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160 results on '"Ariel, Federico"'

1. Guselkumab in patients with moderately to severely active ulcerative colitis (QUASAR): phase 3 double-blind, randomised, placebo-controlled induction and maintenance studies

Author

Abrahamovych, Orest, Abu-farsakh, Niazy, Afanasieva, Halyna, Akpinar, Hale, Al Kharrat, Houssam, Altintas, Engin, Altwegg, Romain, Andreev, Pavel, Aomatsu, Kazuki, Araki, Hiroshi, Argollo, Marjorie, Ariel, Federico, Armuzzi, Alessandro, Ashida, Toshifumi, Augustyn, Monika, Aumais, Guy, Azum, Martín, Baert, Filip, Balaz, Jozef, Balderramo, Domingo, Begun, Jakob, Berova, Temenuzhka, Billiauws, Lore, Blanco, Antonio, Bortlik, Martin, Bossa, Fabrizio, Bunkova, Elena, Cabello, Mercedes, Cao, Qian, Caprioli, Flavio, Cerqueira, Rute, Chachu, Karen, Chamouard, Patrick, Chen, Chunxiao, Chen, Yan, Chen, Baili, Chen, Dongfeng, Chen, Hong, Chen, Youxiang, Chen, Chou-chen, Cheon, Jaehee, Chen, Minhu, Chiu, Cheng-tang, Choi, Changhwan, Chow, Elizabeth, Cicala, Michele, Cintra, Aderson, Danilkiewicz, Wit, Datsenko, Olena, De Hertogh, Gert, De María, Julio, Del Valle Torrealba Medina, Leyanira, Deliang, Liu, Desreumaux, Pierre, Dewint, Pieter, Ding, Shigang, Doherty, Glen, Draganova, Raina, Dutré, Joris, Duvall, George, Egan, Laurence, Fahed, Julien, Fechner, Lars, Fedurco, Miroslav, Ferhat Celik, Aykut, Fernandez, Juan, Filip, Rafal, Fishman, Sigal, Flores, Cristina, Fogel, Ronald, Fowler, Sharyle, Francesconi, Carlos, Fujii, Toshimitsu, Fujiya, Mikihiro, Fukata, Masayuki, Fukuhara, Seiichiro, Furumoto, Yohei, G.Kiss, Gyula, Gachowski, Waldemar, Gao, Xiang, Gasbarrini, Antonio, Gawdis-wojnarska, Beata, Gaya, Daniel, Geccherle, Andrea, Gilletta De Saint Joseph, Cyrielle, Gimenez, Edgardo, Gionchetti, Paolo, Goldin, Eran, Golovchenko, Oleksandr, Gonciarz, Maciej, Gonen, Can, Gonzales, Chad, Gonzalez, Raquel, Gonzalez Segura, Gaston Julian, Gridnyev, Oleksiy, Gu, Fang, Gupta, Nitin, Gyokeres, Tibor, Haines, Melissa, Hebuterne, Xavier, Hedin, Charlotte, Hellstrom, Per, Hilmi, Ida Normiha, Hirai, Fumihito, Hisabe, Takashi, Hlavaty, Tibor, Hoentjen, Frank, Holtmann, Gerald, Horiki, Noriyuki, Horny, Ivo, Horvat, Gyula, Horvath, Frantisek, Hoshi, Namiko, Hosomi, Shuhei, Hospodarskyy, Ihor, Hou, Xiaohua, Hrdlicka, Ludek, Hu, Naizhong, Huang, Vivian, Huang, Caibin, Inaba, Tomoki, Ishiguro, Yoh, Ishihara, Shunji, Ishikawa, Takeshi, Iskandar, Heba, Israeli, Eran, Itaba, Soichi, Ivanishyn, Olha, Izbéki, Ferenc, Jain, Animesh, Jairath, Vipul, Jang, Byung Ik, Jiang, Chunmeng, Jones, Michael, Kagaya, Takashi, Kalimullina, Dilara, Karakina, Marina, Karatas, Ali, Kashimura, Hiroshi, Keret, Dan, Khovaeva, Yaroslava, Kierkus, Jaroslaw, Kim, Taeoh, Kim, Youngho, Kim, Hyo Jong, Klaus, Jochen, Kleczkowski, Dariusz, Klopocka, Maria, Kobayashi, Taku, Kobielusz-gembala, Iwona, Kojima, Yuichiro, Koo, Ja Seol, Kopon, Adam, Kopp, James, Koyama, Fumikazu, Koynarski, Vasil, Kravchenko, Tetiana, Kudo, Masatoshi, Kusunoki, Ryusaku, Kwon, Kwangan, Laclav, Martin, Lago, Paula, Laharie, David, Lasa, Juan, Lateef, Syed, Latinovic Radakovic, Tatjana, Lee, Kang Moon, Leszczyszyn, Jaroslaw, Li, Yan, Liu, Mei, Liu, Eashen, Lobaton