Regulation Of Circadian Gene Expression Research Articles

The circadian regulator PER1 promotes cell reprogramming by inhibiting inflammatory signaling from macrophages.

Circadian regulation of gene expression is prevalent and plays critical roles in cell differentiation. However, its roles in the reprogramming of differentiated cells remain largely unknown. Here, we found that one of the master circadian regulators PER1 promoted virus-mediated reprogramming of mouse embryonic fibroblasts (MEFs) to induced neurons (iNs) and induced pluripotent stem cells (iPSCs). Unexpectedly, PER1 achieved this by repressing inflammatory activation of contaminating macrophages in the MEF culture, rather than by directly modulating the reprogrammability of MEFs. More specifically, we found that transduced viruses activated inflammatory genes in macrophages, such as Tnf encoding TNFα, one of the central inflammatory regulators and an autocrine activator of macrophages. TNFα inhibited iN reprogramming, whereas a TNFα inhibitor promoted iN reprogramming, connecting the inflammatory responses to iN reprogramming. In addition, macrophages were induced to proliferate and mature by non-macrophage cells serving as feeders, which also supported up-regulation of TNFα in macrophages without virus transduction. Furthermore, the 2 inflammatory responses were repressed by the circadian regulator PER1 in macrophages, making reprogrammability dependent on time-of-day of virus transduction. Similar results were obtained with iPSC reprogramming, suggesting a wide occurrence of macrophage-mediated inhibition of cell reprogramming. This study uncovers mechanistic links between cell reprogramming, bystander inflammatory macrophages, and circadian rhythms, which are particularly relevant to in vivo reprogramming and organoid formation incorporating immune cells.

Abstract A152: The oncogene MYC as a driver of circadian clock disruption and dedifferentiation in the lung: implications in early lung carcinogenesis

Abstract Circadian rhythms (24-hour cycles) are disrupted in many human cancers, supporting cancer growth. Non-small cell lung cancers (NSCLCs) exhibit a disrupted molecular circadian clock, and associated alterations in circadian gene expression indicate a poor prognosis. However, it remains unclear how clock disruption occurs in NSCLCs and what NSCLCs gain from this disturbance. The oncogene MYC has been functionally implicated in circadian disruption in a variety of cancer cell lines. In NSCLCs, the MYC or one of its related family members is found mutated or amplified in more than 50% of the cases and its expression correlates with worse survival. BMAL1 is a non-redundant component of the circadian clock and is essential for the overall functionality of this machinery and the circadian regulation of gene expression. Using publicly available data we observed an inverse correlation between the expression of MYC and BMAL1 in LUAD. However, it is unknown if MYC drives clock disruption in the lung and whether clock disruption is functionally required for MYC oncogenic effects. Using an organoid model generated from isolated alveolar type II cells (ATII), the cell of origin lung adenocarcinoma (LUAD), the most prevalent type of NSCLC, we showed that MYC suppresses the expression of BMAL1. In parallel, MYC decreased the expression of specific ATII cell-lineage markers, suggesting the activation of a dedifferentiation program. Using an in vivo mouse model of NSCLC with MYC-inducible expression in ATII cells, we further demonstrated that MYC overexpression for 3 days induces an overall suppression of molecular clock genes, including BMAL1. We also observed that MYC increased the expression of proliferative markers such as Ki67 and promoted the loss of cell-lineage markers in ATII cells, which are early events in lung carcinogenesis. However, it is unclear if these effects are applicable to human LUAD. In human LUAD, we found that molecular subtypes that lack epithelial identity markers and are correlated with worse survival, show lower BMAL1 expression. These data corroborate with a potential implication of the molecular clock on the control of differentiation programs and tumor progression. Circadian clock pharmacological restoration in vivo, using the RORα agonist SR1078, attenuated the expression of the proliferation marker Ki67 induced by MYC in the lung, suggesting that clock disruption potentially mediates MYC oncogenic effects to some extent. Additionally, we performed CUT&TAG in a mouse lung epithelial cell line (MLE12) and identified that BMAL1 binds to the promoter of ATII identity genes (Sftpb, Abca3) and cell cycle genes (Cdk4), suggesting that the molecular clock potentially regulates lung epithelial cell identity and proliferation. Overall, our data identify MYC as a driver of circadian clock disruption in lung alveolar cells which is a potential mechanism implicated in MYC-driven proliferation and dedifferentiation in early-lung cancer. Circadian clock restoration might be a valuable tool to target MYC-amplified tumors. Citation Format: Juliana Cazarin de Menezes, Jamison Burchett, Siti Noor Ain Binti Ahmad Shahidan, Rachel E DeRollo, Brian Altman. The oncogene MYC as a driver of circadian clock disruption and dedifferentiation in the lung: implications in early lung carcinogenesis [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A152.

