Working group 2

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  • Working group 2

    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:

    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

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

    Leng X, Ivanov M, Kindgren P, et al. (2020) Organismal benefits of transcription speed control at gene boundariesEMBO 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 ArabidopsisNat 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

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