Transcriptional Profiling of Daily Patterns of mRNA Expression in the C57BL/6J Mouse Cornea

Physiological Effects of Soat1 Inactivation on Homeostasis of the Mouse Ocular Surface

Purpose

Soat1/SOAT1 have been previously reported to be critical for the biosynthesis of cholesteryl esters (CEs) in the mouse Meibomian glands (MGs) as the loss of function led to an arrest of CE production and a substantial accumulation of nonesterified cholesterol in the meibum, causing an increase in its melting temperature. The purpose of this study was to further investigate the role of Soat1 in meibogenesis and ocular surface physiology.

Methods

The mouse ocular features of knockout Soat1-/- and wild type (WT) mice were studied using various ophthalmic and histological techniques, mouse lipidomes were monitored using liquid chromatography/mass spectrometry, whereas their transcriptomes were compared to characterize the effects of the mutation on the gene expression profiles in the MG and cornea.

Results

Soat1-/- mice displayed increased tear production and severe corneal abnormalities, such as corneal thinning, (neo)vascularization, ulceration, and opacification that progressed with aging. Transcriptomic analyses led to identification of a range of significantly disrupted pathways, which included general and specific lipid metabolism-related pathways, keratinization, angiogenesis/(neo)vascularization, muscle contraction, and several other pathways. In addition, histological and histochemical experiments revealed morphological changes in the MG, cornea, and conjunctiva in Soat1-/- mice. Notably, the mRNA microarray expression level of Soat1 in WT MGs (log2 17.5) was 1000 × of that in the mouse cornea (log2 7.5).

Conclusions

These findings suggest a direct involvement of Soat1/SOAT1 in MGs in maintaining ocular surface homeostasis, in general, and corneal health, specifically.

Chronic sleep deprivation impairs retinal circadian transcriptome and visual function

Sleep loss is common in modern society and is increasingly associated with eye diseases. However, the precise effects of sleep loss on retinal structure and function, particularly on the retinal circadian system, remain largely unexplored. This study investigates these effects using a chronic sleep deprivation (CSD) model in mice. Our investigation reveals that CSD significantly alters the retinal circadian transcriptome, leading to remarkable changes in the temporal patterns of enriched pathways. This perturbation extends to metabolic and immune-related transcriptomes, coupled with an accumulation of reactive oxygen species in the retina. Notably, CSD rhythmically affects the thickness of the ganglion cell complex, along with diurnal shifts in microglial migration and morphology within the retina. Most critically, we observe a marked decrease in both scotopic and photopic retinal function under CSD conditions. These findings underscore the broad impact of sleep deprivation on retinal health, highlighting its role in altering circadian gene expression, metabolism, immune response, and structural integrity. Our study provides new insights into the broader impact of sleep loss on retinal health.

Temporal dynamics and composition of ocular surface microbiota in C57BL/6J mice: uncovering a 12h ultradian rhythm

Purpose

This study aimed to investigate the presence of rhythmic fluctuations in the composition, abundance, and functions of commensal core bacteria on the ocular surface of C57BL/6J mice.

Methods

Male C57BL/6J mice, aged 12 weeks, were subjected to a 12-hour light/12-hour dark cycle. Ocular surface tissue samples were collected at four time points (ZT) over a 24-hour period at six-hour intervals. The core ocular surface microbiota's oscillation cycles and frequencies were assessed using 16S rRNA gene sequencing targeting the V3-V4 region, along with the JTK_CYCLE algorithm. Functional predictions of these bacteria were conducted using PICRUSt2.

