Work in our laboratories is supported by German Research Foundation (DFG) Grants WO 1660/6-1 (to S.W.) and GR 2104/4-1 (to T.G.) and SFB1101 (to T.G. and J.U.L) and by a European Research Council consolidator grant (PLANTSTEMS 647148) to T.G.&#160; S.W. is supported through the Emmy Noether Fellowship of the DFG through Grant WO 1660/2.

<ol>
	<li>Moore, I., Samalova, M., Kurup, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transactivated+and+chemically+inducible+gene+expression+in+plants.">Transactivated and chemically inducible gene expression in plants.</a> The Plant Journal. 45 (4), 651-683 (2006).</li><li>Lampropoulos, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GreenGate---a+novel,+versatile,+and+efficient+cloning+system+for+plant+transgenesis.">GreenGate---a novel, versatile, and efficient cloning system for plant transgenesis.</a> PLoS One. 8 (12), e83043 (2013).</li><li>Baroux, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Predictable+activation+of+tissue-specific+expression+from+a+single+gene+locus+using+the+pOp/LhG4+transactivation+system+in+Arabidopsis.">Predictable activation of tissue-specific expression from a single gene locus using the pOp/LhG4 transactivation system in Arabidopsis.</a> Plant Biotechnology Journal. 3 (1), 91-101 (2005).</li><li>Craft, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+pOp/LhG4+vectors+for+stringent+glucocorticoid-dependent+transgene+expression+in+Arabidopsis.">New pOp/LhG4 vectors for stringent glucocorticoid-dependent transgene expression in Arabidopsis.</a> The Plant Journal. 41 (6), 899-918 (2005).</li><li>Moore, I., Galweiler, L., Grosskopf, D., Schell, J., Palme, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+transcription+activation+system+for+regulated+gene+expression+in+transgenic+plants.">A transcription activation system for regulated gene expression in transgenic plants.</a> Proceedings of the National Academy of Sciences of the United States of America. 95 (1), 376-381 (1998).</li><li>Samalova, M., Brzobohaty, B., Moore, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=pOp6/LhGR:+a+stringently+regulated+and+highly+responsive+dexamethasone-inducible+gene+expression+system+for+tobacco.">pOp6/LhGR: a stringently regulated and highly responsive dexamethasone-inducible gene expression system for tobacco.</a> The Plant Journal. 41 (6), 919-935 (2005).</li><li>Picard, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Steroid-binding+domains+for+regulating+the+functions+of+heterologous+proteins+in+cis.">Steroid-binding domains for regulating the functions of heterologous proteins in cis.</a> Trends in Cell Biology. 3 (8), 278-280 (1993).</li><li>Schurholz, A. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Comprehensive+Toolkit+for+Inducible,+Cell+Type-Specific+Gene+Expression+in+Arabidopsis.">A Comprehensive Toolkit for Inducible, Cell Type-Specific Gene Expression in Arabidopsis.</a> Plant Physiology. 178 (1), 40-53 (2018).</li><li>Kubo, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcription+switches+for+protoxylem+and+metaxylem+vessel+formation.">Transcription switches for protoxylem and metaxylem vessel formation.</a> Genes and Development. 19 (16), 1855-1860 (2005).</li><li>Di Laurenzio, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+SCARECROW+gene+regulates+an+asymmetric+cell+division+that+is+essential+for+generating+the+radial+organization+of+the+Arabidopsis+root.">The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root.</a> Cell. 86 (3), 423-433 (1996).</li><li>Wysocka-Diller, J. W., Helariutta, Y., Fukaki, H., Malamy, J. E., Benfey, P. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+analysis+of+SCARECROW+function+reveals+a+radial+patterning+mechanism+common+to+root+and+shoot.">Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot.</a> Development. 127 (3), 595-603 (2000).</li><li>Hellens, R. P., Edwards, E. A., Leyland, N. R., Bean, S., Mullineaux, P. