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3. The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments

Author

De Vos, Stephanie, Rombauts, Stephane, Coussement, Louis, Dermauw, Wannes, Vuylsteke, Marnik, Sorgeloos, Patrick, Clegg, James S, Nambu, Ziro, Van Nieuwerburgh, Filip, Norouzitallab, Parisa, Van Leeuwen, Thomas, De Meyer, Tim, Van Stappen, Gilbert, Van de Peer, Yves, and Bossier, Peter

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Generic health relevance, Animals, Artemia, Extreme Environments, Extremophiles, Heat-Shock Proteins, Salinity, Arthropod, Genome, Transcriptome, Assembly, Annotation, Extremophile, Anoxia, Brine shrimp, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics, Biological sciences, Biomedical and clinical sciences
Abstract

BackgroundBrine shrimp Artemia have an unequalled ability to endure extreme salinity and complete anoxia. This study aims to elucidate its strategies to cope with these stressors.Results and discussionHere, we present the genome of an inbred A. franciscana Kellogg, 1906. We identified 21,828 genes of which, under high salinity, 674 genes and under anoxia, 900 genes were differentially expressed (42%, respectively 30% were annotated). Under high salinity, relevant stress genes and pathways included several Heat Shock Protein and Leaf Embryogenesis Abundant genes, as well as the trehalose metabolism. In addition, based on differential gene expression analysis, it can be hypothesized that a high oxidative stress response and endocytosis/exocytosis are potential salt management strategies, in addition to the expression of major facilitator superfamily genes responsible for transmembrane ion transport. Under anoxia, genes involved in mitochondrial function, mTOR signalling and autophagy were differentially expressed. Both high salt and anoxia enhanced degradation of erroneous proteins and protein chaperoning. Compared with other branchiopod genomes, Artemia had 0.03% contracted and 6% expanded orthogroups, in which 14% of the genes were differentially expressed under high salinity or anoxia. One phospholipase D gene family, shown to be important in plant stress response, was uniquely present in both extremophiles Artemia and the tardigrade Hypsibius dujardini, yet not differentially expressed under the described experimental conditions.ConclusionsA relatively complete genome of Artemia was assembled, annotated and analysed, facilitating research on its extremophile features, and providing a reference sequence for crustacean research.

Published
2021

7. Overexpression of the ribosome-inactivating protein OsRIP1 modulates the jasmonate signaling pathway in rice.

Author

Simin Chen, De Zutter, Noémie, Meijer, Anikó, Koen Gistelinck, Wytynck, Pieter, Verbeke, Isabel, Osterne, Vinicius J. S., Kondeti, Subramanyam, De Meyer, Tim, Audenaert, Kris, and Van Damme, Els J. M.

Subjects
PLANT enzymes, PLANT hormones, RIBOSOMAL proteins, PROTEIN overexpression, GENE expression, GIBBERELLINS
Abstract

Ribosome-inactivating proteins (RIPs) are plant enzymes that target the rRNA. The cytoplasmic RIP, called OsRIP1, plays a crucial role in regulating jasmonate, a key plant hormone. Understanding the role of OsRIP1 can provide insights into enhancing stress tolerance and optimizing growth of rice. Transcription profiling by mRNA sequencing was employed to measure the changes in gene expression in rice plants in response to MeJA treatment. Compared to wild type (WT) plants, OsRIP1 overexpressing rice plants showed a lower increase in mRNA transcripts for genes related to jasmonate responses when exposed to MeJA treatment for 3 h. After 24 h of MeJA exposure, the mRNA transcripts associated with the gibberellin pathway occurred in lower levels in OsRIP1 overexpressing plants compared to WT plants. We hypothesize that the mechanism underlying OsRIP1 antagonization of MeJA-induced shoot growth inhibition involves cytokininmediated leaf senescence and positive regulation of cell cycle processes, probably via OsRIP1 interaction with 40S ribosomal protein S5 and α-tubulin. Moreover, the photosystem II 10kDa polypeptide was identified to favorably bind to OsRIP1, and its involvement may be attributed to the reduction of photosynthesis in OsRIP1-overexpressing plants subjected to MeJA at the early timepoint (3 h). [ABSTRACT FROM AUTHOR]

Published
2024
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8. Loss-of-Imprinting of HM13 Leads to Poor Prognosis in Clear Cell Renal Cell Carcinoma.

