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  • 1. Ahn, Ji Hoon
    et al.
    Schmid, Markus
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Editorial overview: Growth and development: Change is in the air: how plants modulate development in response to the environment2017In: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 35, IV-VI p.Article in journal (Refereed)
  • 2. Alonso, J. M.
    et al.
    Stepanova, A. N.
    Leisse, T. J.
    Kim, C. J.
    Chen, H. M.
    Shinn, P.
    Stevenson, D. K.
    Zimmerman, J.
    Barajas, P.
    Cheuk, R.
    Gadrinab, C.
    Heller, C.
    Jeske, A.
    Koesema, E.
    Meyers, C. C.
    Parker, H.
    Prednis, L.
    Ansari, Y.
    Choy, N.
    Deen, H.
    Geralt, M.
    Hazari, N.
    Hom, E.
    Karnes, M.
    Mulholland, C.
    Ndubaku, R.
    Schmidt, I.
    Guzman, P.
    Aguilar-Henonin, L.
    Schmid, M.
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
    Weigel, D.
    Carter, D. E.
    Marchand, T.
    Risseeuw, E.
    Brogden, D.
    Zeko, A.
    Crosby, W. L.
    Berry, C. C.
    Ecker, J. R.
    Genome-wide Insertional mutagenesis of Arabidopsis thaliana2003In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 301, no 5633, 653-657 p.Article in journal (Refereed)
  • 3. Brandt, Ronny
    et al.
    Salla-Martret, Merce
    Bou-Torrent, Jordi
    Musielak, Thomas
    Stahl, Mark
    Lanz, Christa
    Ott, Felix
    Schmid, Markus
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
    Greb, Thomas
    Schwarz, Martina
    Choi, Sang-Bong
    Barton, M. Kathryn
    Reinhart, Brenda J.
    Liu, Tie
    Quint, Marcel
    Palauqui, Jean-Christophe
    Martinez-Garcia, Jaime F.
    Wenkel, Stephan
    Genome-wide binding-site analysis of REVOLUTA reveals a link between leaf patterning and light-mediated growth responses2012In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 72, no 1, 31-42 p.Article in journal (Refereed)
  • 4. Capovilla, Giovanna
    et al.
    Pajoro, Alice
    Immink, Richard GH
    Schmid, Markus
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72074 Tübingen, Germany.
    Role of alternative pre-mRNA splicing in temperature signaling2015In: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 27, 97-103 p.Article, review/survey (Refereed)
    Abstract [en]

    Developmental plasticity enables plants to respond rapidly to changing environmental conditions, such as temperature fluctuations. Understanding how plants measure temperature and integrate this information into developmental programs at the molecular level will be essential to breed thermo-tolerant crop varieties. Recent studies identified alternative splicing (AS) as a possible 'molecular thermometer', allowing plants to quickly adjust the abundance of functional transcripts to environmental perturbations. In this review, recent advances regarding the effects of temperature-responsive AS on plant development will be discussed, with emphasis on the circadian clock and flowering time control. The challenge for the near future will be to understand the molecular mechanisms by which temperature can influence AS regulation.

  • 5. Capovilla, Giovanna
    et al.
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany.
    Posé, David
    Control of flowering by ambient temperature2015In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 66, no 1, 59-69 p.Article in journal (Refereed)
    Abstract [en]

    The timing of flowering is a crucial decision in the life cycle of plants since favourable conditions are needed to maximize reproductive success and, hence, the survival of the species. It is therefore not surprising that plants constantly monitor endogenous and environmental signals, such as day length (photoperiod) and temperature, to adjust the timing of the floral transition. Temperature in particular has been shown to have a tremendous effect on the timing of flowering: the effect of prolonged periods of cold, called the vernalization response, has been extensively studied and the underlying epigenetic mechanisms are reasonably well understood in Arabidopsis thaliana. In contrast, the effect of moderate changes in ambient growth temperature on the progression of flowering, the thermosensory pathway, is only starting to be understood on the molecular level. Several genes and molecular mechanisms underlying the thermosensory pathway have already been identified and characterized in detail. At a time when global temperature is rising due to climate change, this knowledge will be pivotal to ensure crop production in the future.