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=pGreen:+a+versatile+and+flexible+binary+Ti+vector+for+Agrobacterium-mediated+plant+transformation.">pGreen: a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation.</a> Plant Molecular Biology. 42 (6), 819-832 (2000).</li><li>Zhang, X., Henriques, R., Lin, S. S., Niu, Q. W., Chua, N. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Agrobacterium-mediated+transformation+of+Arabidopsis+thaliana+using+the+floral+dip+method.">Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method.</a> Nature Protocols. 1 (2), 641-646 (2006).</li><li>Kleinboelting, N., Huep, G., Kloetgen, A., Viehoever, P., Weisshaar, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GABI-Kat+SimpleSearch:+new+features+of+the+Arabidopsis+thaliana+T-DNA+mutant+database.">GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database.</a> Nucleic Acids Research. 40 (Database issue), D1211-D1215 (2012).</li><li>. Selection scheme used at GABI-Kat for resistance to sulfadiazine Available from: <a target="_blank" href="https://www.gabi-kat.de/methods/sul-selection-scheme.html">https://www.gabi-kat.de/methods/sul-selection-scheme.html</a> (2018)</li><li>Huang, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Standard+addition+quantitative+real-time+PCR+(SAQPCR):+a+novel+approach+for+determination+of+transgene+copy+number+avoiding+PCR+efficiency+estimation.">Standard addition quantitative real-time PCR (SAQPCR): a novel approach for determination of transgene copy number avoiding PCR efficiency estimation.</a> PLoS One. 8 (1), e53489 (2013).</li><li>Wallner, E. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Strigolactone-+and+Karrikin-Independent+SMXL+Proteins+Are+Central+Regulators+of+Phloem+Formation.">Strigolactone- and Karrikin-Independent SMXL Proteins Are Central Regulators of Phloem Formation.</a> Current Biology. 27 (8), 1241-1247 (2017).</li><li>Fletcher, J. C., Brand, U., Running, M. P., Simon, R., Meyerowitz, E. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Signaling+of+cell+fate+decisions+by+CLAVATA3+in+Arabidopsis+shoot+meristems.">Signaling of cell fate decisions by CLAVATA3 in Arabidopsis shoot meristems.</a> Science. 283 (5409), 1911-1914 (1999).</li><li>Watanabe, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visualization+of+cellulose+synthases+in+Arabidopsis+secondary+cell+walls.">Visualization of cellulose synthases in Arabidopsis secondary cell walls.</a> Science. 350 (6257), 198-203 (2015).</li><li>Yamaguchi, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=VASCULAR-RELATED+NAC-DOMAIN6+and+VASCULAR-RELATED+NAC-DOMAIN7+effectively+induce+transdifferentiation+into+xylem+vessel+elements+under+control+of+an+induction+system.">VASCULAR-RELATED NAC-DOMAIN6 and VASCULAR-RELATED NAC-DOMAIN7 effectively induce transdifferentiation into xylem vessel elements under control of an induction system.</a> Plant Physiology. 153 (3), 906-914 (2010).</li><li>Engineer, C. B., Fitzsimmons, K. C., Schmuke, J. J., Dotson, S. B., Kranz, R. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+and+evaluation+of+a+Gal4-mediated+LUC/GFP/GUS+enhancer+trap+system+in+Arabidopsis.">Development and evaluation of a Gal4-mediated LUC/GFP/GUS enhancer trap system in Arabidopsis.</a> BMC Plant Biology. 5, 9 (2005).</li><li>Aoyama, T., Chua, N. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+glucocorticoid-mediated+transcriptional+induction+system+in+transgenic+plants.">A glucocorticoid-mediated transcriptional induction system in transgenic plants.</a> The Plant Journal. 11 (3), 605-612 (1997).</li><li>Decaestecker, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CRISPR-TSKO+facilitates+efficient+cell+type-,+tissue-,+or+organ-specific+mutagenesis+in+Arabidopsis.">CRISPR-TSKO facilitates efficient cell type-, tissue-, or organ-specific mutagenesis in Arabidopsis.</a> bioRxiv. , (2018).</li></ol>

