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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, p. IV-VIArticle 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, p. 653-657Article 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, p. 31-42Article in journal (Refereed)
  • 4.
    Brunoni, Federica
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden; Present address: Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany, The Czech Academy of Sciences, Šlechtitelů 27, 78371 Olomouc, Czech Republic.
    Collani, Silvio
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Simura, Jan
    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.
    Bellini, Catherine
    Ljung, Karin
    A bacterial assay for rapid screening of IAA catabolic enzymes2019In: Plant Methods, ISSN 1746-4811, E-ISSN 1746-4811, Vol. 15, no 1, article id 126Article in journal (Refereed)
    Abstract [en]

    Background: Plants rely on concentration gradients of the native auxin, indole-3-acetic acid (IAA), to modulate plant growth and development. Both metabolic and transport processes participate in the dynamic regulation of IAA homeostasis. Free IAA levels can be reduced by inactivation mechanisms, such as conjugation and degradation. IAA can be conjugated via ester linkage to glucose, or via amide linkage to amino acids, and degraded via oxidation. Members of the UDP glucosyl transferase (UGT) family catalyze the conversion of IAA to indole-3-acetyl-1-glucosyl ester (IAGlc); by contrast, IAA is irreversibly converted to indole-3-acetyl-L-aspartic acid (IAAsp) and indole-3-acetyl glutamic acid (IAGlu) by Group II of the GRETCHEN HAGEN3 (GH3) family of acyl amido synthetases. Dioxygenase for auxin oxidation (DAO) irreversibly oxidizes IAA to oxindole-3-acetic acid (oxIAA) and, in turn, oxIAA can be further glucosylated to oxindole-3-acetyl-1-glucosyl ester (oxIAGlc) by UGTs. These metabolic pathways have been identified based on mutant analyses, in vitro activity measurements, and in planta feeding assays. In vitro assays for studying protein activity are based on producing Arabidopsis enzymes in a recombinant form in bacteria or yeast followed by recombinant protein purification. However, the need to extract and purify the recombinant proteins represents a major obstacle when performing in vitro assays.

    Results: In this work we report a rapid, reproducible and cheap method to screen the enzymatic activity of recombinant proteins that are known to inactivate IAA. The enzymatic reactions are carried out directly in bacteria that produce the recombinant protein. The enzymatic products can be measured by direct injection of a small supernatant fraction from the bacterial culture on ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UHPLC–ESI-MS/MS). Experimental procedures were optimized for testing the activity of different classes of IAA-modifying enzymes without the need to purify recombinant protein.

    Conclusions: This new method represents an alternative to existing in vitro assays. It can be applied to the analysis of IAA metabolites that are produced upon supplementation of substrate to engineered bacterial cultures and can be used for a rapid screening of orthologous candidate genes from non-model species.

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  • 5. Capovilla, Giovanna
    et al.
    Delhomme, Nicolas
    Collani, Silvio
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany.
    Shutava, Iryna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bezrukov, Ilja
    Symeonidi, Efthymia
    Amorim, Marcella de Francisco
    Laubinger, Sascha
    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. Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany.
    PORCUPINE regulates development in response to temperature through alternative splicing2018In: Nature plants, ISSN 2055-026X, Vol. 4, no 8, p. 534-539Article in journal (Refereed)
    Abstract [en]

    Recent findings suggest that alternative splicing has a critical role in controlling the responses of plants to temperature variations. However, alternative splicing factors in plants are largely uncharacterized. Here we establish the putative splice regulator, PORCUPINE (PCP), as temperature-specific regulator of development in Arabidopsis thaliana. Our findings point to the misregulation of WUSCHEL and CLAVATA3 as the possible cause for the meristem defects affecting the pcp-1 loss-of-function mutants at low temperatures.

  • 6. 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, p. 97-103Article, 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.

  • 7. 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, p. 59-69Article 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.

  • 8. 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, p. 5117-5127Article 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.