Ortega, Triana, Lopatin, Denis, Lopes, Susana, Lovric Jovanovic, Mileva, Lubini, Marcio, Lukas, Milan, Maaser, Christian, Machytka, Evzen, Maemoto, Atsuo, Magro, Fernando, Marcet, Jorge, Marini, Eduardo, Marusawa, Hiroyuki, Matous, Jan, Matsumoto, Takayuki, Mendu, Shoba, Miao, Yinglei, Mihaly, Emese, Miheller, Pal, Ministro, Paula, Miyabayashi, Hideharu, Mohl, Wolfgang, Molnar, Martin, Moore, Gregory, Moran Faienzo, Gabriela, Morral, Eugeni Domenech, Motoya, Satoshi, Murali, Narayanachar, Mustaffa, Nazri Mohamad, Naem, Mohamed, Nakai, Katsuhiko, Nakajima, Koichi, Nakamoto, Yasunari, Nakamura, Masanao, Nancey, Stephane, Navaneethan, Udayakumar, Nawawi, Khairul Najmi Muhammad, Ninomiya, Tomoyuki, Novak, Janos, Oki, Motoji, Oliveira Santana, Genoile, Onizawa, Michio, Ono, Yohei, Osada, Taro, Osipenko, Marina, Owczarek, Danuta, Parente, Jose Miguel, Patel, Kamal, Patel, Bhaktasharan, Pedersen, Peder, Petroniene, Rima, Petrov, Asen, Petrova, Elina, Piquet, Marie-astrid, Pokrotnieks, Juris, Poroshina, Elena, Portela, Francisco, Pruthi, Jatinder S., Prystupa, Lyudmila, Pukitis, Aldis, Qiu, Yun, Rafalsky, Vladimir, Rainis, Tova, Ramos Junior, Odery, Rashid, Mohammed, Rayyan, Yasser, Reshetko, Olga, Ribeiro, Tarsila, Rivero, Montserrat, Roblin, Xavier, Romatowski, Jacek, Rowbotham, David, Ruffinengo, Orlando Enrique, Rydzewska-wyszkowska, Grazyna, Sablin, Oleg, Sai, Souken, Saibeni, Simone, Said, Rosaida Hj. Md., Sakuraba, Hirotake, Samaan, Mark, Sandborn, William, Saruta, Masayuki, Sauk, Jenny, Savarino, Edoardo Vincenzo, Schultz, Michael, Schulze, Joerg, Sedghi, Shahriar, Seidler, Ursula, Seksik, Philippe, Senturk, Omer, Shelton, Edward, Shimizu, Masahito, Shin, Sungjae, Shukla, Richa, Sigal, Michael, Silva Junior, Roberto, Simoes Neto, Joaquim, Siroky Jr., Milan, Smajstrla, Vit, Smid, Vaclav, Smiley, Sarah, Soledad Brunatto, Luciana, Stanislavchuk, Mykola, Stokesberry, David, Stone, Christian, Suiter, Daniel, Suzuki, Takayoshi, Svorcan, Petar, Takagi, Sho, Takagi, Tomohisa, Takamura, Masaaki, Takayama, Tetsuji, Takeuchi, Ken, Tanaka, Akihito, Tanaka, Hiroki, Tanash, Omar, Tang, Wen, Tankova, Ludmila, Teixeira Campos, Luciana, Thin, Lena, Tkachev, Alexander, Tolmanis, Ivars, Tsarynna, Nataliia, Tsonev, Nikolay, Tulassay, Zsolt, Ueo, Tetsuya, Unal, Nalan, Valuyskikh, Ekaterina, Van Dop, Willemijn, Vasilevskaya, Olga, Venugopal, Kannan, Verstockt, Bram, Viamonte, Manuel, Vyshyvanyuk, Vira, Wang, Bangmao, Wang, Xiaoyan, Wang, Jiangbin, Wang, Yufang, Wei, Shu-chen, Weisshof, Roni, Wisam, Sbeit, Wojcik, Katarzyna, Yakovlev, Alexey, Yasuda, Hiroshi, Ye, Byongduk, Yen, Hsu-heng, Yilmaz, Hasan, Yokoyama, Yoko, Yoon, Hyuk, Yoshida, Takeshi, Yurkiv, Andriy, Zaha, Osamu, Zaltman, Cyrla, Zhan, Qiang, Zhang, Hongjie, Zhang, Shutian, Zhu, Lanxiang, Zou, Duowu, Zou, Xiaoping, Zureikat, Firas, Rubin, David T, Allegretti, Jessica R, Panés, Julián, Shipitofsky, Nicole, Yarandi, Shadi S, Huang, Kuan-Hsiang Gary, Germinaro, Matthew, Wilson, Rebbecca, Zhang, Hongyan, Johanns, Jewel, Feagan, Brian G, Hisamatsu, Tadakazu, Lichtenstein, Gary R, Bressler, Brian, Peyrin-Biroulet, Laurent, Sands, Bruce E, and Dignass, Axel

