński P. SP017CALCIUM-SENSING RECEPTOR GENE (CASR) SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) AND CASR TRANSCRIPT LEVEL CONCERNING DYSLIPIDEMIA IN HEMODIALYSIS (HD) PATIENTS: A CROSS-SECTIONAL STUDY. Nephrol Dial Transplant 2018. [DOI: 10.1093/ndt/gfy104.sp017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alicja Grzegorzewska
- Department od Nephrology, Poznań University of Medical Sciences (PUMS), Poznań, Poland
| | - Bartosz Frycz
- Department of Biochemistry and Molecular Biology, PUMS, Poznań, Poland
| | | | | | | | - Ireneusz Stolarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Paweł Jagodziński
- Department of Biochemistry and Molecular Biology, PUMS, Poznań, Poland
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Klonowska K, Handschuh L, Swiercz A, Figlerowicz M, Kozlowski P. MTTE: an innovative strategy for the evaluation of targeted/exome enrichment efficiency. Oncotarget 2018; 7:67266-67276. [PMID: 27572310 PMCID: PMC5341873 DOI: 10.18632/oncotarget.11646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 07/28/2016] [Indexed: 02/06/2023] Open
Abstract
Although currently available strategies for the preparation of exome-enriched libraries are well established, a final validation of the libraries in terms of exome enrichment efficiency prior to the sequencing step is of considerable importance. Here, we present a strategy for the evaluation of exome enrichment, i.e., the Multipoint Test for Targeted-enrichment Efficiency (MTTE), PCR-based approach utilizing multiplex ligation-dependent probe amplification with capillary electrophoresis separation. We used MTTE for the analysis of subsequent steps of the Illumina TruSeq Exome Enrichment procedure. The calculated values of enrichment-associated parameters (i.e., relative enrichment, relative clearance, overall clearance, and fold enrichment) and the comparison of MTTE results with the actual enrichment revealed the high reliability of our assay. Additionally, the MTTE assay enabled the determination of the sequence-associated features that may confer bias in the enrichment of different targets. Importantly, the MTTE is low cost method that can be easily adapted to the region of interest important for a particular project. Thus, the MTTE strategy is attractive for post-capture validation in a variety of targeted/exome enrichment NGS projects.
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Affiliation(s)
- Katarzyna Klonowska
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Luiza Handschuh
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.,Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Aleksandra Swiercz
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Marek Figlerowicz
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Piotr Kozlowski
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.,Institute of Technology and Chemical Engineering, Poznan University of Technology, 60-965 Poznan, Poland
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Strugała A, Bierwagen P, Rybka J, Giersig M, Figlerowicz M, Urbanowicz A. BMV Propagation, Extraction and Purification Using Chromatographic Methods. Bio Protoc 2018; 8:e2935. [DOI: 10.21769/bioprotoc.2935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/06/2018] [Accepted: 07/26/2018] [Indexed: 11/02/2022] Open
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Handschuh L, Kaźmierczak M, Milewski MC, Góralski M, Łuczak M, Wojtaszewska M, Uszczyńska-Ratajczak B, Lewandowski K, Komarnicki M, Figlerowicz M. Gene expression profiling of acute myeloid leukemia samples from adult patients with AML-M1 and -M2 through boutique microarrays, real-time PCR and droplet digital PCR. Int J Oncol 2017; 52:656-678. [PMID: 29286103 PMCID: PMC5807040 DOI: 10.3892/ijo.2017.4233] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/12/2017] [Indexed: 01/25/2023] Open
Abstract
Acute myeloid leukemia (AML) is the most common and severe form of acute leukemia diagnosed in adults. Owing to its heterogeneity, AML is divided into classes associated with different treatment outcomes and specific gene expression profiles. Based on previous studies on AML, in this study, we designed and generated an AML-array containing 900 oligonucleotide probes complementary to human genes implicated in hematopoietic cell differentiation and maturation, proliferation, apoptosis and leukemic transformation. The AML-array was used to hybridize 118 samples from 33 patients with AML of the M1 and M2 subtypes of the French-American-British (FAB) classification and 15 healthy volunteers (HV). Rigorous analysis of the