Fredy Barneche

Plant Nuclear Dynamics & Signaling team

Sorbonne Université - IBPS - LBD - CNRS UMR7622

75005 Paris, France

Tel. +33 (0) 144278118

E-mail: fredy.barneche@sorbonne-universite.fr

• 2024 - Group leader. LBD, Institut de Biologie Paris Seine (IBPS), Sorbonne Université, Paris, France

• 2016 - CNRS Research Director. Bowler lab. Institut de Biologie de l'Ecole Normale Supérieure, ENS, Paris, France
• 2008 - CNRS Research Scientist. Bowler lab. Institut de Biologie de l'Ecole Normale Supérieure, ENS, Paris, France
• 2006 - HFSP Post-doc fellow. Bowler lab, Zoological Station A. Dohrn, Naples, Italy
• 2002 - EMBO post-doc fellow. Jean-David Rochaix lab, Molecular Biology Department, University of Geneva, Switzerland
• 2001 - PhD in Molecular and Cellular Plant Biology. Manuel Echeverría lab, LGDP, Perpignan & Toulouse III Universities, France
• 1998 - Postgraduate Research Assistant. Craig Pikaard lab, Washington University, Saint-Louis, USA

• 1997 - Master degree, Toulouse University, France

• 1995 - Licence degree, Pau University, France

• Department Council, Dev2A, Sorbonne University - since 2025  

• Scientific Advisory Board, CNRS EpiPlant research network (GDR) - since 2017

• Scientific board, Paris Cité Université (UPC), Life Sciences Dpt, 2021-2025

• HCERES evaluation panel - 2024

• Editorial board member, Scientific Reports (NPG) - since 2014

• INRAE Scientific board member (CSS BIP), 2021-2024

• Scientific board, Doctoral School ED567 (SEVE), Paris Saclay University, 2019-2021

• Reviewer for Cell, Mol. Cell, Cell Rep., Nature Com., Nature Plant, Genome Biol., PNAS and others

• Grant evaluation for NSF (USA), DFG (Germany), ANR (France), BBSRC (UK), Israel Science Foundation, FWF Austrian Research Fund, and others

ORCID: 0000-0002-7014-7097

1. Adrien Vidal, Lorenzo Concia, Martin Rougée, Clara Bourbousse✉️  and Fredy Barneche✉️. ChIP-Rx: Arabidopsis chromatin profiling using quantitative ChIP-seq. (2024) Methods in Molecular Biology: Plant Chromatin Dynamics, Methods and Protocols, 2nd Edition. In press

2. Lahlou A, Coghill I, Davidson MLH, Billon R, Barneche F, Lazar D, Le Saux T, Jullien L.  (2024) Leaves to Measure Light Intensity. Adv. Science. e2304420. doi: 10.1002/advs.202304420.

3. Amiard S, Feit L, Vanrobays E, Simon L, Le Goff S, Loizeau L, Wolff L, Butter F, Bourbousse C, Barneche F, Tatout C, Probst AV. (2024) The TELOMERE REPEAT BINDING proteins TRB4 and TRB5 function as transcriptional activators of PRC2-controlled genes to regulate plant development. Plant Commun. 5(7):100890. doi: 10.1016/j.xplc.2024.100890.

4. Blanco-Touriñán N., Pérez-Alemany J., Bourbousse C., Latrasse D., Ait-Mohamed O., Benhamed M., Barneche F., A. Blázquez M., Gallego-Bartolomé J. And D. Alabadí (2024) The plant POLYMERASE ASSOCIATED FACTOR1 complex links transcription and H2B monoubiquitination genome-wide. Plant Physiology Doi: 10.1093/plphys/kiae041

5. Godwin J., March E., Govindasamy M., Bourbousse C., Wolff L., Fort A., KrzysztonM., López J., Swiezewski S., Barneche F., Schubert D. and S. Farrona (2024) The UBP5 histone H2A deubiquitinase counteracts PRC2-mediated repression to regulate Arabidopsis development and stress responses. Nature Communications 15(1):667. doi: 10.1038/s41467-023-44546-8.

