Publications

  • INDEPTH logo
  • Publications

    INDEPTH members publish high quality articles. These highlight the leading role that INDEPTH plays in attempts to gain a wider understanding about the role of nuclear domains on gene expression and the development of plant traits.

    This page lists the publications from each Workgroup during the course of INDEPTH activities. The publications that have acknowledged the role of the Cost Action in the development of collaborations that have led to this research are highlighted in with the INDEPTH logo.In depth logo (web optimised)

  • Workgroup 1:

    Hernandez-Lagana E, Mosca G, Mendocilla-Sato E, Pires N, Frey A, Giraldo-Fonseca A, Michaud C, Grossniklaus U, Hamant O, Godin C, Boudaoud A, Grimanelli D, Autran D, Baroux C (2021) Organ geometry channels reproductive cell fate in the Arabidopsis ovule primordium. Elife. doi: 10.7554/eLife.66031.

    Arpòn J, Sakai K, Gaudin V, Andrey P (2020) Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin. Sci Rep. doi: 10.1038/s41598-020-79158-5

    Dubos T, Poulet A, Gonthier-Gueret C, Mougeot G, Vanrobays E, Li Y, Tutois S, Pery E, Chausse F, Probst AV, Tatout C, Desset S (2020) Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2.0. Nucleus. doi: 10.1080/19491034.2020.1845012.

    Evans DE, Mermet S, Tatout C (2020) Advancing knowledge of the plant nuclear periphery and its application for crop science. Nucleus. 2020 Dec;11(1):347-363. doi: 10.1080/19491034.2020.1838697.

    In depth logo (web optimised)Bilalovic, O, Avdagic, Z.; Omanovic, S, Besic, I, Letic, V, Tatout, C (2020) Mathematical Modelling of Ground Truth Image for 3D Microscopic Objects Using Cascade of Convolutional Neural Networks Optimized with Parameters' Combinations Generators. Symmetry, 12, 416 https://www.mdpi.com/2073-8994/12/3/416

    Biel AM, Moser M, Meier I (2019) A role for plant KASH proteins in regulating stomatal dynamics. Plant Physiol. doi: 10.1104/pp.19.01010

    In depth logo (web optimised)Le Goff S, Nur Keçeli B, Jerabkova H, Heckmann S, Rutten T, Cotterell S, Schubert V, Roitinger E, Mechtler K, Franklin FCH, Tatout C, Houben A, Geelen D, Probst AV, Lermontova I (2019) The H3 histone chaperone NASPSIM3 escorts CenH3 in Arabidopsis. Plant J doi: 10.1111/tpj.14518

    In depth logo (web optimised)Dumur T, Duncan S, Graumann K, Desset S, Randall RS, Scheid OM, Prodanov D, Tatout C, Baroux C (2019) Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions. Nucleus. 181-212. doi: 10.1080/19491034.2019.1644592

    Rutowicz K, Lirski M, Mermaz B, Teano G, Schubert J, Mestiri I, Kroteń MA, Fabrice TN, Fritz S, Grob S, Ringli C, Cherkezyan L, Barneche F, Jerzmanowski A, Baroux C (2019) Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis. Genome Biol. 20(1):157. doi: 10.1186/s13059-019-1767-3

    Goto C, Hashizume S, Fukao Y, Hara-Nishimura I, Tamura K (2019) Comprehensive nuclear proteome of Arabidopsis obtained by sequential extraction. Nucleus 81-92. doi: 10.1080/19491034.2019.1603093

    In depth logo (web optimised)Monica Pradillo, David Evans and Katja Graumann (2019) The nuclear envelope in higher plant mitosis and meiosis. Nucleus DOI: 10.1080/19491034.2019.1587277

    Gumber HK, McKenna JF, Estrada AL, Tolmie AF, Graumann K, Bass HW (2019) Identification and characterization of genes encoding the nuclear envelope LINCcomplex in the monocot species Zea mays. J Cell Sci pii: jcs.221390. doi: 10.1242/jcs.221390

    Newman-Griffis AH, Del Cerro P, Charpentier M, Meier I (2018) Medicago LINC complexes function in nuclear morphology, nuclear movement, and root nodule symbiosis. Plant Physiol. doi: 10.1104/pp.18.01111