Transcriptomics-based analysis of sex-differentiated mechanisms of hepatotoxicity in zebrafish after long-term exposure to bisphenol AF

Bisphenol AF (BPAF) is an emerging endocrine-disrupting chemical (EDC) prevalent in the environment as one of the main substitutes for bisphenol A. Sex-specific effects of EDCs have been commonly reported and closely linked to sexually dimorphic patterns of hormone metabolism and related gene expression during different exposure windows, but our understanding of these mechanisms is still limited. Here, following 28-day exposure of adult zebrafish to an environmentally relevant concentration of BPAF at 10 μg/L, the global transcriptional networks applying RNA sequencing (RNA-seq) and Ingenuity Pathway Analysis (IPA) were respectively investigated in the male and female fish liver, connecting the sex-dependent toxicity of the long-term exposure of BPAF to molecular responses. As a result, more differentially expressed genes (DEGs) were detected in males (811) than in females (195), and spermatogenesis was the most enriched Gene Ontology (GO) functional classification in males, while circadian regulation of gene expression was the most enriched GO term in females. The expression levels of selected DEGs were routinely verified using qRT-PCR, which showed consistent alterations with the transcriptional changes in RNA-seq data. The causal network analysis by IPA suggested that the adverse outcomes of BPAF in males including liver damage, apoptosis, inflammation of organ, and liver carcinoma, associated with the regulation of several key DEGs detected in RNA-seq, could be linked to the activation of upstream regulatory molecules ifnα, yap1, and ptger2; while, the inhibition of upstream regulators hif1α, ifng, and igf1, leading to the down-regulated expression of several key DEGs, might be involved in BPAF’s effects in females. Furthermore, BPAF exposure altered hepatic histological structure and inhibited antioxidant capability in both male and female livers. Overall, this study revealed different regulation networks involved in the sex-dependent effects of BPAF on the fish liver, and these detected DEGs upon BPAF exposure might be used as potential biomarkers for further assessing sex-specific hepatotoxicity following environmental EDC exposure.

Effect of 11-Deoxycorticosterone in the Transcriptomic Response to Stress in Rainbow Trout Skeletal Muscle.

In aquaculture, many stressors can negatively affect growth in teleosts. It is believed that cortisol performs glucocorticoid and mineralocorticoid functions because teleosts do not synthesize aldosterone. However, recent data suggest that 11-deoxycorticosterone (DOC) released during stress events may be relevant to modulate the compensatory response. To understand how DOC modifies the skeletal muscle molecular response, we carried out a transcriptomic analysis. Rainbow trout (Oncorhynchus mykiss) were intraperitoneally treated with physiological doses of DOC in individuals pretreated with mifepristone (glucocorticoid receptor antagonist) or eplerenone (mineralocorticoid receptor antagonist). RNA was extracted from the skeletal muscles, and cDNA libraries were constructed from vehicle, DOC, mifepristone, mifepristone plus DOC, eplerenone, and eplerenone plus DOC groups. The RNA-seq analysis revealed 131 differentially expressed transcripts (DETs) induced by DOC with respect to the vehicle group, mainly associated with muscle contraction, sarcomere organization, and cell adhesion. In addition, a DOC versus mifepristone plus DOC analysis revealed 122 DETs related to muscle contraction, sarcomere organization, and skeletal muscle cell differentiation. In a DOC versus eplerenone plus DOC analysis, 133 DETs were associated with autophagosome assembly, circadian regulation of gene expression, and regulation of transcription from RNA pol II promoter. These analyses indicate that DOC has a relevant function in the stress response of skeletal muscles, whose action is differentially modulated by GR and MR and is complementary to cortisol.