microarray data revealed that 83 genes were differentially expressed between the patients with AML and the HV, including genes not yet discussed in the context of AML pathogenesis. The most overexpressed genes in AML were STMN1, KITLG, CDK6, MCM5, KRAS, CEBPA, MYC, ANGPT1, SRGN, RPLP0, ENO1 and SET, whereas the most underexpressed genes were IFITM1, LTB, FCN1, BIRC3, LYZ, ADD3, S100A9, FCER1G, PTRPE, CD74 and TMSB4X. The overexpression of the CPA3 gene was specific for AML with mutated NPM1 and FLT3. Although the microarray-based method was insufficient to differentiate between any other AML subgroups, quantitative PCR approaches enabled us to identify 3 genes (ANXA3, S100A9 and WT1) whose expression can be used to discriminate between the 2 studied AML FAB subtypes. The expression levels of the ANXA3 and S100A9 genes were increased, whereas those of WT1 were decreased in the AML-M2 compared to the AML-M1 group. We also examined the association between the STMN1, CAT and ABL1 genes, and the FLT3 and NPM1 mutation status. FLT3+/NPM1− AML was associated with the highest expression of STMN1, and ABL1 was upregulated in FLT3+ AML and CAT in FLT3− AML, irrespectively of the NPM1 mutation status. Moreover, our results indicated that CAT and WT1 gene expression levels correlated with the response to therapy. CAT expression was highest in patients who remained longer under complete remission, whereas WT1 expression increased with treatment resistance. On the whole, this study demonstrates that the AML-array can potentially serve as a first-line screening tool, and may be helpful for the diagnosis of AML, whereas the differentiation between AML subgroups can be more successfully performed with PCR-based analysis of a few marker genes.
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Affiliation(s)
- Luiza Handschuh
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Maciej Kaźmierczak
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Marek C Milewski
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Michał Góralski
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Łuczak
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Marzena Wojtaszewska
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Barbara Uszczyńska-Ratajczak
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Krzysztof Lewandowski
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Mieczysław Komarnicki
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Marek Figlerowicz
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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Jackowiak P, Hojka-Osinska A, Gasiorek K, Stelmaszczuk M, Gudanis D, Gdaniec Z, Figlerowicz M. Effects of G-quadruplex topology on translational inhibition by tRNA fragments in mammalian and plant systems in vitro. Int J Biochem Cell Biol 2017; 92:148-154. [PMID: 28989078 DOI: 10.1016/j.biocel.2017.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/05/2017] [Accepted: 10/04/2017] [Indexed: 02/07/2023]
Abstract
The folding of tRNA fragments (tRFs) into G-quadruplex structures and the implications of G-quadruplexes in translational inhibition have been studied mainly in mammalian systems. To increase our knowledge of these phenomena, we determined the influence of human and plant tRFs and model G-quadruplexes on translation in rabbit reticulocyte lysate and wheat germ extract. The efficiency of translational inhibition in the mammalian system was strongly associated with the type of G-quadruplex topology. In the plant system, the ability of a small RNA to adopt the G-quadruplex conformation was not sufficient to repress translation, indicating the importance of other structural determinants.
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Affiliation(s)
- Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Anna Hojka-Osinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Katarzyna Gasiorek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Michal Stelmaszczuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Dorota Gudanis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznan, Poland.
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Szlachcic WJ, Wiatr K, Trzeciak M, Figlerowicz M, Figiel M. Corrigendum: The Generation of Mouse and Human Huntington Disease iPS Cells Suitable for In vitro Studies on Huntingtin Function. Front Mol Neurosci 2017; 10:312. [PMID: 28983241 PMCID: PMC5625326 DOI: 10.3389/fnmol.2017.00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/15/2017] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article on p. 253 in vol. 10, PMID: 28848389.].