Results

Deep sequencing of the ocular surface microbiota highlighted the high abundance of commensal bacteria, with Proteobacteria, Actinobacteriota, and Firmicutes collectively constituting over 90% of the total sample abundance. Among the 22 core bacterial genera, 11 exhibited robust 12-hour rhythms, including Halomonas, Pelagibacterium, Pseudomonas, Nesterenkonia, norank_f_Hyphomonadaceae, Stenotrophomonas, Anoxybacillus, Acinetobacter, Zoogloea, Brevibacillus, and Ralstonia. Further taxonomic analysis indicated significant intra-cluster similarities and inter-cluster differences at the order, family, and genus levels during ZT0/12 and ZT6/18. Community interaction networks and functional prediction analyses revealed synchronized 12-hour rhythmic oscillations in neural, immune, metabolic, and other pathways associated with symbiotic bacteria.

Conclusion

This study demonstrates the presence of ultradian rhythmic oscillations in commensal bacteria on the ocular surface of normal C57BL/6J mice, with a 12-hour cycle. These findings suggest a crucial role for ultradian rhythms in maintaining ocular surface homeostasis in the host.

Sympathetic Nerves Coordinate Corneal Epithelial Wound Healing by Controlling the Mobilization of Ly6Chi Monocytes From the Spleen to the Injured Cornea

Purpose

This study aims to investigate the potential involvement of spleen-derived monocytes in the repair process following corneal epithelial abrasion.

Methods

A corneal epithelial abrasion model was established in male C57BL/6J mice, and the dynamic changes of monocyte subpopulations in the injured cornea were analyzed using flow cytometry. The effects of Ly6Chi monocyte depletion and local adoptive transfer of purified Ly6Chi monocytes on wound closure and neutrophil recruitment to the injured cornea were observed. The effect of sympathetic nerves on the recruitment of spleen-derived Ly6Chi monocytes to the injured cornea was also investigated using multiple methods. The emigration of fluorescence-labeled monocytes to the injured cornea was validated through intravital microscopy. Finally, differential genes between different groups were identified through high-throughput RNA sequencing and analyzed for functional enrichment, followed by verification by quantitative PCR.

Results

Ly6Chi monocytes were present in large numbers in the injured cornea prior to neutrophil recruitment. Predepletion of Ly6Chi monocytes significantly inhibited neutrophil recruitment to the injured cornea. Furthermore, surgical removal of the spleen significantly reduced the number of Ly6Chi monocytes in the injured cornea. Further observations revealed that sympathetic blockade significantly reduced the number of Ly6Chi monocytes recruited to the injured cornea. In contrast, administration of the β2-adrenergic receptor agonist significantly increased the number of Ly6Chi monocytes recruited to the injured cornea in animals treated with sympathectomy and catecholamine synthesis inhibition.

Conclusions

Our results suggest that spleen-derived Ly6Chi monocytes, under the control of the sympathetic nervous system, play a critical role in the inflammatory response following corneal injury.

Preservation of ∼12-h ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock

Introduction: Besides the ∼24-h circadian rhythms, ∼12-h ultradian rhythms of gene expression, metabolism and behaviors exist in animals ranging from crustaceans to mammals. Three major hypotheses were proposed on the origin and mechanisms of regulation of ∼12-h rhythms, namely, that they are not cell-autonomous and controlled by a combination of the circadian clock and environmental cues, that they are regulated by two anti-phase circadian transcription factors in a cell autonomous manner, or that they are established by a cell-autonomous ∼12-h oscillator. Methods: To distinguish among these possibilities, we performed a post hoc analysis of two high temporal resolution transcriptome dataset in animals and cells lacking the canonical circadian clock. Results: In both the liver of BMAL1 knockout mice and Drosophila S2 cells, we observed robust and prevalent ∼12-h rhythms of gene expression enriched in fundamental processes of mRNA and protein metabolism that show large convergence with those identified in wild-type mice liver. Bioinformatics analysis further predicted ELF1 and ATF6B as putative transcription factors regulating the ∼12-h rhythms of gene expression independently of the circadian clock in both fly and mice. Discussion: These findings provide additional evidence to support the existence of an evolutionarily conserved 12-h oscillator that controls ∼12-h rhythms of gene expression of protein and mRNA metabolism in multiple species.