    Poulet A, Zhou X, Tamura K, Meier I, Tatout C, Graumann K, Evans, DE (2018) Computational Methods for Studying the Plant Nucleus in Gregg G Gundersen and Howard J Worman (ed.), The LINC Complex (Methods in Molecular Biology, Vol. 1840). ISBN: 9781493986903 eISBN: 9781493986910


    Workgroup 2:

    Wang Z, Butel N, Santos-González J, Simon L, Wärdig C, Köhler C (2021) Transgenerational effect of mutants in the RNA-directed DNA methylation pathway on the triploid block in Arabidopsis. Genome Biol. doi: 10.1186/s13059-021-02359-2

    Layat E, Bourcy M, Cotterell S, Zdzieszyńska J, Desset S, Duc C, Tatout C, Bailly C, Probst AV (2021) The Histone Chaperone HIRA Is a Positive Regulator of Seed Germination. Int J Mol Sci. doi: 10.3390/ijms22084031

    In depth logo (web optimised)Goswami R, Asnacios A, Milani P, Graindorge S, Houlné G, Mutterer J, Hamant O, Chabouté ME (2020) Mechanical Shielding in Plant Nuclei. Curr Biol. doi: 10.1016/j.cub.2020.03.059 

    Karaaslan ES, Faiß N, Liu C, Berendzen KW (2020) Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes. Plants (Basel). doi: 10.3390/plants9111478. PMID: 33153046.

    Concia L, Veluchamy A, Ramirez-Prado JS et al (2020) Wheat chromatin architecture is organized in genome territories and transcription factories. Genome Biol. doi: 10.1186/s13059-020-01998-1

    Bente H, Mittelsten Scheid O, Donà M (2020) Versatile in vitro assay to recognize Cas9-induced mutations. Plant Direct   doi: 10.1002/pld3.269

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    Picart-Picolo A, Grob S, Picault N, Franek M, Llauro C, Halter T, Maier TR, Jobet E, Descombin J, Zhang P, Paramasivan V, Baum TJ, Navarro L, Dvořáčková M, Mirouze M, Pontvianne F (2020) Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response. Genome Res. doi: 10.1101/gr.261586.120

    In depth logo (web optimised)Santos AP, Gaudin V et al (2020) Tidying-up the plant nuclear space: domains, functions, and dynamics. J Exp Bot. doi: 10.1093/jxb/eraa282

    In depth logo (web optimised)Probst AV, Desvoyes B, Gutierrez (2020) Similar yet critically different: the distribution, dynamics and function of histone variants. J Exp Bot. doi: 10.1093/jxb/eraa230.

    Karaaslan ES, Wang N, Faiß N, et al. (2020) Marchantia TCP transcription factor activity correlates with three-dimensional chromatin structure Nat Plants. doi:10.1038/s41477-020-00766-0

    Leng X, Thomas Q, Rasmussen SH, Marquardt S (2020) A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription, Trends in Plant Science https://doi.org/10.1016/j.tplants.2020.03.005

    Kindgren P, Ivanov M, Marquardt S (2020) Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis. Nucleic Acids Res. doi:10.1093/nar/gkz1189

    Leng X, Ivanov M, Kindgren P, et al. (2020) Organismal benefits of transcription speed control at gene boundaries. EMBO Rep. doi:10.15252/embr.201949315

    Thomas QA, Ard R, Liu J, et al. (2020) Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis. Nat Commun. doi:10.1038/s41467-020-16390-7

    Ariel F, Lucero L, Christ A, Mammarella MF, Jegu T, Veluchamy A, Mariappan K, Latrasse D, Blein T, Liu C, Benhamed M, Crespi M (2020) R-Loop Mediated trans Action of the APOLO Long Noncoding RNA. Mol Cell. doi: 10.1016/j.molcel.2019.12.015

    Batista RA, Moreno-Romero J, Qiu Y, van Boven J, Santos-González J, Figueiredo DD, Köhler C (2019) The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons. Elife. pii: e50541. doi: 10.7554/eLife.50541