The authors have nothing to disclose.

Here, we describe the steps necessary to generate and apply a versatile and comprehensive toolkit for inducible, cell type specific trans-activation. Crossing lines carrying effector cassettes under control of the pOp promoter with driver lines allows studying the mis-expression effects in the F1 generation, enabling the rapid assessment of genetic perturbation in a wide range of cell types. Alternatively, effector constructs can be used to transform driver lines or, by adapting the cloning strategy, dr...

A major limitation in biology in the postgenomic era is to decipher the context specific role of a given factor or genetic perturbation. Constitutive genetic perturbations such as loss-of-function and gain-of-function approaches often only allow end-point analysis of life-long adaptation processes, obfuscating the distinction between primary and secondary effects. In addition, context specific functions can be masked or diluted by large scale effects in distant tissues or during other phases of development. Moreover, in extreme cases, lethality can preclude any mechanistic insight. Ideally, to circumvent these issues, one could analyze the effect of acute genetic perturbation within a specific context such as a specific cell type in a time-resolved manner. To achieve this, genetic tools for inducible, cell type-specific expression are required1. To provide a resource for the rapid assessment of the spatiotemporal dynamics of a response to a given effector, we have combined the ease of cloning provided by the GreenGate system2 with the proven efficacy of the GR-LhG4 system3,4,5,6. We have generated a set of lines expressing the chimeric transcription factor LhG4 fused to the ligand binding domain of the rat corticoid receptor (GR)7 under the control of well-characterized cell type specific promoters8. In resting conditions, the transcription factor remains outside of the nucleus, as the GR domain is bound by the cytosolic HSP90. With the addition of synthetic ligand dexamethasone (Dex), nuclear translocation is induced and LhG4 will mediate transcription of expression cassettes under control of a cognate synthetic pOp-type promoter, such as an mTurquoise2 reporter included in the driver lines to visualize the expression domain after induction.&#160; Thus, the driver lines technically also contain an effector cassette. The crossing of a set of driver lines with a line carrying an effector cassette with, for example, a gene of interest under control of the same pOp-type promoter thus allows the rapid assessment of the acute or long-term consequences of effector expression in a wide range of cell types.
Here, we provide a protocol describing the procedures necessary to generate the driver and effector lines and demonstrate how cell type specific expression can be induced and followed in the shoot apical meristem, the root apical meristem and the cambium of Arabidopsis. To illustrate the prowess and specificity of this approach, we utilize the well-known transcription factor VND7 which is capable of driving xylem-like secondary cell wall thickenings ectopically9. Treating F1 from a cross between the pSCR10,11 driver line and the pOp6:VND7 effector line leads to the formation of ectopic xylem-like cells in the starch sheath cells of the Arabidopsis stem.
To facilitate the generation of large DNA assemblies required for constructing driver and effector expression plasmids, we used the fast and efficient GreenGate cloning method2. GreenGate cloning is based on type II S restriction enzymes such as Eco31I or its isoschizomer BsaI2. These enzymes cut downstream of their asymmetric recognition sites producing overhangs with varying base composition. By incorporating Eco31I/BsaI restriction sites in oligonucleotides and allocating specific overhang sequences to DNA elements, modular cloning is achieved, facilitating the generation of large assemblies. In the GreenGate framework, DNA modules fall into categories A-F based on overhang sequence that serve as adapters and are assembled in that order. Therefore, the primers designed to amplify your desired product should be in accordance with the selected module2 (Figure 1A). If there is an internal Eco31I/BsaI site and the sequence is not compatible with the GreenGate entry and destination modules, you can proceed without mutagenizing, but with lower efficiency. Alternatively, use site-directed mutagenesis to remove Eco31I/BsaI restriction sites taking care not to change amino acids in gene products.