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Affiliation(s)
- Wojciech J Szlachcic
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Kalina Wiatr
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Marta Trzeciak
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Marek Figlerowicz
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Maciej Figiel
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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Szlachcic WJ, Wiatr K, Trzeciak M, Figlerowicz M, Figiel M. The Generation of Mouse and Human Huntington Disease iPS Cells Suitable for In vitro Studies on Huntingtin Function. Front Mol Neurosci 2017; 10:253. [PMID: 28848389 PMCID: PMC5550714 DOI: 10.3389/fnmol.2017.00253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/26/2017] [Indexed: 01/24/2023] Open
Abstract
Huntington disease (HD) is an incurable neurodegenerative disorder caused by expansion of CAG repeats in huntingtin (HTT) gene, resulting in expanded polyglutamine tract in HTT protein. Although, HD has its common onset in adulthood, subtle symptoms in patients may occur decades before diagnosis, and molecular and cellular changes begin much earlier, even in cells that are not yet lineage committed such as stem cells. Studies in induced pluripotent stem cell (iPSC) HD models have demonstrated that multiple molecular processes are altered by the mutant HTT protein and suggested its silencing as a promising therapeutic strategy. Therefore, we aimed to generate HD iPS cells with stable silencing of HTT and further to investigate the effects of HTT knock-down on deregulations of signaling pathways e.g., p53 downregulation, present in cells already in pluripotent state. We designed a gene silencing strategy based on RNAi cassette in piggyBAC vector for constant shRNA expression. Using such system we delivered and tested several shRNA targeting huntingtin in mouse HD YAC128 iPSC and human HD109, HD71, and Control iPSC. The most effective shRNA (shHTT2) reagent stably silenced HTT in all HD iPS cells and remained active upon differentiation to neural stem cells (NSC). When investigating the effects of HTT silencing on signaling pathways, we found that in mouse HD iPSC lines expressing shRNA the level of mutant HTT inversely correlated with p53 levels, resulting in p53 level normalization upon silencing of mutant HTT. We also found that p53 deregulation continues into the NSC developmental stage and it was reversed upon HTT silencing. In addition, we observed subtle effects of silencing on proteins of Wnt/β-catenin and ERK1/2 signaling pathways. In summary, we successfully created the first mouse and human shRNA-expressing HD iPS cells with stable and continuous HTT silencing. Moreover, we demonstrated reversal of HD p53 phenotype in mouse HD iPSC, therefore, the stable knockdown of HTT is well-suited for investigation on HD cellular pathways, and is potentially useful as a stand-alone therapy or component of cell therapy. In addition, the total HTT knock-down in our human cells has further implications for mutant allele selective approach in iPSC.
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Affiliation(s)
- Wojciech J Szlachcic
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznań, Poland
| | - Kalina Wiatr
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznań, Poland
| | - Marta Trzeciak
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznań, Poland
| | - Marek Figlerowicz
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznań, Poland
| | - Maciej Figiel
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznań, Poland
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Philips A, Stolarek I, Kuczkowska B, Juras A, Handschuh L, Piontek J, Kozlowski P, Figlerowicz M. Comprehensive analysis of microorganisms accompanying human archaeological remains. Gigascience 2017; 6:1-13. [PMID: 28609785 PMCID: PMC5965364 DOI: 10.1093/gigascience/gix044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/09/2017] [Accepted: 06/11/2017] [Indexed: 02/01/2023] Open
Abstract
Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains. DNA samples were isolated from the teeth of human skeletons dated from 100 AD to 1200 AD. The skeletons were collected from 7 archaeological sites in Central Europe and stored under different conditions. The majority of identified microbes were ubiquitous environmental bacteria that most likely contaminated the host remains not long ago. We observed that the composition of microbial communities was sample-specific and not correlated with its temporal or geographical origin. Additionally, traces of bacteria and archaea typical for human oral/gut flora, as well as potential pathogens, were identified in two-thirds of the samples. The genetic material of human-related species, in contrast to the environmental species that accounted for the majority of identified bacteria, displayed DNA damage patterns comparable with endogenous human ancient DNA, which suggested that these microbes might have accompanied the individual before death. Our study showed that the microbiome observed in an individual sample is not reliant on the method or duration of sample storage. Moreover, shallow sequencing of DNA extracted from ancient specimens and subsequent bioinformatics analysis allowed both the identification of ancient microbial species, including potential pathogens, and their differentiation from contemporary species that colonized human remains more recently.
