A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

Gregory, Brian D.; O’Malley, Ronan; Lister, Ryan; Urich, Mark A.; Tonti-Filippini, Julian; Chen, Huaming; Millar, A. Harvey; Ecker, Joseph R.

doi:10.1016/j.devcel.2008.04.005

Cited by 376 publications

(380 citation statements)

References 52 publications

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“…Interestingly, mutations in the Arabidopsis genes that encode the two cap-binding complex (CBC) subunits-CAP-BINDING PROTEIN20 (CBP20) and ABSCISIC ACID HYPERSESITIVE1 (ABH1)/CBP80-cause a serrated leaf phenotype and mRNA splicing defects as observed in emu and se-1 mutants (Hugouvieux et al 2001;Papp et al 2004;Kuhn et al 2007;Laubinger et al 2008;Raczynska et al 2010). It is also noteworthy that the abh1-8 mutation enhanced the phyllotaxy defect of ago1-38 mutant inflorescences as seen in emu ago1-27 plants (Gregory et al 2008). Furthermore, emu was sensitive to the exogenous application of abscisic acid (Supplemental Fig.…”

Section: Discussionmentioning

confidence: 98%

“…Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.2265710. miRNA biogenesis pathways has been recently indicated in Arabidopsis, and this has been extended to RNA silencing in animals (Gregory et al 2008;Kim et al 2008;Laubinger et al 2008;Gruber et al 2009;Sabin et al 2009;Büssing et al 2010). Connecting these two processes permits more robust and accurate regulation of gene expression, and further inquiry into the crosstalk is expected to reveal additional roles.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of EMU, the Arabidopsis homolog of the yeast THO complex member HPR1

Furumizu¹,

Tsukaya²,

Komeda³

2010

RNA

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Diverse and precise control is essential for eukaryotic gene expression. This is accomplished through the recruitment of a myriad of proteins to a nascent messenger RNA (mRNA) to mediate modifications, such as capping, splicing, 39-end processing, and export. Despite being important for every cell, however, the mechanism by which the formation of diverse messenger ribonucleoprotein (mRNP) particles contributes to maintaining intricate systems in the multicellular organism remains incompletely defined. We identified and characterized a mutant gene named erecta mRNA under-expressed (emu) that leads to the defective mRNA accumulation of ERECTA, a developmental regulator in the model plant Arabidopsis thaliana. EMU encodes a protein homologous to a component of the THO complex that is required for the generation of functional mRNPs. Further analysis suggested that EMU is genetically associated with SERRATE, HYPONASTIC LEAVES1, and ARGONAUTE1, which are required for proper RNA maturation or action. Furthermore, mutations in another THO-related gene led to embryonic lethality. These findings support the presence and importance of the THO-related complex in plants as well as yeast and vertebrates.

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Section: Discussionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Characterization of EMU, the Arabidopsis homolog of the yeast THO complex member HPR1

Furumizu¹,

Tsukaya²,

Komeda³

2010

RNA

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“…More recently, the method has been extended to the genome scale to map all uncapped mRNA molecules (6)(7)(8)(9)(10). Briefly, the free 5 0 phosphate group of uncapped mRNA is used for the T4 RNA ligase-mediated ligation to an RNA adaptor, which is subsequently used for RNA purification and selective cDNA synthesis.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Profiling of Uncapped mRNA

Jiao

Riechmann

2011

Methods in Molecular Biology

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Gene transcripts are under extensive posttranscriptional regulation, including the regulation of their stability. A major route for mRNA degradation produces uncapped mRNAs, which can be generated by decapping enzymes, endonucleases, and small RNAs. Profiling uncapped mRNA molecules is important for the understanding of the transcriptome, whose composition is determined by a balance between mRNA synthesis and degradation. In this chapter, we describe a method to profile these uncapped mRNAs at the genome scale.

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“…However, smaller amounts of approximately 1 µ g might also be suffi cient. Fragment size depends on the number of sonication cycles applied [4,5] . For example, to obtain fragments of human genomic DNA with an average size of 150 bp using the bioruptor sonicator, ultrasound should be applied during three cycles of 15 min each at low power.…”

Section: Sonicationmentioning

confidence: 99%

Diagnostic applications of next generation sequencing: working towards quality standards/Diagnostische Anwendung von Next Generation Sequencing: Auf dem Weg zu Qualitätsstandards

Vogl¹,

Eck²,

Benet‐Pagès

et al. 2012

LaboratoriumsMedizin

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Over the past 6 years, next generation sequencing (NGS) has been established as a valuable high-throughput method for research in molecular genetics and has successfully been employed in the identifi cation of rare and common genetic variations. All major NGS technology companies providing commercially available instruments (Roche 454, Illumina, Life Technologies) have recently marketed bench top sequencing instruments with lower throughput and shorter run times, thereby broadening the applications of NGS and opening the technology to the potential use for clinical diagnostics. Although the high expectations regarding the discovery of new diagnostic targets and an overall reduction of cost have been achieved, technological challenges in instrument handling, robustness of the chemistry and data analysis need to be overcome. To facilitate the implementation of NGS as a routine method in molecular diagnostics, consistent quality standards need to be developed. Here the authors give an overview of the current standards in protocols and workfl ows and discuss possible approaches to defi ne quality criteria for NGS in molecular genetic diagnostics.Keywords: bioinformatics; genetic variation; Illumina; library preparation; Life Technologies; molecular genetics; molecular genetic diagnostics; next generation sequencing (NGS); rare diseases; Roche. ZusammenfassungIn den vergangenen 6 Jahren hat sich " next generation sequencing " (NGS) als wichtige Hochdurchsatz-Methode f ü r die molekulargenetische Forschung etabliert und wurde erfolgreich zur Identifi kation seltener und h ä ufi ger genetischer Varianten eingesetzt. Alle gr ö ß eren NGS-Technologieunternehmen, die bisher kommerziell erh ä ltliche Ger ä te zu Verf ü gung stellten (Roche 454, Illumina, Life Technologies), haben vor kurzem auch "benchtop " -Ger ä te mit geringerem Durchsatz und k ü rzeren Laufzeiten auf den Markt gebracht, wodurch die Anwendungsgebiete erweitert und der Technologie der m ö gliche Einsatz in der klinischen Diagnostik er ö ffnet wurde. W ä hrend die hohen Erwartungen hinsichtlich der Entdeckung neuer diagnostischer Zielstrukturen und einer Senkung der Kosten erreicht wurden, m ü ssen etliche technologische Herausforderungen hinsichtlich Bedienung der Ger ä te, Robustheit der Chemie und Handhabung der Datenanalyse noch gemeistert werden. Um die Einf ü hrung von NGS in die Routinediagnostik zu erleichtern, m ü ssen nachhaltige Qualit ä tsstandards entwickelt werden. Im Folgenden geben die Autoren einen Ü berblick ü ber die gegenw ä rtigen Standards in den Protokollen und Arbeitsabl ä ufen und diskutieren m ö gliche Ans ä tze Qualit ä tskriterien f ü r NGS in der molekulargenetischen Diagnostik zu defi nieren.

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A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

Cited by 376 publications

References 52 publications

Characterization of EMU, the Arabidopsis homolog of the yeast THO complex member HPR1

Characterization of EMU, the Arabidopsis homolog of the yeast THO complex member HPR1

Genome-Wide Profiling of Uncapped mRNA

Diagnostic applications of next generation sequencing: working towards quality standards/Diagnostische Anwendung von Next Generation Sequencing: Auf dem Weg zu Qualitätsstandards

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