Preservation of ∼12-hour ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock

Besides the ∼24-hour circadian rhythms, ∼12-hour ultradian rhythms of gene expression, metabolism and behaviors exist in animals ranging from crustaceans to mammals. Three major hypotheses were proposed on the origin and mechanisms of regulation of ∼12-hour rhythms, namely that they are not cell-autonomous and controlled by a combination of the circadian clock and environmental cues, that they are regulated by two anti-phase circadian transcriptional factors in a cell-autonomous manner, or that they are established by a cell-autonomous ∼12-hour oscillator. To distinguish among these possibilities, we performed a post-hoc analysis of two high temporal resolution transcriptome dataset in animals and cells lacking the canonical circadian clock. In both the liver of BMAL1 knockout mice and Drosophila S2 cells, we observed robust and prevalent ∼12-hour rhythms of gene expression enriched in fundamental processes of mRNA and protein metabolism that show large convergence with those identified in wild-type mice liver. Bioinformatics analysis further predicted ELF1 and ATF6B as putative transcription factors regulating the ∼12-hour rhythms of gene expression independently of the circadian clock in both fly and mice. These findings provide additional evidence to support the existence of an evolutionarily conserved 12-hour oscillator that controls ∼12-hour rhythms of gene expression of protein and mRNA metabolism in multiple species.

High-fat intake reshapes the circadian transcriptome profile and metabolism in murine meibomian glands

Background

Nutritional and food components reshape the peripheral clock and metabolism. However, whether food challenges affect the circadian clock and metabolism of meibomian glands (MGs) has not been fully explored. This study was designed to analyze alterations in the rhythmic transcriptome and metabolism of MGs of murine fed a balanced diet or a high-fat diet (HFD).

Methods

Male C57BL/6J mice were maintained on a 12/12 h light/dark cycle and fed ad libitum on normal chow (NC) or HFD for 4 weeks. MGs were collected from sacrificed animals at 3-h intervals throughout a 24-h circadian cycle. The circadian transcriptome of MGs was analyzed via bioinformatics approaches using high-throughput RNA sequencing (RNA-seq). In addition, circadian oscillations of lipid components in MGs were analyzed.

Results

Meibomian glands displayed robust transcriptome rhythmicity. HFD feeding significantly altered the circadian transcriptome profile of MGs—including composition and phase—and spatiotemporally affected the enriched signaling pathways. In addition, HFD feeding significantly altered the normal rhythmic oscillations of lipid components in MGs.

Conclusion

Our data show that HFD significantly affects MGs’ rhythmicity, which reveals a high sensitivity of MGs’ clocks to lipid composition in food.

Sleep Loss Causes Dysfunction in Murine Extraorbital Lacrimal Glands

Purpose

Sleep loss markedly affects the structure and function of the lacrimal gland and may cause ocular surface disease as a common public health problem. This study aims to investigate the circadian disturbance caused by sleep loss leading to dysfunction of extraorbital lacrimal glands (ELGs).

Methods

A mouse sleep deprivation (SD) model for sleep loss studies was built in C57BL/6J male mice. After four weeks, the ELGs were collected at three-hour intervals during a 24-hour period. The Jonckheere-Terpstra-Kendall algorithm was used to determine the composition, phase, and rhythmicity of transcriptomic profiles in ELGs. Furthermore, we compared the non-sleep-deprived and SD-treated mouse ELG (i) reactive oxygen species (ROS) by fluorescein staining, (ii) DNA damage by immunostaining for γ-H2Ax, and (iii) circadian migration of immune cells by immunostaining for CD4, CD8, γδ-TCR, CD64, and CX3CR1. Finally, we also evaluated (i) the locomotor activity and core body temperature rhythm of mice and (ii) the mass, cell size, and tear secretion of the ELGs.