Hsa_circ_0072309 is a prognostic biomarker and is correlated with immune infiltration in gastric cancer

BackgroundHsa_circ_0072309 has been identified as a tumor suppressor in several carcinomas. However, its precise role in gastric cancer (GC) remains largely unknown. This study was aimed to explore the precise role of Hsa_circ_0072309 in GC. MethodsThe transcriptional and clinical data of stomach adenocarcinoma were downloaded using the University of California SantaCruz (UCSC) Xena browser. The circular RNA (circRNA) datasets were obtained from the Gene Expression Omnibus (GEO) database. The expression profile and survival analysis of differentially expressed micro RNAs (DEMIs) and differentially expressed messenger RNAs (DEMs) were performed. Correlations between the expression and immune infiltration of the DEMS were studied. Additionally, the expression of hsa_circ_0072309 in GC tissues and cell lines were validated, and the relationship between its expression and clinical features was investigated. Gain- and loss-of function experiments and molecular interaction experiments were also conducted. ResultsOverall, 7 differentially expressed circRNAs, 13 DEMIs, and 17 DEMs were screened. Two DEMIs (hsa_miR-34a-3p and hsa_miR-326) and five DEMs (C7, MARCKSL1, UBE2T, OLR1, and HOXC11) showed significant differences in the high- and low-risk groups. The most significantly enriched Gene Ontology terms were the circadian regulation of gene expression and protein binding. The most significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways were the PI3K-Akt and Ras signal pathways. Additionally, six genes were significantly correlated with immune infiltration. The real-time quantitative PCR (RT-qPCR) results revealed a significant downregulation of hsa_circ_0072309 in GC tissues related to tumor size, vascular invasion, and lymph node metastasis. A hsa_circ_0072309 overexpression suppressed whereas a hsa_circ_0072309 knockdown promoted GC cells proliferation and migration in vitro; in addition, hsa_circ_0072309 could directly bind to has-miR-34a-3p and has-miR-330-5p. ConclusionsHsa_circ_0072309 is a potential diagnostic biomarker for GC, and complement component 7 may be a tumor suppressor. These may potentially predict the prognosis of patients with GC and may become new therapeutic targets.

Transcriptomic Profiling Revealed Signaling Pathways Associated with the Spawning of Female Zebrafish under Cold Stress

As one of the critical abiotic factors, temperature controls fish development and reproduction. However, the effects of low temperature on the transcriptional regulation of zebrafish reproduction remain largely unclear. In this study, the fecundity of zebrafish was examined after exposure to cold temperatures at 19.5 °C, 19 °C, 18.5 °C, or 18 °C. The temperature at 19 °C showed no significant influence on the fecundity of zebrafish, but temperature at 18.5 °C or 18 °C significantly blocked the spawning of females, suggesting the existence of a low temperature critical point for the spawning of zebrafish females. Based on these observations, the brains of anesthetized fish under cold stress at different cold temperatures were collected for high-throughput RNA-seq assays. Key genes, hub pathways and important biological processes responding to cold temperatures during the spawning of zebrafish were identified through bioinformatic analysis. The number of down-regulated and up-regulated genes during the temperature reduction from egg-spawning temperatures at 19.5 °C and 19 °C to non-spawning temperatures at 18.5 °C and 18 °C were 2588 and 2527 (fold change ≥ 1.5 and p-value ≤ 0.01), respectively. Venn analysis was performed to identify up- and down-regulated key genes. KEGG enrichment analysis indicated that the hub pathways overrepresented among down-regulated key genes included the GnRH signaling pathway, vascular smooth muscle contraction, C-type lectin receptor signaling pathway, phosphatidylinositol signaling system and insulin signaling pathway. GO enrichment analysis of down-regulated key genes revealed the most important biological processes inhibited under non-spawning temperatures at 18.5 °C and 18 °C were photoreceptor cell outer segment organization, circadian regulation of gene expression and photoreceptor cell maintenance. Furthermore, 99 hormone-related genes were found in the brain tissues of non-spawning and spawning groups, and GnRH signaling pathway and insulin signaling pathway were enriched from down-regulated genes related to hormones at 18.5 °C and 18 °C. Thus, these findings uncovered crucial hormone-related genes and signaling pathways controlling the spawning of female zebrafish under cold stress.