  • 6. Capovilla, Giovanna
    et al.
    Symeonidi, Efthymia
    Wu, Rui
    Schmid, Markus
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstr. 35, 72076 Tübingen, Germany.
    Contribution of major FLM isoforms to temperature-dependent flowering in Arabidopsis thaliana2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 18, 5117-5127 p.Article in journal (Refereed)
    Abstract [en]

    FLOWERING LOCUS M (FLM), a component of the thermosensory flowering time pathway in Arabidopsis thaliana, is regulated by temperature-dependent alternative splicing (AS). The main splicing variant, FLM-beta, is a well-documented floral repressor that is down-regulated in response to increasing ambient growth temperature. Two hypotheses have been formulated to explain how flowering time is modulated by AS of FLM. In the first model a second splice variant, FLM-delta, acts as a dominant negative isoform that competes with FLM-beta at elevated ambient temperatures, thereby indirectly promoting flowering. Alternatively, it has been suggested that the induction of flowering at elevated temperatures is caused only by reduced FLM-beta expression. To better understand the role of the two FLM splice forms, we employed CRISPR/Cas9 technology to specifically delete the exons that characterize each splice variant. Lines that produced repressive FLM-beta but were incapable of producing FLM-delta were late flowering. In contrast, FLM-beta knockout lines that still produced FLM-delta flowered early, but not earlier than the flm-3 loss of function mutant, as would be expected if FLM-delta had a dominant-negative effect on flowering. Our data support the role of FLM-beta as a flower repressor and provide evidence that a contribution of FLM-delta to the regulation of flowering time in wild-type A. thaliana seems unlikely.

  • 7. Conn, Vanessa M.
    et al.
    Hugouvieux, Veronique
    Nayak, Aditya
    Conos, Stephanie A.
    Capovilla, Giovanna
    Cildir, Gokhan
    Jourdain, Agnes
    Tergaonkar, Vinay
    Schmid, Markus
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Zubieta, Chloe
    Conn, Simon J.
    A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation2017In: Nature Plants, ISSN 2055-026X, Vol. 3, no 5, 17053Article in journal (Refereed)
    Abstract [en]

    Circular RNAs (circRNAs) are a diverse and abundant class of hyper-stable, non-canonical RNAs that arise through a form of alternative splicing (AS) called back-splicing. These single-stranded, covalently-closed circRNA molecules have been identified in all eukaryotic kingdoms of life(1), yet their functions have remained elusive. Here, we report that circRNAs can be used as bona fide biomarkers of functional, exon-skipped AS variants in Arabidopsis, including in the homeotic MADS-box transcription factor family. Furthermore, we demonstrate that circRNAs derived from exon 6 of the SEPALLATA3 (SEP3) gene increase abundance of the cognate exon-skipped AS variant (SEP3.3 which lacks exon 6), in turn driving floral homeotic phenotypes. Toward demonstrating the underlying mechanism, we show that the SEP3 exon 6 circRNA can bind strongly to its cognate DNA locus, forming an RNA: DNA hybrid, or R-loop, whereas the linear RNA equivalent bound significantly more weakly to DNA. R-loop formation results in transcriptional pausing, which has been shown to coincide with splicing factor recruitment and AS(2-4). This report presents a novel mechanistic insight for how at least a subset of circRNAs probably contribute to increased splicing efficiency of their cognate exon-skipped messenger RNA and provides the first evidence of an organismal-level phenotype mediated by circRNA manipulation.