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  • 9.
    Collani, Silvio
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Max Planck Institute for Developmental Biology,Department of Molecular Biology, Tübingen, Germany.
    Neumann, Manuela
    Yant, Levi
    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. Max Planck Institute for Developmental Biology,Department of Molecular Biology, Tübingen, Germany; Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, People’s Republic of China.
    FT Modulates Genome-Wide DNA-Binding of the bZIP Transcription Factor FD2019In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 180, no 1, p. 367-380Article in journal (Refereed)
    Abstract [en]

    The transition to flowering is a crucial step in the plant life cycle that is controlled by multiple endogenous and environmental cues, including hormones, sugars, temperature, and photoperiod. Permissive photoperiod induces the expression of FLOWERING LOCUS T (FT) in the phloem companion cells of leaves. The FT protein then acts as a florigen that is transported to the shoot apical meristem, where it physically interacts with the Basic Leucine Zipper Domain transcription factor FD and 14-3-3 proteins. However, despite the importance of FD in promoting flowering, its direct transcriptional targets are largely unknown. Here, we combined chromatin immunoprecipitation sequencing and RNA sequencing to identify targets of FD at the genome scale and assessed the contribution of FT to DNA binding. We further investigated the ability of FD to form protein complexes with FT and TERMINAL FLOWER1 through interaction with 14-3-3 proteins. Importantly, we observed direct binding of FD to targets involved in several aspects of plant development. These target genes were previously unknown to be directly related to the regulation of flowering time. Our results confirm FD as a central regulator of floral transition at the shoot meristem and provide evidence for crosstalk between the regulation of flowering and other signaling pathways, such as pathways involved in hormone signaling.

  • 10. 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, article id 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.

  • 11. 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, p. 1978-1986Article in journal (Refereed)
  • 12. 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, p. 2013-2022Article in journal (Refereed)
  • 13. Engelhorn, Julia
    et al.
    Blanvillain, Robert
    Kroner, Christian
    Parrinello, Hugues
    Rohmer, Marine
    Pose, David
    Ott, Felix
    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, Tübingen, Germany.
    Carles, Cristel C.
    Dynamics of H3K4me3 Chromatin Marks Prevails over H3K27me3 for Gene Regulation during Flower Morphogenesis in Arabidopsis thaliana2017In: Epigenomes, ISSN 2075-4655, Vol. 1, no 2, article id 8Article in journal (Refereed)
    Abstract [en]

    Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes (trxG), respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related Histone 3 trimethylation at lysine 4 (H3K4me3). However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with expression changes, in a developmental series including Arabidopsis thaliana leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prevail over changes in H3K27me3 and quantitatively correlate with expression changes, while H3K27me3 changes occur later. Notably, we found that H3K4me3 increase during the early activation of PcG target genes while H3K27me3 level remain relatively constant at the locus. Our results reveal that H3K4me3 predicts changes in gene expression better than H3K27me3, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.

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  • 14. 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, p. 4072-4082Article in journal (Refereed)
  • 15. 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, p. 517-526Article in journal (Refereed)
  • 16. 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, p. 949-962Article 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.

  • 17. 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)
  • 18. 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, p. 49-58Article in journal (Refereed)
  • 19.
    Goretti, Daniela
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Silvestre, Marina
    Collani, Silvio
    Langenecker, Tobias
    Mendez, Carla
    Madueno, Francisco
    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. Beijing Advanced Innovation Centre for Tree Breedingby Molecular Design, Beijing Forestry University, Beijing, People’s Republic of China.
    TERMINAL FLOWER1 Functions as a Mobile Transcriptional Cofactor in the Shoot Apical Meristem2020In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 182, no 4, p. 2081-2095Article in journal (Refereed)
    Abstract [en]