Circadian Regulation of Gene Expression and Metabolism in the Liver.

Circadian rhythms are approximately 24-hour cycles of variation in physiological processes, gene expression, and behavior. They result from the interplay of internal biological clocks with daily environmental rhythms, including light/dark and feeding/fasting. Note that 24-hour rhythms of liver metabolic processes have been known for almost 100 years. Modern studies reveal that, like metabolism, hepatic gene expression is highly rhythmic. Genetic or environmental changes can disrupt the circadian rhythms of the liver, leading to metabolic disorders and hepatocellular carcinoma. In this review, we summarize the current understanding of mechanisms regulating rhythmic gene expression in the liver, highlighting the roles of transcription factors that comprise the core clock molecular as well as noncanonical regulators. We emphasize the plasticity of circadian rhythms in the liver as it responds to multiple inputs from the external and internal environments as well as the potential of circadian medicine to impact liver-related diseases.

Abstract 9552: RNA Sequencing of Cardiac and Renal Tissue in a Rat Model of Chronic Kidney Disease Reveals Chronodisruption as Common Pathway

Introduction: Chronic kidney disease (CKD) is often accompanied by cardiovascular disease, which is referred to as type 4 cardiorenal syndrome. Management is challenging due to the multifactorial nature of the condition, and treatment of one organ may negatively impact the other. Hypothesis: More insights into the common molecular disease processes in the heart and kidney might provide a source for new therapies. We used RNA sequencing to identify pathways that were dysregulated in both organs. Methods: Cardiac and renal tissue samples from four 5/6 th partial nephrectomized (NX) and four sham-operated (SHAM) female Sprague-Dawley rats were analyzed using RNA sequencing. Strand-specific and rRNA depleted cDNA libraries were generated and were sequenced on NovaSeq (Ilumina) with 20 million reads per library. Results: In comparison to SHAM, the kidneys of NX animals had 290 differentially expressed genes (DEGs), showing increased expression of genes that map to Gene Ontology terms including collagen fibril organization , circadian regulation of gene expression , mitotic cell cycle , neutrophil chemotaxis , and inflammatory response . Within the hearts of NX animals, 8 DEGs were found, including those related to circadian regulation of gene expression (Per2, Per3, Arntl/Bmal1, BHLHE41) , as well as the Adra1d , C2cd4b , Ubtd1 , and Atp2b2 genes. Four genes were differentially expressed in both organs. Three of them were related to circadian rhythm, with Per2 and Per3 being downregulated and Arntl/Bmal1 being upregulated. Furthermore, Adra1d was downregulated in both organs. Conclusions: This comprehensive RNA sequencing in a rat model of type 4 cardiorenal syndrome identified chronodisruption as a common pathway, suggesting that circadian rhythms could be a novel target for intervention. Figure Legend. (A) Venn diagram with number of DEGs and vulcano plots for heart (left) and kidney (right). (B) GO terms for heart. (C) GO terms for kidney.

PSXII-3 Identification of key metabolic mediators during dietary tryptophan supplementation in low-birth-weight pigs by RNA sequencing

Abstract Low birth weight (LBW) is associated with the development of metabolic syndrome, diabetes mellitus and insulin resistance. While tryptophan (Trp), one of essential amino acids supplied by diet, plays an essential role in fetal growth and development, the effects of Trp supplementation on metabolic processes of postnatal LBW individuals remain unclear. The objective of this study was to identify differentially expressed (DE) genes and altered biological processes in liver of LBW and normal birth weight (NBW) piglets supplemented with Trp. RNA was isolated from liver tissues of three weeks old piglets supplemented with Trp (NBW-0% and LBW-0, 0.4, and 0.8%) and was used for RNA sequencing (RNAseq). There were 100, 191 and 39 DE genes in NBW (N0) and LBW tryptophan 0.4%, 0.8% (L4 and L8) when compared to LBW without Trp supplementation (L0). To determine whether Trp supplementation can resume metabolic regulation-related gene expression to N0 level, DE genes from N0 vs. L0 were clustered into 3 groups based on co-expression trends and clusters were enriched for genes associated with lipid catabolic process, circadian regulation of gene expression and fatty acid response. Further, eight hub genes (PID1, PAFAH2, MAP3K15, ANKRD44, CYP2J34, N4BP2L1, RUSC1 and SALL1) identified in co-expression networks based on Pearson correlation coefficient had strong co-expression coefficients (|r| > 0.9) with each other. In particular, PID1 was significantly associated with many neurological, metabolic, environmental and cardiovascular traits based on phenome-wide association analysis (Phe-WAS). In summary, our study provides novel insights into the molecular mechanism underlying LBW metabolic changes with Trp supplementation in porcine liver tissue and highlights that LBW metabolism restoration may be regulated by genes participating in fatty acid response and cardiovascular diseases.

