Genome transcriptional regulation

Campese, Lucia, Luca Russo, Maria Abagnale, Adriana Alberti, Giancarlo Bachi, Cecilia Balestra, Daniele Bellardini, et al. 2024. “The NEREA Augmented Observatory: An Integrative Approach to Marine Coastal Ecology.” Scientific Data 11 (1): 989. https://doi.org/10.1038/s41597-024-03787-y.

Maalouf, Christelle A., Adriana Alberti, and Julie Soutourina. 2024. “Mediator Complex in Transcription Regulation and DNA Repair: Relevance for Human Diseases.” DNA Repair 141 (June):103714. https://doi.org/10.1016/j.dnarep.2024.103714.

Zeitler, Leo, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, and Arach Goldar. 2024. “A Genome-Wide Comprehensive Analysis of Nucleosome Positioning in Yeast.” PLoS Computational Biology 20 (1): e1011799. https://doi.org/10.1371/journal.pcbi.1011799.

Haccard, Olivier, Diletta Ciardo, Hemalatha Narrissamprakash, Odile Bronchain, Akiko Kumagai, William G. Dunphy, Arach Goldar, and Kathrin Marheineke. 2023. “Rif1 Restrains the Rate of Replication Origin Firing in Xenopus Laevis.” Communications Biology 6 (1): 788. https://doi.org/10.1038/s42003-023-05172-8.

Arbona, Jean-Michel, Hadi Kabalane, Jeremy Barbier, Arach Goldar, Olivier Hyrien, and Benjamin Audit. 2023. “Neural Network and Kinetic Modelling of Human Genome Replication Reveal Replication Origin Locations and Strengths.” PLoS Computational Biology 19 (5): e1011138. https://doi.org/10.1371/journal.pcbi.1011138.

André, Kévin M., Nathalie Giordanengo Aiach, Veronica Martinez-Fernandez, Leo Zeitler, Adriana Alberti, Arach Goldar, Michel Werner, Cyril Denby Wilkes, and Julie Soutourina. 2023. “Functional Interplay between Mediator and RSC Chromatin Remodeling Complex Controls Nucleosome-Depleted Region Maintenance at Promoters.” Cell Reports 42 (5): 112465. https://doi.org/10.1016/j.celrep.2023.112465.

Wang, Yucheng, Ana Prohaska, Haoran Dong, Adriana Alberti, Inger Greve Alsos, David W. Beilman, Anders A. Bjørk, et al. 2022. “Reply to: When Did Mammoths Go Extinct?” Nature 612 (7938): E4–6. https://doi.org/10.1038/s41586-022-05417-2.

Guérin, Nina, Marta Ciccarella, Elisa Flamant, Paul Frémont, Sophie Mangenot, Benjamin Istace, Benjamin Noel, et al. 2022. “Genomic Adaptation of the Picoeukaryote Pelagomonas Calceolata to Iron-Poor Oceans Revealed by a Chromosome-Scale Genome Sequence.” Communications Biology 5 (1): 1–14. https://doi.org/10.1038/s42003-022-03939-z.

Zeitler, Leo, Cyril Denby Wilkes, Arach Goldar, and Julie Soutourina. 2022. “A Quantitative Modelling Approach for DNA Repair on a Population Scale.” PLOS Computational Biology 18 (9): e1010488. https://doi.org/10.1371/journal.pcbi.1010488.

Gopaul, Diyavarshini, Cyril Denby Wilkes, Arach Goldar, Nathalie Giordanengo Aiach, Marie-Bénédicte Barrault, Elizaveta Novikova, and Julie Soutourina. 2022. “Genomic Analysis of Rad26 and Rad1-Rad10 Reveals Differences in Their Dependence on Mediator and RNA Polymerase II.” Genome Research 32 (8): 1516–28. https://doi.org/10.1101/gr.276371.121.

Wang, Yucheng, Mikkel Winther Pedersen, Inger Greve Alsos, Bianca De Sanctis, Fernando Racimo, Ana Prohaska, Eric Coissac, et al. 2021. “Late Quaternary Dynamics of Arctic Biota from Ancient Environmental Genomics.” Nature, October. https://doi.org/10.1038/s41586-021-04016-x.