<table>
	<tbody>
		<tr>
			<td>Ampicillin</td>
			<td>Carl Roth GmbH + Co. KG</td>
			<td>K029.1</td>
			<td></td>
		</tr>
		<tr>
			<td>ATP</td>
			<td>Sigma-Aldrich</td>
			<td>A9187</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloramphenicol</td>
			<td>Sigma-Aldrich</td>
			<td>C1919</td>
			<td></td>
		</tr>
		<tr>
			<td>Column purification</td>
			<td>Qiagen</td>
			<td>QIAquick PCR Purification Kit (250)</td>
			<td></td>
		</tr>
		<tr>
			<td>Culture chamber for imaging</td>
			<td>Sarstedt AG &#38; Co. KG</td>
			<td>1-well tissue culture chamber, on cover glass II</td>
			<td></td>
		</tr>
		<tr>
			<td>Dexamethasone</td>
			<td>Sigma-Aldrich</td>
			<td>D4903</td>
			<td></td>
		</tr>
		<tr>
			<td>DMSO</td>
			<td>Fisher Scientific, UK</td>
			<td>D139-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Eco31I</td>
			<td>Thermo Fisher Scientific</td>
			<td>FD0294</td>
			<td></td>
		</tr>
		<tr>
			<td>injection cannula (0.30 x 12 mm, 30 G x 1/2)</td>
			<td>Sterican, Braun</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Kanamycin</td>
			<td>Carl Roth GmbH + Co. KG</td>
			<td>T832.2</td>
			<td></td>
		</tr>
		<tr>
			<td>Leica TCS SP5 CLSM, HCX PL APO lambda blue 63x water immersion objectiv</td>
			<td>Leica, Wetzlar, Germany</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>MS medium</td>
			<td>Duchefa, Haarlem, Netherlands</td>
			<td>M0221.0050</td>
			<td></td>
		</tr>
		<tr>
			<td>Nikon A1 CLSM, Apo LWD 25x&#160; 1.1 NA water immersion objective</td>
			<td>Nikon, Minato, Tokyo, Japan</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Petri dish 35/10 mm</td>
			<td>Greiner Bio-One GmbH, Germany</td>
			<td>627102</td>
			<td></td>
		</tr>
		<tr>
			<td>Petri dish 60/150 mm</td>
			<td>Greiner Bio-One GmbH, Germany</td>
			<td>628102</td>
			<td></td>
		</tr>
		<tr>
			<td>Petri dish 120/120/17</td>
			<td>Greiner Bio-One GmbH, Germany</td>
			<td>688102</td>
			<td></td>
		</tr>
		<tr>
			<td>Plant agar</td>
			<td>Duchefa, Haarlem, Netherlands</td>
			<td>P1001</td>
			<td></td>
		</tr>
		<tr>
			<td>Plasmid extraction</td>
			<td>Qiagen</td>
			<td>QIAprep Spin Miniprep Kit</td>
			<td></td>
		</tr>
		<tr>
			<td>Propidium iodide (PI)</td>
			<td>Sigma-Aldrich</td>
			<td>P4170</td>
			<td></td>
		</tr>
		<tr>
			<td>Razorblade</td>
			<td>Classic, Wilkinson Sword GmbH</td>
			<td>7005115E</td>
			<td></td>
		</tr>
		<tr>
			<td>Reaction tubes</td>
			<td>Sarstedt AG &#38; Co. KG</td>
			<td>72.690.001</td>
			<td></td>
		</tr>
		<tr>
			<td>Silwet L-77</td>
			<td>Kurt Obermeier GmbH &#38; Co. KG, Bad Berleburg, Germany</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Spectinomycin</td>
			<td>AppliChem GmbH</td>
			<td>3834.001</td>
			<td></td>
		</tr>
		<tr>
			<td>Spectrophotometer</td>
			<td>Thermo Fisher Scientific</td>
			<td>NanoDrop 2000c</td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Carl Roth GmbH + Co. KG</td>
			<td>4621.1</td>
			<td></td>
		</tr>
		<tr>
			<td>Sulfadiazine</td>
			<td>Sigma-Aldrich</td>
			<td>S6387</td>
			<td></td>
		</tr>
		<tr>
			<td>Tetracycline</td>
			<td>AppliChem GmbH</td>
			<td>2228.0025</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 Ligase 5 U/&#181;l</td>
			<td>Thermo Fisher Scientific</td>
			<td>EL0011</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 Ligase 30 U/&#181;l</td>
			<td>Thermo Fisher Scientific</td>
			<td>EL0013</td>
			<td></td>
		</tr>
	</tbody>
</table>

inducible, cell type-specific expression in arabidopsis thaliana through lhgr-mediated trans-activation

Inducible, tissue-specific expression is an important and powerful tool to study the spatio-temporal dynamics of genetic perturbation. Combining the flexible and efficient GreenGate cloning system with the proven and benchmarked LhGR system (here termed GR-LhG4) for the inducible expression, we have generated a set of transgenic Arabidopsis lines that can drive the expression of an effector cassette in a range of specific cell types in the three main plant meristems. To this end, we chose the previously developed GR-LhG4 system based on a chimeric transcription factor and a cognate pOp-type promoter ensuring tight control over a wide range of expression levels. In addition, to visualize the expression domain where the synthetic transcription factor is active, an ER-localized mTurquoise2 fluorescent reporter under control of the pOp4 or pOp6 promoter is encoded in driver lines. Here, we describe the steps necessary to generate a driver or effector line and demonstrate how cell type specific expression can be induced and followed in the shoot apical meristem, the root apical meristem and the cambium of Arabidopsis. By using several or all driver lines, the context specific effect of expressing one or multiple factors (effectors) under control of the synthetic pOp promoter can be assessed rapidly, for example in F1 plants of a cross between one effector and multiple driver lines. This approach is exemplified by the ectopic expression of VND7, a NAC transcription factor capable of inducing ectopic secondary cell wall deposition in a cell autonomous manner.