Published
2025
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5. HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions

Author

Huang, Ying, An, Jing, Sircar, Sanchari, Bergis, Clara, Lopes, Chloé Dias, He, Xiaoning, Da Costa, Barbara, Tan, Feng-Quan, Bazin, Jeremie, Antunez-Sanchez, Javier, Mammarella, Maria Florencia, Devani, Ravi-sureshbhai, Brik-Chaouche, Rim, Bendahmane, Abdelhafid, Frugier, Florian, Xia, Chongjing, Rothan, Christophe, Probst, Aline V., Mohamed, Zouine, Bergounioux, Catherine, Delarue, Marianne, Zhang, Yijing, Zheng, Shaojian, Crespi, Martin, Fragkostefanakis, Sotirios, Mahfouz, Magdy M., Ariel, Federico, Gutierrez-Marcos, Jose, Raynaud, Cécile, Latrasse, David, and Benhamed, Moussa

Published
2023
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10. Apoplastic class III peroxidases PRX62 and PRX69 promote Arabidopsis root hair growth at low temperature

Author

Pacheco, Javier Martínez, Ranocha, Philippe, Kasulin, Luciana, Fusari, Corina M., Servi, Lucas, Aptekmann, Ariel. A., Gabarain, Victoria Berdion, Peralta, Juan Manuel, Borassi, Cecilia, Marzol, Eliana, Rodríguez-Garcia, Diana Rosa, del Carmen Rondón Guerrero, Yossmayer, Sardoy, Mariana Carignani, Ferrero, Lucía, Botto, Javier F., Meneses, Claudio, Ariel, Federico, Nadra, Alejandro D., Petrillo, Ezequiel, Dunand, Christophe, and Estevez, José M.

Published
2022
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13. Efficacy and safety of baricitinib for the treatment of hospitalised adults with COVID-19 (COV-BARRIER): a randomised, double-blind, parallel-group, placebo-controlled phase 3 trial

Author

Ahn, Mi-Young, Akasbi, Miriam, Alatorre-Alexander, Jorge, Altclas, Javier David, Ariel, Federico, Ariza, Horacio Alberto, Atkar, Chandrasekhar, Bertetti, Anselmo, Bhattacharya, Meenakshi, Briones, Maria Luisa, Budhraja, Akshay, Burza, Aaliya, Camacho Ortiz, Adrian, Caricchio, Roberto, Casas, Marcelo, Cevoli Recio, Valeria, Choi, Won Suk, Cohen, Emilia, Comulada-Rivera, Angel, Cook, Paul, Cornejo Juarez, Dora Patricia, Daniel, Carnevali, Degrecci Relvas, Luiz Fernando, Dominguez Cherit, Jose Guillermo, Ellerin, Todd, Enikeev, Dmitry, Erico Tanni Minamoto, Suzana, Estrada, Vicente, Fiss, Elie, Furuichi, Motohiko, Giovanni Luz, Kleber, Goldman, Jason D., Gonzalez, Omar, Gordeev, Ivan, Gruenewald, Thomas, Hamamoto Sato, Victor Augusto, Heo, Eun Young, Heo, Jung Yeon, Hermida, Maria, Hirai, Yuji, Hutchinson, David, Iastrebner, Claudio, Ioachimescu, Octavian, Jain, Manish, Juliani Souza Lima, Maria Patelli, Khan, Akram, Kremer, Andreas E., Lawrie, Thomas, MacElwee, Mark, Madhani-Lovely, Farah, Malhotra, Vinay, Martínez Resendez, Michel Fernando, McKinnell, James, Milligan, Patrick, Minelli, Cesar, Moran Rodriguez, Miguel Angel, Parody, Maria Leonor, Paulin, Priscila, Pellegrini, Rita de Cassia, Pemu, Priscilla, Procopio Carvalho, Ana Carolina, Puoti, Massimo, Purow, Joshua, Ramesh, Mayur, Rea Neto, Alvaro, Robinson, Philip, Rodrigues, Cristhieni, Rojas Velasco, Gustavo, Saraiva, Jose Francisco Kerr, Scheinberg, Morton, Schreiber, Stefan, Scublinsky, Dario, Sevciovic Grumach, Anete, Shawa, Imad, Simon Campos, Jesus, Sofat, Nidhi, Som, Mousumi, Spinner, Christoph D., Sprinz, Eduardo, Stienecker, Roger, Suarez, Jose, Tachikawa, Natsuo, Tahir, Hasan, Tiffany, Brian, Vishnevsky, Alexander, Westheimer Cavalcante, Adilson, Zirpe, Kapil, Marconi, Vincent C, Ramanan, Athimalaipet V, de Bono, Stephanie, Kartman, Cynthia E, Krishnan, Venkatesh, Liao, Ran, Piruzeli, Maria Lucia B, Goldman, Jason D, de Cassia Pellegrini, Rita, Cardoso, Anabela, Chakladar, Sujatro, Crowe, Brenda, Reis, Paulo, Zhang, Xin, Adams, David H, and Ely, E Wesley

Published
2021
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16. Genetic–epigenetic interplay in the determination of plant 3D genome organization.