Neurofibromin 1 in mushroom body neurons mediates circadian wake drive through activating cAMP\u2013PKA signaling

Various behavioral and cognitive states exhibit circadian variations in animals across phyla including Drosophila melanogaster, in which only ~0.1% of the brain’s neurons contain circadian clocks. Clock neurons transmit the timing information to a plethora of non-clock neurons via poorly understood mechanisms. Here, we address the molecular underpinning of this phenomenon by profiling circadian gene expression in non-clock neurons that constitute the mushroom body, the center of associative learning and sleep regulation. We show that circadian clocks drive rhythmic expression of hundreds of genes in mushroom body neurons, including the Neurofibromin 1 (Nf1) tumor suppressor gene and Pka-C1. Circadian clocks also drive calcium rhythms in mushroom body neurons via NF1-cAMP/PKA-C1 signaling, eliciting higher mushroom body activity during the day than at night, thereby promoting daytime wakefulness. These findings reveal the pervasive, non-cell-autonomous circadian regulation of gene expression in the brain and its role in sleep.

Evidence for a dysfunction and disease-promoting role of the circadian clock in the diabetic retina

Diabetic retinopathy is a major complication of chronic hyperglycemia and a leading cause of blindness in developed countries. In the present study the interaction between diabetes and retinal clocks was investigated in mice. It was seen that in the db/db mouse – a widely used animal model of diabetic retinopathy – clock function and circadian regulation of gene expression was disturbed in the retina. Remarkably, elimination of clock function by Bmal1-deficiency mitigates the progression of pathophysiology of the diabetic retina. Thus high-fat diet was seen to induce histopathology and molecular markers associated with diabetic retinopathy in wild type but not in Bmal1-deficient mice. The data of the present study suggest that Bmal1/the retinal clock system is both, a target and an effector of diabetes mellitus in the retina and hence represents a putative therapeutic target in the pathogenesis of diabetic retinopathy.

Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi.

The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we investigated whether core circadian clock genes in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply re-wired to different core clock genes. We identified candidate core clock genes based on gene expression features and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between this new set of core candidates and known core clock genes in Kalanchoë fedtschenkoi. We further inferred stomata-related gene targets for known and candidate core clock genes and constructed a gene regulatory network for core clock and stomata-related genes. Our results provide new insight into the mechanism of circadian control of CAM-related genes in K. fedtschenkoi, facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments.

Effect of hyaluronic acid: Mechanistic investigations via topological and functional analysis of its protein interaction network

Purpose: To predict molecular targets and the mechanism of action of hyaluronic acid against various disease conditions.
 Methods: The present study was designed and conducted based on the principle of network pharmacology, protein-protein interaction (PPI) database, and biological process analysis. At a high confidence score, a protein network comprising seventeen human protein targets was achieved from STITCH (Search Tool for Interaction of Chemicals).
 Results: Cytoscape-based protein-protein interaction network (PPIN) with 342 nodes was developed and analyzed to ascertain the molecular basis of hyaluronic acid actions. It revealed that hyaluronic acid was mainly involved in various physiological processes including extracellular matrix (ECM) disassembly, collagen catabolic process, mucopolysaccharide metabolic process, and circadian regulation of gene expression.
 Conclusion: The retrieved pathways are known to be involved in causing several pathologies such as leukemia, psoriasis, tick-borne encephalitis, etc. These pathways are influenced by hyaluronic acid. However, further explanations are required to elucidate whether these targets of hyaluronic acid have a therapeutic or toxicological role.

