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Transcriptome profiling of inflorescence stem tissues from Arabidopsis thaliana series

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE142034 | GEO | 2020/02/10

REPOSITORIES: GEO

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Transcriptome profiling of inflorescence stem tissues from Arabidopsis thaliana series 2

Project description:We report the application of laser capture microdissection (LCM) for high resolution transcriptome profiling of the second internode of the Arabidopsis thaliana inflorescence stem. In this series, we used LCM to determine and compare the transcriptome profiles of the phloem cap, the pith, and the remaining vascular bundle area.

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Transcriptome profiling of inflorescence stem tissues from Arabidopsis thaliana series 1

Project description:We report the Fluorescence Activated Nucleus Sorting (FANS)-based RNA sequencing for high resolution transcriptome profiling of the second internode of the Arabidopsis thaliana inflorescence stem. We compared GFP-positive nuclei and GFP negative nuclei from promoter reporter lines expressing Histone 4-GFP (NST3pro:H4-GFP, SMXL5pro:H4-GFP, APLpro:H4-GFP), and compared GFP positive nuclei from seven lines expressing Histone 4-GFP under the control of different tissue-specific promoters (NST3pro:H4-GFP, VND7pro:H4-GFP, PXYpro:H4-GFP, SMXL5pro:H4-GFP, APLpro:H4-GFP, SCRpro:H4-GFP, LTP1pro:H4-GFP).

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Transcriptome profiling of inflorescence stem tissues from Arabidopsis thaliana series

Project description:Transcriptome profiling of inflorescence stem tissues from Arabidopsis thaliana series

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Transcriptome profiling of inflorescence stem tissues from Arabidopsis thaliana series 2

Project description:Transcriptome profiling of inflorescence stem tissues from Arabidopsis thaliana series 2

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Transcriptome profiling of inflorescence stem tissues from Arabidopsis thaliana series 1

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Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures.

Project description:Genome-wide gene expression maps with a high spatial resolution have substantially accelerated plant molecular science. However, the number of characterized tissues and growth stages is still small due to the limited accessibility of most tissues for protoplast isolation. Here, we provide gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues. By combining fluorescence-activated nucleus sorting and laser-capture microdissection with next-generation RNA sequencing, we characterized the transcriptomes of xylem vessels, fibers, the proximal and distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classified more than 15,000 genes as being differentially expressed among different stem tissues and revealed known and novel tissue-specific cellular signatures. By determining overrepresented transcription factor binding regions in the promoters of differentially expressed genes, we identified candidate tissue-specific transcriptional regulators. Our datasets predict the expression profiles of an exceptional number of genes and allow hypotheses to be generated about the spatial organization of physiological processes. Moreover, we demonstrate that information about gene expression in a broad range of mature plant tissues can be established at high spatial resolution by nuclear mRNA profiling. Tissue-specific gene expression values can be accessed online at https://arabidopsis-stem.cos.uni-heidelberg.de/.

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Project description:This study presents the first large-scale analysis of plant intact glycopeptides. Using wheat germ agglutinin lectin weak affinity chromatography to enrich modified peptides, followed by electron transfer dissociation (ETD)(1) fragmentation tandem mass spectrometry, glycan compositions on over 1100 glycopeptides from 270 proteins found in Arabidopsis inflorescence tissue were characterized. While some sites were only detected with a single glycan attached, others displayed up to 16 different glycoforms. Among the identified glycopeptides were four modified in nonconsensus glycosylation motifs. While most of the modified proteins are secreted, membrane, endoplasmic reticulum (ER), or Golgi-localized proteins, surprisingly, N-linked sugars were detected on a protein predicted to be cytosolic or nuclear.

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Project description:This SuperSeries is composed of the SubSeries listed below.

2024-06-24 | GSE267649 | GEO

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Project description:Heterosis occurs where F1 offspring display superior characteristics to the parents. Heterosis is usually considered to result from crosses of genetically distinct (e.g. homozygous inbred) parents producing heterozygous F1 offspring. Most mechanistic models for heterosis require genetically heterozygous F1 hybrid offspring harbouring allelic diversity. Epigenetic or dosage models for heterosis could allow for heterosis effects in F1 offspring that display no allelic diversity with their parents. Reciprocal inter-ploidy crosses between diploid (2x) and tetraploid (4x) lines in the same genetic background generates genetically identical F1 triploids (3x). Such reciprocal F1 triploids differ according to whether the additional chromosome set is either maternally (maternal excess) or paternally inherited (paternal excess). Biomass accumulation and abiotic stress tolerance between the parental (2x and 4x) and reciprocal F1 triploid (3x) offspring of Arabidopsis thaliana accession C24 reveals a strong parental genome-dosage induced heterosis in the paternal-excess triploid F1 plants. In these F1 triploids, the circadian clock related genes CCA1 and TOC1, and the growth factors PIF4 and PIF5, display different expression levels compared to the non-heterotic maternal excess F1 triploid siblings. Whole transcriptome profiling reveals a paternal genome dosage effect on gene expression levels with strong enrichment for dysregulated abiotic stress-related genes in the paternal excess F1 triploids. This study demonstrates that heterosis can be triggered without allelic diversity in F1 triploid plants. Heterosis without heterozygosity in plants can be induced via an epigenetic “chromosome imprinting” like parental genome dosage effect requiring paternal transmission of an additional chromosome set

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