Author

Voorthuijzen, Floris, Stroobandt, Cedric, Van Criekinge, Wim, Goovaerts, Tine, and De Meyer, Tim

Subjects
GENOMIC imprinting, RENAL cell carcinoma, PEPTIDES, TUMOR classification, EPIGENETICS
Abstract

Genomic imprinting refers to the epigenetic silencing of one of both alleles in a parent-of-origin-specific manner, particularly in genes regulating growth and development. Impaired genomic imprinting leading to the activation of the silenced allele, also called canonical loss-of-imprinting (LOI), is considered an early factor in oncogenesis. As LOI studies in clear cell renal cell carcinoma (ccRCC) are limited to IGF2, we performed a genome-wide analysis in 128 kidney normal solid tissue and 240 stage 1 ccRCC samples (TCGA RNA-seq data) to screen for canonical LOI in early oncogenesis. In ccRCC, we observed LOI (adj. p = 2.74 × 10−3) of HM13 (Histocompatibility Minor 13), a signal peptide peptidase involved in epitope generation. HM13 LOI samples featured HM13 overexpression, both compared to normal solid tissues (p = 3.00 × 10−7) and non-LOI (p = 1.27 × 10−2) samples. Upon adjustment for age and sex, HM13 expression was significantly associated with poor survival (p = 7.10 × 10−5). Moreover, HM13 overexpression consistently exacerbated with increasing tumor stage (p = 2.90 × 10−8). For IGF2, LOI was observed in normal solid tissues, but the prevalence did not increase in cancer. In conclusion, HM13 LOI is an early event in ccRCC, causing overexpression leading to poor prognosis. [ABSTRACT FROM AUTHOR]

Published
2024
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9. The RNA Atlas expands the catalog of human non-coding RNAs

Author

Lorenzi, Lucia, Chiu, Hua-Sheng, Avila Cobos, Francisco, Gross, Stephen, Volders, Pieter-Jan, Cannoodt, Robrecht, Nuytens, Justine, Vanderheyden, Katrien, Anckaert, Jasper, Lefever, Steve, Tay, Aidan P., de Bony, Eric J., Trypsteen, Wim, Gysens, Fien, Vromman, Marieke, Goovaerts, Tine, Hansen, Thomas Birkballe, Kuersten, Scott, Nijs, Nele, Taghon, Tom, Vermaelen, Karim, Bracke, Ken R., Saeys, Yvan, De Meyer, Tim, Deshpande, Nandan P., Anande, Govardhan, Chen, Ting-Wen, Wilkins, Marc R., Unnikrishnan, Ashwin, De Preter, Katleen, Kjems, Jørgen, Koster, Jan, Schroth, Gary P., Vandesompele, Jo, Sumazin, Pavel, and Mestdagh, Pieter

Published
2021
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14. Concurrent invasions of European starlings in Australia and North America reveal population‐specific differentiation in shared genomic regions

Author

Hofmeister, Natalie R., primary, Stuart, Katarina C., additional, Warren, Wesley C., additional, Werner, Scott J., additional, Bateson, Melissa, additional, Ball, Gregory F., additional, Buchanan, Katherine L., additional, Burt, David W., additional, Cardilini, Adam P. A., additional, Cassey, Phillip, additional, De Meyer, Tim, additional, George, Julia, additional, Meddle, Simone L., additional, Rowland, Hannah M., additional, Sherman, Craig D. H., additional, Sherwin, William B., additional, Vanden Berghe, Wim, additional, Rollins, Lee Ann, additional, and Clayton, David F., additional

Published
2023
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17. Identification of Novel Genetic Loci Associated with Thyroid Peroxidase Antibodies and Clinical Thyroid Disease

