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Identification of microRNAs in response to blue light irridiation by high-throughput sequencing in Saccharina japonica

ABSTRACT: Blue light (BL) is an important environmental factor that plays critical role in algae growth and development. Saccharina japonica, as a typical brown alga, showed greatly affected by BL. However, little has been known about the regulation pathway of BL response in algae. microRNAs (miRNAs) participated in great number of life process regulation and may be also involved in the BL response in plants. To identify miRNAs from S. japonica and characterize their probable roles in BL response, we sequenced and compared small RNA libraries under BL irradiation and dark conditions. 20 potential novel miRNAs were identified from S. japonica. Bioinformatics analysis of the miRNAs indicated that their potential targets were involved in various biological processes. Based on differential expression analysis and qRT-PCR experiment, some probable miRNAs related to BL responses were selected for further verification of their function, such as miR398. Our results demonstrated that miRNAs might play vital roles in metabolism of S. japonica, including BL responses.

ORGANISM(S): Saccharina japonica

PROVIDER: GSE36704 | GEO | 2017/06/12

SECONDARY ACCESSION(S): PRJNA153567

REPOSITORIES: GEO

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Project description:Regulation of gene expression by reactive oxygen species (ROS) is an important component of abiotic stress signal transduction mechanisms. Previous genome-wide analysis of chilling-induced changes in gene expression suggested a potential role of H2O2 and other ROS as key signals in the induction of early response genes in japonica rice (cv. Nipponbare). Candidate regulators including bZIP-, Myb- or WRKY-types of transcription factors that were responsive to both chilling (10oC) and exogenous H2O2, and their probable target clusters (as1/ocs/TGA1-like, MybR-like element containing genes) were inferred by integrative analysis of qPCR expression profiles and ab initio promoter motif data. In an effort to define the composition and hierarchical organization of the ROS-mediated chilling response regulatory networks, we examined the effect of exogenous H2O2 (6 hours in 4mM H2O2 at 28oC and then 6 hours of recovery in water at 28oC) on the transcriptome of Nipponbare in a genome-wide scale and compared them with the chilling stress transcriptome. Results of this study were consistent with our earlier model that a ROSbZIP-as1/ocs/TGA1 regulatory module is a direct consequence of chilling-induced elevation of intracellular ROS during the initial 24 hours. Keywords: time course (response to exogenous H2O2) This experiment describes the analysis of the temporal changes in gene expression in response to exogenous H2O2 in Nipponbare rice. A total of 5 treatment regimes were examined (1, 3, and 6 hours at 4 mM H2O2 and then 3 and 6 hours of recovery in water after 6 hours of exposure to H2O2). The microarray platform used in this study was the 45K oligonucleotide microarray (www.ricearray.org) which comes in pairs of slides A and B (each containing about 50% of the total number of features). The data described in this series include all hybridizations with slide A and with slide B. All experiments were performed with two independent biological replicates (R1 and R2) for each time point.

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Identification of microRNAs in response to blue light irridiation by high-throughput sequencing in Saccharina japonica

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