Generation of driver and effector lines through GreenGate cloning
The GreenGate cloning system is based on GoldenGate cloning and use the type IIS restriction endonuclease BsaI or its isoschizomer Eco31I. As the enzyme produces overhangs distant from its asymmetric recognition site, the base composition of the overhangs can be freely chosen, which is the basis form the modularity of the system. Each PCR-generated element, for example, a promoter sequence, CDS...

Watch this Scientific Journal Video about Inducible, Cell Type-Specific Expression in Arabidopsis thaliana Through LhGR-Mediated Trans-Activation at JoVE.com

Inducible, Cell Type-Specific Expression in Arabidopsis thaliana Through LhGR-Mediated Trans-Activation

Here, we describe the generation and application of a set of transgenic Arabidopsis thaliana lines enabling inducible, tissue-specific expression in the three main meristems, the shoot apical meristem, the root apical meristem, and the cambium.

Inducible, Cell Type-Specific Expression in Arabidopsis thaliana Through LhGR-Mediated Trans-Activation

Inducible, tissue-specific expression is an important and powerful tool to study the spatio-temporal dynamics of genetic perturbation. Combining the ...

inducible-cell-type-specific-expression-arabidopsis-thaliana-through

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Genetics

9.4K Views.  Centre for Organismal Studies (COS) Heidelberg. Here, we describe the generation and application of a set of transgenic Arabidopsis thaliana lines enabling inducible, tissue-specific expression in the three main meristems, the shoot apical meristem, the root apical meristem, and the cambium.

Video: Inducible, Cell Type-Specific Expression in Arabidopsis thaliana Through LhGR-Mediated Trans-Activation

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

Terroir refers to the combination of environmental factors that affect the characteristics of crops such as grapevine (Vitis vinifera) according to particular habitats and management practices. This article shows how certain terroir signatures can be detected in the berry metabolome and transcriptome of the grapevine cultivar Corvina using multivariate statistical analysis. The method first requires an appropriate sampling plan. In this case study, a specific clone of the Corvina cultivar was selected to minimize genetic differences, and samples were collected from seven vineyards representing three different macro-zones during three different growing seasons. An untargeted LC-MS metabolomics approach is recommended due to its high sensitivity, accompanied by efficient data processing using MZmine software and a metabolite identification strategy based on fragmentation tree analysis. Comprehensive transcriptome analysis can be achieved using microarrays containing probes covering ~99% of all predicted grapevine genes, allowing the simultaneous analysis of all differentially expressed genes in the context of different terroirs. Finally, multivariate data analysis based on projection methods can be used to overcome the strong vintage-specific effect, allowing the metabolomics and transcriptomics data to be integrated and analyzed in detail to identify informative correlations.

This article describes the application of untargeted metabolomics, transcriptomics and multivariate statistical analysis to grape berry transcripts and metabolites in order to gain insight into the terroir concept, i.e., the impact of the environment on berry quality traits.

Terroir refers to the combination of environmental factors that affect the characteristics of crops such as grapevine (Vitis vinifera) according to ...

Parallel Measurement of Circadian Clock Gene Expression and Hormone Secretion in Human Primary Cell Cultures

Circadian clocks are functional in all light-sensitive organisms, allowing for an adaptation to the external world by anticipating daily environmental changes. Considerable progress in our understanding of the tight connection between the circadian clock and most aspects of physiology has been made in the field over the last decade. However, unraveling the molecular basis that underlies the function of the circadian oscillator in humans stays of highest technical challenge. Here, we provide a detailed description of an experimental approach for long-term (2-5 days) bioluminescence recording and outflow medium collection in cultured human primary cells. For this purpose, we have transduced primary cells with a lentiviral luciferase reporter that is under control of a core clock gene promoter, which allows for the parallel assessment of hormone secretion and circadian bioluminescence. Furthermore, we describe the conditions for disrupting the circadian clock in primary human cells by transfecting siRNA targeting CLOCK. Our results on the circadian regulation of insulin secretion by human pancreatic islets, and myokine secretion by human skeletal muscle cells, are presented here to illustrate the application of this methodology. These settings can be used to study the molecular makeup of human peripheral clocks and to analyze their functional impact on primary cells under physiological or pathophysiological conditions.