Author

Medici, Marco, Porcu, Eleonora, Pistis, Giorgio, Teumer, Alexander, Brown, Suzanne J, Jensen, Richard A, Rawal, Rajesh, Roef, Greet L, Plantinga, Theo S, Vermeulen, Sita H, Lahti, Jari, Simmonds, Matthew J, Husemoen, Lise Lotte N, Freathy, Rachel M, Shields, Beverley M, Pietzner, Diana, Nagy, Rebecca, Broer, Linda, Chaker, Layal, Korevaar, Tim IM, Plia, Maria Grazia, Sala, Cinzia, Völker, Uwe, Richards, J Brent, Sweep, Fred C, Gieger, Christian, Corre, Tanguy, Kajantie, Eero, Thuesen, Betina, Taes, Youri E, Visser, W Edward, Hattersley, Andrew T, Kratzsch, Jürgen, Hamilton, Alexander, Li, Wei, Homuth, Georg, Lobina, Monia, Mariotti, Stefano, Soranzo, Nicole, Cocca, Massimiliano, Nauck, Matthias, Spielhagen, Christin, Ross, Alec, Arnold, Alice, van de Bunt, Martijn, Liyanarachchi, Sandya, Heier, Margit, Grabe, Hans Jörgen, Masciullo, Corrado, Galesloot, Tessel E, Lim, Ee M, Reischl, Eva, Leedman, Peter J, Lai, Sandra, Delitala, Alessandro, Bremner, Alexandra P, Philips, David IW, Beilby, John P, Mulas, Antonella, Vocale, Matteo, Abecasis, Goncalo, Forsen, Tom, James, Alan, Widen, Elisabeth, Hui, Jennie, Prokisch, Holger, Rietzschel, Ernst E, Palotie, Aarno, Feddema, Peter, Fletcher, Stephen J, Schramm, Katharina, Rotter, Jerome I, Kluttig, Alexander, Radke, Dörte, Traglia, Michela, Surdulescu, Gabriela L, He, Huiling, Franklyn, Jayne A, Tiller, Daniel, Vaidya, Bijay, de Meyer, Tim, Jørgensen, Torben, Eriksson, Johan G, O'Leary, Peter C, Wichmann, Eric, Hermus, Ad R, Psaty, Bruce M, Ittermann, Till, Hofman, Albert, Bosi, Emanuele, Schlessinger, David, Wallaschofski, Henri, Pirastu, Nicola, Aulchenko, Yurii S, de la Chapelle, Albert, Netea-Maier, Romana T, Gough, Stephen CL, Schwabedissen, Henriette Meyer zu, Frayling, Timothy M, and Kaufman, Jean-Marc

Subjects
Biological Sciences, Genetics, Prevention, Clinical Research, Autoimmune Disease, 2.1 Biological and endogenous factors, Aetiology, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, Metabolic and endocrine, Autoantibodies, Genetic Loci, Genome-Wide Association Study, Graves Disease, Hashimoto Disease, Humans, Iodide Peroxidase, Risk Factors, Thyroiditis, Autoimmune, Thyrotropin, Developmental Biology
Abstract

Autoimmune thyroid diseases (AITD) are common, affecting 2-5% of the general population. Individuals with positive thyroid peroxidase antibodies (TPOAbs) have an increased risk of autoimmune hypothyroidism (Hashimoto's thyroiditis), as well as autoimmune hyperthyroidism (Graves' disease). As the possible causative genes of TPOAbs and AITD remain largely unknown, we performed GWAS meta-analyses in 18,297 individuals for TPOAb-positivity (1769 TPOAb-positives and 16,528 TPOAb-negatives) and in 12,353 individuals for TPOAb serum levels, with replication in 8,990 individuals. Significant associations (P

Published
2014

19. Publisher Correction: The RNA Atlas expands the catalog of human non-coding RNAs

Author

Lorenzi, Lucia, Chiu, Hua-Sheng, Avila Cobos, Francisco, Gross, Stephen, Volders, Pieter-Jan, Cannoodt, Robrecht, Nuytens, Justine, Vanderheyden, Katrien, Anckaert, Jasper, Lefever, Steve, Tay, Aidan P., de Bony, Eric J., Trypsteen, Wim, Gysens, Fien, Vromman, Marieke, Goovaerts, Tine, Hansen, Thomas Birkballe, Kuersten, Scott, Nijs, Nele, Taghon, Tom, Vermaelen, Karim, Bracke, Ken R., Saeys, Yvan, De Meyer, Tim, Deshpande, Nandan P., Anande, Govardhan, Chen, Ting-Wen, Wilkins, Marc R., Unnikrishnan, Ashwin, De Preter, Katleen, Kjems, Jørgen, Koster, Jan, Schroth, Gary P., Vandesompele, Jo, Sumazin, Pavel, and Mestdagh, Pieter

Published
2021
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20. Liver transcriptomic and methylomic analyses identify transcriptional mitogen-activated protein kinase regulation in facultative hibernation of Syrian hamster

Author

Coussement, Louis, primary, Oosterhof, Marloes M., additional, Guryev, Victor, additional, Reitsema, Vera A., additional, Bruintjes, Jojanneke J., additional, Goris, Maaike, additional, Bouma, Hjalmar R., additional, de Meyer, Tim, additional, Rots, Marianne G., additional, and Henning, Robert H., additional

Published
2023
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26. Supplementary Figure S2 from A Four-Gene Promoter Methylation Marker Panel Consisting of GREM1, NEURL, LAD1, and NEFH Predicts Survival of Clear Cell Renal Cell Cancer Patients