  • 8. Dinh, Thanh Theresa
    et al.
    Girke, Thomas
    Liu, Xigang
    Yant, Levi
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tuebingen, Germany.
    Chen, Xuemei
    The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element2012In: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 139, no 11, 1978-1986 p.Article in journal (Refereed)
  • 9. Dohmann, Esther M. N.
    et al.
    Levesque, Mitchell P.
    De Veylder, Lieven
    Reichardt, Ilka
    Juergens, Gerd
    Schmid, Markus
    Tübingen University, Center for Plant Molecular Biology, Department of Developmental Genetics, Auf der Morgenstelle 3-5, 72076 Tübingen, Germany.
    Schwechheimer, Claus
    The Arabidopsis COP9 signalosome is essential for G2 phase progression and genomic stability2008In: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 135, no 11, 2013-2022 p.Article in journal (Refereed)
  • 10. Galvao, Vinicius C.
    et al.
    Horrer, Daniel
    Kuettner, Frank
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tuebingen, Germany.
    Spatial control of flowering by DELLA proteins in Arabidopsis thaliana2012In: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 139, no 21, 4072-4082 p.Article in journal (Refereed)
  • 11. Galvao, Vinicius C.
    et al.
    Nordstroem, Karl J. V.
    Lanz, Christa
    Sulz, Patric
    Mathieu, Johannes
    Pose, David
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tuebingen, Germany.
    Weigel, Detlef
    Schneeberger, Korbinian
    Synteny-based mapping-by-sequencing enabled by targeted enrichment2012In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 71, no 3, 517-526 p.Article in journal (Refereed)
  • 12. Galvao, Vinicius Costa
    et al.
    Collani, Silvio
    Horrer, Daniel
    Schmid, Markus
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana2015In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 84, no 5, 949-962 p.Article in journal (Refereed)
    Abstract [en]

    Distinct molecular mechanisms integrate changes in ambient temperature into the genetic pathways that govern flowering time in Arabidopsis thaliana. Temperature-dependent eviction of the histone variant H2A.Z from nucleosomes has been suggested to facilitate the expression of FT by PIF4 at elevated ambient temperatures. Here we show that, in addition to PIF4, PIF3 and PIF5, but not PIF1 and PIF6, can promote flowering when expressed specifically in phloem companion cells (PCC), where they can induce FT and its close paralog, TSF. However, despite their strong potential to promote flowering, genetic analyses suggest that the PIF genes seem to have only a minor role in adjusting flowering in response to photoperiod or high ambient temperature. In addition, loss of PIF function only partially suppressed the early flowering phenotype and FT expression of the arp6 mutant, which is defective in H2A.Z deposition. In contrast, the chemical inhibition of gibberellic acid (GA) biosynthesis resulted in a strong attenuation of early flowering and FT expression in arp6. Furthermore, GA was able to induce flowering at low temperature (15 degrees C) independently of FT, TSF, and the PIF genes, probably directly at the shoot apical meristem. Together, our results suggest that the timing of the floral transition in response to ambient temperature is more complex than previously thought and that GA signaling might play a crucial role in this process.