Here, we describe settings to monitor in parallel circadian bioluminescence and the secretory activity of human islet cells and primary myotubes. For this, we employed lentiviral gene delivery of a luciferase core clock reporter, followed by in vitro synchronization and collection of outflow medium by continuous cell perifusion.

Circadian clocks are functional in all light-sensitive organisms, allowing for an adaptation to the external world by anticipating daily environmental ...

Single-cell Gene Expression Using Multiplex RT-qPCR to Characterize Heterogeneity of Rare Lymphoid Populations

Gene expression heterogeneity is an interesting feature to investigate in lymphoid populations. Gene expression in these cells varies during cell activation, stress, or stimulation. Single-cell multiplex gene expression enables the simultaneous assessment of tens of genes1,2,3. At the single-cell level, multiplex gene expression determines population heterogeneity4,5. It allows for the distinction of population heterogeneity by determining both the probable mix of diverse precursor stages among mature cells and also the diversity of cell responses to stimuli.
Innate lymphoid cells (ILC) have been recently described as a population of innate effectors of the immune response6,7. In this protocol, cell heterogeneity of the ILC hepatic compartment is investigated during homeostasis.
Currently, the most widely used technique to assess gene expression is RT-qPCR. This method measures gene expression only one gene at a time. Additionally, this method cannot estimate heterogeneity of gene expression, since multiple cells are needed for one test. This leads to the measurement of the average gene expression of the population. When assessing large numbers of genes, RT-qPCR becomes a time-, reagent-, and sample-consuming method. Hence, the trade-offs limit the number of genes or cell populations that can be evaluated, increasing the risk of missing the global picture.
This manuscript describes how single-cell multiplex RT-qPCR can be used to overcome these limitations. This technique has benefited from recent microfluidics technological advances1,2. Reactions occurring in multiplex RT-qPCR chips do not exceed the nanoliter-level. Hence, single-cell gene expression, as well as simultaneous multiple gene expression, can be performed in a reagent-, sample-, and cost-effective manner. It is possible to test cell gene signature heterogeneity at the clonal level between cell subsets within a population at different developmental stages or under different conditions4,5. Working on rare populations with large numbers of conditions at the single-cell level is no longer a restriction.

This protocol describes how to assess the expression of a large array of genes at the clonal level. Single-cell RT-qPCR produces highly reliable results with a strong sensitivity for hundreds of samples and genes.

Gene expression heterogeneity is an interesting feature to investigate in lymphoid populations. Gene expression in these cells varies during cell ...

Rearing and Double-stranded RNA-mediated Gene Knockdown in the Hide Beetle, Dermestes maculatus

Advances in genomics have raised the possibility of probing biodiversity at an unprecedented scale. However, sequence alone will not be informative without tools to study gene function. The development and sharing of detailed protocols for the establishment of new model systems in laboratories, and for tools to carry out functional studies, is thus crucial for leveraging the power of genomics. Coleoptera (beetles) are the largest clade of insects and occupy virtually all types of habitats on the planet. In addition to providing ideal models for fundamental research, studies of beetles can have impacts on pest control as they are often pests of households, agriculture, and food industries. Detailed protocols for rearing and maintenance of D. maculatus laboratory colonies and for carrying out dsRNA-mediated interference in D. maculatus are presented. Both embryonic and parental RNAi procedures-including apparatus set up, preparation, injection, and post-injection recovery-are described. Methods are also presented for analyzing embryonic phenotypes, including viability, patterning defects in hatched larvae, and cuticle preparations for unhatched larvae. These assays, together with in situ hybridization and immunostaining for molecular markers, make D. maculatus an accessible model system for basic and applied research. They further provide useful information for establishing procedures in other emerging insect model systems.

Rearing and Double-stranded RNA-mediated Gene Knockdown in the Hide Beetle, Dermestes maculatus

Here, we present protocols for rearing an intermediate-germ beetle, Dermestes maculatus (D. maculatus) in the lab. We also share protocols for embryonic and parental RNAi and methods for analyzing embryonic phenotypes to study gene function in this species.

Advances in genomics have raised the possibility of probing biodiversity at an unprecedented scale. However, sequence alone will not be informative ...

