Unknown,Transcriptomics,Genomics,Proteomics

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The Arabidopsis Tandem Zinc Finger 9 (TZF9) is involved in global post-transcriptional regulation during PTI

ABSTRACT: The Arabidopsis Tandem Zinc Finger 9 (TZF9) is a putative RNA-binding protein that is localized to Processing Body-like structures. A tzf9 knock out line showed attenuated response to the Pattern-Associated Molecular Pattern (PAMP), flg22 (doi: 10.1093/pcp/pct175). To uncover the molecular mechanism for this phenotype, global gene expression analysis covering total RNA (transcriptome) and polysome-associated mRNAs (translatome) was performed. For the latter, a transgenic line expressing a FLAG-tagged ribosomal protein RPL18 was crossed to the tzf9 mutant. The results show a strong 'uncoupling' between transcriptome and translatome in the mutant, indicating that TZF9 could be involved in global post-transcriptional regulation process.

INSTRUMENT(S): Affymetrix GeneAtlas

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Naheed Tabassum

PROVIDER: E-MTAB-6918 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Plant organs are comprised of distinct cell types with unique assemblages of mRNAs. This is a collection of CEL files of mRNA profiles of the total steady-state mRNAs and polysomal mRNAs of distinct cell types of the whole root and shoot of 7-d-old Arabidopsis thaliana seedlings. The cell type specific mRNA populations are those present in ribosome-mRNA complexes. This sub-population of mRNAs was obtained by first establishing a collection of Arabidopsis lines that express a FLAG-epitope tagged ribosomal protein L18 (RPL18) directed by promoters expressed in specific cell types and regions. Thirteen different promoter:FLAG-RPL18 lines were used. The targeted cell types and promoters included root atrichoblast (non-hair) epidermal cells (pGL2), root endodermis (pSCR), root stelar xylem and pericycle (pWOL, pSHR), root phloem companion cells (phloem CC) (pSUC2, pSultr2;2), root proliferating cells (pRPL11C), root cortex meristematic cells (pCO2), root cortex elongation/maturation cells (pPEP), shoot mesophyll (pRBCS), shoot epidermis (pCER5), shoot guard cells (pKAT1), shoot bundle sheath (pSultr2;2), shoot phloem CC (pSUC2) and shoot trichomes (pGL2). A CaMV 35S promoter:FLAG-RPL18 line was used to obtain the polysomal mRNA of multiple cell types. The immunopurification of ribosome-mRNA complexes of specific cell types/regions was accomplished by the method described in Zanetti et al. (Plant Physiology, 138, 624-635; 2005). Hybridization of the immunopurified mRNAs to the Affymetrix ATH1 DNA microarray platform and subsequent data analysis permitted the identification of transcripts that are enriched or depleted in specific cell types/regions of roots and shoots. The dataset includes samples from cell types/regions from seedlings grown under control conditions and cell types/regions of seedlings exposed to low oxygen stress (hypoxia) for 2 h. Experiment Overall Design: 79 samples, 2 conditions (2 h hypoxia stress, 2 h non-stress), 2 RNA pools (Total mRNA and polysomal mRNA), 2 organs, 13 promoter lines, 2-4 replicates

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The Arabidopsis Tandem Zinc Finger 9 (TZF9) is involved in global post-transcriptional regulation during PTI

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