Results

SD dramatically altered the composition and phase-associated functional enrichment of the circadian transcriptome, immune cell trafficking, metabolism, cell differentiation, and neural secretory activities of mouse ELGs. Additionally, SD caused the ROS accumulation and consequent DNA damage in the ELGs, and the ELG dysfunction caused by SD was irreversible.

Conclusions

SD damages the structure, function, and diurnal oscillations of ELGs. These results highlight comprehensive characterization of insufficient sleep–affected ELG circadian transcriptome that may provide a new therapeutic approach to counteract the effects of SD on ELG function.

TRPV1+ sensory nerves modulate corneal inflammation after epithelial abrasion via RAMP1 and SSTR5 signaling

Timely initiation and termination of inflammatory response after corneal epithelial abrasion is critical for the recovery of vision. The cornea is innervated with rich sensory nerves with highly dense TRPV1 nociceptors. However, the roles of TRPV1⁺ sensory neurons in corneal inflammation after epithelial abrasion are not completely understood. Here, we found that depletion of TRPV1⁺ sensory nerves using resiniferatoxin (RTX) and blockade of TRPV1 using AMG-517 delayed corneal wound closure and enhanced the infiltration of neutrophils and γδ T cells to the wounded cornea after epithelial abrasion. Furthermore, depletion of TRPV1⁺ sensory nerves increased the number and TNF-α production of corneal CCR2⁺ macrophages and decreased the number of corneal CCR2^- macrophages and IL-10 production. In addition, the TRPV1⁺ sensory nerves inhibited the recruitment of neutrophils and γδ T cells to the cornea via RAMP1 and SSTR5 signaling, decreased the responses of CCR2⁺ macrophages via RAMP1 signaling, and increased the responses of CCR2^- macrophages via SSTR5 signaling. Collectively, our results suggest that the TRPV1⁺ sensory nerves suppress inflammation to support corneal wound healing via RAMP1 and SSTR5 signaling, revealing potential approaches for improving defective corneal wound healing in patients with sensory neuropathy.

Tip60 might be a candidate for the acetylation of hepatic carbonic anhydrase I and III in mice

BACKGROUND

Carbonic anhydrases (CAs) play a significant role in maintaining pH balance by catalyzing the conversion of carbon dioxide to bicarbonate. The regulation of pH is critical for all living organisms. Although there are many studies in the literature on the biochemical, functional, and structural features of CAs, there is not sufficient information about the epigenetic regulation of CAs.

METHODS AND RESULTS

The lysine acetyltransferase TIP60 (60 kDa Tat-interactive protein) was knocked out specifically in mouse liver using the Cre/loxP system, and knockout rate was shown as 83-88% by Southern blot analysis. The impact of Tip60 on the expression of Ca1, Ca3, and Ca7 was investigated at six Zeitgeber time (ZT) points in the control and liver-specific Tip60 knockout mice (mutant) groups by real-time PCR. In the control group, while Ca1 showed the highest expression at ZT8 and ZT12, the lowest expression profile was observed at ZT0 and ZT20. Hepatic Ca1 displayed robust circadian expression. However, hepatic Ca3 exhibited almost the same level of expression at all ZT points. The highest expression of Ca7 was observed at ZT12, and the lowest expression was determined at ZT4. Furthermore, hepatic Ca7 also showed robust circadian expression. The expression of Ca1 and Ca3 significantly decreased in mutant mice at all time periods, but the expression of Ca7 used as a negative control was not affected.

CONCLUSIONS

It was suggested for the first time that Tip60 might be considered a candidate protein in the regulation of the Ca1 and Ca3 genes, possibly by acetylation.

Short-Term High Fructose Intake Impairs Diurnal Oscillations in the Murine Cornea

Purpose

Endogenous and exogenous stressors, including nutritional challenges, may alter circadian rhythms in the cornea. This study aimed to determine the effects of high fructose intake (HFI) on circadian homeostasis in murine cornea.

