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1. Articulated Animal AI: An Environment for Animal-like Cognition in a Limbed Agent

Author

Lucas, Jeremy and Prémont-Schwarz, Isabeau

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Computer Science - Robotics
Abstract

This paper presents the Articulated Animal AI Environment for Animal Cognition, an enhanced version of the previous AnimalAI Environment. Key improvements include the addition of agent limbs, enabling more complex behaviors and interactions with the environment that closely resemble real animal movements. The testbench features an integrated curriculum training sequence and evaluation tools, eliminating the need for users to develop their own training programs. Additionally, the tests and training procedures are randomized, which will improve the agent's generalization capabilities. These advancements significantly expand upon the original AnimalAI framework and will be used to evaluate agents on various aspects of animal cognition., Comment: 8 pages, accepted to Workshop on Open-World Agents (OWA-2024) at NeurIPS 2024 in Vancouver, Canada

Published
2024

4. JASPAR 2024:20th anniversary of the open-access database of transcription factor binding profiles

Author

Rauluseviciute, Ieva, Riudavets-puig, Rafael, Blanc-mathieu, Romain, Castro-mondragon, Jaime a, Ferenc, Katalin, Kumar, Vipin, Lemma, Roza Berhanu, Lucas, Jérémy, Chèneby, Jeanne, Baranasic, Damir, Khan, Aziz, Fornes, Oriol, Gundersen, Sveinung, Johansen, Morten, Hovig, Eivind, Lenhard, Boris, Sandelin, Albin, Wasserman, Wyeth w, Parcy, François, Mathelier, Anthony, Rauluseviciute, Ieva, Riudavets-puig, Rafael, Blanc-mathieu, Romain, Castro-mondragon, Jaime a, Ferenc, Katalin, Kumar, Vipin, Lemma, Roza Berhanu, Lucas, Jérémy, Chèneby, Jeanne, Baranasic, Damir, Khan, Aziz, Fornes, Oriol, Gundersen, Sveinung, Johansen, Morten, Hovig, Eivind, Lenhard, Boris, Sandelin, Albin, Wasserman, Wyeth w, Parcy, François, and Mathelier, Anthony

Abstract

JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs’ structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest., JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs’ structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.

Published
2024

5. The ALOG domain defines a family of plant-specific transcription factors acting during Arabidopsis flower development

Author

Rieu, Philippe, primary, Beretta, Veronica Maria, additional, Caselli, Francesca, additional, Thévénon, Emmanuel, additional, Lucas, Jérémy, additional, Rizk, Mahmoud, additional, Franchini, Emanuela, additional, Caporali, Elisabetta, additional, Paleni, Chiara, additional, Nanao, Max H., additional, Kater, Martin M., additional, Dumas, Renaud, additional, Zubieta, Chloe, additional, Parcy, François, additional, and Gregis, Veronica, additional

Published
2024
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8. JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles

Author

Rauluseviciute, Ieva, primary, Riudavets-Puig, Rafael, additional, Blanc-Mathieu, Romain, additional, Castro-Mondragon, Jaime A, additional, Ferenc, Katalin, additional, Kumar, Vipin, additional, Lemma, Roza Berhanu, additional, Lucas, Jérémy, additional, Chèneby, Jeanne, additional, Baranasic, Damir, additional, Khan, Aziz, additional, Fornes, Oriol, additional, Gundersen, Sveinung, additional, Johansen, Morten, additional, Hovig, Eivind, additional, Lenhard, Boris, additional, Sandelin, Albin, additional, Wasserman, Wyeth W, additional, Parcy, François, additional, and Mathelier, Anthony, additional

Published
2023
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10. JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles.