    Hu B, Wang N, Bi X, Karaaslan ES, Weber AL, Zhu W, Berendzen KW, Liu C (2019) Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery. Genome Biol. 20(1):87. doi: 10.1186/s13059-019-1694-3

    Rutowicz K, Lirski M, Mermaz B, Teano G, Schubert J, Mestiri I, Kroteń MA, Fabrice TN, Fritz S, Grob S, Ringli C, Cherkezyan L, Barneche F, Jerzmanowski A, Baroux C (2019) Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis. Genome Biol. 20(1):157. doi: 10.1186/s13059-019-1767-3

    Wijnker E, Harashima H, Müller K, Parra-Nuñez P, de Snoo CB, van de Belt J, Dissmeyer N, Bayer M, Pradillo M, Schnittger A (2019) The Cdk1/Cdk2 homolog CDKA;1 controls the recombination landscape in Arabidopsis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1820753116

    Prusicki MA, Keizer EM, van Rosmalen RP, Komaki S, Seifert F, Müller K, Wijnker E, Fleck C, Schnittger A (2019) Live cell imaging of meiosis in Arabidopsis thaliana . Elife. doi: 10.7554/eLife.42834

    Goto C, Hashizume S, Fukao Y, Hara-Nishimura I, Tamura K (2019) Comprehensive nuclear proteome of Arabidopsis obtained by sequential extraction. Nucleus 81-92. doi: 10.1080/19491034.2019.1603093

    Yang C, Hamamura Y, Sofroni K, Böwer F, Stolze SC, Nakagami H, Schnittger A (2019) SWITCH 1/DYAD is a WINGS APART-LIKE antagonist that maintains sister chromatid cohesion in meiosis. Nat Commun. 10(1):1755. doi: 10.1038/s41467-019-09759-w

    Mikulski P, Hohenstatt ML, Farrona S, Smaczniak C, Stahl Y, Kalyanikrishna K, Kaufmann K, Angenent GC, Schubert D (2019) The chromatin-associated protein PWO1 interacts with plant nuclear lamin-like components to regulate nuclear size. Plant Cell. doi: 10.1105/tpc.18.00663

    Ariadna Picart-Picolo, Nathalie Picault & Frédéric Pontvianne (2019) Ribosomal RNA genes shape chromatin domains associating with the nucleolus Nucleus, DOI: 10.1080/19491034.2019.1591106

    Völz R, Kim SK, Mi J, Rawat AA, Veluchamy A, Mariappan KG, Rayapuram N, Daviere JM, Achard P, Blilou I, Al-Babili S, Benhamed M, Hirt H (2019) INDETERMINATE-DOMAIN 4 (IDD4) coordinates immune responses with plant-growth in Arabidopsis thaliana. PLoS Pathog. 2019 Jan 24;15(1):e1007499. doi: 10.1371/journal.ppat.1007499

    Iwabuchi K, Ohnishi H, Tamura K, Fukao Y, Furuya T, Hattori K, Tsukaya H, Hara-Nishimura I (2018) ANGUSTIFOLIA Regulates Actin Filament Alignment for Nuclear Positioning in Leaves. Plant Physiol. 2018 Nov 7. pii: pp.01150.2018. doi: 10.1104/pp.18.01150

    Schmid MW, Heichinger C, Coman Schmid D, Guthörl D, Gagliardini V, Bruggmann R, Aluri S, Aquino C, Schmid B, Turnbull LA, Grossniklaus U (2018) Contribution of epigenetic variation to adaptation in Arabidopsis. Nat Commun. doi: 10.1038/s41467-018-06932-5

    Benoit M, Simon L, Desset S, Duc C, Cotterell S, Poulet A, Le Goff S,Tatout C, Probst AV* (2018) Replication-coupled histone H3.1 depositio determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development. NewPhytol. doi: 10.1111/nph.15248

    Doğan SE and Liu C (2018) Chromatin packing and positioning of plant genomes in 3D. Nature Plants 4, 521-229. doi:10.1038/s41477-018-0199-5

    Bi X and Liu C. (2018) Genome-wide identification of chromatin domains anchored at the nuclear periphery in plants. Methods in Molecular Biology 1830, 381-393. doi:10.1007/978-1-4939-8657-6_23