Author

van Vlodrop, Iris J.H., primary, Joosten, Sophie C., primary, De Meyer, Tim, primary, Smits, Kim M., primary, Van Neste, Leander, primary, Melotte, Veerle, primary, Baldewijns, Marcella M.L.L., primary, Schouten, Leo J., primary, van den Brandt, Piet A., primary, Jeschke, Jana, primary, Yi, Joo Mi, primary, Schuebel, Kornel E., primary, Ahuja, Nita, primary, Herman, James G., primary, Aarts, Maureen J., primary, Bosman, Fred T., primary, Van Criekinge, Wim, primary, and van Engeland, Manon, primary

Published
2023
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27. Supplementary Figure Legends and Supplementary Tables from A Four-Gene Promoter Methylation Marker Panel Consisting of GREM1, NEURL, LAD1, and NEFH Predicts Survival of Clear Cell Renal Cell Cancer Patients

Author

van Vlodrop, Iris J.H., primary, Joosten, Sophie C., primary, De Meyer, Tim, primary, Smits, Kim M., primary, Van Neste, Leander, primary, Melotte, Veerle, primary, Baldewijns, Marcella M.L.L., primary, Schouten, Leo J., primary, van den Brandt, Piet A., primary, Jeschke, Jana, primary, Yi, Joo Mi, primary, Schuebel, Kornel E., primary, Ahuja, Nita, primary, Herman, James G., primary, Aarts, Maureen J., primary, Bosman, Fred T., primary, Van Criekinge, Wim, primary, and van Engeland, Manon, primary

Published
2023
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32. MAGE enables population level RNAseq driven genotyping and (differential) allelic divergence detection in healthy kidney and carcinoma

Author

Stroobandt Cedric, Goovaerts Tine, Coussement Louis, De Graeve Femke, Voorthuijzen Floris, Van Steenbergen Laure, Galle Jeroen, Van Criekinge Wim, and De Meyer Tim

Abstract

Decreasing sequencing costs have instigated large-scale RNAseq experiments, yet genetic polymorphisms in such data remain poorly exploited. Currently, allele-specific expression (ASE) studies focus almost exclusively on genetic variants explaining expression differences (cis-eQTLs), largely ignoring other ASE effects. The latter are typically associated with higher variance in expression of both copies of a gene, here called Allelic Divergence (AD). We therefore developed an RNAseq-driven population-level beta-binomial mixture model for (differential) AD detection. The model simultaneously enables RNAseq-driven genotyping, which outperforms alternative RNA genotyping methods when applied on healthy kidney data from The Cancer Genome Atlas. Moreover, we identify well-known non-cis-eQTL ASE, e.g. random monoallelic expression of HLA and immunoglobulin genes in healthy kidney, as well as allele-specific aberrations in clear cell kidney carcinoma, including long-range epigenetic silencing of protocadherins, copy-number alterations, and loss of imprinting. These methods are available as the Modeller of Allelic Gene Expression (MAGE) tool suite: https://biobix.github.io/MAGE/.