Author

He, Xiaoning, Dias Lopes, Chloé, Pereyra-Bistrain, Leonardo I, Huang, Ying, An, Jing, Chaouche, Rim Brik, Zalzalé, Hugo, Wang, Qingyi, Ma, Xing, Antunez-Sanchez, Javier, Bergounioux, Catherine, Piquerez, Sophie, Fragkostefanakis, Sotirios, Zhang, Yijing, Zheng, Shaojian, Crespi, Martin, Mahfouz, Magdy M, Mathieu, Olivier, Ariel, Federico, and Gutierrez-Marcos, Jose

Published
2024
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20. Ixekizumab for patients with non-radiographic axial spondyloarthritis (COAST-X): a randomised, placebo-controlled trial

Author

Morin, Frederic, Rahman, Proton, Ariel, Federico, Berman, Alberto, Carrio, Judith, Lucero, Eleonora, Cocco, Jose Maldonado, Hidalgo, Rodolfo Pardo, Velasco, Jorge, Viola, Diego O., Grisar, Johannes, Resch, Heinrich, Scheinecker, Clemens, Melazzi, Ana Claudia, Roimicher, Luis, Scotton, Antonio Scafuto, Rodriguez, Aaron Alejandro Barrera, Molina, Francisco Fidencio Cons, Barragan, Sergio Duran, Skinner, Cassandra M., Tena, Cesar Francisco Pacheco, Remus, Cesar Ricardo Ramos, Rodriguez, Juan Cruz Rizo, Hong, Seung-Jae, Kang, Seong Wook, Lee, Chang Keun, Lee, Eun Bong, Lee, Sang Heon, Park, Min-Chan, Lee, Sang-Hoon, Dokoupilova, Eva, Dvorak, Zdenek, Malcova, Martina, Pvelka, Karel, Eklund, Kari K., Jarvinen, Pentti, Karjalainen, Anna, Paimela, Leena, Taniguchi, Yoshinori, Tsuda, Tokutaro, Tada, Kurisu, Dobashi, Hiroaki, Inui, Kentaro, Ueki, Yukitaka, Matsumoto, Yoshifuji, Hatta, Kazuhiro, Atsumi, Tatsuya, Goto, Hitoshi, Honjo, Shigeru, Matsui, Kiyoshi, Takakubo, Yuya, Neeck, Gunther, Wagner, Sylke, Braun, Jürgen, Blicharshi, Tomasz, Dudek, Anna, Hrycai, Pawel, Plebanski, Rafal, Drabiszcak-Piatkowska, Janina, Brzezicki, Jan, Krogulec, Marek, Opris-Belinski, Daniela, Ramazan, Ana Maria, Tronaru, Luminita, van de Sande, Marleen G., Matsievskaya, Galina, Schmidt, Evgeniya, Stanislav, Marina, Yakushin, Sergey, Ershova, Olga, Rebroy, Andrey, Churchill, Melvin A., Flint, Kathleen P., Greenwald, Maria, Howell, Mary P., Kaine, Jeffrey L., Kivitz, Alan, Klein, Steven J., Mueller, Eric C., Peters, Eric A., Querubin, Roel, Sayers, Michael E., Scoville, Craig D., Shanahan, Joseph C., Roseff, Richard, Hull, John E., Mallepalli, Jyothi R., Sebai, Mohamed B., Kimmel, Steven C., Goddard, David H., Mease, Philip J., Harris, Mark D., Mabaquiao, Arthur R., Diegel, Roger J., Thai, Christine, Rivera, Tania L., Perez-De Jesus, Amarilis, Soto-Raices, Oscar, Toro-Torres, Ramon, Pantojas, Carlos, Deodhar, Atul, van der Heijde, Désirée, Gensler, Lianne S, Kim, Tae-Hwan, Maksymowych, Walter P, Østergaard, Mikkel, Poddubnyy, Denis, Marzo-Ortega, Helena, Bessette, Louis, Tomita, Tetsuya, Leung, Ann, Hojnik, Maja, Gallo, Gaia, Li, Xiaoqi, Adams, David, Carlier, Hilde, and Sieper, Joachim

Published
2020
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22. sincFold: end-to-end learning of short- and long-range interactions in RNA secondary structure.