Author

Rauluseviciute, Ieva, Riudavets-Puig, Rafael, Blanc-Mathieu, Romain, Castro-Mondragon, Jaime A, Ferenc, Katalin, Kumar, Vipin, Lemma, Roza Berhanu, Lucas, Jérémy, Chèneby, Jeanne, Baranasic, Damir, Khan, Aziz, Fornes, Oriol, Gundersen, Sveinung, Johansen, Morten, Hovig, Eivind, Lenhard, Boris, Sandelin, Albin, Wasserman, Wyeth W, Parcy, François, and Mathelier, Anthony

Published
2024
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12. Cauliflower fractal forms arise from perturbations of floral gene networks

Author

Azpeitia, Eugenio, primary, Tichtinsky, Gabrielle, additional, Le Masson, Marie, additional, Serrano-Mislata, Antonio, additional, Lucas, Jérémy, additional, Gregis, Veronica, additional, Gimenez, Carlos, additional, Prunet, Nathanaël, additional, Farcot, Etienne, additional, Kater, Martin M., additional, Bradley, Desmond, additional, Madueño, Francisco, additional, Godin, Christophe, additional, and Parcy, Francois, additional

Published
2021
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13. The LEAFY floral regulator displays pioneer transcription factor properties

Author

Lai, Xuelei, Blanc-Mathieu, Romain, GrandVuillemin, Loïc, Huang, Ying, Stigliani, Arnaud, Lucas, Jérémy, Thévenon, Emmanuel, Loue-Manifel, Jeanne, Turchi, Laura, Daher, Hussein, Brun-Hernandez, Eugenia, Vachon, Gilles, Latrasse, David, Benhamed, Moussa, Dumas, Renaud, Zubieta, Chloe, Parcy, François, Lai, Xuelei, Blanc-Mathieu, Romain, GrandVuillemin, Loïc, Huang, Ying, Stigliani, Arnaud, Lucas, Jérémy, Thévenon, Emmanuel, Loue-Manifel, Jeanne, Turchi, Laura, Daher, Hussein, Brun-Hernandez, Eugenia, Vachon, Gilles, Latrasse, David, Benhamed, Moussa, Dumas, Renaud, Zubieta, Chloe, and Parcy, François

Abstract

Pioneer transcription factors (TFs) are a special category of TFs with the capacity to bind to closed chromatin regions in which DNA is wrapped around histones and may be highly methylated. Subsequently, pioneer TFs are able to modify the chromatin state to initiate gene expression. In plants, LEAFY (LFY) is a master floral regulator and has been suggested to act as a pioneer TF in Arabidopsis. Here, we demonstrate that LFY is able to bind both methylated and non-methylated DNA using a combination of in vitro genome-wide binding experiments and structural modeling. Comparisons between regions bound by LFY in vivo and chromatin accessibility data suggest that a subset of LFY bound regions is occupied by nucleosomes. We confirm that LFY is able to bind nucleosomal DNA in vitro using reconstituted nucleosomes. Finally, we show that constitutive LFY expression in seedling tissues is sufficient to induce chromatin accessibility in the LFY direct target genes APETALA1 and AGAMOUS. Taken together, our study suggests that LFY possesses key pioneer TF features that contribute to launching the floral gene expression program.

Published
2021

14. The LEAFY floral regulator displays pioneer transcription factor properties

Author

Lai, Xuelei, primary, Blanc-Mathieu, Romain, additional, GrandVuillemin, Loïc, additional, Huang, Ying, additional, Stigliani, Arnaud, additional, Lucas, Jérémy, additional, Thévenon, Emmanuel, additional, Loue-Manifel, Jeanne, additional, Turchi, Laura, additional, Daher, Hussein, additional, Brun-Hernandez, Eugenia, additional, Vachon, Gilles, additional, Latrasse, David, additional, Benhamed, Moussa, additional, Dumas, Renaud, additional, Zubieta, Chloe, additional, and Parcy, François, additional

Published
2021
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15. The Intervening Domain Is Required For DNA-binding and Functional Identity of Plant MADS Transcription Factors

Author

Lai, Xuelei, primary, Vega-Leon, Rosario, additional, Hugouvieux, Veronique, additional, Blanc-Mathieu, Romain, additional, van der Wal, Froukje, additional, Lucas, Jérémy, additional, Silva, Catarina S., additional, Jourdain, Agnès, additional, Muino, Jose, additional, Nanao, Max H., additional, Immink, Richard, additional, Kaufmann, Kerstin, additional, Parcy, François, additional, Smaczniak, Cezary, additional, and Zubieta, Chloe, additional