Inducible T7 RNA Polymerase-mediated Multigene Expression System, pMGX

Co-expression of multiple proteins is increasingly essential for synthetic biology, studying protein-protein complexes, and characterizing and harnessing biosynthetic pathways. In this manuscript, the use of a highly effective system for the construction of multigene synthetic operons under the control of an inducible T7 RNA polymerase is described. This system allows many genes to be expressed simultaneously from one plasmid. Here, a set of four related vectors, pMGX-A, pMGX-hisA, pMGX-K, and pMGX-hisK, with either the ampicillin or kanamycin resistance selectable marker (A and K) and either possessing or lacking an N-terminal hexahistidine tag (his) are disclosed. Detailed protocols for the construction of synthetic operons using this vector system are provided along with the corresponding data, showing that a pMGX-based system containing five genes can be readily constructed and used to produce all five encoded proteins in Escherichia coli. This system and protocol enables researchers to routinely express complex multi-component modules and pathways in E. coli.

This study describes methods for the T7-mediated co-expression of multiple genes from a single plasmid in Escherichia coli using the pMGX plasmid system.

Co-expression of multiple proteins is increasingly essential for synthetic biology, studying protein-protein complexes, and characterizing and harnessing ...

Single-cell Gene Expression Profiling Using FACS and qPCR with Internal Standards

Gene expression measurements from bulk populations of cells can obscure the considerable transcriptomic variation of individual cells within those populations. Single-cell gene expression measurements can help assess the role of noise in gene expression, identify correlations in the expression of pairs of genes, and reveal subpopulations of cells that respond differently to a stimulus. Here, we describe a procedure to measure the expression of up to 96 genes in single mammalian cells isolated from a population growing in tissue culture. Cells are sorted into lysis buffer by fluorescence-activated cell sorting (FACS), and the mRNA species of interest are reverse-transcribed and amplified. Gene expression is then measured using a microfluidic real-time PCR machine, which performs up to 96 qPCR assays on up to 96 samples at a time. We also describe the generation and use of PCR amplicon standards to enable the estimation of the absolute number of each transcript. Compared with other methods of measuring gene expression in single cells, this approach allows for the quantification of more distinct transcripts than RNA FISH at a lower cost than RNA-Seq.

We describe a method to sort single mammalian cells and to quantify the expression of up to 96 target genes of interest in each cell. This method includes the use of internal qPCR standards to enable the estimation of absolute transcript counts.

Gene expression measurements from bulk populations of cells can obscure the considerable transcriptomic variation of individual cells within those ...

Controllable Ion Channel Expression through Inducible Transient Transfection

Transfection, the delivery of foreign nucleic acids into a cell, is a powerful tool in protein research. Through this method, ion channels can be investigated through electrophysiological analysis, biochemical characterization, mutational studies, and their effects on cellular processes. Transient transfections offer a simple protocol in which the protein becomes available for analysis within a few hours to days. Although this method presents a relatively straightforward and time efficient protocol, one of the critical components is calibrating the expression of the gene of interest to physiological relevant levels or levels that are suitable for analysis. To this end, many different approaches that offer the ability to control the expression of the gene of interest have emerged. Several stable cell transfection protocols provide a way to permanently introduce a gene of interest into the cellular genome under the regulation of a tetracycline-controlled transcriptional activation. While this technique produces reliable expression levels, each gene of interest requires a few weeks of skilled work including calibration of a killing curve, selection of cell colonies, and overall more resources. Here we present a protocol that uses transient transfection of the Transient Receptor Potential cation channel subfamily V member 1 (TRPV1) gene in an inducible system as an efficient way to express a protein in a controlled manner which is essential in ion channel analysis. We demonstrate that using this technique, we are able to perform calcium imaging, whole cell, and single channel analysis with controlled channel levels required for each type of data collection with a single transfection. Overall, this provides a replicable technique that can be used to study ion channels structure and function.

Studying ion channels through a heterologously expressing system has become a core technique in biomedical research. In this manuscript, we present a time efficient method to achieve tightly controlled ion channel expression by performing transient transfection under the control of an inducible promoter.

Transfection, the delivery of foreign nucleic acids into a cell, is a powerful tool in protein research. Through this method, ion channels can be ...