    TERMINAL FLOWER1 acts in the shoot apical meristem as a mobile cell-non-autonomous transcriptional cofactor that associates with DNA to regulate meristem indeterminacy and flowering. The floral transition is a critical step in the life cycle of flowering plants, and several mechanisms control this finely orchestrated process. TERMINAL FLOWER1 (TFL1) is a floral repressor and close relative of the florigen, FLOWERING LOCUS T (FT). During the floral transition, TFL1 expression is up-regulated in the inflorescence apex to maintain the indeterminate growth of the shoot apical meristem (SAM). Both TFL1 and FT are mobile proteins, but they move in different ways. FT moves from the leaves to the SAM, while TFL1 appears to move within the SAM. The importance of TFL1 movement for its function in the regulation of flowering time and shoot indeterminacy and its molecular function are still largely unclear. Our results using Arabidopsis (Arabidopsis thaliana) indicate that TFL1 moves from its place of expression in the center of the SAM to the meristem layer L1 and that the movement in the SAM is required for the regulation of the floral transition. Chromatin immunoprecipitation sequencing and RNA sequencing demonstrated that TFL1 functions as a cotranscription factor that associates with and regulates the expression of hundreds of genes. These newly identified direct TFL1 targets provide the possibility to discover new roles for TFL1 in the regulation of floral transition and inflorescence development.

  • 20. 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, p. 1049-1062Article in journal (Refereed)
  • 21. 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, p. 1247-1255Article in journal (Refereed)
  • 22. 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, p. 4117-4129Article in journal (Refereed)
  • 23. 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, p. 433-449Article in journal (Refereed)
  • 24. 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, p. 807-816Article in journal (Refereed)
  • 25. 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, p. 628-632Article in journal (Refereed)
  • 26.
    Lee, Joanne E.
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Neumann, Manuela
    Duro, Daniel Iglesias
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    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. Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tu ¨bingen, Germany; Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, People's Republic of China.
    CRISPR-based tools for targeted transcriptional and epigenetic regulation in plants2019In: PLoS ONE, E-ISSN 1932-6203, Vol. 14, no 9, article id e0222778Article in journal (Refereed)
    Abstract [en]

    Programmable gene regulators that can modulate the activity of selected targets in trans are a useful tool for probing and manipulating gene function. CRISPR technology provides a convenient method for gene targeting that can also be adapted for multiplexing and other modifications to enable strong regulation by a range of different effectors. We generated a vector toolbox for CRISPR/dCas9-based targeted gene regulation in plants, modified with the previously described MS2 system to amplify the strength of regulation, and using Golden Gate-based cloning to enable rapid vector assembly with a high degree of flexibility in the choice of promoters, effectors and targets. We tested the system using the floral regulator FLOWERING LOCUS T (FT) as a target and a range of different effector domains including the transcriptional activator VP64, the H3K27 acetyltransferase p300 and the H3K9 methyltransferase KRYPTONITE. When transformed into Arabidopsis thaliana, several of the constructs caused altered flowering time phenotypes that were associated with changes in FT expression and/or epigenetic status, thus demonstrating the effectiveness of the system. The MS2-CRISPR/dCas9 system can be used to modulate transcriptional activity and epigenetic status of specific target genes in plants, and provides a versatile tool that can easily be used with different targets and types of regulation for a range of applications.

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  • 27. 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, p. 109-118Article in journal (Refereed)
  • 28. 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, article id 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.

  • 29. 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, p. 1055-1060Article in journal (Refereed)
  • 30. 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)
  • 31. 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, p. 1369-1379Article in journal (Refereed)
  • 32. 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, p. 1293-1306Article in journal (Refereed)
  • 33. Pfeiffer, Anne
    et al.
    Janocha, Denis
    Dong, Yihan
    Medzihradszky, Anna
    Schöne, Stefanie
    Daum, Gabor
    Suzaki, Takuya
    Forner, Joachim
    Longenecker, Tobias
    Rempel, Eugen
    Schmid, Markus
    Department 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, article id 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.

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  • 34. 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)
  • 35. 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, p. 414-+Article in journal (Refereed)
  • 36. 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, p. 45-50Article in journal (Refereed)
  • 37. Prát, Tomáš
    et al.
    Hajný, Jakub
    Grunewald, Wim
    Vasileva, Mina
    Molnár, Gergely
    Tejos, Ricardo
    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).
    Sauer, Michael
    Friml, Jiří
    WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity2018In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 14, no 1, article id e1007177Article in journal (Refereed)
    Abstract [en]

    Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17-and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain-and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development.

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  • 38. 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, article id 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.