6. Teano G., Concia L., Carron L., Wolff L., Adamusová K., Fojtová M., Bourge M., Kramdi A., Colot V., Grossniklaus U., Bowler C., Baroux C., Carbone A., Probst A.V., Procházková Schrumpfová P., Fajkus J., Amiard S., Grob S., Bourbousse C. and F. Barneche✉️ (2023) Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis. Cell Reports. doi.org/10.1016/j.celrep.2023.112894

7. *Johann to Berens P, *Schivre G, Barneche F, Bourbousse C, and Molinier J. (2022) Advanced methods for segmentation of Arabidopsis nuclei and chromocenters. Epigenomes 6(4), 34. doi.org/10.3390/epigenomes6040034

8. Patitaki E., Schivre G., Zioutopoulou A., Perrella G., Bourbousse C., ✉️Barneche F. and ✉️Kaiserli E. (2022) Light, chromatin, action: nuclear events regulating light signaling in Arabidopsis. Tansley review in New Phytologist. doi: 10.1111/nph.18424

9. Méteignier LV, Lecampion C, Vrieta C, Térèsee M, Rougée M, Breuerh C, Soubigou-Taconnat L, Sugimoto K, Barneche F and C Laloi (2022) Topoisomerase VI participates to a chromatin boundary function that prevents heterochromatin spreading into nearby euchromatic islands. PNAS 119(27):e2001290119. https://doi.org/10.1073/pnas.2001290119

10. Jurdak Y, de Almeida Garcia Rodrigues G, Chaumont N, Schivre G, Bourbousse C, Barneche F, Bou Dagher Kharrat M and C Bailly (2022) Intracellular reactive oxygen species trafficking participates in seed dormancy alleviation in Arabidopsis seeds. New Phytol. 234(3):850-866. doi: 10.1111/nph.18038

11. Huang Y, Sicar S, Ramirez-Prado JS, Manza-Mianza D, Antunez-Sanchez J, Brik-Chaouche R, Rodriguez-Granados NY, An J, Bergounioux C, Mahfouz MM, Hirt H, Crespi M, Concia L, Barneche F, Amiard S, Probst AV, Gutierrez-Marcos J, Ariel F, Raynaud C, Latrasse D, Benhamed M. (2021) Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis. Genome Res. 31(7):1230-44. doi:10.1101/gr.273771.120

12. *Cañibano E, *Bourbousse B, Garcia-Leon M, Wolff L, Garcia-Baudino C, Barneche F, Rubio V and S Fonseca (2021). DET1-mediated COP1 regulation avoids HY5 activity over second-site targets to tune plant photomorphogenesis. Molecular Plant. doi.org/10.1016/j.molp.2021.03.009

13. KD Grasser✉️, V Rubio✉️ and F Barneche✉️ (2020) Multifaceted activities of the plant SAGA complex. BBA Gene Regul. Mech. doi:10.1016/j.bbagrm.2020.194613

14. Meco V, Egea I, Ortíz-Atienza A, Drevensek S, Esch E, Yuste-Lisbona FY, Barneche, Vriezen W, Bolarin MC,  Lozano R and FB Flores. (2020) The Salt Sensitivity Induced by Disruption of Cell Wall-Associated Kinase 1 (SlWAK1) Tomato Gene Is Linked to Altered Osmotic and Metabolic Homeostasis. Int. J. Mol. Sci. 21(17), 6308. doi:10.3390/ijms21176308

15. ✉️Bourbousse C, ✉️Barneche F. and C. Laloi (2020) Plant Chromatin Catches the Sun. Front. Plant Sci. 10:1728. doi:10.3389/fpls.2019.01728

16. Rutowicz K, Lirski M, Mermaz B, Schubert J, Teano G, Mestiri I, Kroten M, Tohnyui F, Fritz S, Grob S, Ringli C, Cherkezeyan L, Barneche F, Jerzmanowski A, Baroux C (2019) Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis. Genome Biology 20: 157. Doi:10.1186/s13059-019-1767-3

17. Fiorucci AS, Bourbousse C, Concia L, Rougée M, Deton-Cabanillas AF, Zabulon G, Layat E, Latrasse D, Kim SK, Chaumont N, Lombard B, Stroebel D, Lemoine S, Mohammad A, Blugeon C, Loew D, Bailly C, Bowler C, Benhamed M and F. Barneche✉️ (2019) Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination. Genome Biology 20(1):100. doi:10.1186/s13059-019-1705-4

18. Bourbousse C. and F. Barneche✉️ (2019) A dynamic signaling path to chromatin-level control of plant drought response. Molecular Plant. pii: S1674-2052(19)30053-X. doi:10.1016/j.molp.2019.01.022