Author

Bugnon, Leandro A, Persia, Leandro Di, Gerard, Matias, Raad, Jonathan, Prochetto, Santiago, Fenoy, Emilio, Chorostecki, Uciel, Ariel, Federico, Stegmayer, Georgina, and Milone, Diego H

Subjects
NUCLEOTIDE sequence, NON-coding RNA, DEEP learning, RNA, DYNAMIC programming
Abstract

Motivation Coding and noncoding RNA molecules participate in many important biological processes. Noncoding RNAs fold into well-defined secondary structures to exert their functions. However, the computational prediction of the secondary structure from a raw RNA sequence is a long-standing unsolved problem, which after decades of almost unchanged performance has now re-emerged due to deep learning. Traditional RNA secondary structure prediction algorithms have been mostly based on thermodynamic models and dynamic programming for free energy minimization. More recently deep learning methods have shown competitive performance compared with the classical ones, but there is still a wide margin for improvement. Results In this work we present sincFold, an end-to-end deep learning approach, that predicts the nucleotides contact matrix using only the RNA sequence as input. The model is based on 1D and 2D residual neural networks that can learn short- and long-range interaction patterns. We show that structures can be accurately predicted with minimal physical assumptions. Extensive experiments were conducted on several benchmark datasets, considering sequence homology and cross-family validation. sincFold was compared with classical methods and recent deep learning models, showing that it can outperform the state-of-the-art methods. [ABSTRACT FROM AUTHOR]

Published
2024
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23. A lateral organ boundaries domain transcription factor acts downstream of the auxin response factor 2 to control nodulation and root architecture in Medicago truncatula.

Author

Kirolinko, Cristina, Hobecker, Karen, Cueva, Marianela, Botto, Florencia, Christ, Aurélie, Niebel, Andreas, Ariel, Federico, Blanco, Flavio Antonio, Crespi, Martín, and Zanetti, María Eugenia

Subjects
ROOT-tubercles, MEDICAGO truncatula, TRANSCRIPTION factors, AUXIN, ROOT formation, PROTHROMBIN, LEGUMES
Abstract

Summary: Legume plants develop two types of root postembryonic organs, lateral roots and symbiotic nodules, using shared regulatory components. The module composed by the microRNA390, the Trans‐Acting SIRNA3 (TAS3) RNA and the Auxin Response Factors (ARF)2, ARF3, and ARF4 (miR390/TAS3/ARFs) mediates the control of both lateral roots and symbiotic nodules in legumes.Here, a transcriptomic approach identified a member of the Lateral Organ Boundaries Domain (LBD) family of transcription factors in Medicago truncatula, designated MtLBD17/29a, which is regulated by the miR390/TAS3/ARFs module. ChIP‐PCR experiments evidenced that MtARF2 binds to an Auxin Response Element present in the MtLBD17/29a promoter. MtLBD17/29a is expressed in root meristems, lateral root primordia, and noninfected cells of symbiotic nodules.Knockdown of MtLBD17/29a reduced the length of primary and lateral roots and enhanced lateral root formation, whereas overexpression of MtLBD17/29a produced the opposite phenotype. Interestingly, both knockdown and overexpression of MtLBD17/29a reduced nodule number and infection events and impaired the induction of the symbiotic genes Nodulation Signaling Pathway (NSP) 1 and 2.Our results demonstrate that MtLBD17/29a is regulated by the miR390/TAS3/ARFs module and a direct target of MtARF2, revealing a new lateral root regulatory hub recruited by legumes to act in the root nodule symbiotic program. [ABSTRACT FROM AUTHOR]

Published
2024
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26. The C subunit of the nuclear factor Y binds to the Cyclin P4;1 promoter to modulate nodule organogenesis and infection during symbiosis in Phaseolus vulgaris.

Author

Roda, Carla, Clúa, Joaquín, Eylenstein, Andrés, Greco, Micaela, Ariel, Federico, Zanetti, María Eugenia, and Blanco, Flavio Antonio

Subjects
CYCLINS, NITROGEN fixation, SYMBIOSIS, MORPHOGENESIS, COMMON bean, SOIL microbiology
Abstract

This article explores the role of the C subunit of the nuclear factor Y (NF-Y) in the symbiotic relationship between Phaseolus vulgaris (common bean) plants and soil microorganisms. The interaction between the plants and rhizobia leads to the formation of nodules, where nitrogen fixation occurs. The study found that the NF-Y subunit PvNF-YC1 directly binds to a gene involved in the cell cycle and nodule formation. Additionally, the study identified the PvCYCP4;1 cyclin gene as being crucial for root growth, nodule formation, and rhizobial infection in common bean. The findings shed light on the regulatory mechanisms of the cell cycle during symbiotic interactions in common bean plants. [Extracted from the article]

Published
2024
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27. Transcription factor NAC1 activates expression of peptidase-encoding AtCEPs in roots to limit root hair growth.

