[{"ddc":["570"],"quality_controlled":"1","publisher":"MDPI","article_processing_charge":"Yes","doi":"10.3390/cells12121613","type":"journal_article","_id":"13214","date_updated":"2024-03-06T14:00:33Z","status":"public","publication":"Cells","project":[{"grant_number":"26130","name":"Functional asymmetry of medial habenula outputs in mice","_id":"62883ed7-2b32-11ec-9570-93580204e56b"}],"acknowledgement":"This work was supported by the Austrian Academy of Sciences ÖAW: Doc fellowship (26130) to Stefan Riegler.","date_published":"2023-06-13T00:00:00Z","pmid":1,"external_id":{"isi":["001017033600001"],"pmid":["37371083"]},"isi":1,"year":"2023","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        12","abstract":[{"lang":"eng","text":"Nitrogen is an important macronutrient required for plant growth and development, thus directly impacting agricultural productivity. In recent years, numerous studies have shown that nitrogen-driven growth depends on pathways that control nitrate/nitrogen homeostasis and hormonal networks that act both locally and systemically to coordinate growth and development of plant organs. In this review, we will focus on recent advances in understanding the role of the plant hormones auxin and cytokinin and their crosstalk in nitrate-regulated growth and discuss the significance of novel findings and possible missing links."}],"has_accepted_license":"1","file_date_updated":"2023-07-12T10:01:54Z","publication_status":"published","publication_identifier":{"issn":["2073-4409"]},"oa_version":"Published Version","title":"Nitrate, auxin and cytokinin - a trio to tango","day":"13","author":[{"first_name":"R","full_name":"Abualia, R","last_name":"Abualia"},{"id":"FF6018E0-D806-11E9-8E43-0B14E6697425","full_name":"Riegler, Stefan","last_name":"Riegler","orcid":"0000-0003-3413-1343","first_name":"Stefan"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"date_created":"2023-07-12T07:41:25Z","article_type":"review","volume":12,"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Abualia, R., Riegler, S., &#38; Benková, E. (2023). Nitrate, auxin and cytokinin - a trio to tango. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells12121613\">https://doi.org/10.3390/cells12121613</a>","mla":"Abualia, R., et al. “Nitrate, Auxin and Cytokinin - a Trio to Tango.” <i>Cells</i>, vol. 12, no. 12, 1613, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/cells12121613\">10.3390/cells12121613</a>.","chicago":"Abualia, R, Stefan Riegler, and Eva Benková. “Nitrate, Auxin and Cytokinin - a Trio to Tango.” <i>Cells</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/cells12121613\">https://doi.org/10.3390/cells12121613</a>.","ista":"Abualia R, Riegler S, Benková E. 2023. Nitrate, auxin and cytokinin - a trio to tango. Cells. 12(12), 1613.","ieee":"R. Abualia, S. Riegler, and E. Benková, “Nitrate, auxin and cytokinin - a trio to tango,” <i>Cells</i>, vol. 12, no. 12. MDPI, 2023.","short":"R. Abualia, S. Riegler, E. Benková, Cells 12 (2023).","ama":"Abualia R, Riegler S, Benková E. Nitrate, auxin and cytokinin - a trio to tango. <i>Cells</i>. 2023;12(12). doi:<a href=\"https://doi.org/10.3390/cells12121613\">10.3390/cells12121613</a>"},"issue":"12","month":"06","file":[{"creator":"alisjak","date_updated":"2023-07-12T10:01:54Z","date_created":"2023-07-12T10:01:54Z","file_size":1066802,"file_id":"13218","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_cells_Abualia.pdf","checksum":"6dc9df5f4f59fc27c509c275060354a5","relation":"main_file"}],"article_number":"1613","department":[{"_id":"EvBe"}]},{"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"R. Zhang, R. Kuo, M. Coulter, C.P.G. Calixto, J.C. Entizne, W. Guo, Y. Marquez, L. Milne, S. Riegler, A. Matsui, M. Tanaka, S. Harvey, Y. Gao, T. Wießner-Kroh, A. Paniagua, M. Crespi, K. Denby, A.B. Hur, E. Huq, M. Jantsch, A. Jarmolowski, T. Koester, S. Laubinger, Q.Q. Li, L. Gu, M. Seki, D. Staiger, R. Sunkar, Z. Szweykowska-Kulinska, S.L. Tu, A. Wachter, R. Waugh, L. Xiong, X.N. Zhang, A. Conesa, A.S.N. Reddy, A. Barta, M. Kalyna, J.W.S. Brown, Genome Biology 23 (2022).","ieee":"R. Zhang <i>et al.</i>, “A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis,” <i>Genome Biology</i>, vol. 23. BioMed Central, 2022.","ama":"Zhang R, Kuo R, Coulter M, et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. 