Versatile Gene-Specific Sequence Tags for<i>Arabidopsis</i>Functional Genomics: Transcript Profiling and Reverse Genetics Applications

Hilson, Pierre; Allemeersch, Joke; Altmann, Thomas; Aubourg, Santiago P.; Avon, Alexandra; Beynon, Jim; Bhalerao, Rishikesh P.; Bitton, Frédérique; Caboche, Michel; Cannoot, Bernard; Chardakov, Vasil; Cognet-Holliger, Cecile; Colot, Vincent; Crowe, Mark L.; Darimont, Caroline; Durinck, Steffen; Eickhoff, Holger; Longevialle, Andéol Falcon de; Farmer, Edward E.; Grant, Murray; Kuiper, Martin; Lehrach, Hans; Léon, Céline; Leyva, Antonio; Lundeberg, Joakim; Lurin, Claire; Moreau, Yves; Nietfeld, Wilfried; Paz‐Ares, Javier; Reymond, Philippe; Rouzé, Pierre; Sandberg, Göran; Segura, Maria Dolores; Serizet, Carine; Tabrett, Alexandra; Taconnat, Ludivine; Thareau, Vincent; Hummelen, Paul Van; Vercruysse, Steven; Vuylsteke, Marnik; Weingartner, Magdalena; Weisbeek, Peter; Wirta, Valtteri; Wittink, Floyd R.A.; Zabeau, Marc; Small, Ian

doi:10.1101/gr.2544504

Cited by 288 publications

(318 citation statements)

References 81 publications

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“…However, despite all these observations, the activation of AtNUC-L2 is nonnatural in Atnuc-L1 plants and raises the major question about the biological role of this second nucleolin-like gene in A. thaliana. Transcriptome analysis revealed that 333 genes (of ϳ25,000 gst; http:// www.catma.org/) are deregulated in the Atnuc-L1 plants, i.e., their expression is enhanced or repressed by more than 1.66 times (Hilson et al, 2004). The AtNUC-L2 gene is ranked 124th among 148 up-regulated genes.…”

Section: Discussionmentioning

confidence: 99%

Characterization of AtNUC-L1 Reveals a Central Role of Nucleolin in Nucleolus Organization and Silencing of AtNUC-L2 Gene in Arabidopsis

Pontvianne

Matı́a

Douet

et al. 2007

MBoC

125

207

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Nucleolin is one of the most abundant protein in the nucleolus and is a multifunctional protein involved in different steps of ribosome biogenesis. In contrast to animals and yeast, the genome of the model plant Arabidopsis thaliana encodes two nucleolin-like proteins, AtNUC-L1 and AtNUC-L2. However, only the AtNUC-L1 gene is ubiquitously expressed in normal growth conditions. Disruption of this AtNUC-L1 gene leads to severe plant growth and development defects. AtNUC-L1 is localized in the nucleolus, mainly in the dense fibrillar component. Absence of this protein in Atnuc-L1 plants induces nucleolar disorganization, nucleolus organizer region decondensation, and affects the accumulation levels of pre-rRNA precursors. Remarkably, in Atnuc-L1 plants the AtNUC-L2 gene is activated, suggesting that AtNUC-L2 might rescue, at least partially, the loss of AtNUC-L1. This work is the first description of a higher eukaryotic organism with a disrupted nucleolin-like gene and defines a new role for nucleolin in nucleolus structure and rDNA chromatin organization.

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Section: Discussionmentioning

confidence: 99%

Characterization of AtNUC-L1 Reveals a Central Role of Nucleolin in Nucleolus Organization and Silencing of AtNUC-L2 Gene in Arabidopsis

Pontvianne

Matı́a

Douet

et al. 2007

MBoC

125

207

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“…The gene studied in this work (At1g74900) was first flagged as worthy of interest from a high-throughput RNA interference screen of a large number of Arabidopsis genes, including many genes encoding PPR proteins (Hilson et al, 2004). Different independent lines of knockdown expression of At1g74900 showed delayed development and delayed flowering, so three T-DNA insertion lines putatively mutated in At1g74900 were obtained and analyzed.…”

Section: Macroscopic Phenotypementioning

confidence: 99%

The Pentatricopeptide Repeat GeneOTP43Is Required fortrans-Splicing of the Mitochondrialnad1Intron 1 inArabidopsis thaliana

et al. 2007

Self Cite

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The mitochondrial NADH:ubiquinone oxidoreductase complex (Complex I) is a large protein complex formed from both nuclearly and mitochondrially encoded subunits. Subunit ND1 is encoded by a mitochondrial gene comprising five exons, and the mature transcript requires four RNA splicing events, two of which involve trans-splicing independently transcribed RNAs. We have identified a nuclear gene (OTP43) absolutely required for trans-splicing of intron 1 (and only intron 1) of Arabidopsis thaliana nad1 transcripts. This gene encodes a previously uncharacterized pentatricopeptide repeat protein.Mutant Arabidopsis plants with a disrupted OTP43 gene do not present detectable mitochondrial Complex I activity and show severe defects in seed development, germination, and to a lesser extent in plant growth. The alternative respiratory pathway involving alternative oxidase is significantly induced in the mutant.

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“…Microarray analysis was performed with CATMA version 2 arrays (complete Arabidopsis transcriptome microarray) (Allemeersch et al 2005;Hilson et al 2004). CATMA version 2 contained 24,411 gene-specific tags (GST).…”

Section: Catma Arraysmentioning

confidence: 99%

Disease-Specific Expression of Host Genes During Downy Mildew Infection of Arabidopsis

Huibers¹,

Jong²,

Dekter³

et al. 2009

MPMI

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Here, we report on the identification of Arabidopsis genes that are induced during compatible but not during incompatible interactions with the downy mildew pathogen Hyaloperonospora arabidopsidis. This set of so-called compatible specific (CS) genes contrasts with the large group of defense-associated genes that is differentially expressed during both compatible and incompatible interactions. From the 17 identified CS genes, 6 belong to the ethylene response factor (ERF) family of transcription factor genes, suggesting that these ERF have a role during compatibility. The majority of CS genes are differentially regulated in response to various forms of abiotic stress. In silico analysis of the CS genes revealed an over-representation of dehydration-responsive element/C-repeat binding factor (DREB1A/ CBF3) binding sites and EveningElement motifs in their promoter regions. The CS-ERF are closely related to the CBF transcription factors and could potentially bind the DREB1A/CBF3 promoter elements in the CS genes. Transcript levels of CS genes peak at 2 to 3 days postinoculation, when pathogen growth is highest, and decline at later stages of infection. The induction of several CS genes was found to be isolate specific. This suggests that the identified CS genes could be the direct or indirect targets of downy mildew effector proteins that promote disease susceptibility.

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Versatile Gene-Specific Sequence Tags forArabidopsisFunctional Genomics: Transcript Profiling and Reverse Genetics Applications

Cited by 288 publications

References 81 publications

Characterization of AtNUC-L1 Reveals a Central Role of Nucleolin in Nucleolus Organization and Silencing of AtNUC-L2 Gene in Arabidopsis

Characterization of AtNUC-L1 Reveals a Central Role of Nucleolin in Nucleolus Organization and Silencing of AtNUC-L2 Gene in Arabidopsis

The Pentatricopeptide Repeat GeneOTP43Is Required fortrans-Splicing of the Mitochondrialnad1Intron 1 inArabidopsis thaliana

Disease-Specific Expression of Host Genes During Downy Mildew Infection of Arabidopsis

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