  • 13. Galvao, Vinicius Costa
    et al.
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
    Regulation of Flowering by Endogenous Signals2014In: Molecular Genetics of Floral Transition and Flower Development, 2014Chapter in book (Refereed)
  • 14. Gietl, C.
    et al.
    Schmid, M.
    Lehrstuhl für Botanik, Biologikum-Weihenstephan, Technische Universität München, Am Hochanger 4, 85350 Freising, Germany.
    Ricinosomes: an organelle for developmentally regulated programmed cell death in senescing plant tissues2001In: Die Naturwissenschaften, ISSN 0028-1042, E-ISSN 1432-1904, Vol. 88, no 2, 49-58 p.Article in journal (Refereed)
  • 15. Helm, Michael
    et al.
    Schmid, Markus
    Technische Universität München, Lehrstuhl für Botanik, Biologikum-Weihenstephan, Am Hochanger 4, D-85350 Freising, Germany.
    Hierl, Georg
    Terneus, Kimberly
    Tan, Li
    Lottspeich, Friedrich
    Kieliszewski, Marcia J.
    Gietl, Christine
    KDEL-tailed cysteine endopeptidases involved in programmed cell death, intercalation of new cells, and dismantling of extensin scaffolds2008In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 95, no 9, 1049-1062 p.Article in journal (Refereed)
  • 16. Henz, Stefan R.
    et al.
    Cumbie, Jason S.
    Kasschau, Kristin D.
    Lohmann, Jan U.
    Carrington, James C.
    Weigel, Detlef
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tuebingen, Germany.
    Distinct expression patterns of natural antisense transcripts in arabidopsis2007In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 144, no 3, 1247-1255 p.Article in journal (Refereed)
  • 17. Huijser, Peter
    et al.
    Schmid, Markus
    Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
    The control of developmental phase transitions in plants2011In: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 138, no 19, 4117-4129 p.Article in journal (Refereed)
  • 18. Immink, Richard G. H.
    et al.
    Pose, David
    Ferrario, Silvia
    Ott, Felix
    Kaufmann, Kerstin
    Valentim, Felipe Leal
    de Folter, Stefan
    van der Wal, Froukje
    van Dijk, Aalt D. J.
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tuebingen, Germany.
    Angenent, Gerco C.
    Characterization of SOC1's Central Role in Flowering by the Identification of Its Upstream and Downstream Regulators2012In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 160, no 1, 433-449 p.Article in journal (Refereed)
  • 19. Koo, Sung C.
    et al.
    Bracko, Oliver
    Park, Mi S.
    Schwab, Rebecca
    Chun, Hyun J.
    Park, Kyoung M.
    Seo, Jun S.
    Grbic, Vojislava
    Balasubramanian, Sureshkumar
    Schmid, Markus
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany.
    Godard, Francois
    Yun, Dae-Jin
    Lee, Sang Y.
    Cho, Moo J.
    Weigel, Detlef
    Kim, Min C.
    Control of lateral organ development and flowering time by the Arabidopsis thaliana MADS-box Gene AGAMOUS-LIKE62010In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 62, no 5, 807-816 p.Article in journal (Refereed)
  • 20. Lee, Jeong Hwan
    et al.
    Ryu, Hak-Seung
    Chung, Kyung Sook
    Pose, David
    Kim, Soonkap
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
    Ahn, Ji Hoon
    Regulation of Temperature-Responsive Flowering by MADS-Box Transcription Factor Repressors2013In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 342, no 6158, 628-632 p.Article in journal (Refereed)
  • 21. Lempe, J.
    et al.
    Balasubramanian, S.
    Sureshkumar, S.
    Singh, A.
    Schmid, M.
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany .
    Weigel, D.
    Diversity of flowering responses in wild Arabidopsis thaliana strains2005In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 1, no 1, 109-118 p.Article in journal (Refereed)
  • 22. Lutz, Ulrich
    et al.
    Posé, David
    Pfeifer, Matthias
    Gundlach, Heidrun
    Hagmann, Jörg
    Wang, Congmao
    Weigel, Detlef
    Mayer, Klaus F. X.
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
    Schwechheimer, Claus
    Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M2015In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 11, no 10, e1005588Article in journal (Refereed)
    Abstract [en]

    Plants integrate seasonal cues such as temperature and day length to optimally adjust their flowering time to the environment. Compared to the control of flowering before and after winter by the vernalization and day length pathways, mechanisms that delay or promote flowering during a transient cool or warm period, especially during spring, are less well understood. Due to global warming, understanding this ambient temperature pathway has gained increasing importance. In Arabidopsis thalianaFLOWERING LOCUS M (FLM) is a critical flowering regulator of the ambient temperature pathway. FLM is alternatively spliced in a temperature-dependent manner and the two predominant splice variants, FLM-ß and FLM-δ, can repress and activate flowering in the genetic background of the Athaliana reference accession Columbia-0. The relevance of this regulatory mechanism for the environmental adaptation across the entire range of the species is, however, unknown. Here, we identify insertion polymorphisms in the first intron of FLM as causative for accelerated flowering in many natural A. thaliana accessions, especially in cool (15°C) temperatures. We present evidence for a potential adaptive role of this structural variation and link it specifically to changes in the abundance of FLM-ß. Our results may allow predicting flowering in response to ambient temperatures in the Brassicaceae.

