[{"main_file_link":[{"url":"https://doi.org/10.1093/pcp/pcab149","open_access":"1"}],"isi":1,"doi":"10.1093/pcp/pcab149","year":"2022","external_id":{"pmid":["34791413"],"isi":["000877899400009"]},"title":"Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density","article_processing_charge":"No","date_updated":"2023-08-02T13:40:43Z","oa":1,"volume":63,"quality_controlled":"1","oa_version":"Published Version","acknowledgement":"The authors thank Ralf Stracke (Bielefeld University, Bielefeld, Germany) for providing the myb mutants and their colleagues Bert De Rybel for the tmo5t;mo5l1 double mutant, Boris Parizot for tips on the RNA-seq analysis, Veronique Storme for statistical help on both the RNA-seq and lateral root density, and Martine De Cock for help in preparing the manuscript.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1471-9053"],"issn":["0032-0781"]},"_id":"10583","pmid":1,"citation":{"ista":"Struk S, Braem L, Matthys C, Walton A, Vangheluwe N, Van Praet S, Jiang L, Baster P, De Cuyper C, Boyer F-D, Stes E, Beeckman T, Friml J, Gevaert K, Goormachtig S. 2022. Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. Plant &#38; Cell Physiology. 63(1), 104–119.","short":"S. Struk, L. Braem, C. Matthys, A. Walton, N. Vangheluwe, S. Van Praet, L. Jiang, P. Baster, C. De Cuyper, F.-D. Boyer, E. Stes, T. Beeckman, J. Friml, K. Gevaert, S. Goormachtig, Plant &#38; Cell Physiology 63 (2022) 104–119.","ama":"Struk S, Braem L, Matthys C, et al. Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. <i>Plant &#38; Cell Physiology</i>. 2022;63(1):104-119. doi:<a href=\"https://doi.org/10.1093/pcp/pcab149\">10.1093/pcp/pcab149</a>","mla":"Struk, Sylwia, et al. “Transcriptional Analysis in the Arabidopsis Roots Reveals New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol Accumulation, Root Hair Elongation and Lateral Root Density.” <i>Plant &#38; Cell Physiology</i>, vol. 63, no. 1, Oxford University Press, 2022, pp. 104–19, doi:<a href=\"https://doi.org/10.1093/pcp/pcab149\">10.1093/pcp/pcab149</a>.","chicago":"Struk, Sylwia, Lukas Braem, Cedrick Matthys, Alan Walton, Nick Vangheluwe, Stan Van Praet, Lingxiang Jiang, et al. “Transcriptional Analysis in the Arabidopsis Roots Reveals New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol Accumulation, Root Hair Elongation and Lateral Root Density.” <i>Plant &#38; Cell Physiology</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/pcp/pcab149\">https://doi.org/10.1093/pcp/pcab149</a>.","ieee":"S. Struk <i>et al.</i>, “Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density,” <i>Plant &#38; Cell Physiology</i>, vol. 63, no. 1. Oxford University Press, pp. 104–119, 2022.","apa":"Struk, S., Braem, L., Matthys, C., Walton, A., Vangheluwe, N., Van Praet, S., … Goormachtig, S. (2022). Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. <i>Plant &#38; Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcab149\">https://doi.org/10.1093/pcp/pcab149</a>"},"publication_status":"published","keyword":["flavonols","MAX2","rac-Gr24","RNA-seq","root development","transcriptional regulation"],"author":[{"full_name":"Struk, Sylwia","last_name":"Struk","first_name":"Sylwia"},{"first_name":"Lukas","last_name":"Braem","full_name":"Braem, Lukas"},{"full_name":"Matthys, Cedrick","last_name":"Matthys","first_name":"Cedrick"},{"first_name":"Alan","full_name":"Walton, Alan","last_name":"Walton"},{"full_name":"Vangheluwe, Nick","last_name":"Vangheluwe","first_name":"Nick"},{"first_name":"Stan","full_name":"Van Praet, Stan","last_name":"Van Praet"},{"last_name":"Jiang","full_name":"Jiang, Lingxiang","first_name":"Lingxiang"},{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","full_name":"Baster, Pawel","last_name":"Baster","first_name":"Pawel"},{"full_name":"De Cuyper, Carolien","last_name":"De Cuyper","first_name":"Carolien"},{"last_name":"Boyer","full_name":"Boyer, Francois-Didier","first_name":"Francois-Didier"},{"full_name":"Stes, Elisabeth","last_name":"Stes","first_name":"Elisabeth"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kris","last_name":"Gevaert","full_name":"Gevaert, Kris"},{"last_name":"Goormachtig","full_name":"Goormachtig, Sofie","first_name":"Sofie"}],"abstract":[{"text":"The