Transcriptome and Degradome Profiling Reveals a Role of miR530 in the Circadian Regulation of Gene Expression in Kalanchoë marnieriana.

Crassulacean acid metabolism (CAM) is an important photosynthetic pathway for plant adaptation to dry environments. CAM plants feature a coordinated interaction between mesophyll and epidermis functions that involves refined regulations of gene expression. Plant microRNAs (miRNAs) are crucial post-transcription regulators of gene expression, however, their roles underlying the CAM pathway remain poorly investigated. Here, we present a study characterizing the expression of miRNAs in an obligate CAM species Kalanchoë marnieriana. Through sequencing of transcriptome and degradome in mesophyll and epidermal tissues under the drought treatments, we identified differentially expressed miRNAs that were potentially involved in the regulation of CAM. In total, we obtained 84 miRNA genes, and eight of them were determined to be Kalanchoë-specific miRNAs. It is widely accepted that CAM pathway is regulated by circadian clock. We showed that miR530 was substantially downregulated in epidermal peels under drought conditions; miR530 targeted two tandem zinc knuckle/PLU3 domain encoding genes (TZPs) that were potentially involved in light signaling and circadian clock pathways. Our work suggests that the miR530-TZPs module might play a role of regulating CAM-related gene expression in Kalanchoë.

CRYPTOCHROMES confer robustness, not rhythmicity, to circadian timekeeping.

Circadian rhythms are a pervasive property of mammalian cells, tissues and behaviour, ensuring physiological adaptation to solar time. Models of cellular timekeeping revolve around transcriptional feedback repression, whereby CLOCK and BMAL1 activate the expression of PERIOD (PER) and CRYPTOCHROME (CRY), which in turn repress CLOCK/BMAL1 activity. CRY proteins are therefore considered essential components of the cellular clock mechanism, supported by behavioural arrhythmicity of CRY‐deficient (CKO) mice under constant conditions. Challenging this interpretation, we find locomotor rhythms in adult CKO mice under specific environmental conditions and circadian rhythms in cellular PER2 levels when CRY is absent. CRY‐less oscillations are variable in their expression and have shorter periods than wild‐type controls. Importantly, we find classic circadian hallmarks such as temperature compensation and period determination by CK1δ/ε activity to be maintained. In the absence of CRY‐mediated feedback repression and rhythmic Per2 transcription, PER2 protein rhythms are sustained for several cycles, accompanied by circadian variation in protein stability. We suggest that, whereas circadian transcriptional feedback imparts robustness and functionality onto biological clocks, the core timekeeping mechanism is post‐translational.

A high-salt/high fat diet alters circadian locomotor activity and glucocorticoid synthesis in mice.

Salt is an essential nutrient; however, excessive salt intake is a prominent public health concern worldwide. Various physiological functions are associated with circadian rhythms, and disruption of circadian rhythms is a prominent risk factor for cardiovascular diseases, cancer, and immune disease. Certain nutrients are vital regulators of peripheral circadian clocks. However, the role of a high-fat and high-salt (HFS) diet in the regulation of circadian gene expression is unclear. This study aimed to investigate the effect of an HFS diet on rhythms of locomotor activity, caecum glucocorticoid secretion, and clock gene expression in mice. Mice administered an HFS diet displayed reduced locomotor activity under normal light/dark and constant dark conditions in comparison with those administered a normal diet. The diurnal rhythm of caecum glucocorticoid secretion and the expression levels of glucocorticoid-related genes and clock genes in the adrenal gland were disrupted with an HFS diet. These results suggest that an HFS diet alters locomotor activity, disrupts circadian rhythms of glucocorticoid secretion, and downregulates peripheral adrenal gland circadian clock genes.