2022;23. doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>","mla":"Zhang, Runxuan, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>, vol. 23, 149, BioMed Central, 2022, doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>.","apa":"Zhang, R., Kuo, R., Coulter, M., Calixto, C. P. G., Entizne, J. C., Guo, W., … Brown, J. W. S. (2022). A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>","chicago":"Zhang, Runxuan, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>. BioMed Central, 2022. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>.","ista":"Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS. 2022. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. 23, 149."},"month":"07","file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2022_GenomeBiology_Zhang.pdf","checksum":"2c30ef84151d257a6b835b4e069b70ac","relation":"main_file","date_updated":"2022-07-18T08:15:24Z","creator":"dernst","date_created":"2022-07-18T08:15:24Z","file_size":3146207,"file_id":"11597"}],"article_number":"149","department":[{"_id":"FyKo"}],"abstract":[{"text":"Background: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.\r\nResults: We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage.\r\nConclusions: AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        23","has_accepted_license":"1","publication_identifier":{"eissn":["1474-760X"]},"publication_status":"published","file_date_updated":"2022-07-18T08:15:24Z","oa_version":"Published Version","title":"A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis","author":[{"first_name":"Runxuan","full_name":"Zhang, Runxuan","last_name":"Zhang"},{"first_name":"Richard","last_name":"Kuo","full_name":"Kuo, Richard"},{"first_name":"Max","full_name":"Coulter, Max","last_name":"Coulter"},{"last_name":"Calixto","full_name":"Calixto, Cristiane P.G.","first_name":"Cristiane P.G."},{"last_name":"Entizne","full_name":"Entizne, Juan Carlos","first_name":"Juan Carlos"},{"first_name":"Wenbin","last_name":"Guo","full_name":"Guo, Wenbin"},{"full_name":"Marquez, Yamile","last_name":"Marquez","first_name":"Yamile"},{"full_name":"Milne, Linda","last_name":"Milne","first_name":"Linda"},{"id":"FF6018E0-D806-11E9-8E43-0B14E6697425","full_name":"Riegler, Stefan","last_name":"Riegler","orcid":"0000-0003-3413-1343","first_name":"Stefan"},{"full_name":"Matsui, Akihiro","last_name":"Matsui","first_name":"Akihiro"},{"first_name":"Maho","full_name":"Tanaka, Maho","last_name":"Tanaka"},{"last_name":"Harvey","full_name":"Harvey, Sarah","first_name":"Sarah"},{"full_name":"Gao, Yubang","last_name":"Gao","first_name":"Yubang"},{"full_name":"Wießner-Kroh, Theresa","last_name":"Wießner-Kroh","first_name":"Theresa"},{"full_name":"Paniagua, Alejandro","last_name":"Paniagua","first_name":"Alejandro"},{"full_name":"Crespi, Martin","last_name":"Crespi","first_name":"Martin"},{"last_name":"Denby","full_name":"Denby, Katherine","first_name":"Katherine"},{"first_name":"Asa Ben","full_name":"Hur, Asa Ben","last_name":"Hur"},{"first_name":"Enamul","last_name":"Huq","full_name":"Huq, Enamul"},{"first_name":"Michael","full_name":"Jantsch, Michael","last_name":"Jantsch"},{"first_name":"Artur","full_name":"Jarmolowski, Artur","last_name":"Jarmolowski"},{"last_name":"Koester","full_name":"Koester, Tino","first_name":"Tino"},{"first_name":"Sascha","last_name":"Laubinger","full_name":"Laubinger, Sascha"},{"first_name":"Qingshun Quinn","full_name":"Li, Qingshun Quinn","last_name":"Li"},{"first_name":"Lianfeng","last_name":"Gu","full_name":"Gu, Lianfeng"},{"last_name":"Seki","full_name":"Seki, Motoaki","first_name":"Motoaki"},{"full_name":"Staiger, Dorothee","last_name":"Staiger","first_name":"Dorothee"},{"first_name":"Ramanjulu","last_name":"Sunkar","full_name":"Sunkar, Ramanjulu"},{"last_name":"Szweykowska-Kulinska","full_name":"Szweykowska-Kulinska, Zofia","first_name":"Zofia"},{"first_name":"Shih Long","full_name":"Tu, Shih Long","last_name":"Tu"},{"first_name":"Andreas","full_name":"Wachter, Andreas","last_name":"Wachter"},{"first_name":"Robbie","full_name":"Waugh, Robbie","last_name":"Waugh"},{"first_name":"Liming","last_name":"Xiong","full_name":"Xiong, Liming"},{"last_name":"Zhang","full_name":"Zhang, Xiao Ning","first_name":"Xiao Ning"},{"full_name":"Conesa, Ana","last_name":"Conesa","first_name":"Ana"},{"full_name":"Reddy, Anireddy S.N.","last_name":"Reddy","first_name":"Anireddy S.N."