Published
2021
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16. The making of cauliflowers: the story of unsuccessful flowers

Author

Azpeitia, Eugenio, primary, Tichtinsky, Gabrielle, additional, Le Masson, Marie, additional, Serrano-Mislata, Antonio, additional, Gregis, Veronica, additional, Gimenez, Carlos, additional, Prunet, Nathanaёl, additional, Lucas, Jérémy, additional, Farcot, Etienne, additional, Kater, Martin M., additional, Bradley, Desmond, additional, Madueño, Francisco, additional, Godin, Christophe, additional, and Parcy, Francois, additional

Published
2021
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19. Structural and functional evolutionary dynamics of duplicated genes and genomes in nascent and natural B. napus

Author

Rousseau-Gueutin, Mathieu, Lucas, Jérémy, Denoeud, France, Ferreira de Carvalho, Julie, He, Zhesi, Boutte, Julien, Deniot, Gwenaëlle, Falentin, Cyril, Filangi, Olivier, Gilet, Marie-Madeleine, Legeai, Fabrice, Lodé-Taburel, Maryse, Morice, Jérôme, Trotoux, Gwenn, Aury, Jean-Marc, Barbe, Valérie, Snowdon, Rod J., Wincker, Patrick, Bancroft, Ian, Chèvre, Anne-Marie, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of York [York, UK], Institut für Insektenbiotechnologie [Justus-Liebig-Universität Gießen], Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Rousseau-Gueutin, Mathieu, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Justus-Liebig-Universität Gießen (JLU)

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

20. Co-evolution of chloroplast and nuclear genomes in flowering plants and impact of allopolyploidy on fine tune cytonuclear interactions

Author

Rousseau-Gueutin, Mathieu, Ferreira de Carvalho, Julie, Lucas, Jérémy, Deniot, Gwenaëlle, Falentin, Cyril, Archambeau, Heloïse, Gilet, Marie-Madeleine, Legeai, Fabrice, Lodé-Taburel, Maryse, Morice, Jérôme, Trotoux, Gwenn, Montes, Emilie, Aury, Jean-Marc, Barbe, Valérie, Snowdon, Rod J., He, Zhesi, Denoeud, France, Wincker, Patrick, Bancroft, Ian, Chèvre, Anne-Marie, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut für Insektenbiotechnologie [Justus-Liebig-Universität Gießen], Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), University of York [York, UK], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Justus-Liebig-Universität Gießen (JLU), and Rousseau-Gueutin, Mathieu

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

21. Cytonuclear interactions overcome inter-genomic conflict resulting from interspecific hybridization and genome doubling

Author

Ferreira De Carvalho, Julie, Lucas, Jérémy, Falentin, Cyril, Deniot, Gwenaëlle, Filangi, Olivier, Gilet, Marie-Madeleine, Legeai, Fabrice, Lodé-Taburel, Maryse, Morice, Jérôme, Trotoux, Gwenn, Aury, Jean-Marc, Barbe, Valérie, Keller, Jean, Snowdon, Rod J., He, Zhesi, Denoeud, France, Wincker, Patrick, Bancroft, Ian, Chèvre, Anne-Marie, Rousseau-Gueutin, Mathieu, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Justus-Liebig-Universität Gießen (JLU), University of York [York, UK], Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), and Rousseau-Gueutin, Mathieu

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

23. Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole‐genome duplications in Brassica

Author

Ferreira de Carvalho, Julie, primary, Lucas, Jérémy, additional, Deniot, Gwenaëlle, additional, Falentin, Cyril, additional, Filangi, Olivier, additional, Gilet, Marie, additional, Legeai, Fabrice, additional, Lode, Maryse, additional, Morice, Jérôme, additional, Trotoux, Gwenn, additional, Aury, Jean‐Marc, additional, Barbe, Valérie, additional, Keller, Jean, additional, Snowdon, Rod, additional, He, Zhesi, additional, Denoeud, France, additional, Wincker, Patrick, additional, Bancroft, Ian, additional, Chèvre, Anne‐Marie, additional, and Rousseau‐Gueutin, Mathieu, additional

Published
2019
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24. OsFD4 promotes the rice floral transition via florigen activation complex formation in the shoot apical meristem.

