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Identification and functional characterization of circular RNAs in response to blue light induction in Saccharina japonica

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Abstract

Blue light is one of the important factors that influences Saccharina japonica growth and development. Circular RNAs (circRNAs) are a class of abundant endogenous stable RNAs that play vital roles in many biological activities. To explore the blue light-mediated regulation of circRNAs, the transcript profiles of circRNAs in response to blue light (RB), white light (RW) and dark (RD) were characterized in the sporophytes of S. japonica using rRNA-depleted circular RNA sequencing and bioinformatics analysis. In total, 1768 circRNAs were identified in sporophytes, and 969 (54.81%) were derived from exons. Enrichment analysis showed that the parental genes of S. japonica circRNAs were involved in spliceosome, RNA transport, protein processing in the endoplasmic reticulum and endocytosis pathways. In total, 37 and 14 differentially expressed circRNAs were identified in the RB vs. RD and RB vs. RW comparisons, respectively. The sja-circ-000945, sja-circ-000944, sja-circ-000486 and sja-circ-000518 were differentially expressed in both the RB vs. RD and RB vs. RW comparisons, which indicating that they may play vital roles in blue light-mediated signal transduction. Based on the circRNA-microRNA-mRNA network analysis, sja-circ-000518 and sja-circ-000486 were related to sporophyte growth and development. In addition, sja-circ-000518 was involved in signal transduction by competing for binding sites in novel-m3940-3p with both CBL-interacting protein kinase 31 and phosphatidylinositol 4-phosphate 5-kinase. In conclusion, circRNAs may function as posttranscriptional regulators in blue light-mediated growth and development of S. japonica. Our study provides an understanding of the regulation of circRNAs from the perspective of circRNA-related competitive endogenous RNAs in the brown macroalgae.

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Abbreviations

CIPK31:

CBL-interacting protein kinase 31

DAVID:

Database for annotation, visualization and integrated discovery

PIP5K:

Phosphatidylinositol 4-phosphate 5-kinase

qRT-PCR:

Quantitative real-time PCR

lncRNA:

Long non-coding RNA

microRNA:

MiRNA

RB:

Blue light

RD:

Dark

RW:

White light

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Funding

This research was funded by Joint Research Project Between China and Japan, grant number 2017YFE0130900, National Natural Science Foundation of China, grant number 31772848, and China Postdoctoral Science Foundation, grant number 2022M713183.

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Authors and Affiliations

  1. CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China

    Xiaoqi Yang, Xiuliang Wang, Jianting Yao & Delin Duan

  2. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China

    Xiaoqi Yang, Xiuliang Wang, Jianting Yao & Delin Duan

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  1. Xiaoqi Yang
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  2. Xiuliang Wang
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  4. Delin Duan
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Contributions

Methodology: XY; Validation: XY; formal analysis: XY; writing—original draft preparation: XY, XW, JY, DD, writing—review and editing: DD; funding acquisition: XW; DD.

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Correspondence to Delin Duan.

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Communicated by Hong-Xia Zhang.

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Yang, X., Wang, X., Yao, J. et al. Identification and functional characterization of circular RNAs in response to blue light induction in Saccharina japonica. Plant Growth Regul 100, 161–170 (2023). https://doi.org/10.1007/s10725-022-00947-1

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  • DOI: https://doi.org/10.1007/s10725-022-00947-1

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