    Wang G, Jiang H, Del Toro de León G, Martinez G, Köhler C (2018) Sequestration of a Transposon-Derived siRNA by a Target Mimic Imprinted Gene Induces Postzygotic Reproductive Isolation in Arabidopsis. Dev Cell. pii: S1534-5807(18)30599-9. doi: 10.1016/j.devcel.2018.07.014

    Nassrallah A, Rougée 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, Barneche F (2018) DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis. Elife. pii: e37892. doi: 10.7554/eLife.37892


    Workgroup 3:

    Liu B, Jin C, De Storme N, Schotte S, Schindfessel C, De Meyer T, Geelen D (2021) A Hypomorphic Mutant of PHD Domain Protein Male Meiocytes Death 1. Genes (Basel) doi: 10.3390/genes12040516
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    Varotto S, Tani E, et al (2020) Epigenetics: possible applications in climate-smart crop breeding. J Exp Bot. doi: 10.1093/jxb/eraa188.

    In depth logo (web optimised)Fernández-Jiménez N, Pradillo M (2020) The role of the nuclear envelope in the regulation of chromatin dynamics during cell division. J Exp Bot. doi: 10.1093/jxb/eraa299.

    Nowicka A, Tokarz B, Zwyrtková J, Dvořák Tomaštíková E, Procházková K, Ercan U, Finke A, Rozhon W, Poppenberger B, Otmar M, Niezgodzki I, Krečmerová M, Schubert I, Pecinka A (2019) Comparative analysis of epigenetic inhibitors reveals different degrees of interference with transcriptional gene silencing and induction of DNA damage. Plant Jn doi: 10.1111/tpj.14612

    Boudichevskaia A, Houben A, Fiebig A, Prochazkova K, Pecinka A, Lermontova I (2019) Depletion of KNL2 Results in Altered Expression of Genes Involved in Regulation of the Cell Cycle, Transcription, and Development in Arabidopsis. Int J Mol Sci. doi: 10.3390/ijms20225726

    In depth logo (web optimised)Pecinka A, Chevalier C, Colas I, Kalantidis K, Varotto S, Krugman T, Michaelidis C, Vallés MP, Muñoz A, Pradillo M (2019) Chromatin dynamics during interphase and cell division: similarities and differences between model and crop plants. J Exp Bot. doi: 10.1093/jxb/erz457

    Le Goff S, Nur Keçeli B, Jerabkova H, Heckmann S, Rutten T, Cotterell S, Schubert V, Roitinger E, Mechtler K, Franklin FCH, Tatout C, Houben A, Geelen D, Probst AV, Lermontova I (2019) The H3 histone chaperone NASPSIM3 escorts CenH3 in Arabidopsis. Plant J doi: 10.1111/tpj.14518

    Wijnker E, Harashima H, Müller K, Parra-Nuñez P, de Snoo CB, van de Belt J, Dissmeyer N, Bayer M, Pradillo M, Schnittger A (2019) The Cdk1/Cdk2 homolog CDKA;1 controls the recombination landscape in Arabidopsis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1820753116

    Prusicki MA, Keizer EM, van Rosmalen RP, Komaki S, Seifert F, Müller K, Wijnker E, Fleck C, Schnittger A (2019) Live cell imaging of meiosis in Arabidopsis thaliana . Elife. doi: 10.7554/eLife.42834

    Yang C, Hamamura Y, Sofroni K, Böwer F, Stolze SC, Nakagami H, Schnittger A (2019) SWITCH 1/DYAD is a WINGS APART-LIKE antagonist that maintains sister chromatid cohesion in meiosis. Nat Commun. 10(1):1755. doi: 10.1038/s41467-019-09759-w

    Ghorbel M, Zaidi I, Ebel C, Hanin M (2019) Differential regulation of the durum wheat MAPK phosphatase 1 by calmodulin, bivalent cations and possibly mitogen activated protein kinase 3. Plant Physiol Biochem. doi: 10.1016/j.plaphy.2018.12.016