Studying Cell Cycle-regulated Gene Expression by Two Complementary Cell Synchronization Protocols

The gene expression program of the cell cycle represents a critical step for understanding cell cycle-dependent processes and their role in diseases such as cancer. Cell cycle-regulated gene expression analysis depends on cell synchronization into specific phases. Here we describe a method utilizing two complementary synchronization protocols that is commonly used for studying periodic variation of gene expression during the cell cycle. Both procedures are based on transiently blocking the cell cycle in one defined point. The synchronization protocol by hydroxyurea (HU) treatment leads to cellular arrest in late G1/early S phase, and release from HU-mediated arrest provides a cellular population uniformly progressing through S and G2/M. The synchronization protocol by thymidine and nocodazole (Thy-Noc) treatment blocks cells in early mitosis, and release from Thy-Noc mediated arrest provides a synchronized cellular population suitable for G1 phase and S phase-entry studies. Application of both procedures requires monitoring of the cell cycle distribution profiles, which is typically performed after propidium iodide (PI) staining of the cells and flow cytometry-mediated analysis of DNA content. We show that the combined use of two synchronization protocols is a robust approach to clearly determine the transcriptional profiles of genes that are differentially regulated in the cell cycle (i.e. E2F1 and E2F7), and consequently to have a better understanding of their role in cell cycle processes. Furthermore, we show that this approach is useful for the study of mechanisms underlying drug-based therapies (i.e. mitomycin C, an anticancer agent), because it allows to discriminate genes that are responsive to the genotoxic agent from those solely affected by cell cycle perturbations imposed by the agent.

We report two cell synchronization protocols that provide a context for studying events related to specific phases of the cell cycle. We show that this approach is useful for analyzing the regulation of specific genes in an unperturbed cell cycle or upon exposure to agents affecting the cell cycle.

The gene expression program of the cell cycle represents a critical step for understanding cell cycle-dependent processes and their role in diseases such ...

Constitutive and Inducible Systems for Genetic In Vivo Modification of Mouse Hepatocytes Using Hydrodynamic Tail Vein Injection

In research models of liver cancer, regeneration, inflammation, and fibrosis, flexible systems for in vivo gene expression and silencing are highly useful. Hydrodynamic tail vein injection of transposon-based constructs is an efficient method for genetic manipulation of hepatocytes in adult mice. In addition to constitutive transgene expression, this system can be used for more advanced applications, such as shRNA-mediated gene knock-down, implication of the CRISPR/Cas9 system to induce gene mutations, or inducible systems. Here, the combination of constitutive CreER expression together with inducible expression of a transgene or miR-shRNA of choice is presented as an example of this technique. We cover the multi-step procedure starting from the preparation of sleeping beauty-transposon constructs, to the injection and treatment of mice, and the preparation of liver tissue for analysis by immunostaining. The system presented is a reliable and efficient approach to achieve complex genetic manipulations in hepatocytes. It is specifically useful in combination with Cre/loxP-based mouse strains and can be applied to a variety of models in the research of liver disease.

Constitutive and Inducible Systems for Genetic In Vivo Modification of Mouse Hepatocytes Using Hydrodynamic Tail Vein Injection

Hydrodynamic tail vein injection of transposon-based integration vectors enables stable transfection of murine hepatocytes in vivo. Here, we present a practical protocol for transfection systems that enables the long-term constitutive expression of a single transgene or combined constitutive and doxycycline-inducible expression of a transgene or miR-shRNA in the liver.

In research models of liver cancer, regeneration, inflammation, and fibrosis, flexible systems for in vivo gene expression and silencing are highly ...

An Optogenetic Method to Control and Analyze Gene Expression Patterns in Cell-to-cell Interactions

Cells should respond properly to temporally changing environments, which are influenced by various factors from surrounding cells. The Notch signaling pathway is one of such essential molecular machinery for cell-to-cell communications, which plays key roles in normal development of embryos. This pathway involves a cell-to-cell transfer of oscillatory information with ultradian rhythms, but despite the progress in molecular biology techniques, it has been challenging to elucidate the impact of multicellular interactions on oscillatory gene dynamics. Here, we present a protocol that permits optogenetic control and live monitoring of gene expression patterns in a precise temporal manner. This method successfully revealed that intracellular and intercellular periodic inputs of Notch signaling entrain intrinsic oscillations by frequency tuning and phase shifting at the single-cell resolution. This approach is applicable to the analysis of the dynamic features of various signaling pathways, providing a unique platform to test a functional significance of dynamic gene expression programs in multicellular systems.

Here, we present a protocol to analyze cell-to-cell transfer of oscillatory information by optogenetic control and live monitoring of gene expression. This approach provides a unique platform to test a functional significance of dynamic gene expression programs in multicellular systems.

Cells should respond properly to temporally changing environments, which are influenced by various factors from surrounding cells. The Notch signaling ...