Author

Rodríguez-García, Diana R, Rondón Guerrero, Yossmayer del Carmen, Ferrero, Lucía, Rossi, Andrés Hugo, Miglietta, Esteban A, Aptekmann, Ariel A, Marzol, Eliana, Martínez Pacheco, Javier, Carignani, Mariana, Berdion Gabarain, Victoria, Lopez, Leonel E, Díaz Dominguez, Gabriela, Borassi, Cecilia, Sánchez-Serrano, José Juan, Xu, Lin, Nadra, Alejandro D, Rojo, Enrique, Ariel, Federico, and Estevez, José M

Published
2024
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28. Long noncoding RNA‐mediated epigenetic regulation of auxin‐related genes controls shade avoidance syndrome in Arabidopsis.

Author

Mammarella, María Florencia, Lucero, Leandro, Hussain, Nosheen, Muñoz‐Lopez, Aitor, Huang, Ying, Ferrero, Lucia, Fernandez‐Milmanda, Guadalupe L, Manavella, Pablo, Benhamed, Moussa, Crespi, Martin, Ballare, Carlos L, Gutiérrez Marcos, José, Cubas, Pilar, and Ariel, Federico

Subjects
GENETIC regulation, EPIGENETICS, LINCRNA, ARABIDOPSIS, SUSTAINABLE agriculture, ARABIDOPSIS thaliana
Abstract

The long noncoding RNA (lncRNA) AUXIN‐REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA–DNA hybrids (R‐loops) and modulating local three‐dimensional chromatin conformation. Here, we show that APOLO regulates shade avoidance syndrome by dynamically modulating expression of key factors. In response to far‐red (FR) light, expression of APOLO anti‐correlates with that of its target BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis thaliana. APOLO deregulation results in BRC1 transcriptional repression and an increase in the number of branches. Accumulation of APOLO transcription fine‐tunes the formation of a repressive chromatin loop encompassing the BRC1 promoter, which normally occurs only in leaves and in a late response to far‐red light treatment in axillary buds. In addition, our data reveal that APOLO participates in leaf hyponasty, in agreement with its previously reported role in the control of auxin homeostasis through direct modulation of auxin synthesis gene YUCCA2, and auxin efflux genes PID and WAG2. We show that direct application of APOLO RNA to leaves results in a rapid increase in auxin signaling that is associated with changes in the plant response to far‐red light. Collectively, our data support the view that lncRNAs coordinate shade avoidance syndrome in A. thaliana, and reveal their potential as exogenous bioactive molecules. Deploying exogenous RNAs that modulate plant–environment interactions may therefore become a new tool for sustainable agriculture. Synopsis: The Arabidopsis lncRNA APOLO influences chromatin architecture to regulate transcription of specific genes, including auxin‐responsive genes which are involved in the plant's response to shade avoidance. Here, APOLO is shown to respond to changes in light by influencing transcription and plant behavior. APOLO modulates the expression of BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis, through chromatin looping around the BRC1 promoter.APOLO‐mediated chromatin looping is influenced by changes in light exposure and regulates branching behavior.Low‐red/far‐red light ratio‐mediated leaf hyponasty depends on APOLO regulation of auxin‐related genes.In vitro‐transcribed APOLO directly sprayed onto plants is sufficient to alter plant auxin homeostasis in response to light conditions. [ABSTRACT FROM AUTHOR]

Published
2023
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34. The plant noncoding transcriptome: a versatile environmental sensor.

Author

Chorostecki, Uciel, Bologna, Nicolas G., and Ariel, Federico

Subjects
PLANT RNA, NON-coding RNA, MOLECULAR structure, TRANSCRIPTOMES, MORPHOLOGY, LINCRNA
Abstract

Plant noncoding RNA transcripts have gained increasing attention in recent years due to growing evidence that they can regulate developmental plasticity. In this review article, we comprehensively analyze the relationship between noncoding RNA transcripts in plants and their response to environmental cues. We first provide an overview of the various noncoding transcript types, including long and small RNAs, and how the environment modulates their performance. We then highlight the importance of noncoding RNA secondary structure for their molecular and biological functions. Finally, we discuss recent studies that have unveiled the functional significance of specific long noncoding transcripts and their molecular partners within ribonucleoprotein complexes during development and in response to biotic and abiotic stress. Overall, this review sheds light on the fascinating and complex relationship between dynamic noncoding transcription and plant environmental responses, and highlights the need for further research to uncover the underlying molecular mechanisms and exploit the potential of noncoding transcripts for crop resilience in the context of global warming. [ABSTRACT FROM AUTHOR]

Published
2023
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35. The long intergenic noncoding RNA ARES modulates root architecture in Arabidopsis.