    Liu B, Mo WJ, Zhang D, De Storme N, Geelen D (2019) Cold Influences Male Reproductive Development in Plants: A Hazard to Fertility, but a Window for Evolution. Plant Cell Physiol. doi: 10.1093/pcp/pcy209

    Carvalho A, Reis S, Pavia I, Lima-Brito JE (2018) Influence of seed priming with iron and/or zinc in the nucleolar activity and protein content of bread wheat. Protoplasma. doi: 10.1007/s00709-018-01335-1

    Carvalho A, Leal F, Matos M, Lima-Brito J (2018) Effects of heat stress in the leaf mitotic cell cycle and chromosomes of four wine-producing grapevine varieties.Protoplasma. doi: 10.1007/s00709-018-1267-4

    Klymiuk V, Yaniv E, Huang L, Raats D, Fatiukha A, Chen S, Feng L, Frenkel Z, Krugman T, Lidzbarsky G, Chang W, Jääskeläinen MJ, Schudoma C, Paulin L, Laine P, Bariana H, Sela H, Saleem K, Sørensen CK, Hovmøller MS, Distelfeld A, Chalhoub B, Dubcovsky J, Korol AB, Schulman AH, Fahima T (2018) Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family. Nat Commun. doi: 10.1038/s41467-018-06138-9

    Pradillo M, Santos JL (2018) Genes involved in miRNA biogenesis affect meiosis and fertility. Chromosome Res. doi: 10.1007/s10577-018-9588-x

    Groves NR, Biel AM, Newman-Griffis AH, Meier I (2018) Dynamic Changes in Plant Nuclear Organization in Response to Environmental and Developmental Signals. Plant Physiol. 176(1):230-241. doi: 10.1104/pp.17.00788.

    Varas J, Pradillo M (2018) Immunolabeling Protocols for Studying Meiosis in Plant Mutants Defective for Nuclear Envelope Components. Methods Mol Biol.1840:237-247. doi: 10.1007/978-1-4939-8691-0_17

    Gigli-Bisceglia N, Engelsdorf T, Strnad M, Vaahtera L, Khan GA, Jamoune A, Alipanah L, Novák O, Persson S, Hejatko J, Hamann T (2018) Cell wall integrity modulates Arabidopsis thaliana cell cycle gene expression in a cytokinin- and nitrate reductase-dependent manner. Development. pii: dev.166678. doi: 10.1242/dev.166678

    Forestan C, Farinati S, Rouster J, Lassagne H, Lauria M, Dal Ferro N, Varotto S (2018) Control of Maize Vegetative and Reproductive Development, Fertility, and rRNAs Silencing by HISTONE DEACETYLASE 108. Genetics. doi: 10.1534/genetics.117.300625

    In depth logo (web optimised)Vogel A, Schwacke R, Denton AK, Usadel B, Hollmann J, Fischer K, Bolger A, Schmidt MH, Bolger ME, Gundlach H, Mayer KFX, Weiss-Schneeweiss H, Temsch EM, Krause K (2018) Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris . Nat Commun. doi: 10.1038/s41467-018-04344-z > PUBLICATION SUPPORTED BY INDEPTH FUNDING .


    Workgroup 4:

    Grob S, Grossniklaus U (2019) Invasive DNA elements modify the nuclear architecture of their insertion site by KNOT-linked silencing in Arabidopsis thaliana . Genome Biol. 2019 Jun 11;20(1):120. doi: 10.1186/s13059-019-1722-3


    Workgroup 5:

    In depth logo (web optimised)Parry G, Pradillo M, Probst AV, Tatout C (2020) Untangling chromatin interactions. J Exp Bot. doi: 10.1093/jxb/eraa334

    Parry G, Harrison CJ (2018) GARNet gene editing workshop. New Phytol. doi: 10.1111/nph.15573

    In depth logo (web optimised)Parry G, Probst AV, Baroux C, Tatout C. (2018) Meeting report - INDEPTH kick-off meeting. J Cell Sci. 131(12). pii: jcs220558.



  • Joining the INDEPTH COST Action

    If you are interested in joining Action please contact the INDEPTH Chairman stating why the research program of your lab would enhance the overall activity of the Action.

    Christophe Tatout

    christophe.tatout@uca.fr