19. *Nassrallah A, *Rougee M, Bourbousse C, Drevensek S, Fonseca S, Iniesto E, Ait-Mohamed O, Deton-Cabanillas AF, Zabulon G, Ahmed I, Stroebel D, Masson V, Lombard B, Eeckhout D, Gevaert K, Loew D, Genovesio A, Breyton C, de Jaeger G, Bowler C, Rubio V and F Barneche✉️ (2018) DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis. eLife  e37892. doi:10.7554/eLife.37892

20. Egea I, Pineda B, Ortíz-Atienza A, Plasencia FA, Drevensek S, García-Sogo B, Yuste-Lisbona FJ, Barrero J, Atarés A, Flores FB, Barneche F, Angosto T, Capel C, Salinas J, Vriezen W, Esch E, Bowler C, Bolarin MC, Moreno V and Lozano R (2017) The SlCBL10 calcineurin B-like protein ensures plant growth under salt stress by regulating Na+ and Ca2+ homeostasis. Plant Physiol. doi:10.1104/pp.17.01605

21. ✉️Barneche F, Baroux C. (2017) Unreeling the chromatin thread: a genomic perspective on organization around the periphery of the Arabidopsis nucleus. Genome Biology 18(1):97 doi:10.1186/s13059-017-1239-6

22. Bourbousse C., Benhamed M. and F. Barneche✉️ (2017) Profiling developmentally and environmentally controlled chromatin reprogramming. Methods in Molecular Biology. 2018;1675:3-30. DOI 10.1007/978-1-4939-7318-7_1

23. Jégu T, Veluchamy A, Ramirez-Prado JS, Rizzi-Paillet C, Perez M, Lhomme A, Latrasse D, Coleno E, Vicaire S, Legras S, Jost B, Rougée M, Barneche F, Bergounioux C, Crespi M, Mahfouz M, Hirt H, Raynaud C and Benhamed M. (2017) The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility. Genome Biology 18(1):114. doi:10.1186/s13059-017-1246-7

24. Snoek BL, Pavlova P, Tessadori F, Peeters AJM, Bourbousse C, Barneche F, de Jong JH, Fransz PF, van Zanten M. (2017) Genetic Dissection of Morphometric Traits Reveals that Phytochrome B Affects Nucleus Size and Heterochromatin Organization in Arabidopsis thaliana. G3. doi:10.1534/g3.117.043539

25. Schalk C, Drevensek S, Kramdi A, Kassam M, Ahmed I, Cognat V, Graindorge S, Bergdoll M, Baumberger N, Heintz D, Bowler C, Genschik P, Barneche F, Colot V, Molinier J. (2016) DNA DAMAGE BINDING PROTEIN 2 (DDB2) Shapes the DNA Methylation Landscape.  Plant Cell. doi/10.1105/tpc.16.00474

26. Venturelli S, Belz RG, Kämper A, Berger A, von Horn K, Wegner A, Böcker A, Zabulon G, Langenecker T, Kohlbacher O, Barneche F, Weigel D, Lauer UM, Bitzer M, Becker C. (2015) Plants Release Precursors of Histone Deacetylase Inhibitors to Suppress Growth of Competitors. Plant Cell. 27(11):3175-89. doi:10.1105/tpc.15.00585

27. Bourbousse C, Mestiri I, Zabulon G, Bourge M, Formiggini F, Koini MA, Brown SC, Fransz P, Bowler C and F Barneche✉️ (2015) Light signaling controls nuclear architecture reorganization during seedling establishment. PNAS. 112(21):E2836-44. doi:10.1073/pnas.1503512112 [FB4] 

28. ✉️Barneche F., Malapeira J. and P. Mas (2014) The impact of chromatin dynamics on plant light responses and circadian clock function. J. Exp. Bot.,  65:2895-2913. (Review). doi:10.1093/jxb/eru011

29. Bourbousse C., Ahmed I., Roudier F., Zabulon G., Blondet E., Balzergue S., Colot V., Bowler C. and F. Barneche✉️ (2012) Histone H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis. PLoS Genetics. 8: e1002825. doi:10.1371/journal.pgen.1002825

30. Roudier F., Ahmed I., Bérard C., Sarazin A., Mary-Huard T., Cortijo S., Caillieux E., Al-Shikley L., Duvernois-Berthet E., Giraut L., Després B., Drevensek S., Barneche F., Bowler C., Brunaud V.,Aubourg S., Martin-Magniette M.-L., Robin S. and Colot V.  (2011) Integrative epigenomic mapping defines four major chromatin types in Arabidopsis. EMBO J. 30: 1928-38. doi:10.1038/emboj.2011.103