The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation

The circadian clock in plants temporally coordinates biological processes throughout the day, synchronizing gene expression with diurnal environmental changes. Circadian oscillator proteins are known to regulate the expression of clock-controlled plant genes by controlling their transcription. Here, using a high-throughput RNA-Seq approach, we examined genome-wide circadian and diurnal control of the Arabidopsis transcriptome, finding that the oscillation patterns of different transcripts of multitranscript genes can exhibit substantial differences and demonstrating that the circadian clock affects posttranscriptional regulation. In parallel, we found that two major posttranscriptional mechanisms, alternative splicing (AS; especially intron retention) and alternative polyadenylation (APA), display circadian rhythmicity resulting from oscillation in the genes involved in AS and APA. Moreover, AS-related genes exhibited rhythmic AS and APA regulation, adding another layer of complexity to circadian regulation of gene expression. We conclude that the Arabidopsis circadian clock not only controls transcription of genes but also affects their posttranscriptional regulation by influencing alternative splicing and alternative polyadenylation.

Changes in microRNAs Expression Profile of Mimetic Aging Mice Treated with Melanin from Sepiella japonica Ink.

A natural melanin extracted from Sepiella japonica ink (MSJI) is a polymer with antioxidant properties. In this study, the effects of MSJI treatment on microRNAs differentially expressed during aging in mimetic mice were investigated. The results revealed that 8 miRNAs: mmu-miR-1971, mmu-miR-3070b-3p, mmu-miR-320-3p, mmu-miR-342-3p, mmu-miR-350-3p, mmu-miR-5132-5p, mmu-miR-697, and mmu-miR-712-5p showed significantly different expression between mice treated with MSJI gavage and aging mice. GO analysis and signaling pathway analysis revealed that the predicted target genes were involved in diverse biological processes such as steroid and cholesterol metabolism, xenobiotic, demethylation, and circadian regulation of gene expression, suggesting a potential role in antiaging. The dual-luciferase reporter gene assay confirmed the downregulation of mmu-miR-697 in HS samples and targeting of the Gpt2 which plays an important role in aging. This study supports the hypothesis that MSJI prolongs the cell cycle by acting as an antioxidant to delay decrepitude.

Beyond Transcription: Fine-Tuning of Circadian Timekeeping by Post-Transcriptional Regulation.

The circadian clock is an important endogenous timekeeper, helping plants to prepare for the periodic changes of light and darkness in their environment. The clockwork of this molecular timer is made up of clock proteins that regulate transcription of their own genes with a 24 h rhythm. Furthermore, the rhythmically expressed clock proteins regulate time-of-day dependent transcription of downstream genes, causing messenger RNA (mRNA) oscillations of a large part of the transcriptome. On top of the transcriptional regulation by the clock, circadian rhythms in mRNAs rely in large parts on post-transcriptional regulation, including alternative pre-mRNA splicing, mRNA degradation, and translational control. Here, we present recent insights into the contribution of post-transcriptional regulation to core clock function and to regulation of circadian gene expression in Arabidopsis thaliana.

Comparative transcriptomic analysis of high and low egg-producing duck ovaries

The egg-laying rate is an important indicator of egg production of laying ducks. Egg production directly impacts the economic benefits of the duck industry. In order to obtain better insight into the molecular mechanisms associated with the process of egg production, comparative transcriptomic analysis of the ovaries of Jinding ducks with high and low egg production was performed using the Illumina HiSeq 2500 system. A total of 843 differentially expressed genes (DEGs) was identified, 367 that were down-regulated and 476 that were up-regulated in high egg production (HEP) ovaries, as compared with low egg production (LEP) ovaries. Some genes, such as MC5R, APOD, ORAI1, and DYRK4, were more active in HEP ovaries, indicating that these genes may play important roles in regulation of egg production. Among these 843 DEGs, 685 were assigned to gene ontology (GO) categories. Of these, 25 genes were related to reproduction, and 30 were related to the reproductive process, including some associated with ovarian follicle development, circadian regulation of gene expression, circadian rhythm, and estrogen receptor binding. Furthermore, some important functional pathways were revealed, such as the steroid biosynthesis pathway, the endocrine and other factor-regulated calcium reabsorption pathways, circadian rhythm, the neuroactive ligand-receptor interaction pathway, fatty acid biosynthesis, and the calcium-signaling pathway, which appear to be much more active in the HEP group, as compared to those of the LEP group. The results of this study provide very useful information that may contribute to future functional studies of genes involved in bird reproduction.