  • 23. Mathieu, Johannes
    et al.
    Warthmann, Norman
    Kuettner, Frank
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstrasse 37 - 39, D - 72076 Tübingen, Germany.
    Export of FT protein from phloem companion cells is sufficient for floral induction in Arabidopsis2007In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 17, no 12, 1055-1060 p.Article in journal (Refereed)
  • 24. Mathieu, Johannes
    et al.
    Yant, Levi J.
    Muerdter, Felix
    Kuettner, Frank
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany.
    Repression of Flowering by the miR172 Target SMZ2009In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 7, no 7Article in journal (Refereed)
  • 25. Mirjam, Esther
    et al.
    Dohmann, Natascha
    Levesque, Mitchell Paul
    Isono, Erika
    Schmid, Markus
    Department of Developmental Genetics, Center for Plant Molecular Biology, Tübingen University, 72076 Tuebingen, Germany.
    Schwechheimer, Claus
    Auxin responses in mutants of the Arabidopsis CONSTITUTIVE PHOTOMORPHOGENIC9 signalosome2008In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 147, no 3, 1369-1379 p.Article in journal (Refereed)
  • 26. Moyroud, Edwige
    et al.
    Minguet, Eugenio Gomez
    Ott, Felix
    Yant, Levi
    Pose, David
    Monniaux, Marie
    Blanchet, Sandrine
    Bastien, Olivier
    Thevenon, Emmanuel
    Weigel, Detlef
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tuebingen, Germany .
    Parcy, Francois
    Prediction of Regulatory Interactions from Genome Sequences Using a Biophysical Model for the Arabidopsis LEAFY Transcription Factor2011In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 23, no 4, 1293-1306 p.Article in journal (Refereed)
  • 27. Pfeiffer, Anne
    et al.
    Janocha, Denis
    Dong, Yihan
    Medzihradszky, Anna
    Schöne, Stefanie
    Daum, Gabor
    Suzaki, Takuya
    Forner, Joachim
    Longenecker, Tobias
    Rempel, Eugen
    Schmid, Markus
    3Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
    Wirtz, Markus
    Hell, Rüdiger
    Lohmann, Jan U.
    Integration of light and metabolic signals for stem cell activation at the shoot apical meristem2016In: eLIFE, E-ISSN 2050-084X, Vol. 5, e17023Article in journal (Refereed)
    Abstract [en]

    A major feature of embryogenesis is the specification of stem cell systems, but in contrast to the situation in most animals, plant stem cells remain quiescent until the postembryonic phase of development. Here, we dissect how light and metabolic signals are integrated to overcome stem cell dormancy at the shoot apical meristem. We show on the one hand that light is able to activate expression of the stem cell inducer WUSCHEL independently of photosynthesis and that this likely involves inter-regional cytokinin signaling. Metabolic signals, on the other hand, are transduced to the meristem through activation of the TARGET OF RAPAMYCIN (TOR) kinase. Surprisingly, TOR is also required for light signal dependent stem cell activation. Thus, the TOR kinase acts as a central integrator of light and metabolic signals and a key regulator of stem cell activation at the shoot apex.

  • 28. Ponnu, Jathish
    et al.
    Wahl, Vanessa
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tuebingen, Germany.
    Trehalose-6-phosphate: connecting plant metabolism and development2011In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 2Article in journal (Refereed)
  • 29. Pose, David
    et al.
    Verhage, Leonie
    Ott, Felix
    Yant, Levi
    Mathieu, Johannes
    Angenent, Gerco C.
    Immink, Richard G. H.
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
    Temperature-dependent regulation of flowering by antagonistic FLM variants2013In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 503, no 7476, 414-+ p.Article in journal (Refereed)
  • 30. Pose, David
    et al.
    Yant, Levi
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tuebingen, Germany.
    The end of innocence: flowering networks explode in complexity2012In: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 15, no 1, 45-50 p.Article in journal (Refereed)
  • 31. Sayou, Camille
    et al.
    Nanao, Max H.
    Jamin, Marc
    Pose, David
    Thevenon, Emmanuel
    Gregoire, Laura
    Tichtinsky, Gabrielle
    Denay, Gregoire
    Ott, Felix
    Llobet, Marta Peirats
    Schmid, Markus
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Dumas, Renaud
    Parcy, Francois
    A SAM oligomerization domain shapes the genomic binding landscape of the LEAFY transcription factor2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, 11222Article in journal (Refereed)
    Abstract [en]