Methods

Corneas of male C57BL/6J mice subjected to 10 days of HFI (15% fructose in drinking water) were collected at 3-hour intervals over a 24-hour circadian cycle. Total extracted RNA was subjected to high-throughput RNA sequencing. Rhythmic transcriptional data were analyzed to determine the phase, rhythmicity, unique signature, metabolic pathways, and cell signaling pathways of transcripts with temporally coordinated expression. Corneas of HFI mice were collected for whole-mounted techniques after immunofluorescent staining to quantify mitotic cell number in the epithelium and trafficking of neutrophils and γδ-T cells to the limbal region over a circadian cycle.

Results

HFI significantly reprogrammed the circadian transcriptomic profiles of the normal cornea and reorganized unique temporal and clustering enrichment pathways, but did not affect core-clock machinery. HFI altered the distribution pattern and number of corneal epithelial mitotic cells and enhanced recruitment of neutrophils and γδ-T cell immune cells to the limbus across a circadian cycle. Cell cycle, immune function, metabolic processes, and neuronal-related transcription and associated pathways were altered in the corneas of HFI mice.

Conclusions

HFI significantly reprograms diurnal oscillations in the cornea based on temporal and spatial distributions of epithelial mitosis, immune cell trafficking, and cell signaling pathways. Our findings reveal novel molecular targets for treating pathologic alterations in the cornea after HFI.

The daily gene transcription cycle in mouse retina

Many physiological retinal processes, such as outer segment disk shedding and visual sensitivity, exhibit a daily rhythm. However, the detailed transcriptome dynamics and related biological processes of the retina are not fully understood. Retinal tissues were collected from C57BL/6J male mice housed in a 12h light/12h dark (LD) cycle for 4 weeks, at Zeitgeber time (ZT) 0, 4, 8, 12, 16, and 20. Total RNA was extracted from the tissues and used for unique identifier RNA sequencing experiments. The rhythmicity of gene expression was determined using the MetaCycle R package. We found that 1741 genes (10.26%) were rhythmically expressed in the retina. According to the expression patterns, the rhythmically expressed genes were assigned to four clusters, each with about 361-492 genes, using the Mfuzz R package. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were conducted to identify pathways and biological processes of the profiled genes. Genes in Clusters 1 and 4 were associated with glycolysis and energy production, showed higher activity at night (from ZT16 to ZT20), and were enriched in the Hif-1α signaling pathway and low-oxygen-related terms. Genes in Cluster 2 were predominantly involved in cilium assembly and organization and were relatively upregulated during the day. Genes in Cluster 3 were associated with ribosome biosynthesis and were highly expressed during the day-night transition period. Taken together, these results demonstrate that a large proportion of retinal genes are expressed rhythmically. Genes involved in energy production and glycolysis are highly expressed at night, leading to relative hypoxia and activation of the Hif-1α signaling pathway. Genes associated with the formation of photoreceptor cilia are expressed during the day.

Diurnal Control of Sensory Axon Growth and Shedding in the Mouse Cornea

Purpose

The circadian clock plays an important role in the expression and regulation of various genes and cellular processes in the body. Here, we study diurnal regulation of the growth and shedding of the sensory axons in the mouse cornea.

Methods

Male and female BALB/cN mice were euthanized 90 minutes before and after the lights are turned on and off; at 5:30 AM, 8:30 AM, 5:30 PM, and 8:30 PM. Nerve terminal growth, shedding and overall axon density were assessed at these four time points using confocal imaging after staining axons in en face whole mount corneas with antibodies against βIII tubulin, GAP43, and L1CAM. In addition, corneal epithelial cell proliferation, thickness, and desquamation were assessed using ki67, LAMP1, Involucrin, and ZO1.

Results

Nerve terminal shedding took place between 5:30 AM and 8:30 AM and correlated positively with the timing of apical cell desquamation. After shedding the tips of the nerve terminals, axonal growth increased as indicated by increased axonal GAP43 expression. At 5:30 PM and 8:30 PM before and after the lights are turned off, cell proliferation was reduced, and epithelial thickness was maximal.

