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SRX5356925: GSM3596768: RNAseq Migrant ZT04 rep2; Danaus plexippus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 17.8M spots, 890.4M bases, 436.1Mb downloads

Submitted by: NCBI (GEO)
Study: Circadian clock genes and the vitamin A pathway regulate seasonal photoperiodic responsiveness in an insect
show Abstracthide Abstract
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. Overall design: Determine the identify of rhythmic genes underlying photoperiodic responses in monarch butterfly brains using RNA-seq.
Sample: RNAseq Migrant ZT04 rep2
SAMN10907706 • SRS4347770 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Brains of wild-caught migrants and of monarchs raised indoors in LP and SP were dissected in 0.5X RNA later (Invitrogen) to prevent RNA degradation, the retinal pigmented photoreceptor layer was removed, and the brains were stored at -80oC until use. For each seasonal phenotype/photoperiodic condition, three pooled brains were collected in two replicates at ZT1, ZT4, ZT7, ZT10, ZT13, ZT16, ZT19, and ZT22. For each sample, total RNA was extracted using an RNeasy Mini kit (Qiagen). For samples from wild-caught migrants, polyA+ RNA was isolated from 2 μg of total RNA with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), and multiplexed libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos (New England Biolabs) and amplified with 12 PCR cycles, following the manufacturer's recommendations. For samples from monarchs raised in LP and SP, multiplexed libraries were prepared by the Texas A&M AgriLife Genomics and Bioinformatics Facility using polyA+ RNA isolated from 1 μg of total RNA, and multiplexed libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina), following the manufacturer's recommendations. Libraries quality and size distribution was verified on a Bioanalyzer, libraries were quantified by real-time quantitative PCR, and 16 multiplexed libraries were mixed in equimolar ratios and sequenced on a Hi-seq 2500 (Illumina) using 50bp single end reads.
Experiment attributes:
GEO Accession: GSM3596768
Links:
Runs: 1 run, 17.8M spots, 890.4M bases, 436.1Mb
Run# of Spots# of BasesSizePublished
SRR855515117,808,260890.4M436.1Mb2019-11-14

ID:
7247655

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