Published
2022

33. Genome-wide analyses identify a role for SLC17A4 and AADAT in thyroid hormone regulation

Author

Teumer, Alexander, Chaker, Layal, Groeneweg, Stefan, Li, Yong, Di Munno, Celia, Barbieri, Caterina, Schultheiss, Ulla T., Traglia, Michela, Ahluwalia, Tarunveer S., Akiyama, Masato, Appel, Emil Vincent R., Arking, Dan E., Arnold, Alice, Astrup, Arne, Beekman, Marian, Beilby, John P., Bekaert, Sofie, Boerwinkle, Eric, Brown, Suzanne J., De Buyzere, Marc, Campbell, Purdey J., Ceresini, Graziano, Cerqueira, Charlotte, Cucca, Francesco, Deary, Ian J., Deelen, Joris, Eckardt, Kai-Uwe, Ekici, Arif B., Eriksson, Johan G., Ferrrucci, Luigi, Fiers, Tom, Fiorillo, Edoardo, Ford, Ian, Fox, Caroline S., Fuchsberger, Christian, Galesloot, Tessel E., Gieger, Christian, Gögele, Martin, De Grandi, Alessandro, Grarup, Niels, Greiser, Karin Halina, Haljas, Kadri, Hansen, Torben, Harris, Sarah E., van Heemst, Diana, den Heijer, Martin, Hicks, Andrew A., den Hollander, Wouter, Homuth, Georg, Hui, Jennie, Ikram, M. Arfan, Ittermann, Till, Jensen, Richard A., Jing, Jiaojiao, Jukema, J. Wouter, Kajantie, Eero, Kamatani, Yoichiro, Kasbohm, Elisa, Kaufman, Jean-Marc, Kiemeney, Lambertus A., Kloppenburg, Margreet, Kronenberg, Florian, Kubo, Michiaki, Lahti, Jari, Lapauw, Bruno, Li, Shuo, Liewald, David C. M., Lifelines Cohort Study, Lim, Ee Mun, Linneberg, Allan, Marina, Michela, Mascalzoni, Deborah, Matsuda, Koichi, Medenwald, Daniel, Meisinger, Christa, Meulenbelt, Ingrid, De Meyer, Tim, Meyer zu Schwabedissen, Henriette E., Mikolajczyk, Rafael, Moed, Matthijs, Netea-Maier, Romana T., Nolte, Ilja M., Okada, Yukinori, Pala, Mauro, Pattaro, Cristian, Pedersen, Oluf, Petersmann, Astrid, Porcu, Eleonora, Postmus, Iris, Pramstaller, Peter P., Psaty, Bruce M., Ramos, Yolande F. M., Rawal, Rajesh, Redmond, Paul, Richards, J. Brent, Rietzschel, Ernst R., Rivadeneira, Fernando, Roef, Greet, Rotter, Jerome I., Sala, Cinzia F., Schlessinger, David, Selvin, Elizabeth, Slagboom, P. Eline, Soranzo, Nicole, Sørensen, Thorkild I. A., Spector, Timothy D., Starr, John M., Stott, David J., Taes, Youri, Taliun, Daniel, Tanaka, Toshiko, Thuesen, Betina, Tiller, Daniel, Toniolo, Daniela, Uitterlinden, Andre G., Visser, W. Edward, Walsh, John P., Wilson, Scott G., Wolffenbuttel, Bruce H. R., Yang, Qiong, Zheng, Hou-Feng, Cappola, Anne, Peeters, Robin P., Naitza, Silvia, Völzke, Henry, Sanna, Serena, Köttgen, Anna, Visser, Theo J., and Medici, Marco

Published
2018
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36. Transcript‐ and annotation‐guided genome assembly of the European starling

Author

Stuart, Katarina C., primary, Edwards, Richard J., additional, Cheng, Yuanyuan, additional, Warren, Wesley C., additional, Burt, David W., additional, Sherwin, William B., additional, Hofmeister, Natalie R., additional, Werner, Scott J., additional, Ball, Gregory F., additional, Bateson, Melissa, additional, Brandley, Matthew C., additional, Buchanan, Katherine L., additional, Cassey, Phillip, additional, Clayton, David F., additional, De Meyer, Tim, additional, Meddle, Simone L., additional, and Rollins, Lee A., additional

Published
2022
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41. Trans-driven variation in expression is common among detoxification genes in the extreme generalist herbivore Tetranychus urticae

Author

Kurlovs, Andre H., De Beer, Berdien, Ji, Meiyuan, Vandenhole, Marilou, De Meyer, Tim, Feyereisen, René, Clark, Richard M., Van Leeuwen, Thomas, Kurlovs, Andre H., De Beer, Berdien, Ji, Meiyuan, Vandenhole, Marilou, De Meyer, Tim, Feyereisen, René, Clark, Richard M., and Van Leeuwen, Thomas

Abstract

The extreme adaptation potential of the generalist herbivore Tetranychus urticae (the two-spotted spider mite) to pesticides as well as diverse host plants has been associated with clade-specific gene expansions in known detoxifying enzyme families, and with extensive and rapid transcriptional responses. However, how this broad transcriptional potential is regulated remains largely unknown. Using a parental/F1 design in which four inbred strains were crossed to a common inbred strain, we assessed the genetic basis and inheritance of gene expression variation in T. urticae. Mirroring known phenotypic variation in the progenitor strains of the inbreds, we confirmed that the inbred strains we created were genetically distinct, varied markedly in pesticide resistance, and also captured variation in host plant fitness as is commonly observed in this species. By examining differences in gene expression between parents and allele-specific expression in F1s, we found that variation in RNA abundance was more often explained in trans as compared to cis, with the former associated with dominance in inheritance. Strikingly, in a gene ontology analysis, detoxification genes of the cytochrome P450 monooxygenase (CYP) family, as well as dioxygenases (DOGs) acquired from horizontal gene transfer from fungi, were specifically enriched at the extremes of trans-driven up- and downregulation. In particular, multiple CYPs and DOGs with broad substrate-specificities for pesticides or plant specialized compounds were exceptionally highly upregulated as a result of trans-regulatory variation, or in some cases synergism of cis and trans, in the most multi-pesticide resistant strains. Collectively, our findings highlight the potential importance of trans-driven expression variation in genes associated with xenobiotic metabolism and host plant use for rapid adaptation in T. urticae, and also suggests modular control of these genes, a regulatory architecture that might ameliorate negative p

Published
2022

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