Transcriptional regulation through association of chromatin domains with nuclear compartments
The position of a genomic locus within the nucleus and relative to nuclear domains such as the nuclear periphery, the nucleolus, chromocenters or Polycomb bodies has the potential to affect its expression.
Recent developments including techniques such as ChIP-seq and RNA-seq coupled to Chromatin Conformation Capture (3C) applied to the whole genome (Hi- C) have greatly improved our understanding of genome organization in nuclear space and revealed plant-specific features of nuclear architecture. Uniting these approaches with the power of genetics will provide breakthroughs in our understanding of plant nuclear architecture and genome expression. WG2 will integrate these different methodologies and deploy a series of complementary approaches to study the spatial organization of genomic loci in relation to its local chromatin features and its transcriptional activity.
Members of WG2:
- Rita Abranches, Universidade Nova de Lisboa, Portugal
- Phillippe Andrey, INRA Centre de Versailles-Grignon, France
- Rafal Archaki, University of Warsaw, Poland
- Fredy Barneche, Institut de Biologie de l’École Normale Supérieure, France
- Célia Baroux, University of Zürich, Switzerland
- Hank Bass, Florida State University, United States
- Moussa Benhamed, Institute of Plant Science Paris Saclay, France
- Allessandra Carbone, Sorbonne Université, France
- Marie-Edith Chabouté, Institut de Biologie Moléculaire des plantes, France
- Jaroslav Dolezel, Institute of Experimental Botany, Czech Republic
- Susan Duncan, Earlham Institute, UK
- Martina Dvorackova, CEITEC/Masaryk University, Czech Republic
- Sara Farrona, National University of Ireland Galway, Ireland
- Attila Feher, University of Szeged, Hungary
- Duarte Figueiredo, University of Potsdam, Germany
- Paul Fransz, University of Amsterdam, Netherlands
- Valérie Gaudin, INRA Centre de Versailles-Grignon, France
- Ueli Grossniklaus, University of Zürich, Switzerland
- Hana Jerabkova, Institute of Experimental Botany, Czech Republic
- Hua Jiang, IPK Gatersleben, Germany
- Marta Koblowska, University of Warsaw, Poland
- Claudia Köhler, Swedish University of Agricultural Sciences, Sweden
- László Kozma-Bognár, University of Szeged, Hungary
- Elodie Laine, Sorbonne Université
- Inna Lermontova, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Germany
- Chang Liu, Center for Molecular Biology of Plants, Germany
- Kristine Margaryan, Yerevan State University, Armenia
- Sebastian Marquardt, University of Copenhagen
- Rainer Melzer, University College Dublin, Ireland
- Ortrun Mittelsten Scheid, Gregor Mendel Institute of Molecular Plant Biology, Austria
- Iva Mozgova, Institute of Microbiology, Czech Republic
- Hans Nützmann, University of Bath, UK
- Etienne Paux, INRA, France
- Ales Pecinka, Institute of Experimental Botany, Czech Republic
- Beata Petrovksa, Institute of Experimental Botany, Czech Republic
- Frederic Pontvianne, Laboratoire Génome et Développement des Plantes, France
- Robert Possee, Oxford Expression Technologies Ltd, UK
- Aline Probst, Genetics, Reproduction and Development, France
- Stefanie Rosa, Swedish University of Agricultural Sciences, Sweden
- François Roudier, ENS Lyon, France
- Julio Saez-Vasquez, Laboratoire Génome et Développement des Plantes, France
- Anne-Catherine Schmit, Institut de Biologie Moléculaire des Plantes, France
- Arp Schnittger, University of Hamburg, Germany
- Daniel Schubert, Freie Universität Berlin, Germany
- Veit Schubert, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Germany
- Marek Sebela, Palacky University Olomouc, Czech Republic
- Hana Simkova, Institute of Experimental Botany, Czech Republic
- Nils Stein, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Germany
- Szymon Swiezewski, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Poland
- Kentaro Tamura, Kyoto University, Japan
- Christophe Tatout, Genetics, Reproduction and Development, France
- Ahmet Tek, Niğde Ömer Halisdemir Üniversitesi, Turkey
- Valya Vassileva, Institute of Plant Physiology and Genetics, Bulgaria
- Paul Wyatt, Biogemma, France
Recent publications from members of WG2:
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