    Deciphering the mechanisms directing transcription factors (TFs) to specific genome regions is essential to understand and predict transcriptional regulation. TFs recognize short DNA motifs primarily through their DNA-binding domain. Some TFs also possess an oligomerization domain suspected to potentiate DNA binding but for which the genome-wide influence remains poorly understood. Here we focus on the LEAFY transcription factor, a master regulator of flower development in angiosperms. We have determined the crystal structure of its conserved amino-terminal domain, revealing an unanticipated Sterile Alpha Motif oligomerization domain. We show that this domain is essential to LEAFY floral function. Moreover, combined biochemical and genome-wide assays suggest that oligomerization is required for LEAFY to access regions with low-affinity binding sites or closed chromatin. This finding shows that domains that do not directly contact DNA can nevertheless have a profound impact on the DNA binding landscape of a TF.

  • 32. Schlereth, Alexandra
    et al.
    Moller, Barbara
    Liu, Weilin
    Kientz, Marika
    Flipse, Jacky
    Rademacher, Eike H.
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstrasse 37–39, 72076 Tübingen, Germany.
    Juergens, Gerd
    Weijers, Dolf
    MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor2010In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 464, no 7290, 913-U128 p.Article in journal (Refereed)
  • 33.
    Schmid, M.
    et al.
    Max Planck Institute for Developmental Biology, Spemannstrasse 37-39, 72076 Tübingen, Germany.
    Davison, T. S.
    Henz, S. R.
    Pape, U. J.
    Demar, M.
    Vingron, M.
    Scholkopf, B.
    Weigel, D.
    Lohmann, J. U.
    A gene expression map of Arabidopsis thaliana development2005In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 37, no 5, 501-506 p.Article in journal (Refereed)
  • 34.
    Schmid, M.
    et al.
    Lehrstuhl für Botanik, Biologikum-Weihenstephan, Technische Universität München, Am Hochanger 4, D-85350 Freising, Germany.
    Simpson, D.
    Gietl, C.
    Programmed cell death in castor bean endosperm is associated with the accumulation and release of a cysteine endopeptidase from ricinosomes1999In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 96, no 24, 14159-14164 p.Article in journal (Refereed)
  • 35.
    Schmid, M.
    et al.
    Lehrstuhl für Botanik, Biologikum-Weihenstephan, Technische Universität München, Am Hochanger 4, D-85350 Freising, Germany.
    Simpson, D. J.
    Sarioglu, H.
    Lottspeich, F.
    Gietl, C.
    The ricinosomes of senescing plant tissue bud from the endoplasmic reticulum2001In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 98, no 9, 5353-5358 p.Article in journal (Refereed)
  • 36.
    Schmid, M.
    et al.
    Lehrstuhl für Botanik, Technische Universität München, Germany..
    Simpson, D.
    Kalousek, F.
    Gietl, C.
    A cysteine endopeptidase with a C-terminal KDEL motif isolated from castor bean endosperm is a marker enzyme for the ricinosome, a putative lytic compartment1998In: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 206, no 3, 466-475 p.Article in journal (Refereed)
  • 37.
    Schmid, M.
    et al.
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany.
    Uhlenhaut, N. H.
    Godard, F.
    Demar, M.
    Bressan, R.
    Weigel, D.
    Lohmann, J. U.
    Dissection of floral induction pathways using global expression analysis2003In: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 130, no 24, 6001-6012 p.Article in journal (Refereed)
  • 38. Schumann, U.
    et al.
    Wanner, G.
    Veenhuis, M.
    Schmid, M.
    Lehrstuhl für Botanik, Technische Universität München, Am Hochanger 4, D-85350 Freising, Germany.
    Gietl, C.
    AthPEX10, ariuclear gene essential for peroxisome and storage organelle formation during Arabidopsis embryogenesis2003In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 100, no 16, 9626-9631 p.Article in journal (Refereed)
  • 39. Schwab, R.
    et al.
    Palatnik, J. F.
    Riester, M.
    Schommer, C.
    Schmid, M.
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
    Weigel, D.
    Specific effects of MicroRNAs on the plant transcriptome2005In: Developmental Cell, ISSN 1534-5807, E-ISSN 1878-1551, Vol. 8, no 4, 517-527 p.Article in journal (Refereed)
  • 40. Slane, Daniel
    et al.
    Kong, Jixiang
    Berendzen, Kenneth W.
    Kilian, Joachim
    Henschen, Agnes
    Kolb, Martina
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
    Harter, Klaus
    Mayer, Ulrike
    De Smet, Ive
    Bayer, Martin
    Juergens, Gerd
    Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo2014In: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 141, no 24, 4831-4840 p.Article in journal (Refereed)
  • 41. Slane, Daniel
    et al.
    Kong, Jixiang
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany.
    Jürgens, Gerd
    Bayer, Martin
    Profiling of embryonic nuclear vs. cellular RNA in Arabidopsis thaliana2015In: Genomics Data, ISSN 1025-6059, E-ISSN 2213-5960, Vol. 4, 96-98 p.Article in journal (Refereed)
    Abstract [en]