Ciardo, Diletta, Olivier Haccard, Hemalatha Narassimprakash, David Cornu, Ida Chiara Guerrera, Arach Goldar, and Kathrin Marheineke. 2021. “Polo-like Kinase 1 (Plk1) Regulates DNA Replication Origin Firing and Interacts with Rif1 in Xenopus.” Nucleic Acids Research 49 (17): 9851–69. https://doi.org/10.1093/nar/gkab756.

Ciardo, Diletta, Olivier Haccard, Hemalatha Narassimprakash, Jean-Michel Arbona, Olivier Hyrien, Benjamin Audit, Kathrin Marheineke, and Arach Goldar. 2021. “Organization of DNA Replication Origin Firing in Xenopus Egg Extracts: The Role of Intra-S Checkpoint.” Genes 12 (8): 1224. https://doi.org/10.3390/genes12081224.

Sipos, Eliet H., Adélaïde Léty-Stefanska, Cyril Denby Wilkes, Julie Soutourina, and Florent Malloggi. 2021. “Microfluidic Platform for Monitoring Saccharomyces Cerevisiae Mutation Accumulation.” Lab on a Chip 21 (12): 2407–16. https://doi.org/10.1039/d1lc00086a.

André, Kévin M., Eliet H. Sipos, and Julie Soutourina. 2021. “Mediator Roles Going Beyond Transcription.” Trends in Genetics 37 (3): 224–34. https://doi.org/10.1016/j.tig.2020.08.015.

Forey, Romain, Antoine Barthe, Mireille Tittel-Elmer, Maxime Wery, Marie-Bénédicte Barrault, Cécile Ducrot, Andrew Seeber, et al. 2021. “A Role for the Mre11-Rad50-Xrs2 Complex in Gene Expression and Chromosome Organization.” Molecular Cell 81 (1): 183-197.e6. https://doi.org/10.1016/j.molcel.2020.11.010.

Ciardo, Diletta, Olivier Haccard, Hemalatha Narassimprakash, Virginie Chiodelli, Arach Goldar, and Kathrin Marheineke. 2020. “Polo-like Kinase 1 (Plk1) Is a Positive Regulator of DNA Replication in the Xenopus in Vitro System.” Cell Cycle (Georgetown, Tex.) 19 (14): 1817–32. https://doi.org/10.1080/15384101.2020.1782589.

Georges, Adrien, Diyavarshini Gopaul, Cyril Denby Wilkes, Nathalie Giordanengo Aiach, Elizaveta Novikova, Marie-Bénédicte Barrault, Olivier Alibert, and Julie Soutourina. 2019. “Functional Interplay between Mediator and RNA Polymerase II in Rad2/XPG Loading to the Chromatin.” Nucleic Acids Research 47 (17): 8988–9004. https://doi.org/10.1093/nar/gkz598.

Soutourina, Julie. 2019. “Mammalian Mediator as a Functional Link between Enhancers and Promoters.” Cell 178 (5): 1036–38. https://doi.org/10.1016/j.cell.2019.07.040.

Carvalho, Cyril, Valentin L’Hôte, Régis Courbeyrette, Gueorgui Kratassiouk, Guillaume Pinna, Jean-Christophe Cintrat, Cyril Denby-Wilkes, et al. 2019. “Glucocorticoids Delay RAF-Induced Senescence Promoted by EGR1.” Journal of Cell Science 132 (16): jcs230748. https://doi.org/10.1242/jcs.230748.

Ciardo, Diletta, Arach Goldar, and Kathrin Marheineke. 2019. “On the Interplay of the DNA Replication Program and the Intra-S Phase Checkpoint Pathway.” Genes 10 (2): 94. https://doi.org/10.3390/genes10020094.

Arbona, Jean-Michel, Arach Goldar, Olivier Hyrien, Alain Arneodo, and Benjamin Audit. 2018. “The Eukaryotic Bell-Shaped Temporal Rate of DNA Replication Origin Firing Emanates from a Balance between Origin Activation and Passivation.” Edited by Bruce Stillman. ELife 7 (June):e35192. https://doi.org/10.7554/eLife.35192.