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Affiliation(s)
- Anna Philips
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Ireneusz Stolarek
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Bogna Kuczkowska
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty
of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland
| | - Luiza Handschuh
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Department of Hematology and Bone Marrow Transplantation, University of
Medical Sciences, Poznan, 60-569, Poland
- Institute of Technology and Chemical Engineering, Poznan University of
Technology, Poznan, 60-965, Poland
| | - Janusz Piontek
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty
of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland
| | - Piotr Kozlowski
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Institute of Technology and Chemical Engineering, Poznan University of
Technology, Poznan, 60-965, Poland
| | - Marek Figlerowicz
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan,
60-965, Poland
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Jackowiak P, Hojka-Osinska A, Philips A, Zmienko A, Budzko L, Maillard P, Budkowska A, Figlerowicz M. Small RNA fragments derived from multiple RNA classes - the missing element of multi-omics characteristics of the hepatitis C virus cell culture model. BMC Genomics 2017; 18:502. [PMID: 28666407 PMCID: PMC5493846 DOI: 10.1186/s12864-017-3891-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/21/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND A pool of small RNA fragments (RFs) derived from diverse cellular RNAs has recently emerged as a rich source of functionally relevant molecules. Although their formation and accumulation has been connected to various stress conditions, the knowledge on RFs produced upon viral infections is very limited. Here, we applied the next generation sequencing (NGS) to characterize RFs generated in the hepatitis C virus (HCV) cell culture model (HCV-permissive Huh-7.5 cell line). RESULTS We found that both infected and non-infected cells contained a wide spectrum of RFs derived from virtually all RNA classes. A significant fraction of identified RFs accumulated to similar levels as miRNAs. Our analysis, focused on RFs originating from constitutively expressed non-coding RNAs, revealed three major patterns of parental RNA cleavage. We found that HCV infection induced significant changes in the accumulation of low copy number RFs, while subtly altered the levels of high copy number ones. Finally, the candidate RFs potentially relevant for host-virus interactions were identified. CONCLUSIONS Our results indicate that RFs should be considered an important component of the Huh-7.5 transcriptome and suggest that the main factors influencing the RF biogenesis are the RNA structure and RNA protection by interacting proteins. The data presented here significantly complement the existing transcriptomic, miRnomic, proteomic and metabolomic characteristics of the HCV cell culture model.
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Affiliation(s)
- Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Anna Hojka-Osinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Anna Philips
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965, Poznan, Poland
| | - Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Patrick Maillard
- Institut Pasteur, Hepacivirus and Innate Immunity, CNRS, UMR3569, 75724, Paris, France
| | - Agata Budkowska
- Institut Pasteur, Hepacivirus and Innate Immunity, CNRS, UMR3569, 75724, Paris, France.,Scientific Advisor for the Department of International Affairs, Institut Pasteur, 75724, Paris, France
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965, Poznan, Poland.
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Budzko L, Jackowiak P, Kamel K, Sarzynska J, Bujnicki JM, Figlerowicz M. Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro. Sci Rep 2017. [PMID: 28634398 PMCID: PMC5478644 DOI: 10.1038/s41598-017-03936-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) is known for its established role in antibody production. AID induces the diversification of antibodies by deaminating deoxycytidine (C) within immunoglobulin genes. The capacity of AID to deaminate 5-methyldeoxycytidine (5 mC) and/or 5-hydroxymethyldeoxycytidine (5 hmC), and consequently AID involvement in active DNA demethylation, is not fully resolved. For instance, structural determinants of AID activity on different substrates remain to be identified. To better understand the latter issue, we tested how mutations in human AID (hAID) influence its ability to deaminate C, 5 mC, and 5 hmC in vitro. We showed that each of the selected mutations differentially affects hAID’s ability to deaminate C and 5 mC. At the same time, we did not observe hAID activity on 5 hmC. Surprisingly, we found that the N51A hAID mutant, with no detectable activity on C, efficiently deaminated 5 mC, which may suggest different requirements for C and 5 mC deamination. Homology modeling and molecular dynamics simulations revealed that the pattern of enzyme-substrate recognition is one of the important factors determining enzyme activity on C and 5 mC. Consequently, we have proposed mechanisms that explain why wild type hAID more efficiently deaminates C than 5 mC in vitro and why 5 hmC is not deaminated.