Author

Roulé, Thomas, Legascue, María Florencia, Barrios, Andana, Gaggion, Nicolás, Crespi, Martin, Ariel, Federico, and Blein, Thomas

Subjects
LINCRNA, ROOT development, GENE expression, REGULATOR genes, PLANT genes, EPIGENETICS, ARABIDOPSIS
Abstract

Long noncoding RNAs (lncRNAs) have emerged as important regulators of gene expression in plants. They have been linked to a wide range of molecular mechanisms, including epigenetics, miRNA activity, RNA processing and translation, and protein localization or stability. In Arabidopsis, characterized lncRNAs have been implicated in several physiological contexts, including plant development and the response to the environment. Here we searched for lncRNA loci located nearby key genes involved in root development and identified the lncRNA ARES (AUXIN REGULATOR ELEMENT DOWNSTREAM SOLITARYROOT) downstream of the lateral root master gene IAA14/SOLITARYROOT (SLR). Although ARES and IAA14 are co‐regulated during development, the knockdown and knockout of ARES did not affect IAA14 expression. However, in response to exogenous auxin, ARES knockdown impairs the induction of its other neighboring gene encoding the transcription factor NF‐YB3. Furthermore, knockdown/out of ARES results in a root developmental phenotype in control conditions. Accordingly, a transcriptomic analysis revealed that a subset of ARF7‐dependent genes is deregulated. Altogether, our results hint at the lncRNA ARES as a novel regulator of the auxin response governing lateral root development, likely by modulating gene expression in trans. [ABSTRACT FROM AUTHOR]

Published
2023
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37. Beyond transcription: compelling open questions in plant RNA biology.

Author

Manavella, Pablo A, Herz, Micaela A Godoy, Kornblihtt, Alberto R, Sorenson, Reed, Sieburth, Leslie E, Nakaminami, Kentaro, Seki, Motoaki, Ding, Yiliang, Sun, Qianwen, Kang, Hunseung, Ariel, Federico D, Crespi, Martin, Giudicatti, Axel J, Cai, Qiang, Jin, Hailing, Feng, Xiaoqi, Qi, Yijun, and Pikaard, Craig S

Published
2023
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42. Plant long non-coding RNAs: biologically relevant and mechanistically intriguing.

Author

Yang, Jun, Ariel, Federico, and Wang, Dong

Subjects
*MOLECULAR interactions, *PLANT life cycles, *NUCLEOTIDES, *RNA sequencing, *PLANT breeding, *LINCRNA, *CIRCULAR RNA
Abstract

Long non-coding RNAs (lncRNAs) are a group of RNAs greater than 200 nucleotides in length exhibiting low or no coding potential that are involved in diverse biological functions through their molecular interaction with proteins, DNA, or other RNAs. With the emergence of advanced high-throughput RNA sequencing technologies, tens of thousands of novel long non-coding RNAs have been identified in plant transcriptomes in the last decade. More importantly, functional studies revealed that several lncRNAs play key regulatory roles in plant development and stress responses. In this review, we focus on summarizing recent progress uncovering regulatory roles and mechanisms of lncRNAs during the plant life cycle, and briefly discuss the possible biotechnological applications of lncRNAs for plant breeding. [ABSTRACT FROM AUTHOR]

Published
2023
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43. Exogenous RNAs: promising tools for the second green revolution.

Author

Melo, Johan Rodríguez, Mammarella, Florencia, and Ariel, Federico

Subjects
SUSTAINABLE agriculture, PEST control, RNA, RNA synthesis, GLOBAL warming, PESTICIDES, GREEN Revolution
Abstract

The impending need for increasing amounts of food for the world population poses enormous challenges to agriculture. Moreover, global warming has exacerbated abiotic and biotic stresses, accelerating the emergence of new pests and pathogens which threatens crop productivity. Therefore, the scientific community urgently needs to develop innovative solutions for sustainable agriculture, notably replacing synthetic pesticides by active and highly specific biomolecules for pest control. In this context, RNA-based technologies emerge as an outstanding genetically modified organism-free approach offering versatile solutions to boost productivity while conserving and harnessing the wide variety of local landraces. Here we review recent advances in the field, including RNA synthesis approaches and the development of the nanotechnology required for RNA stabilization and delivery, and we discuss the potential of RNA as the key molecule for versatile applications in the second green revolution. [ABSTRACT FROM AUTHOR]

Published
2023
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44. Trichoderma root colonization in maize triggers epigenetic changes in genes related to the jasmonic and salicylic acid pathways that prime defenses against Colletotrichum graminicola leaf infection.

