To cope with seasonal environmental changes, animals adapt their physiology and behaviour in response to photoperiod. However, the molecular mechanisms underlying these adaptive changes are not completely understood. Here, using genome-wide expression analysis, we show that an uncharacterized long noncoding RNA (lncRNA), LDAIR, is strongly regulated by photoperiod in Japanese medaka fish (Oryzias latipes). Numerous transcripts and signalling pathways are activated during the transition from short- to long-day conditions; however, LDAIR is one of the first genes to be induced and its expression shows a robust daily rhythm under long-day conditions. Transcriptome analysis of LDAIR knockout fish reveals that the LDAIR locus regulates a gene neighbourhood, including corticotropin releasing hormone receptor 2, which is involved in the stress response. Behavioural analysis of LDAIR knockout fish demonstrates that LDAIR affects self-protective behaviours under long-day conditions. Therefore, we propose that photoperiodic regulation of corticotropin releasing hormone receptor 2 by LDAIR modulates adaptive behaviours to seasonal environmental changes.
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The microarray and RNA-Seq data are available at the NCBI Gene Expression Omnibus (accession no. GSE119905). All other data are available from the authors upon request.
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We thank NBRP-Medaka (National Bio-Resource Project of MEXT, Japan) and the Data Integration and Analysis Facility for use of their facilities. We also thank M. Okubo, A. Akama, N. Baba and C. Kinoshita for technical assistance, and T.K. Tamai for comments on the manuscript. This work was supported in part by the JSPS KAKENHI Grant-in-Aid for Specially Promoted Research (grant no. 26000013), the Human Frontier Science Program (grant no. RGP0030/2015) and Grant-in-Aid for JSPS Fellows (grant no. 18J10936). The WPI-ITbM is supported by the World Premier International Research Center Initiative, MEXT, Japan.
The authors declare no competing interests.
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Supplementary Figs. 1–6 and Supplementary Table 1
Supplementary Data 1: List of photoperiodically-regulated transcripts. Supplementary Data 2: List of differentially expressed transcripts between wild type (WT) and LDAIR knockout (KO) medaka.
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Nakayama, T., Shimmura, T., Shinomiya, A. et al. Seasonal regulation of the lncRNA LDAIR modulates self-protective behaviours during the breeding season. Nat Ecol Evol 3, 845–852 (2019). https://doi.org/10.1038/s41559-019-0866-6