31. Castells E., Molinier J., Benvenuto G., Bourbousse C., Zabulon G., Zalc A., Cazzaniga S., Genschik P., ✉️Barneche F. and C. Bowler (2011) The conserved factor DE-ETIOLATED 1 cooperates with CUL4-DDB1DDB2 to maintain genome integrity upon UV stress. EMBO J. 30: 1162-72 doi:10.1038/emboj.2011.20

32. Enfissi E.M., Barneche F., Ahmed I., Lopez, E. Lichtlé, C. McQuinn, R. Giovannoni J., Bowler C., Bramley P. and P. Fraser. (2010) Transcriptomic and Metabolomic Characterisation of Nutritionally Enhanced Tomato Fruit Associated with the Fruit Specific Silencing of DE-ETIOLATED1 reveals links between primary and secondary metabolism. Plant Cell. 22: 1190-215. doi:10.1105/tpc.110.073866

33. Castells E., Molinier J., Genschick P., Drevensek S., ✉️Barneche F. & C. ✉️Bowler (2010) det1-1 induced UV-C hyposensitivity through UVR3 and PHR1 photolyase overexpression. The Plant J., 63: 392–404. doi:10.1111/j.1365-313X.2010.04249.x 

34. Barneche F., Winter V., Crèvecœur M. and J.-D. Rochaix. (2006) ATAB2 is a novel factor in the signalling pathway of light-controlled synthesis of photosystem proteins. EMBO J. 25: 5907-5918. doi:10.1038/sj.emboj.7601472

35. Bellafiore S., Barneche F., Peltier G. and J.-D. Rochaix. (2005) State transitions and adaptation to changing light require chloroplast thylakoid protein kinase STN7. Nature. 433: 892-895. doi:10.1038/nature03286

36. Falciatore A., *Merendino L., *Barneche F., *Ceol M., Meskauskiene R., Apel K. and J.-D. Rochaix.  (2005) The FLP proteins act as regulators of chlorophyll synthesis in response to light and plastid signals in Chlamydomonas. Genes & Dev. 19: 176–187. doi:10.1101/gad.321305

37. Sáez-Vasquez J., Caparros-Ruiz D., Barneche F. and M. Echeverría. (2004) A plant snoRNP complex containing snoRNAs, fibrillarin and nucleolin-like proteins is competent for both rDNA binding and pre-rRNA processing in vitro. Mol. Cell. Biol. 24: 7284-7297. doi:10.1128/MCB.24.16.7284-7297.2004

38. Sáez-Vasquez J., Caparros-Ruiz D., Barneche F. and M. Echeverría. (2004) Characterization of a plant pre-rRNA processing complex that interacts with 5’ETS rDNA. Biochem. Soc. T. 32: 578-80. doi:10.1042/BST0320578

39. *Kruszka K., *Barneche F., Guyot R., Ailhas J., Meneau I., Schiffer S., Marchfelder A. and M. Echeverría.  (2003) Plant dicistronic tRNA-snoRNA genes: a new mode of expression of the small nucleolar RNAs processed by RNase Z. EMBO J. 22: 621-632. doi:10.1093/emboj/cdg040

40. Barneche F., Gaspin C., Guyot R. and M. Echeverría. (2001) Identification of sixty-six box C/D snoRNAs in Arabidopsis thaliana: extensive gene duplications generated multiple isoforms predicting new ribosomal RNA 2’-O-methylation sites.  J. Mol. Biol. 311: 57-73. doi:10.1006/jmbi.2001.4851

41. Barneche F., Steinmetz F. and M. Echeverría. (2000) Fibrillarin genes encode both a conserved nucleolar protein and a novel snoRNA involved in rRNA methylation in Arabidopsis thaliana. J. Biol. Chem. 275: 27212-20. doi:10.1074/jbc.M002996200

42. Lahmy S., Barneche F., Derancourt J., Filipowicz W., Delseny M. and M. Echeverría. (2000) A chloroplastic RNA-binding protein is a new member of the PPR family. FEBS Lett. 480: 255-60. doi:10.1016/s0014-5793(00)01935-9

✉️ Corresponding author

*Equal contribution