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  • 39. 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, p. 913-U128Article in journal (Refereed)
  • 40.
    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, p. 501-506Article in journal (Refereed)
  • 41.
    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, p. 14159-14164Article in journal (Refereed)
  • 42.
    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, p. 5353-5358Article in journal (Refereed)
  • 43.
    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, p. 466-475Article in journal (Refereed)
  • 44.
    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, p. 6001-6012Article in journal (Refereed)
  • 45. 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, p. 9626-9631Article in journal (Refereed)
  • 46. 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, p. 517-527Article in journal (Refereed)
  • 47. Shanks, Carly M.
    et al.
    Hecker, Andreas
    Cheng, Chia-Yi
    Brand, Luise
    Collani, Silvio
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
    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.
    Schaller, G. Eric
    Wanke, Dierk
    Harter, Klaus
    Kieber, Joseph J.
    Role of BASIC PENTACYSTEINE transcription factors in a subset of cytokinin signaling responses2018In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 95, no 3, p. 458-473Article in journal (Refereed)
    Abstract [en]

    Cytokinin plays diverse roles in plant growth and development, generally acting by modulating gene transcription in target tissues. The type-B Arabidopsis response regulators (ARR) transcription factors have emerged as primary targets of cytokinin signaling and are required for essentially all cytokinin-mediated changes in gene expression. The diversity of cytokinin function is likely imparted by the activity of various transcription factors working with the type-B ARRs to alter specific sets of target genes. One potential set of co-regulators modulating the cytokinin response are the BARLEY B-RECOMBINANT/BASIC PENTACYSTEINE (BBR/BPC) family of plant-specific transcription factors. Here, we show that disruption of multiple BPCs results in reduced sensitivity to cytokinin. Further, the BPCs are necessary for the induction of a subset of genes in response to cytokinin. We identified direct invivo targets of BPC6 using ChIP-Seq and found an enrichment of promoters of genes differentially expressed in response to cytokinin. Further, a significant number of BPC6 regulated genes are also direct targets of the type-B ARRs. Potential cis-binding elements for a number of other transcription factors linked to cytokinin action are enriched in the BPC binding fragments, including those for the cytokinin response factors (CRFs). In addition, several BPCs interact with a subset of type-A ARRs. Consistent with these results, a significant number of genes whose expression is altered in bpc mutant roots are also mis-expressed in crf1,3,5,6 and type-A arr3,4,5,6,7,8,9,15 mutant roots. These results suggest that the BPCs are part of a complex network of transcription factors that are involved in the response to cytokinin.

  • 48. 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, p. 4831-4840Article in journal (Refereed)
  • 49. 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, p. 96-98Article 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.

  • 50. Speth, Corinna
    et al.
    Szabo, Emese Xochitl
    Martinho, Claudia
    Collani, Silvio
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    zur Oven-Krockhaus, Sven
    Richter, Sandra
    Droste-Borel, Irina
    Macek, Boris
    Stierhof, York-Dieter
    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.
    Liu, Chang
    Laubinger, Sascha
    Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes2018In: eLIFE, E-ISSN 2050-084X, Vol. 7, article id e37078Article in journal (Refereed)
    Abstract [en]

    Intron splicing increases proteome complexity, promotes RNA stability, and enhances transcription. However, introns and the concomitant need for splicing extend the time required for gene expression and can cause an undesirable delay in the activation of genes. Here, we show that the plant microRNA processing factor SERRATE (SE) plays an unexpected and pivotal role in the regulation of intronless genes. Arabidopsis SE associated with more than 1000, mainly intronless, genes in a transcription-dependent manner. Chromatin-bound SE liaised with paused and elongating polymerase II complexes and promoted their association with intronless target genes. Our results indicate that stress-responsive genes contain no or few introns, which negatively affects their expression strength, but that some genes circumvent this limitation via a novel SE-dependent transcriptional activation mechanism. Transcriptome analysis of a Drosophila mutant defective in ARS2, the metazoan homologue of SE, suggests that SE/ARS2 function in regulating intronless genes might be conserved across kingdoms.

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