--- _id: '10583' abstract: - lang: eng 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. 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. article_processing_charge: No article_type: original author: - first_name: Sylwia full_name: Struk, Sylwia last_name: Struk - first_name: Lukas full_name: Braem, Lukas last_name: Braem - first_name: Cedrick full_name: Matthys, Cedrick last_name: Matthys - first_name: Alan full_name: Walton, Alan last_name: Walton - first_name: Nick full_name: Vangheluwe, Nick last_name: Vangheluwe - first_name: Stan full_name: Van Praet, Stan last_name: Van Praet - first_name: Lingxiang full_name: Jiang, Lingxiang last_name: Jiang - first_name: Pawel full_name: Baster, Pawel id: 3028BD74-F248-11E8-B48F-1D18A9856A87 last_name: Baster - first_name: Carolien full_name: De Cuyper, Carolien last_name: De Cuyper - first_name: Francois-Didier full_name: Boyer, Francois-Didier last_name: Boyer - first_name: Elisabeth full_name: Stes, Elisabeth last_name: Stes - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Kris full_name: Gevaert, Kris last_name: Gevaert - first_name: Sofie full_name: Goormachtig, Sofie last_name: Goormachtig citation: 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. Plant & Cell Physiology. 2022;63(1):104-119. doi:10.1093/pcp/pcab149 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. Plant & Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcab149 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.” Plant & Cell Physiology. Oxford University Press, 2022. https://doi.org/10.1093/pcp/pcab149. ieee: S. Struk 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,” Plant & Cell Physiology, vol. 63, no. 1. Oxford University Press, pp. 104–119, 2022. 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 & Cell Physiology. 63(1), 104–119. 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.” Plant & Cell Physiology, vol. 63, no. 1, Oxford University Press, 2022, pp. 104–19, doi:10.1093/pcp/pcab149. 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 & Cell Physiology 63 (2022) 104–119. date_created: 2021-12-28T11:44:18Z date_published: 2022-01-21T00:00:00Z date_updated: 2023-08-02T13:40:43Z day: '21' department: - _id: JiFr doi: 10.1093/pcp/pcab149 external_id: isi: - '000877899400009' pmid: - '34791413' intvolume: ' 63' isi: 1 issue: '1' keyword: - flavonols - MAX2 - rac-Gr24 - RNA-seq - root development - transcriptional regulation language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/pcp/pcab149 month: '01' oa: 1 oa_version: Published Version page: 104-119 pmid: 1 publication: Plant & Cell Physiology publication_identifier: eissn: - 1471-9053 issn: - 0032-0781 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public 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 type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 63 year: '2022' ... --- _id: '5556' abstract: - lang: eng 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" article_processing_charge: No author: - first_name: Martin full_name: Lukacisin, Martin id: 298FFE8C-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisin orcid: 0000-0001-6549-4177 - first_name: Matthieu full_name: Landon, Matthieu last_name: Landon - first_name: Rishi full_name: Jajoo, Rishi last_name: Jajoo citation: 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:10.15479/AT:ISTA:45 apa: 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. https://doi.org/10.15479/AT:ISTA:45 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. https://doi.org/10.15479/AT:ISTA:45. 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. 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, 10.15479/AT:ISTA:45. mla: Lukacisin, Martin, et al. 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, doi:10.15479/AT:ISTA:45. short: M. Lukacisin, M. Landon, R. Jajoo, (2016). datarep_id: '45' date_created: 2018-12-12T12:31:31Z date_published: 2016-08-25T00:00:00Z date_updated: 2024-02-21T13:51:53Z day: '25' ddc: - '571' department: - _id: ToBo doi: 10.15479/AT:ISTA:45 file: - access_level: open_access checksum: ee697f2b1ade4dc14d6ac0334dd832ab content_type: application/zip creator: system date_created: 2018-12-12T13:02:58Z date_updated: 2020-07-14T12:47:02Z file_id: '5616' file_name: IST-2016-45-v1+1_PaperCode.zip file_size: 296722548 relation: main_file file_date_updated: 2020-07-14T12:47:02Z has_accepted_license: '1' keyword: - transcription - pausing - backtracking - polymerase - RNA - NET-seq - nucleosome - basepairing license: https://creativecommons.org/licenses/by-sa/4.0/ month: '08' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '8431' relation: used_in_publication status: deleted - id: '1029' relation: research_paper status: public status: public title: MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '6161' 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.' author: - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: J. full_name: Hodgkin, J. last_name: Hodgkin citation: ama: 'de Bono M, Hodgkin J. Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences. Genetics. 1996;144(2):587-595.' apa: 'de Bono, M., & Hodgkin, J. (1996). Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences. Genetics. Genetics Society of America.' chicago: 'Bono, Mario de, and J. Hodgkin. “Evolution of Sex Determination in Caenorhabditis: Unusually High Divergence of Tra-1 and Its Functional Consequences.” Genetics. Genetics Society of America, 1996.' ieee: 'M. de Bono and J. Hodgkin, “Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences,” Genetics, vol. 144, no. 2. Genetics Society of America, pp. 587–595, 1996.' 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.' mla: 'de Bono, Mario, and J. Hodgkin. “Evolution of Sex Determination in Caenorhabditis: Unusually High Divergence of Tra-1 and Its Functional Consequences.” Genetics, vol. 144, no. 2, Genetics Society of America, 1996, pp. 587–95.' short: M. de Bono, J. Hodgkin, Genetics 144 (1996) 587–595. date_created: 2019-03-21T11:50:37Z date_published: 1996-10-01T00:00:00Z date_updated: 2021-01-12T08:06:28Z day: '01' extern: '1' external_id: pmid: - '8889522' intvolume: ' 144' issue: '2' 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 language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1207552/ month: '10' oa: 1 oa_version: Published Version page: 587-595 pmid: 1 publication: Genetics publication_identifier: issn: - '00166731' publication_status: published publisher: Genetics Society of America quality_controlled: '1' status: public title: 'Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 144 year: '1996' ...