Conclusions

Intraepithelial corneal nerve growth and shedding are under diurnal control regulated by the time of day and whether lights are on or off. Axons extend during the day and are shed within 90 minutes after lights are turned on. The data presented in this article shed light on the potential role that circadian clock plays in corneal pain and discomfort.

Light cycle phase advance as a model for jet lag reprograms the circadian rhythms of murine extraorbital lacrimal glands

PURPOSE

Jet lag causes a disruption in physiological rhythms in humans. This study aims to explore the extent to which jet lag affects the circadian rhythmicity in the lacrimal glands.

METHODS

C57BL/6J mice were subjected to a 12-h light/12-h dark (LD) cycle and an 8-h advanced LD schedule as a model for jet lag. On day 5 after the LD advance, the extraorbital lacrimal glands (ELGs) were collected at 3-h intervals during a 24-h cycle. Total mRNA was extracted from normal and advanced LD-treated ELGs and assayed using high-throughput RNA sequencing. The rhythmic transcripts were identified, analyzed, and visualized by bioinformatics techniques. Finally, (i) animal behavior; (ii) the mass, cell size, and secretion response of ELGs; and (iii) circadian migration of immune cells to ELGs were also assayed.

RESULTS

Jet lag treatment drastically altered the phase and composition of the rhythmic transcripts compared to that of normal ELGs. The key biological processes, signaling pathways, and protein-protein association networks were also dramatically altered in a spatiotemporal pattern. Furthermore, the circadian migration of neutrophils, T cells, B cells, and macrophages to the ELGs increased and shifted later by 6-h. Finally, the circadian rhythms of the ELGs with respect to mass, cell size, and secretion response were also impaired in jet lag-treated animals.

CONCLUSIONS

Jet lag impairs the circadian rhythm of the transcriptomic profile, structure, and secretion function of the lacrimal glands. This information provides novel insight into the negative effects of jet lag on ELGs.

Revealing the hidden reality of the mammalian 12-h ultradian rhythms

Biological oscillations often cycle at different harmonics of the 24-h circadian rhythms, a phenomenon we coined "Musica Universalis" in 2017. Like the circadian rhythm, the 12-h oscillation is also evolutionarily conserved, robust, and has recently gained new traction in the field of chronobiology. Originally thought to be regulated by the circadian clock and/or environmental cues, recent new evidences support the notion that the majority of 12-h rhythms are regulated by a distinct and cell-autonomous pacemaker that includes the unfolded protein response (UPR) transcription factor spliced form of XBP1 (XBP1s). 12-h cycle of XBP1s level in turn transcriptionally generates robust 12-h rhythms of gene expression enriched in the central dogma information flow (CEDIF) pathway. Given the regulatory and functional separation of the 12-h and circadian clocks, in this review, we will focus our attention on the mammalian 12-h pacemaker, and discuss our current understanding of its prevalence, evolutionary origin, regulation, and functional roles in both physiological and pathological processes.

Recent advances in modulators of circadian rhythms: an update and perspective

Circadian rhythm is a universal life phenomenon that plays an important role in maintaining the multiple physiological functions and regulating the adaptability to internal and external environments of flora and fauna. Circadian alignment in humans has the greatest effect on human health, and circadian misalignment is closely associated with increased risk for metabolic syndrome, cardiovascular diseases, neurological diseases, immune diseases, cancer, sleep disorders, and ophthalmic diseases. The recent description of clock proteins and related post-modification targets was involved in several diseases, and numerous lines of evidence are emerging that small molecule modulators of circadian rhythms can be used to rectify circadian disorder. Herein, we attempt to update the disclosures about the modulators targeting core clock proteins and related post-modification targets, as well as the relationship between circadian rhythm disorders and human health as well as the therapeutic role and prospect of these small molecule modulators in circadian rhythm related disease.

