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Staiger D.,Bielefeld University | Staiger D.,Institute for Genome Research and Systems Biology | Green R.,Hebrew University of Jerusalem
Trends in Plant Science | Year: 2011

The circadian clock is an endogenous, approximately 24-h timer that enables plants to anticipate daily changes in their environment and regulates a considerable fraction of the transcriptome. At the core of the circadian system is the oscillator, made up of interconnected feedback loops, involving transcriptional regulation of clock genes and post-translational modification of clock proteins. Recently, it has become clear that post-transcriptional events are also critical for shaping rhythmic mRNA and protein profiles. This review covers regulation at the RNA level of both the core clock and output genes in Arabidopsis (Arabidopsis thaliana), with comparisons with other model organisms. We discuss the role of splicing, mRNA decay and translational regulation as well as recent insights into rhythms of noncoding regulatory RNAs. © 2011. Source

Staiger D.,Bielefeld University | Staiger D.,Institute for Genome Research and Systems Biology | Brown J.W.S.,James Hutton Institute
Plant Cell | Year: 2013

High-throughput sequencing for transcript profiling in plants has revealed that alternative splicing (AS) affects a much higher proportion of the transcriptome than was previously assumed. AS is involved in most plant processes and is particularly prevalent in plants exposed to environmental stress. The identification of mutations in predicted splicing factors and spliceosomal proteins that affect cell fate, the circadian clock, plant defense, and tolerance/sensitivity to abiotic stress all point to a fundamental role of splicing/AS in plant growth, development, and responses to external cues. Splicing factors affect the AS of multiple downstream target genes, thereby transferring signals to alter gene expression via splicing factor/AS networks. The last two to three years have seen an ever-increasing number of examples of functional AS. At a time when the identification of AS in individual genes and at a global level is exploding, this review aims to bring together such examples to illustrate the extent and importance of AS, which are not always obvious from individual publications. It also aims to ensure that plant scientists are aware that AS is likely to occur in the genes that they study and that dynamic changes in AS and its consequences need to be considered routinely. © 2013 American Society of Plant Biologists. All rights reserved. Source

Lohr B.,Bielefeld University | Streitner C.,Bielefeld University | Steffen A.,Bielefeld University | Lange T.,TU Braunschweig | And 2 more authors.
Molecular Biology Reports | Year: 2014

The RNA-binding protein Arabidopsis thaliana glycine-rich RNA-binding protein 7 (AtGRP7) regulates the steady-state abundance of numerous target transcripts in A. thaliana. Here we show that the GA1 and GA2 transcripts encoding the first enzymes of the gibberellin biosynthetic pathway are expressed at reduced levels in transgenic plants ectopically over-expressing AtGRP7 (AtGRP7-ox plants). Furthermore, the levels of the bioactive phytohormone GA4 as well as of several intermediates of the GA biosynthetic pathway are reduced in AtGRP7-ox plants. The transgenic plants show a reduced length of the vegetative stem. The application of exogenous GA largely reverses the phenotype by increasing the number of vegetative internodes. AtGRP7-ox plants flower with fewer leaves than wt plants, suggesting that the floral promotive effect of AtGRP7 bypasses the effect of a reduced GA level in AtGRP7-ox plants. Upon GA treatment, AtGRP7-ox plants flower only slightly earlier than wild type plants. Thus, exogenous GA has only a small additional effect in reducing the number of leaves at the onset of flowering in AtGRP7-ox plants. © 2013 Springer Science+Business Media Dordrecht. Source

Streitner C.,Bielefeld University | Koster T.,Bielefeld University | Simpson C.G.,James Hutton Institute | Shaw P.,James Hutton Institute | And 4 more authors.
Nucleic Acids Research | Year: 2012

Alternative splicing (AS) of pre-mRNAs is an important regulatory mechanism shaping the transcriptome. In plants, only few RNA-binding proteins are known to affect AS. Here, we show that the glycine-rich RNA-binding protein AtGRP7 influences AS in Arabidopsis thaliana. Using a high-resolution RT-PCR-based AS panel, we found significant changes in the ratios of AS isoforms for 59 of 288 analyzed AS events upon ectopic AtGRP7 expression. In particular, AtGRP7 affected the choice of alternative 5′ splice sites preferentially. About half of the events are also influenced by the paralog AtGRP8, indicating that AtGRP7 and AtGRP8 share a network of downstream targets. For 10 events, the AS patterns were altered in opposite directions in plants with elevated AtGRP7 level or lacking AtGRP7. Importantly, RNA immunoprecipitation from plant extracts showed that several transcripts are bound by AtGRP7 in vivo and indeed represent direct targets. Furthermore, the effect of AtGRP7 on these AS events was abrogated by mutation of a single arginine that is required for its RNA-binding activity. This indicates that AtGRP7 impacts AS of these transcripts via direct interaction. As several of the AS events are also controlled by other splicing regulators, our data begin to provide insights into an AS network in Arabidopsis. © 2012 The Author(s). Source

Ramos R.T.J.,Federal University of Para | Carneiro A.R.,Federal University of Para | de Castro Soares S.,Federal University of Minas Gerais | Barbosa S.,Federal University of Para | And 6 more authors.
Journal of Microbiological Methods | Year: 2013

With the advent of high-throughput DNA sequencing platforms, there has been a reduction in the cost and time of sequencing. With these advantages, new challenges have emerged, such as the handling of large amounts of data, quality assessment, and the assembly of short reads. Currently, benchtop high-throughput sequencers enable the genomes of prokaryotic organisms to be sequenced within two hours with a reduction in coverage compared with the SOLiD, Illumina and 454 FLX Titanium platforms, making it necessary to evaluate the efficiency of less expensive benchtop instruments for prokaryotic genomics. In the present work, we evaluate and propose a methodology for the use of the Ion Torrent PGM platform for decoding the gram-positive bacterium Corynebacterium pseudotuberculosis, for which 15 complete genome sequences have already been deposited based on fragment and mate-paired libraries with a 3-kb insert size. Despite the low coverage, a single sequencing run using a mate-paired library generated 39 scaffolds after de novo assembly without data curation. This result is superior to that obtained by sequencing using libraries generated from fragments marketed by the equipment's manufacturer, as well as that observed for mate-pairs sequenced by SOLiD. The generated sequence added an extra 91. kb to the genome available at NCBI. © 2013. Source

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