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Affiliation(s)
- Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Karol Kamel
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109, Warsaw, Poland.,Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965, Poznan, Poland.
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Budny B, Szczepanek-Parulska E, Zemojtel T, Szaflarski W, Rydzanicz M, Wesoly J, Handschuh L, Wolinski K, Piatek K, Niedziela M, Ziemnicka K, Figlerowicz M, Zabel M, Ruchala M. Mutations in proteasome-related genes are associated with thyroid hemiagenesis. Endocrine 2017; 56:279-285. [PMID: 28390009 PMCID: PMC5395596 DOI: 10.1007/s12020-017-1287-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 03/20/2017] [Indexed: 12/11/2022]
Abstract
PURPOSE Human thyroid development is a complex and still unexplained process. Thyroid hemiagenesis is a congenital anomaly, where one of the thyroid lobes fails to develop. In the majority of patients with thyroid hemiagenesis, the genetic background remains unknown. The aim of the study was to search for novel genetic contributors to the etiology of thyroid hemiagenesis. METHODS A cohort of 34 sporadic patients diagnosed with thyroid hemiagenesis and one three-generation family were subjected to comprehensive genomic examination. Initially, targeted screening of associated transcription factors, known to be linked to thyroid development, was performed. As a next step, genomic examinations were applied using high-resolution microarrays, whereas for the thyroid hemiagenesis family, additionally the whole exome sequencing was performed. RESULTS Screening of transcription factors revealed no causative mutations in the studied cohort. Genomic examinations revealed the presence of four recurrent defects (three deletions and one duplication) affecting highly conservative proteasome genes PSMA1, PSMA3, and PSMD3. In a thyroid hemiagenesis family a splice site mutation in a proteasome gene PSMD2 (c.612T > C cDNA.1170T > C, g.3271T > C) was found in both affected mother and daughter. CONCLUSIONS Our results shed a new light on etiology of thyroid hemiagenesis, so far suspected to be linked only to mutations in the genes directly involved in the thyroid development. We demonstrated, for the first time, that genomic alterations in proteasome-associated genes co-occur in patients presenting this developmental anomaly.
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Affiliation(s)
- Bartlomiej Budny
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Ewelina Szczepanek-Parulska
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Tomasz Zemojtel
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Science, Poznan, Poland
| | - Witold Szaflarski
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznan, Poland
| | - Malgorzata Rydzanicz
- Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Joanna Wesoly
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Luiza Handschuh
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Science, Poznan, Poland
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Kosma Wolinski
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Katarzyna Piatek
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Marek Niedziela
- Department of Paediatric Endocrinology and Rheumatology, Poznan University of Medical Sciences, Poznan, Poland
| | - Katarzyna Ziemnicka
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Marek Figlerowicz
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Science, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Maciej Zabel
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marek Ruchala
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland.
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Grzegorzewska A, Niepolski L, Świderska M, Mostowska A, Stolarek I, Figlerowicz M, Jagodziński P. MP710ENHO, RXRA, AND LXRA POLYMORPHISMS AND DYSLIPIDEMIA, RELATED COMORBIDITIES AND SURVIVAL IN HEMODIALYSIS PATIENTS. Nephrol Dial Transplant 2017. [DOI: 10.1093/ndt/gfx180.mp710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Milewski MC, Kamel K, Kurzynska-Kokorniak A, Chmielewski MK, Figlerowicz M. EvOligo: A Novel Software to Design and Group Libraries of Oligonucleotides Applicable for Nucleic Acid-Based Experiments. J Comput Biol 2017; 24:1014-1028. [PMID: 28294640 DOI: 10.1089/cmb.2016.0154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Experimental methods based on DNA and RNA hybridization, such as multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification, or microarray analysis, require the use of mixtures of multiple oligonucleotides (primers or probes) in a single test tube. To provide an optimal reaction environment, minimal self- and cross-hybridization must be achieved among these oligonucleotides. To address this problem, we developed EvOligo, which is a software package that provides the means to design and group DNA and RNA molecules with defined lengths. EvOligo combines two modules. The first module performs oligonucleotide design, and the second module performs oligonucleotide grouping. The software applies a nearest-neighbor model of nucleic acid interactions coupled with a parallel evolutionary algorithm to construct individual oligonucleotides, and to group the molecules that are characterized by the weakest possible cross-interactions. To provide optimal solutions, the evolutionary algorithm sorts oligonucleotides into sets, preserves preselected parts of the oligonucleotides, and shapes their remaining parts. In addition, the oligonucleotide sets can be designed and grouped based on their melting temperatures. For the user's convenience, EvOligo is provided with a user-friendly graphical interface. EvOligo was used to design individual oligonucleotides, oligonucleotide pairs, and groups of oligonucleotide pairs that are characterized by the following parameters: (1) weaker cross-interactions between the non-complementary oligonucleotides and (2) more uniform ranges of the oligonucleotide pair melting temperatures than other available software products. In addition, in contrast to other grouping algorithms, EvOligo offers time-efficient sorting of paired and unpaired oligonucleotides based on various parameters defined by the user.
