Genome Sequencing and Transcriptome Analyses of the Siberian Hamster Hypothalamus Identify Mechanisms for Seasonal Energy Balance

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Genome Sequencing and Transcriptome Analyses of the Siberian Hamster Hypothalamus Identify Mechanisms for Seasonal Energy Balance Genome sequencing and transcriptome analyses of the Siberian hamster hypothalamus identify mechanisms for seasonal energy balance Riyue Baoa,b, Kenneth G. Onishic, Elisabetta Tollad, Fran J. P. Eblinge, Jo E. Lewisf, Richard L. Andersong, Perry Barrettg, Brian J. Prendergastc,h, and Tyler J. Stevensond,1 aCenter for Research Informatics, University of Chicago, Chicago, IL 60637; bDepartment of Pediatrics, University of Chicago, Chicago, IL 60637; cInstitute for Mind and Biology, University of Chicago, Chicago, IL 60637; dInstitute for Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G61 1QH, United Kingdom; eSchool of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom; fInstitute of Metabolic Sciences, University of Cambridge, Cambridge CB2 0QQ, United Kingdom; gRowett Institute, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom; and hDepartment of Psychology, University of Chicago, Chicago, IL 60637 Edited by Donald Pfaff, The Rockefeller University, New York, NY, and approved May 13, 2019 (received for review February 18, 2019) Synthesis of triiodothyronine (T3) in the hypothalamus induces service of timing seasonal biology (6, 7). Enzymes that act on marked seasonal neuromorphology changes across taxa. How thyroid hormones, in particular the iodothyronine deiodinases species-specific responses to T3 signaling in the CNS drive annual (type 2 and 3; DIO2 and DIO3, respectively) respond to seasonal changes in body weight and energy balance remains uncharacterized. changes in photoperiod-driven melatonin secretion and govern These experiments sequenced and annotated the Siberian hamster peri-hypothalamic catabolism of the prohormone thyroxine (T4), (Phodopus sungorus) genome, a model organism for seasonal phys- which limits T3-driven changes in neuroendocrine activity. T3 induces iology research, to facilitate the dissection of T3-dependent molecular ligand-dependent rearrangement of the thyroid hormone receptor mechanisms that govern predictable, robust, and long-term changes (TR), and T drives the vast majority of TR-induced gene expression in body weight. Examination of the Phodopus genome, in combina- 3 (8). Increased hypothalamic T production in long summer days, tion with transcriptome sequencing of the hamster diencephalon un- 3 der winter and summer conditions, and in vivo-targeted expression driven in most amniotes by peri-hypothalamic DIO2-mediated con- PHYSIOLOGY analyses confirmed that proopiomelanocortin (pomc) is a primary ge- version of T4 to the biologically active hormone T3, activates anabolic neuroendocrine pathways that maintain reproductive competence nomic target for the long-term T3-dependent regulation of body weight. Further in silico analyses of pomc promoter sequences and increase body weight. Decreased T3 signaling is afforded by peri- revealed that thyroid hormone receptor 1β-binding motif insertions hypothalamic DIO3 expression, which catabolizes T4 and T3 into have evolved in several genera of the Cricetidae family of rodents. receptor-inactive amines, and is associated with adaptation to re- Finally, experimental manipulation of food availability confirmed that productively inhibitory photoperiods (9–12).Indiversetaxa,DIO2 hypothalamic pomc mRNA expression is dependent on longer-term photoperiod cues and is unresponsive to acute, short-term food avail- Significance ability. These observations suggest that species-specific responses to hypothalamic T3, driven in part by the receptor-binding motif inser- The genome and hypothalamic transcriptome of the Siberian tions in some cricetid genomes, contribute critically to the long-term hamster were sequenced and annotated to identify transcrip- regulation of energy balance and the underlying physiological and tional pathways that exhibit seasonal plasticity in energy bal- behavioral adaptations associated with the seasonal organization ance. Adaptation to short winter days reversed seasonal of behavior. obesity and down-regulated hypothalamic proopiomelano- cortin, and exogenous triiodothyronine reinstated weight triiodothyronine | proopiomelanocortin | seasonal | obesity gain and proopiomelanocortin expression. In silico analyses identified the evolution of thyroid hormone receptor binding heostatic regulation of physiological processes is pervasive motifs in the proximal promoter of the proopiomelanocortin R(1), and naturally occurring, long-term programmed seasonal gene of hamsters and other Cricetidae. Energetic challenges reproduction and energy balance is one salient example. High- imposed by food restriction elicited orexigenic and anorexi- amplitude