Author

Agostini, Romina B, Ariel, Federico, Rius, Sebastián P, Vargas, Walter A, and Campos-Bermudez, Valeria A

Subjects
*PLANT colonization, *SALICYLIC acid, *JASMONIC acid, *TRICHODERMA, *COLLETOTRICHUM, *CORN
Abstract

Beneficial interactions between plant roots and Trichoderma species lead to both local and systemic enhancements of the plant immune system through a mechanism known as priming of defenses. Previously, we have reported a number of genes and proteins that are differentially regulated in distant tissues of maize plants following inoculation with Trichoderma atroviride. To further investigate the mechanisms involved in the systemic activation of plant responses, here we have further evaluated the regulatory aspects of a selected group of genes when priming is triggered in maize plants. Time-course experiments from the beginning of the interaction between T. atroviride and maize roots followed by leaf infection with Colletotrichum graminicola allowed us to identify a gene set regulated by priming in the leaf tissue. In the same experiment, phytohormone measurements revealed a decrease in jasmonic acid concentration while salicylic acid increased at 2 d and 6 d post-inoculation. In addition, chromatin structure and modification assays showed that chromatin was more open in the primed state compared with unprimed control conditions, and this allowed for quicker gene activation in response to pathogen attack. Overall, the results allowed us to gain insights on the interplay between the phytohormones and epigenetic regulatory events in the systemic and long-lasting regulation of maize plant defenses following Trichoderma inoculation. [ABSTRACT FROM AUTHOR]

Published
2023
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45. Differential chromatin binding preference is the result of the neo‐functionalization of the TB1 clade of TCP transcription factors in grasses.

Author

Mansilla, Natanael, Fonouni‐Farde, Camille, Ariel, Federico, and Lucero, Leandro

Subjects
TRANSCRIPTION factors, GENETIC regulation, CHROMATIN, CORN, GENE expression
Abstract

Summary: The understanding of neo‐functionalization of plant transcription factors (TFs) after gene duplication has been extensively focused on changes in protein–protein interactions, the expression pattern of TFs, or the variation of cis‐elements bound by TFs. Yet, the main molecular role of a TF, that is, its specific chromatin binding for the direct regulation of target gene expression, continues to be mostly overlooked.Here, we studied the TB1 clade of the TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTORS (TCP) TF family within the grasses (Poaceae).We identified an Asp/Gly amino acid replacement within the TCP domain, originated within a paralog TIG1 clade exclusive for grasses. The heterologous expression of Zea mays TB1 and its two paralogs BAD1 and TIG1 in Arabidopsis mutant plants lacking the TB1 ortholog BRC1 revealed distinct functions in plant development. Notably, the Gly acquired in the TIG1 clade does not impair TF homodimerization and heterodimerization, while it modulates chromatin binding preferences. We found that in vivo TF recognition of target promoters depends on this Asp/Gly mutation and directly impacts downstream gene expression and subsequent plant development.These results provided new insights into how natural selection fine‐tunes gene expression regulation after duplication of TFs to define plant architecture. [ABSTRACT FROM AUTHOR]

Published
2023
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46. Transcriptional Control of a Plant Stem Cell Niche

Author

Busch, Wolfgang, Miotk, Andrej, Ariel, Federico D., Zhao, Zhong, Forner, Joachim, Daum, Gabor, Suzaki, Takuya, Schuster, Christoph, Schultheiss, Sebastian J., Leibfried, Andrea, Haubeiß, Silke, Ha, Nati, Chan, Raquel L., and Lohmann, Jan U.

Published
2010
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47. The Potential Use of the Epigenetic Remodeler LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) as a Tool for Crop Improvement.

Author

Mansilla, Natanael, Ferrero, Lucia, Ariel, Federico D., and Lucero, Leandro E.

Subjects
CROP improvement, HETEROCHROMATIN, GENETIC regulation, EPIGENETICS, LINCRNA
Abstract

The vast diversity of traits exhibited by horticultural crops largely depends upon variation in gene expression regulation. The uppermost layer of gene expression regulation is chromatin compaction. In plants, the LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) is a member of the Polycomb Repressive Complex 1 (PRC1) that controls the spreading of the H3K27me3 mark throughout the genome to regulate gene expression. Much of the epigenetic control exerted by LHP1 has been deeply explored on the model species Arabidopsis thaliana. Recent advances in melon, tomato, and soybean highlight the relevance of LHP1 in controlling the development and physiology of a plethora of traits in crops. However, whether LHP1 exerts its diverse roles through similar mechanisms and through modulating the same target genes has been overlooked. In this review, we gather a wealth of knowledge about the LHP1 mode of action, which involves a tight connection with histone marks and long noncoding RNAs to modulate gene expression. Strikingly, we found that LHP1 may be linked to H3K27me3 regulation across the plant lineage, yet, through epigenetic regulation of a distinct set of target genes. This is supported by subtle differences in subcellular LHP1 localization between species found here. In addition, we summarize the variety of developmental outputs modulated by LHP1 across land plants pinpointing its importance for plant breeding. Hence, LHP1 has probably been co-opted in different lineages to modulate diverse traits contributing to crop diversification. [ABSTRACT FROM AUTHOR]

Published
2023
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