Author

Cerise, Martina, Giaume, Francesca, Galli, Mary, Khahani, Bahman, Lucas, Jérémy, Podico, Federico, Tavakol, Elahe, Parcy, François, Gallavotti, Andrea, Brambilla, Vittoria, and Fornara, Fabio

Subjects
MERISTEMS, DNA-protein interactions, LEUCINE zippers, TRANSCRIPTION factors, PROTEIN-protein interactions, RICE, INFLORESCENCES
Abstract

Summary: In rice, the florigens Heading Date 3a (Hd3a) and Rice Flowering Locus T 1 (RFT1), OsFD‐like basic leucine zipper (bZIP) transcription factors, and Gf14 proteins assemble into florigen activation/repressor complexes (FACs/FRCs), which regulate transition to flowering in leaves and apical meristem. Only OsFD1 has been described as part of complexes promoting flowering at the meristem, and little is known about the role of other bZIP transcription factors, the combinatorial complexity of FAC formation, and their DNA‐binding properties.Here, we used mutant analysis, protein–protein interaction assays and DNA affinity purification (DAP) sequencing coupled to in silico prediction of binding syntaxes to study several bZIP proteins that assemble into FACs or FRCs.We identified OsFD4 as a component of a FAC promoting flowering at the shoot apical meristem, downstream of OsFD1. The osfd4 mutants are late flowering and delay expression of genes promoting inflorescence development. Protein–protein interactions indicate an extensive network of contacts between several bZIPs and Gf14 proteins. Finally, we identified genomic regions bound by bZIPs with promotive and repressive effects on flowering.We conclude that distinct bZIPs orchestrate floral induction at the meristem and that FAC formation is largely combinatorial. While binding to the same consensus motif, their DNA‐binding syntax is different, suggesting discriminatory functions. [ABSTRACT FROM AUTHOR]

Published
2021
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26. Impact of whole genome triplication on the evolutionary history and the functional dynamics of regulatory genes involved in Brassicaself-incompatibility signalling pathway

Author

Azibi, Thanina, Hadj-Arab, Houria, Lodé, Maryse, Ferreira de Carvalho, Julie, Trotoux, Gwenn, Nègre, Sylvie, Gilet, Marie-Madeleine, Boutte, Julien, Lucas, Jérémy, Vekemans, Xavier, Chèvre, Anne-Marie, and Rousseau-Gueutin, Mathieu

Abstract

Polyploidy or whole genome duplication is a frequent and recurrent phenomenon in flowering plants that has played a major role in their diversification, adaptation and speciation. The adaptive success of polyploids relates to the different evolutionary fates of duplicated genes. In this study, we explored the impact of the whole genome triplication (WGT) event in the Brassiceae tribe on the genes involved in the self-incompatibility (SI) signalling pathway, a mechanism allowing recognition and rejection of self-pollen in hermaphrodite plants. By taking advantage of the knowledge acquired on this pathway as well as of several reference genomes in Brassicaceae species, we determined copy number of the different genes involved in this pathway and investigated their structural and functional evolutionary dynamics. We could infer that whereas most genes involved in the SI signalling returned to single copies after the WGT event (i.e. ARC1, JDP1, THL1, THL2, Exo70A01) in diploid Brassicaspecies, a few were retained in duplicated (GLO1and PLDα) or triplicated copies (MLPK). We also carefully studied the gene structure of these latter duplicated genes (including the conservation of functional domains and active sites) and tested their transcription in the stigma to identify which copies seem to be involved in the SI signalling pathway. By taking advantage of these analyses, we then explored the putative origin of a contrasted SI phenotype between two Brassica rapavarieties that have been fully sequenced and shared the same S-allele (S60).

Published
2020
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