Cell‐type specific analysis of translating RNAs in developing flowers reveals new levels of control

Jiao, Yuling; Meyerowitz, Elliot M.

doi:10.1038/msb.2010.76

Cited by 164 publications

(167 citation statements)

References 76 publications

Supporting

Mentioning

154

Contrasting

Unclassified

Order By: Relevance

“…Poly(A + ) RNAs were purified by two rounds of hybridization to oligo(dT)-coated Dynal magnetic beads (Life Technology). Sequencing libraries were prepared from poly(A + ) RNA as described previously (Jiao and Meyerowitz, 2010). The libraries were sequenced as 50-mers using HiSeq2000 (Illumina) with standard settings.…”

Section: Preparation Of Rna-seq Librariesmentioning

confidence: 99%

“…After reads that aligned to ribosomal RNA or transfer RNA were removed, the expression counts of gene locus were calculated based on mapping outputs by Cuffdiff2 (version 2.1.1) and were normalized to reads per kilobase per million mapped read using edgeR (Robinson et al, 2010). The cutoff value for significant expression was 0.5 reads per kilobase per million mapped read according to previous control experiments (Jiao and Meyerowitz, 2010). Differential expression was also assessed using edgeR (Robinson et al, 2010).…”

Section: Analysis Of Rna-seq Datamentioning

confidence: 99%

See 1 more Smart Citation

Suppression of Photosynthetic Gene Expression in Roots Is Required for Sustained Root Growth under Phosphate Deficiency

Kang

Tian

et al. 2014

Plant Physiology

Self Cite

View full text Add to dashboard Cite

Plants cope with inorganic phosphate (Pi) deficiencies in their environment by adjusting their developmental programs and metabolic activities. For Arabidopsis (Arabidopsis thaliana), the developmental responses include the inhibition of primary root growth and the enhanced formation of lateral roots and root hairs. Pi deficiency also inhibits photosynthesis by suppressing the expression of photosynthetic genes. Early studies showed that photosynthetic gene expression was also suppressed in Pi-deficient roots, a nonphotosynthetic organ; however, the biological relevance of this phenomenon remains unknown. In this work, we characterized an Arabidopsis mutant, hypersensitive to Pi starvation7 (hps7), that is hypersensitive to Pi deficiency; the hypersensitivity includes an increased inhibition of root growth. HPS7 encodes a tyrosylprotein sulfotransferase. Accumulation of HPS7 proteins in root tips is enhanced by Pi deficiency. Comparative RNA sequencing analyses indicated that the expression of many photosynthetic genes is activated in roots of hps7. Under Pi deficiency, the expression of photosynthetic genes in hps7 is further increased, which leads to enhanced accumulation of chlorophyll, starch, and sucrose. Pi-deficient hps7 roots also produce a high level of reactive oxygen species. Previous research showed that the overexpression of GOLDEN-like (GLK) transcription factors in transgenic Arabidopsis activates photosynthesis in roots. The GLK overexpressing (GLK OX) lines also exhibit increased inhibition of root growth under Pi deficiency. The increased inhibition of root growth in hps7 and GLK OX lines by Pi deficiency was completely reversed by growing the plants in the dark. Based on these results, we propose that suppression of photosynthetic gene expression is required for sustained root growth under Pi deficiency.

show abstract

Section: Preparation Of Rna-seq Librariesmentioning

confidence: 99%

Section: Analysis Of Rna-seq Datamentioning

confidence: 99%

Suppression of Photosynthetic Gene Expression in Roots Is Required for Sustained Root Growth under Phosphate Deficiency

Kang

Tian

et al. 2014

Plant Physiology

Self Cite

View full text Add to dashboard Cite

show abstract

“…However, RNA-Seq data can distinguish between the two genes and indicate that in flower tissue (Jiao and Meyerowitz, 2010;Niederhuth et al, 2013), shoot apical meristem (Torti et al, 2012), developing embryos (Nodine and Bartel, 2012), and the central cell of the female gamete (Schmid et al, 2012), EIF4E1B mRNA is expressed and associates with polysomes in flowers (Jiao and Meyerowitz, 2010); however, EIF4E1C mRNA was at much lower to undetectable levels in these tissues. In an analysis of 80 genomes released by the 1001 Genomes Project, EIF4E1C was predicted to be spontaneously deleted in 12 strains, suggesting that it is likely not providing any advantage to promote its retention in the genome .…”