seasonal cycles in energy balance and somatic growth are genic neuropeptide responses in the hypothalamus, but did not common in nature and provide a unique and valuable opportunity affect proopiomelanocortin, which was regulated only by to identify the genomic and molecular pathways involved in rheo- photoperiod. Hypothalamic proopiomelanocortin is main- static control of physiology (2–5). Siberian hamsters (Phodopus tained by photoperiod-driven triiodothyronine signaling and sungorus) exhibit marked changes in energy balance as they adapt thereby affords adaptive long-term temporal organization of from a summer to a winter environment in nature: a decrease in day physiological systems that regulate energy balance. length (i.e., photoperiod) below ∼13 h light/day triggers seasonal infertility, anorexia, and a dramatic decrease in body fat (2). Con- Author contributions: R.B., E.T., F.J.P.E., P.B., B.J.P., and T.J.S. designed research; R.B., K.G.O., E.T., J.E.L., R.L.A., and T.J.S. performed research; R.B., K.G.O., E.T., F.J.P.E., J.E.L., sequently, Phodopus provide a unique and important model for R.L.A., P.B., and T.J.S. analyzed data; and R.B., B.J.P., and T.J.S. wrote the paper. neuroendocrine, physiological, and behavioral mechanisms that The authors declare no conflict of interest. govern long-term seasonal regulation of body weight and re- This article is a PNAS Direct Submission. production (2, 5); these robust phenotypic changes in physiology This open access article is distributed under Creative Commons Attribution-NonCommercial- and behavior can be recapitulated in the laboratory with manipu- NoDerivatives License 4.0 (CC BY-NC-ND). lations of day length (photoperiod) alone. Data deposition: The Siberian hamster genome is available in GenBank (https://www.ncbi. Triiodothyronine (T3)-responsive neuro-glial substrates figure nlm.nih.gov/nuccore/1056038647). prominently in the transduction of photoperiod signals into the 1To whom correspondence may be addressed. Email: [email protected]. neuroendocrine system. T3-responsive targets in the central This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. nervous system (CNS) constitute an evolutionarily conserved 1073/pnas.1902896116/-/DCSupplemental. system that orchestrates morphological brain plasticity in the www.pnas.org/cgi/doi/10.1073/pnas.1902896116 PNAS Latest Articles | 1of6 Downloaded by guest on September 28, 2021 and DIO3 responses to environmental cues (e.g., photoperiod, or through daily torpor, which conserves energy (14). The absence hours of light per day) have established links between tissue-specific of comprehensive genomic information for Phodopus has limited patterns of T3 signaling and seasonal changes in reproduction and molecular insights into the physiological processes that regulate ponderal growth/regression (2, 6). Conspicuously absent are insights these seasonal adaptations in energy balance. To address this into how T3 signaling impacts hypothalamic orexigenic/anorexigenic deficiency, we used Illumina sequencing to draft the Siberian neuropeptide systems that govern changes in energy balance man- hamster genome (SI Appendix, Table S1 and Fig. S1; ref. 15). To datory to support these seasonal cycles of reproduction and complement genome annotation and to identify molecular pathways life history. involved in energy balance, a seasonal hypothalamic transcriptome was also sequenced and annotated.Transcriptomicanalyseswere Results and Discussion performed on hypothalamic RNA from adult male hamsters fol- Characterization of the Siberian Hamster Genome and Photoperiodic lowing adaptation to long-day (LD) and SD photoperiods. Over Diencephalon. Seasonal changes in day length are sufficient to 5,000 unique transcripts were identified, and 32 exhibited significant induce a constellation of changes in Siberian hamster physiology expression changes between the photoperiods [false discovery rate that support adaptation to and survival of winter: exposure to a (FDR) < 0.05-corrected; SI Appendix,TableS2]withthetopdif- short-day photoperiod (SD) causes molt to a more insulative fur ferentially expressed protein-coding transcripts shown (Fig. 1D). (Fig. 1A) and gonadal involution (P < 0.001; Fig. 1B), body Multiple RNAs that have previously been implicated individually in weight is strikingly reduced in SD, white adipose tissue is de- the long-term, neuroendocrine control of reproductive physiology pleted (P < 0.001; Fig. 1C), and brown adipose tissue thermo- were identified, including thyrotropin-stimulating hormone subunit-β genic capacity is augmented (13). Nocturnal foraging persists (tshβ), neuropeptide VF precursor (npvf), and iodothyronine throughout the winter months, but metabolic rate is decreased deiodinase type III (dio3;Fig.1E and SI Appendix,Fig.S2). Gene A B 1000 C 60 50 800 40 600 *** 30 400
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