synthetic strigolactone (SL) analog, rac-GR24, has been instrumental in studying the role of SLs as well as karrikins because it activates the receptors DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2) of their signaling pathways, respectively. Treatment with rac-GR24 modifies the root architecture at different levels, such as decreasing the lateral root density (LRD), while promoting root hair elongation or flavonol accumulation. Previously, we have shown that the flavonol biosynthesis is transcriptionally activated in the root by rac-GR24 treatment, but, thus far, the molecular players involved in that response have remained unknown. To get an in-depth insight into the changes that occur after the compound is perceived by the roots, we compared the root transcriptomes of the wild type and the more axillary growth2 (max2) mutant, affected in both SL and karrikin signaling pathways, with and without rac-GR24 treatment. Quantitative reverse transcription (qRT)-PCR, reporter line analysis and mutant phenotyping indicated that the flavonol response and the root hair elongation are controlled by the ELONGATED HYPOCOTYL 5 (HY5) and MYB12 transcription factors, but HY5, in contrast to MYB12, affects the LRD as well. Furthermore, we identified the transcription factors TARGET OF MONOPTEROS 5 (TMO5) and TMO5 LIKE1 as negative and the Mediator complex as positive regulators of the rac-GR24 effect on LRD. Altogether, hereby, we get closer toward understanding the molecular mechanisms that underlay the rac-GR24 responses in the root.","lang":"eng"}],"department":[{"_id":"JiFr"}],"date_created":"2021-12-28T11:44:18Z","article_type":"original","date_published":"2022-01-21T00:00:00Z","month":"01","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"Oxford University Press","page":"104-119","publication":"Plant & Cell Physiology","issue":"1","type":"journal_article","day":"21","status":"public","intvolume":"        63"},{"related_material":{"record":[{"id":"8431","relation":"used_in_publication","status":"deleted"},{"relation":"research_paper","id":"1029","status":"public"}]},"ddc":["571"],"file":[{"file_id":"5616","creator":"system","content_type":"application/zip","relation":"main_file","date_created":"2018-12-12T13:02:58Z","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","file_name":"IST-2016-45-v1+1_PaperCode.zip","file_size":296722548,"date_updated":"2020-07-14T12:47:02Z","access_level":"open_access"}],"date_created":"2018-12-12T12:31:31Z","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"license":"https://creativecommons.org/licenses/by-sa/4.0/","department":[{"_id":"ToBo"}],"title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","publisher":"Institute of Science and Technology Austria","datarep_id":"45","doi":"10.15479/AT:ISTA:45","year":"2016","month":"08","date_published":"2016-08-25T00:00:00Z","_id":"5556","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:02Z","article_processing_charge":"No","date_updated":"2024-02-21T13:51:53Z","oa":1,"abstract":[{"text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions","lang":"eng"}],"author":[{"first_name":"Martin","last_name":"Lukacisin","full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Landon, Matthieu","last_name":"Landon","first_name":"Matthieu"},{"last_name":"Jajoo","full_name":"Jajoo, Rishi","first_name":"Rishi"}],"status":"public","keyword":["transcription","pausing","backtracking","polymerase","RNA","NET-seq","nucleosome","basepairing"],"day":"25","citation":{"short":"M. Lukacisin, M. Landon, R. Jajoo, (2016).","ista":"Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","ama":"Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>","mla":"Lukacisin, Martin, et al. <i>MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.”