},{"first_name":"Andrea","last_name":"Barta","full_name":"Barta, Andrea"},{"first_name":"Maria","last_name":"Kalyna","full_name":"Kalyna, Maria"},{"first_name":"John W.S.","full_name":"Brown, John W.S.","last_name":"Brown"}],"scopus_import":"1","day":"07","article_type":"original","date_created":"2022-07-17T22:01:53Z","volume":23,"status":"public","publication":"Genome Biology","acknowledgement":"This work was jointly supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) BB/P009751/1 to JB; BB/R014582/1 to RW and RZ; BB/S020160/1 to RZ; BB/S004610/1 (16 ERA-CAPS BARN) to RW; the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to RZ, RW, and JB]; the\r\nNational Science Foundation (MCB-2014408) and the National Institute of Health (NIH) (GM-114297) to E.H.; S. H. was supported by funding to K.D. from the University of York; the Austrian Science Fund (FWF) SFB F43 to AB and MJ and [P26333] to MK; The French Agence Nationale de la Recherche grant ANR-16-CE12-0032 to MC; the Japan Science and\r\nTechnology Agency (JST), the Core Research for Evolutionary Science and Technology (CREST; Grant Number JPMJCR13B4) to M.S.; the National Science Foundation (Grant No. DBI1949036 to A.b.H and A.S.N.R, and Grant No. MCB 2014542 to E.H. and A.S.N.R.); and the DOE Office of Science, Office of Biological and Environmental Research (Grant\r\nNo. DE-SC0010733) to A.S.N.R and A.b.H.; the Deutsche Forschungsgemeinschaft (DFG) STA653/14-1 and STA653/15-1 to DS; the National Science Foundation grant (IOS-154173) to Q.Q.L.; the German Research Foundation (DFG) WA2167/8-1 to AW and SFB1101/C03 to AW and TWK; the Research Grants Council (RGC) of Hong Kong (GRF 12103020) to LX. NSF grant IOS-1849708 and NSF EPSCoR grant 1826836 to RS; the Academia Sinica to S.-L. T.","date_published":"2022-07-07T00:00:00Z","external_id":{"isi":["000821915500002"]},"year":"2022","isi":1,"ddc":["570"],"quality_controlled":"1","publisher":"BioMed Central","doi":"10.1186/s13059-022-02711-0","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-03T12:04:18Z","_id":"11587"},{"oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Nimeth BA, Riegler S, Kalyna M. Alternative splicing and DNA damage response in plants. <i>Frontiers in Plant Science</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fpls.2020.00091\">10.3389/fpls.2020.00091</a>","short":"B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020).","ieee":"B. A. Nimeth, S. Riegler, and M. Kalyna, “Alternative splicing and DNA damage response in plants,” <i>Frontiers in Plant Science</i>, vol. 11. Frontiers, 2020.","chicago":"Nimeth, Barbara Anna, Stefan Riegler, and Maria Kalyna. “Alternative Splicing and DNA Damage Response in Plants.” <i>Frontiers in Plant Science</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fpls.2020.00091\">https://doi.org/10.3389/fpls.2020.00091</a>.","ista":"Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 11, 91.","mla":"Nimeth, Barbara Anna, et al. “Alternative Splicing and DNA Damage Response in Plants.” <i>Frontiers in Plant Science</i>, vol. 11, 91, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fpls.2020.00091\">10.3389/fpls.2020.00091</a>.","apa":"Nimeth, B. A., Riegler, S., &#38; Kalyna, M. (2020). Alternative splicing and DNA damage response in plants. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2020.00091\">https://doi.org/10.3389/fpls.2020.00091</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"02","department":[{"_id":"FyKo"}],"article_number":"91","file":[{"relation":"main_file","checksum":"57c37209f7b6712ced86c0f11b2be74e","file_name":"2020_FrontiersPlants_Nimeth.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"7607","date_created":"2020-03-23T09:03:40Z","file_size":507414,"creator":"dernst","date_updated":"2020-07-14T12:48:01Z"}],"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        11","abstract":[{"lang":"eng","text":"Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants."}],"file_date_updated":"2020-07-14T12:48:01Z","publication_identifier":{"eissn":["1664462X"]},"publication_status":"published","day":"19","scopus_import":"1","author":[{"first_name":"Barbara Anna","last_name":"Nimeth","full_name":"Nimeth, Barbara Anna"},{"orcid":"0000-0003-3413-1343","first_name":"Stefan","last_name":"Riegler","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","full_name":"Riegler, Stefan"},{"last_name":"Kalyna","full_name":"Kalyna, Maria","first_name":"Maria"}],"oa_version":"Published Version","title":"Alternative splicing and DNA damage response in plants","volume":11,"date_created":"2020-03-22T23:00:46Z","article_type":"original","status":"public","publication":"Frontiers in Plant Science","date_published":"2020-02-19T00:00:00Z","year":"2020","isi":1,"external_id":{"isi":["000518903600001"]},"ddc":["580"],"quality_controlled":"1","article_processing_charge":"No","doi":"10.3389/fpls.2020.00091","publisher":"Frontiers","_id":"7603","date_updated":"2023-08-18T07:05:18Z","type":"journal_article"}]