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Time-course small RNA sequencing across photoperiods in Arabidopsis thaliana

ABSTRACT: Small RNAs play important roles in photoperiodism, but a comprehensive characterization of miRNAs and the more recently recognized tRFs within this context is lacking. Herein, we characterize the patterns of miRNAs and tRFs in Arabidopsis by performing time-course sRNA-sequencing across three photoperiods. By comparing with our previous mRNA-sequencing time-courses (GSE221846), we identified 14 negatively-correlated miRNA-mRNA pairs between the two co-sequenced datasets that suggest photoperiodic sRNA regulations. Furthermore, we identified 20 patterns of photoperiodic tRFs. These patterns are linked to the tRNA isotypes and positions they derive from, suggesting that tRFs are subjected to photoperiodic regulations.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE289155 | GEO | 2025/08/07

REPOSITORIES: GEO

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Project description:Seasonal adaptation to changes in light:dark regimes (i.e., photoperiod) allows organisms living at temperate latitudes to anticipate environmental change and adjust their physiology and behavior accordingly. The circadian system has been implicated in measurement and response to changes in photoperiod in nearly all animals studied so far (Saunders, 2011). The use of both traditional and non-traditional model insects with robust seasonal responses has recently genetically demonstrated the central role that clock genes play in photoperiodic response. Yet, the molecular pathways involved in insect photoperiodic responses remain largely unknown. Here, using the Eastern North American monarch butterfly (Reppert et al, 2016; Denlinger et al, 2017), we identified the vitamin A pathway as a novel pathway downstream of the circadian clock mediating insect photoperiod responsiveness. We found that interrupting clock function by disrupting circadian activation and repression abolishes photoperiodic responses in reproductive output, providing a functional link between clock genes and photoperiodic responsiveness in the monarch. Through transcriptomic approaches, we identified a molecular signature of seasonal-specific rhythmic gene expression in the brain, the organ known to function in photoperiodic reception in both Lepidoptera and some flies (Bowen et al, 1984; Saunders & Cymborowski, 1996). Among genes differentially expressed between both long and short photoperiods and between seasonal forms, several were belonging to the vitamin A pathway. The rhythmic expression of all of these genes was abolished in clock-deficient mutants. We also showed that a CRISPR/Cas9-mediated loss-of-function mutation in the pathway’s rate-limiting enzyme, ninaB1, impaired the monarch ability to respond to the photoperiod independently of visual function in the compound eye and without affecting circadian rhythms. Our finding that the vitamin A pathway is a key mediator of photoperiodic responses in insects could have broad implications for understanding the molecular mechanisms underlying photoperiodism.

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Time-course small RNA sequencing across photoperiods in Arabidopsis thaliana

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