    In Arabidopsis, various cell type-specific whole-genome expression analyses have been conducted. However, the vast majority of these were performed with cellular RNA from root tissues or other easily accessible cell types [1]. Nuclear RNA was neglected for a long time as not being representative for transcriptomic studies. In recent years, however, there have been reports describing the validity of nuclear RNA for these types of studies [2] and [3]. Here we describe the generation, quality assessment and analysis of nuclear transcriptomic data from Arabidopsis embryos published by Slane et al. (2014) [4]. Comparison of nuclear with cellular gene expression demonstrated the usefulness of nuclear transcriptomics.

  • 42. Srikanth, Anusha
    et al.
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tuebingen, Germany.
    Regulation of flowering time: all roads lead to Rome2011In: Cellular and Molecular Life Sciences (CMLS), ISSN 1420-682X, E-ISSN 1420-9071, Vol. 68, no 12, 2013-2037 p.Article in journal (Refereed)
  • 43. Valentim, Felipe Leal
    et al.
    van Mourik, Simon
    Pose, David
    Kim, Min C
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
    van Ham, Roeland C H J
    Busscher, Marco
    Sanchez-Perez, Gabino F
    Molenaar, Jaap
    Angenent, Gerco C
    Immink, Richard G H
    van Dijk, Aalt D J
    A Quantitative and Dynamic Model of the Arabidopsis Flowering Time Gene Regulatory Network2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 2, e0116973Article in journal (Refereed)
    Abstract [en]

    Various environmental signals integrate into a network of floral regulatory genes leading to the final decision on when to flower. Although a wealth of qualitative knowledge is available on how flowering time genes regulate each other, only a few studies incorporated this knowledge into predictive models. Such models are invaluable as they enable to investigate how various types of inputs are combined to give a quantitative readout. To investigate the effect of gene expression disturbances on flowering time, we developed a dynamic model for the regulation of flowering time in Arabidopsis thaliana. Model parameters were estimated based on expression time-courses for relevant genes, and a consistent set of flowering times for plants of various genetic backgrounds. Validation was performed by predicting changes in expression level in mutant backgrounds and comparing these predictions with independent expression data, and by comparison of predicted and experimental flowering times for several double mutants. Remarkably, the model predicts that a disturbance in a particular gene has not necessarily the largest impact on directly connected genes. For example, the model predicts that SUPPRESSOR OF OVEREXPRESSION OF CONSTANS (SOC1) mutation has a larger impact on APETALA1 (AP1), which is not directly regulated by SOC1, compared to its effect on LEAFY (LFY) which is under direct control of SOC1. This was confirmed by expression data. Another model prediction involves the importance of cooperativity in the regulation of APETALA1 (AP1) by LFY, a prediction supported by experimental evidence. Concluding, our model for flowering time gene regulation enables to address how different quantitative inputs are combined into one quantitative output, flowering time.