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Affiliation(s)
| | - Karol Kamel
- 1 Institute of Bioorganic Chemistry PAS , Poznan, Poland
| | | | | | - Marek Figlerowicz
- 1 Institute of Bioorganic Chemistry PAS , Poznan, Poland .,2 Institute of Computing Science, Poznan University of Technology , Poznan, Poland
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Samelak-Czajka A, Marszalek-Zenczak M, Marcinkowska-Swojak M, Kozlowski P, Figlerowicz M, Zmienko A. MLPA-Based Analysis of Copy Number Variation in Plant Populations. Front Plant Sci 2017; 8:222. [PMID: 28270823 PMCID: PMC5318451 DOI: 10.3389/fpls.2017.00222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/06/2017] [Indexed: 05/18/2023]
Abstract
Copy number variants (CNVs) are intraspecies duplications/deletions of large DNA segments (>1 kb). A growing number of reports highlight the functional and evolutionary impact of CNV in plants, increasing the need for appropriate tools that enable locus-specific CNV genotyping on a population scale. Multiplex ligation-dependent probe amplification (MLPA) is considered a gold standard in genotyping CNV in humans. Consequently, numerous commercial MLPA assays for CNV-related human diseases have been created. We routinely genotype complex multiallelic CNVs in human and plant genomes using the modified MLPA procedure based on fully synthesized oligonucleotide probes (90-200 nt), which greatly simplifies the design process and allows for the development of custom assays. Here, we present a step-by-step protocol for gene-specific MLPA probe design, multiplexed assay setup and data analysis in a copy number genotyping experiment in plants. As a case study, we present the results of a custom assay designed to genotype the copy number status of 12 protein coding genes in a population of 80 Arabidopsis accessions. The genes were pre-selected based on whole genome sequencing data and are localized in the genomic regions that display different levels of population-scale variation (non-variable, biallelic, or multiallelic, as well as CNVs overlapping whole genes or their fragments). The presented approach is suitable for population-scale validation of the CNV regions inferred from whole genome sequencing data analysis and for focused analysis of selected genes of interest. It can also be very easily adopted for any plant species, following optimization of the template amount and design of the appropriate control probes, according to the general guidelines presented in this paper.
