Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Identification of WRKY22 direct targets under submergence in Arabidopsis with ChIP

ABSTRACT: To identify direct targets of WRKY22, we created a transgenic Arabidopsis line that expresses a c-myc epitope-tagged WRKY22 and used ChIP followed by microarray hybridization (ChIP-chip) to screen for candidates and validate the in vivo protein-DNA interactions with ChIP followed by quantitative PCR (ChIP-Q-PCR). The WRKY22 and c-myc epitope tag fusion construct was generated and transformed into wrky22-ko2 plants. The resulting transgenic lines should have better ChIP efficiency than the wild-type background, due to the reduced competition for WRKY22 binding sites from endogenous WRKY22. ChIP-enriched DNA fragments were identified using criteria of a window of +300 to M-oM- 2 or < 0.5-fold induction in any time point under submergence treatments in expression array data. Comparison of c-myc tagged WRKY22 transgenic plants vs wild-type (Columbia) plants. Both materials were submergence treated for 3 hours.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Fu-Chiun Hsu

PROVIDER: E-GEOD-40138 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Switchgrass plants were grown in a Sandwich tube system to induce gradual drought stress by withholding watering. After 29 days, leaf photosynthetic rate decreased significantly, compared to the control plants which were watered regularly. The drought-treated plants recovered to the same leaf water content after three days of re-watering. Root tip (1cm basal fragment, designated as RT1 hereafter) and the elongation/maturation zone (the next upper 1 cm tissue, designated as RT2 hereafter) tissues were collected at the 29th day of drought stress treatment, (named SDT for severe drought treated), one (D1W) and three days (D3W) of re-watering. The tandem mass tags mass spectrometry-based quantitative proteomics analysis was performed to identify the proteomes, and drought-induced differentially expressed proteins (DEPs). From RT1 tissues, 6,156, 7,687 and 7,699 proteins were quantified, and 296, 535 and 384 DEPs were identified in the SDT, D1W and D3W samples, respectively. From RT2 tissues, 7,382, 7,255 and 6,883 proteins were quantified, and 393, 587 and 321 proteins DEPs were identified in the SDT, D1W and D3W samples. Between RT1 and RT2 tissues, very few DEPs overlapped at SDT, but the number of such proteins increased during the recovery phase. A large number of hydrophilic proteins and stress-responsive proteins were induced during SDT and remained at a higher level during the recovery stages. A large number of DEPs in RT1 tissues maintained the same expression pattern throughout drought treatment and the recovery phases. The DEPs in RT1 tissues were classified in cell proliferation, mitotic cell division, and chromatin modification, and those in RT2 were placed in cell wall remodeling and cell expansion processes. This study provided information pertaining to root zone-specific proteome changes during drought and recover phases, which will allow us to choose the proteins (genes) as better defined targets for developing drought tolerant plants.

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Identification of WRKY22 direct targets under submergence in Arabidopsis with ChIP

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