</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>.","apa":"Lukacisin, M., Landon, M., &#38; Jajoo, R. (2016). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016."},"type":"research_data"},{"status":"public","intvolume":"       144","type":"journal_article","day":"01","page":"587-595","publication":"Genetics","issue":"2","language":[{"iso":"eng"}],"publisher":"Genetics Society of America","date_published":"1996-10-01T00:00:00Z","month":"10","date_created":"2019-03-21T11:50:37Z","keyword":["amino acid sequence","article","caenorhabditis elegans","evolution","genetic variability","nonhuman","priority journal","sex determination","Amino Acid Sequence","Animals","Animals","Genetically Modified","Base Sequence","Caenorhabditis","Caenorhabditis elegans","Caenorhabditis elegans Proteins","DNA","Helminth","DNA-Binding Proteins","Evolution","Molecular","Female","Helminth Proteins","Membrane Proteins","Molecular Sequence Data","Mutagenesis","RNA","Messenger","Sequence Homology","Amino Acid","Sex Determination (Analysis)","Transcription Factors","Transgenes","Turner Syndrome","Animalia","Caenorhabditis","Caenorhabditis briggsae","Caenorhabditis elegans","Nematoda"],"author":[{"last_name":"de Bono","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hodgkin, J.","last_name":"Hodgkin","first_name":"J."}],"abstract":[{"lang":"eng","text":"The tra-1 gene is a terminal regulator of somatic sex in Caenorhabditis elegans: high tra-1 activity elicits female development, low tra-1 activity elicits male development. To investigate the function and evolution of tra- 1, we examined the tra-1 gene from the closely related nematode C. briggsae. Ce-tra-1 and Cb-tra-1 are unusually divergent. Each gene generates two transcripts, but only one of these is present in both species. This common transcript encodes TRA-1A, which shows only 44% amino acid identity between the species, a figure much lower than that for previously compared genes. A Cb-tra-1 transgene rescues many tissues of tra-1(null) mutants of C. elegans but not the somatic gonad or germ line. This transgene also causes nongonadal feminization of XO animals, indicating incorrect sexual regulation. Alignment of Ce-TRA-1A and Cb-TRA-1A defined several conserved regions likely to be important for tra-1 function. The phenotype differences between Ce-tra- 1(null) mutants rescued by Cb-tra-1 transgenes and wild-type C. elegans indicate significant divergence of regulatory regions. These molecular and functional studies suggest that evolution of sex determination in nematodes is rapid and genetically complex."}],"citation":{"ama":"de Bono M, Hodgkin J. Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences. <i>Genetics</i>. 1996;144(2):587-595.","mla":"de Bono, Mario, and J. Hodgkin. “Evolution of Sex Determination in Caenorhabditis: Unusually High Divergence of Tra-1 and Its Functional Consequences.” <i>Genetics</i>, vol. 144, no. 2, Genetics Society of America, 1996, pp. 587–95.","ista":"de Bono M, Hodgkin J. 1996. Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences. Genetics. 144(2), 587–595.","short":"M. de Bono, J. Hodgkin, Genetics 144 (1996) 587–595.","apa":"de Bono, M., &#38; Hodgkin, J. (1996). Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences. <i>Genetics</i>. Genetics Society of America.","ieee":"M. de Bono and J. Hodgkin, “Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences,” <i>Genetics</i>, vol. 144, no. 2. Genetics Society of America, pp. 587–595, 1996.","chicago":"Bono, Mario de, and J. Hodgkin. “Evolution of Sex Determination in Caenorhabditis: Unusually High Divergence of Tra-1 and Its Functional Consequences.” <i>Genetics</i>. Genetics Society of America, 1996."},"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","publication_identifier":{"issn":["00166731"]},"pmid":1,"_id":"6161","oa":1,"volume":144,"date_updated":"2021-01-12T08:06:28Z","title":"Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences","external_id":{"pmid":["8889522"]},"year":"1996","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1207552/"}]}]