Soutourina, Julie. 2018. “Transcription Regulation by the Mediator Complex.” Nature Reviews. Molecular Cell Biology 19 (4): 262–74. https://doi.org/10.1038/nrm.2017.115.

Calderari, Sophie, Massimiliano Ria, Christelle Gérard, Tatiane C. Nogueira, Olatz Villate, Stephan C. Collins, Helen Neil, et al. 2018. “Molecular Genetics of the Transcription Factor GLIS3 Identifies Its Dual Function in Beta Cells and Neurons.” Genomics 110 (2): 98–111. https://doi.org/10.1016/j.ygeno.2017.09.001.

Bhullar, Simran, Cyril Denby Wilkes, Olivier Arnaiz, Mariusz Nowacki, Linda Sperling, and Eric Meyer. 2018. “A Mating-Type Mutagenesis Screen Identifies a Zinc-Finger Protein Required for Specific DNA Excision Events in Paramecium.” Nucleic Acids Research 46 (18): 9550–62. https://doi.org/10.1093/nar/gky772.

Bischerour, Julien, Simran Bhullar, Cyril Denby Wilkes, Vinciane Régnier, Nathalie Mathy, Emeline Dubois, Aditi Singh, et al. 2018. “Six Domesticated PiggyBac Transposases Together Carry out Programmed DNA Elimination in Paramecium.” ELife 7:e37927. https://doi.org/10.7554/eLife.37927.

Eychenne, Thomas, Michel Werner, and Julie Soutourina. 2017. “Toward Understanding of the Mechanisms of Mediator Function in Vivo: Focus on the Preinitiation Complex Assembly.” Transcription 8 (5): 328–42. https://doi.org/10.1080/21541264.2017.1329000.

Eychenne, Thomas, Elizaveta Novikova, Marie-Bénédicte Barrault, Olivier Alibert, Claire Boschiero, Nuno Peixeiro, David Cornu, et al. 2016. “Functional Interplay between Mediator and TFIIB in Preinitiation Complex Assembly in Relation to Promoter Architecture.” Genes & Development 30 (18): 2119–32. https://doi.org/10.1101/gad.285775.116.

Goldar, A., A. Arneodo, B. Audit, F. Argoul, A. Rappailles, G. Guilbaud, N. Petryk, M. Kahli, and O. Hyrien. 2016. “Deciphering DNA Replication Dynamics in Eukaryotic Cell Populations in Relation with Their Averaged Chromatin Conformations.” Scientific Reports 6 (March):22469. https://doi.org/10.1038/srep22469.

Dieuleveult, Maud de, Kuangyu Yen, Isabelle Hmitou, Arnaud Depaux, Fayçal Boussouar, Daria Bou Dargham, Sylvie Jounier, et al. 2016. “Genome-Wide Nucleosome Specificity and Function of Chromatin Remodellers in ES Cells.” Nature 530 (7588): 113–16. https://doi.org/10.1038/nature16505.

Eyboulet, Fanny, Sandra Wydau-Dematteis, Thomas Eychenne, Olivier Alibert, Helen Neil, Claire Boschiero, Marie-Claire Nevers, et al. 2015. “Mediator Independently Orchestrates Multiple Steps of Preinitiation Complex Assembly in Vivo.” Nucleic Acids Research 43 (19): 9214–31. https://doi.org/10.1093/nar/gkv782.

Bridier-Nahmias, Antoine, Aurélie Tchalikian-Cosson, Joshua A. Baller, Rachid Menouni, Hélène Fayol, Amando Flores, Ali Saïb, Michel Werner, Daniel F. Voytas, and Pascale Lesage. 2015. “Retrotransposons. An RNA Polymerase III Subunit Determines Sites of Retrotransposon Integration.” Science (New York, N.Y.) 348 (6234): 585–88. https://doi.org/10.1126/science.1259114.

Platel, Marie, Arach Goldar, Jennifer M. Wiggins, Pedro Barbosa, Pierre Libeau, Pierre Priam, Hemalatha Narassimprakash, Xenia Grodzenski, and Kathrin Marheineke. 2015. “Tight Chk1 Levels Control Replication Cluster Activation in Xenopus.” PloS One 10 (6): e0129090. https://doi.org/10.1371/journal.pone.0129090.