Type 1 diabetes mellitus impairs diurnal oscillations in murine extraorbital lacrimal glands

PURPOSE

People with diabetes are at high risk of lacrimal gland dysfunction, but the underlying mechanism is not well understood. In this study, we determined how type 1 diabetes mellitus (T1DM) influences circadian homeostasis of the murine extraorbital lacrimal glands (ELGs).

METHODS

A T1DM animal model was established by systemic streptozotocin injection in C57BL/6J mice. After 5 weeks, ELGs were collected at 3-h intervals over a 24-h circadian cycle. Total extracted RNA was subjected to high-throughput RNA sequencing, and rhythmic transcriptional data were evaluated using the Jonckheere-Terpstra-Kendall algorithm, Kyoto Encyclopedia of Genes and Genomes pathway analysis, Phase Set Enrichment Analysis, and time series cluster analysis to determine the phase, rhythmicity, and unique signature of the transcripts over temporally coordinated expression. Additionally, mass, cell size, histology, and tear secretion of the ELGs were evaluated.

RESULTS

T1DM globally altered the composition of the ELG transcriptome. Specifically, T1DM significantly reprogrammed the circadian transcriptomic profiles of normal ELGs and reorganized core clock machinery. Unique temporal and clustering enrichment pathways were also rewired by T1DM. Finally, normal daily rhythms of mass, cell size, and tear secretion of mouse ELGs were significantly impaired by streptozotocin-induced diabetes.

CONCLUSIONS

T1DM significantly reprograms the diurnal oscillations of the lacrimal glands and impairs their structure and tear secretion. This information may reveal potential targets for improving lacrimal gland dysfunction in patients with diabetes.

Circadian analysis of the mouse retinal pigment epithelium transcriptome

The presence of a phagocytic peak of photoreceptor outer segments by the retinal pigment epithelium (RPE) one or 2 h after the onset of light has been reported for several diurnal and nocturnal species. This peak in phagocytic activity also persists under constant lighting conditions (i.e., constant light or dark) thus demonstrating that the timing of this peak is driven by a circadian clock. The aim of this study was to investigate the change in RPE whole transcriptome at two different circadian times (CT; 1 h before (CT23) and 1 h after (CT1) subjective light onset). C57BL/6J male mice were maintained in constant dark conditions for three days and euthanized under red light (<1 lux) at CT23 and CT1. RPE was isolated from whole eyes for RNA library preparation and sequencing on an Illumina HiSeq4000 platform. 14,083 mouse RPE transcripts were detected in common between CT23 and CT1. 12,005 were protein coding transcripts and 2078 were non-protein coding transcripts. 2421 protein coding transcripts were significantly upregulated whereas only 3 transcripts were significantly downregulated and 12 non-protein coding transcripts were significantly upregulated and 31 non-protein coding transcripts were significantly downregulated at CT1 when compared to CT23 (p < 0.05, fold change ≥ ±2.0). Of the protein coding transcripts, most of them were characterized as: enzymes, kinases, and transcriptional regulators with a large majority of activity in the cytoplasm, nucleus, and plasma membrane. Non-protein coding transcripts included biotypes such as long-non coding RNAs and pseudogenes. Gene ontology analysis and ingenuity pathway analysis revealed that differentially expressed transcripts were associated with integrin signaling, oxidative phosphorylation, protein phosphorylation, and actin cytoskeleton remodeling suggesting that these previously identified phagocytic pathways are under circadian control. Our analysis identified new pathways (e.g., increased mitochondrial respiration via increased oxidative phosphorylation) that may be involved in the circadian control of phagocytic activity. In addition, our dataset suggests a possible regulatory role for the identified non-protein coding transcripts in mediating the complex function of RPE phagocytosis. Finally, our results also indicate, as seen in other tissues, about 20% of the whole RPE transcriptome may be under circadian clock regulation.