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Affiliation(s)
- Anna Samelak-Czajka
- Institute of Computing Science, Faculty of Computing, Poznan University of TechnologyPoznan, Poland
| | - Malgorzata Marszalek-Zenczak
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | | | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Marek Figlerowicz
- Institute of Computing Science, Faculty of Computing, Poznan University of TechnologyPoznan, Poland
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Agnieszka Zmienko
- Institute of Computing Science, Faculty of Computing, Poznan University of TechnologyPoznan, Poland
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
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Mickiewicz A, Sarzyńska J, Miłostan M, Kurzyńska-Kokorniak A, Rybarczyk A, Łukasiak P, Kuliński T, Figlerowicz M, Błażewicz J. Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA. Comput Biol Chem 2016; 66:44-56. [PMID: 27907832 DOI: 10.1016/j.compbiolchem.2016.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/11/2016] [Accepted: 11/16/2016] [Indexed: 12/20/2022]
Abstract
Plant Dicer-like proteins (DCLs) belong to the Ribonuclease III (RNase III) enzyme family. They are involved in the regulation of gene expression and antiviral defense through RNA interference pathways. A model plant, Arabidopsis thaliana encodes four DCL proteins (AtDCL1-4) that produce different classes of small regulatory RNAs. Our studies focus on AtDCL4 that processes double-stranded RNAs (dsRNAs) into 21 nucleotide trans-acting small interfering RNAs. So far, little is known about the structures of plant DCLs and the complexes they form with dsRNA. In this work, we present models of the catalytic core of AtDCL4 and AtDCL4-dsRNA complex constructed by computational methods. We built a homology model of the catalytic core of AtDCL4 comprising Platform, PAZ, Connector helix and two RNase III domains. To assemble the AtDCL4-dsRNA complex two modeling approaches were used. In the first method, to establish conformations that allow building a consistent model of the complex, we used Normal Mode Analysis for both dsRNA and AtDCL4. The second strategy involved template-based approach for positioning of the PAZ domain and manual arrangement of the Connector helix. Our results suggest that the spatial orientation of the Connector helix, Platform and PAZ relative to the RNase III domains is crucial for measuring dsRNA of defined length. The modeled complexes provide information about interactions that may contribute to the relative orientations of these domains and to dsRNA binding. All these information can be helpful for understanding the mechanism of AtDCL4-mediated dsRNA recognition and binding, to produce small RNA of specific size.
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Affiliation(s)
- Agnieszka Mickiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland
| | - Joanna Sarzyńska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland.
| | - Maciej Miłostan
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland
| | - Anna Kurzyńska-Kokorniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Agnieszka Rybarczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland
| | - Piotr Łukasiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland
| | - Tadeusz Kuliński
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland
| | - Jacek Błażewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland
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Zmienko A, Samelak-Czajka A, Kozlowski P, Szymanska M, Figlerowicz M. Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2, AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location. BMC Genomics 2016; 17:893. [PMID: 27825302 PMCID: PMC5101643 DOI: 10.1186/s12864-016-3221-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/27/2016] [Indexed: 12/28/2022] Open
Abstract
Background Intraspecies copy number variations (CNVs), defined as unbalanced structural variations of specific genomic loci, ≥1 kb in size, are present in the genomes of animals and plants. A growing number of examples indicate that CNVs may have functional significance and contribute to phenotypic diversity. In the model plant Arabidopsis thaliana at least several hundred protein-coding genes might display CNV; however, locus-specific genotyping studies in this plant have not been conducted. Results We analyzed the natural CNVs in the region overlapping MSH2 gene that encodes the DNA mismatch repair protein, and AT3G18530 and AT3G18535 genes that encode poorly characterized proteins. By applying multiplex ligation-dependent probe amplification and droplet digital PCR we genotyped those genes in 189 A. thaliana accessions. We found that AT3G18530 and AT3G18535 were duplicated (2–14 times) in 20 and deleted in 101 accessions. MSH2 was duplicated in 12 accessions (up to 12-14 copies) but never deleted. In all but one case, the MSH2 duplications were associated with those of AT3G18530 and AT3G18535. Considering the structure of the CNVs, we distinguished 5 genotypes for this region, determined their frequency and geographical distribution. We defined the CNV breakpoints in 35 accessions with AT3G18530 and AT3G18535 deletions and tandem duplications and showed that they were reciprocal events, resulting from non-allelic homologous recombination between 99 %-identical sequences flanking these genes. The widespread geographical distribution of the deletions supported by the SNP and linkage disequilibrium analyses of the genomic sequence confirmed the recurrent nature of this CNV. Conclusions We characterized in detail for the first time the complex multiallelic CNV in Arabidopsis genome. The region encoding MSH2, AT3G18530 and AT3G18535 genes shows enormous variation of copy numbers among natural ecotypes, being a remarkable example of high Arabidopsis genome plasticity. We provided the molecular insight into the mechanism underlying the recurrent nature of AT3G18530-AT3G18535 duplications/deletions. We also performed the first direct comparison of the two leading experimental methods, suitable for assessing the DNA copy number status. Our comprehensive case study provides foundation information for further analyses of CNV evolution in Arabidopsis and other plants, and their possible use in plant breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3221-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Maja Szymanska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.
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