Section: Eif4e1b/eif4e1c Expressionmentioning

confidence: 99%

Two Arabidopsis Loci Encode Novel Eukaryotic Initiation Factor 4E Isoforms That Are Functionally Distinct from the Conserved Plant Eukaryotic Initiation Factor 4E

et al. 2014

View full text Add to dashboard Cite

Canonical translation initiation in eukaryotes begins with the Eukaryotic Initiation Factor 4F (eIF4F) complex, made up of eIF4E, which recognizes the 7-methylguanosine cap of messenger RNA, and eIF4G, which serves as a scaffold to recruit other translation initiation factors that ultimately assemble the 80S ribosome. Many eukaryotes have secondary EIF4E genes with divergent properties. The model plant Arabidopsis (Arabidopsis thaliana) encodes two such genes in tandem loci on chromosome 1, EIF4E1B (At1g29550) and EIF4E1C (At1g29590). This work identifies EIF4E1B/EIF4E1C-type genes as a Brassicaceae-specific diverged form of EIF4E. There is little evidence for EIF4E1C gene expression; however, the EIF4E1B gene appears to be expressed at low levels in most tissues, though microarray and RNA Sequencing data support enrichment in reproductive tissue. Purified recombinant eIF4E1b and eIF4E1c proteins retain cap-binding ability and form functional complexes in vitro with eIF4G. The eIF4E1b/eIF4E1c-type proteins support translation in yeast (Saccharomyces cerevisiae) but promote translation initiation in vitro at a lower rate compared with eIF4E. Findings from surface plasmon resonance studies indicate that eIF4E1b and eIF4E1c are unlikely to bind eIF4G in vivo when in competition with eIF4E. This study concludes that eIF4E1b/eIF4E1c-type proteins, although bona fide cap-binding proteins, have divergent properties and, based on apparent limited tissue distribution in Arabidopsis, should be considered functionally distinct from the canonical plant eIF4E involved in translation initiation.

show abstract

“…To facilitate the capture of ribosome-associated mRNA, we developed a method for translating ribosome affinity immunopurification (TRAP) incorporating FLAG-tagged ribosomal protein L18 (RPL18) into functional ribosomes in the model plant Arabidopsis thaliana (1). Two advantages of TRAP are that it reduces contamination of polysome preparations with mRNA-ribonucleoprotein (mRNP) complexes of similar density and can be used to obtain mRNAs from subpopulations of cells of a multicellular organ or tissue in plants (2,3), as well as in mammals and insects (4,5).…”

mentioning

confidence: 99%

“…Translation is also modulated by regulatory molecules, including auxin (22,23), gibberellins (24), and polyamines (25). Most of the recent studies documenting dynamics in mRNA translation were performed using microarrays, but the application of high-throughput mRNA sequencing (mRNA-seq) to evaluate translatomes has provided greater detail of RNAs associated with ribosomes (3,26). In yeast, the translatome is recognized as an accessible proxy of de novo protein synthesis (27).…”

mentioning

confidence: 99%

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

Juntawong

Girke

Bazin

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

361

415

View full text Add to dashboard Cite

Translational regulation contributes to plasticity in metabolism and growth that enables plants to survive in a dynamic environment. Here, we used the precise mapping of ribosome footprints (RFs) on mRNAs to investigate translational regulation under control and sublethal hypoxia stress conditions in seedlings of Arabidopsis thaliana. Ribosomes were obtained by differential centrifugation or immunopurification and were digested with RNase I to generate footprint fragments that were deep-sequenced. Comparison of RF number and position on genic regions with fragmented total and polysomal mRNA illuminated numerous aspects of posttranscriptional and translational control under both growth conditions. When seedlings were oxygen-deprived, the frequency of ribosomes at the start codon was reduced, consistent with a global decline in initiation of translation. Hypoxia-up-regulated gene transcripts increased in polysome complexes during the stress, but the number of ribosomes per transcript relative to normoxic conditions was not enhanced. On the other hand, many mRNAs with limited change in steady-state abundance had significantly fewer ribosomes but with an overall similar distribution under hypoxia, consistent with restriction of initiation rather than elongation of translation. RF profiling also exposed the inhibitory effect of upstream ORFs on the translation of downstream protein-coding regions under normoxia, which was further modulated by hypoxia. The data document translation of alternatively spliced mRNAs and expose ribosome association with some noncoding RNAs. Altogether, we present an experimental approach that illuminates prevalent and nuanced regulation of protein synthesis under optimal and energy-limiting conditions. ribosome profiling | uORF | alternative splicing | long intergenic noncoding RNA | translational efficiency

show abstract

Cell‐type specific analysis of translating RNAs in developing flowers reveals new levels of control

Cited by 164 publications

References 76 publications

Suppression of Photosynthetic Gene Expression in Roots Is Required for Sustained Root Growth under Phosphate Deficiency

Suppression of Photosynthetic Gene Expression in Roots Is Required for Sustained Root Growth under Phosphate Deficiency

Two Arabidopsis Loci Encode Novel Eukaryotic Initiation Factor 4E Isoforms That Are Functionally Distinct from the Conserved Plant Eukaryotic Initiation Factor 4E

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

Contact Info

Product

Resources

About