  • 44. Wahl, Vanessa
    et al.
    Brand, Luise H.
    Guo, Ya-Long
    Schmid, Markus
    Department of Molecular Biology, AG Schmid, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany.
    The FANTASTIC FOUR proteins influence shoot meristem size in Arabidopsis thaliana2010In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 10Article in journal (Refereed)
  • 45. Wahl, Vanessa
    et al.
    Ponnu, Jathish
    Schlereth, Armin
    Arrivault, Stephanie
    Langenecker, Tobias
    Franke, Annika
    Feil, Regina
    Lunn, John E.
    Stitt, Mark
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
    Regulation of Flowering by Trehalose-6-Phosphate Signaling in Arabidopsis thaliana2013In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 339, no 6120, 704-707 p.Article in journal (Refereed)
  • 46. Wigge, P. A.
    et al.
    Kim, M. C.
    Jaeger, K. E.
    Busch, W.
    Schmid, M.
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
    Lohmann, J. U.
    Weigel, D.
    Integration of spatial and temporal information during floral induction in Arabidopsis2005In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 309, no 5737, 1056-1059 p.Article in journal (Refereed)
  • 47. Wimmer, C.
    et al.
    Schmid, M.
    Institute of Botany, Technische Universitaet Muenchen, Munich, Germany.
    Veenhuis, M.
    Gietl, C.
    The plant PTS1 receptor: similarities and differences to its human and yeast counterparts1998In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 16, no 4, 453-464 p.Article in journal (Refereed)
  • 48. Yant, Levi
    et al.
    Mathieu, Johannes
    Dinh, Thanh Theresa
    Ott, Felix
    Lanz, Christa
    Wollmann, Heike
    Chen, Xuemei
    Schmid, Markus
    Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany.
    Orchestration of the Floral Transition and Floral Development in Arabidopsis by the Bifunctional Transcription Factor APETALA22010In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 22, no 7, 2156-2170 p.Article in journal (Refereed)
  • 49. Yant, Levi
    et al.
    Mathieu, Johannes
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstrasse 37-39, D-72076 Tübingen, Germany.
    Just say no: floral repressors help Arabidopsis bide the time2009In: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 12, no 5, 580-586 p.Article in journal (Refereed)
  • 50. You, Yuan
    et al.
    Sawikowska, Aneta
    Neumann, Manuela
    Pose, David
    Capovilla, Giovanna
    Langenecker, Tobias
    Neher, Richard A.
    Krajewski, Pawel
    Schmid, Markus
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
    Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, 15120Article in journal (Refereed)
    Abstract [en]

    Plants can produce organs throughout their entire life from pluripotent stem cells located at their growing tip, the shoot apical meristem (SAM). At the time of flowering, the SAM of Arabidopsis thaliana switches fate and starts producing flowers instead of leaves. Correct timing of flowering in part determines reproductive success, and is therefore under environmental and endogenous control. How epigenetic regulation contributes to the floral transition has eluded analysis so far, mostly because of the poor accessibility of the SAM. Here we report the temporal dynamics of the chromatin modifications H3K4me3 and H3K27me3 and their correlation with transcriptional changes at the SAM in response to photoperiod-induced flowering. Emphasizing the importance of tissue-specific epigenomic analyses we detect enrichments of chromatin states in the SAM that were not apparent in whole seedlings. Furthermore, our results suggest that regulation of translation might be involved in adjusting meristem function during the induction of flowering.

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