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Vincent EP, Perry BW, Kelley JL, Robbins CT, Jansen HT. Circadian gene transcription plays a role in cellular metabolism in hibernating brown bears, Ursus arctos. J Comp Physiol B 2023; 193:699-713. [PMID: 37819371 DOI: 10.1007/s00360-023-01513-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 10/13/2023]
Abstract
Hibernation is a highly seasonal physiological adaptation that allows brown bears (Ursus arctos) to survive extended periods of low food availability. Similarly, daily or circadian rhythms conserve energy by coordinating body processes to optimally match the environmental light/dark cycle. Brown bears express circadian rhythms in vivo and their cells do in vitro throughout the year, suggesting that these rhythms may play important roles during periods of negative energy balance. Here, we use time-series analysis of RNA sequencing data and timed measurements of ATP production in adipose-derived fibroblasts from active and hibernation seasons under two temperature conditions to confirm that rhythmicity was present. Culture temperature matching that of hibernation body temperature (34 °C) resulted in a delay of daily peak ATP production in comparison with active season body temperatures (37 °C). The timing of peaks of mitochondrial gene transcription was altered as were the amplitudes of transcripts coding for enzymes of the electron transport chain. Additionally, we observed changes in mean expression and timing of key metabolic genes such as SIRT1 and AMPK which are linked to the circadian system and energy balance. The amplitudes of several circadian gene transcripts were also reduced. These results reveal a link between energy conservation and a functioning circadian system in hibernation.
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Affiliation(s)
- Ellery P Vincent
- School of Biological Sciences, Washington State University, Pullman, WA, 99163, USA
| | - Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, WA, 99163, USA
| | - Joanna L Kelley
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Charles T Robbins
- School of Biological Sciences, Washington State University, Pullman, WA, 99163, USA
- School of the Environment, Washington State University, Pullman, WA, 99163, USA
| | - Heiko T Jansen
- School of Biological Sciences, Washington State University, Pullman, WA, 99163, USA.
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, 99163, USA.
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2
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Stenzinger M, Karpova D, Unterrainer C, Harenkamp S, Wiercinska E, Hoerster K, Pfeffer M, Maronde E, Bonig H. Hematopoietic-Extrinsic Cues Dictate Circadian Redistribution of Mature and Immature Hematopoietic Cells in Blood and Spleen. Cells 2019; 8:E1033. [PMID: 31491915 PMCID: PMC6769956 DOI: 10.3390/cells8091033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 12/27/2022] Open
Abstract
Circadian oscillations in circulating leukocyte subsets including immature hematopoietic cells have been appreciated; the origin and nature of these alterations remain elusive. Our analysis of wild-type C57BL/6 mice under constant darkness confirmed circadian fluctuations of circulating leukocytes and clonogenic cells in blood and spleen but not bone marrow. Clock gene deficient Bmal1-/- mice lacked this regulation. Cell cycle analyses in the different hematopoietic compartments excluded circadian changes in total cell numbers, rather favoring shifting hematopoietic cell redistribution as the underlying mechanism. Transplant chimeras demonstrate that circadian rhythms within the stroma mediate the oscillations independently of hematopoietic-intrinsic cues. We provide evidence of circadian CXCL12 regulation via clock genes in vitro and were able to confirm CXCL12 oscillation in bone marrow and blood in vivo. Our studies further implicate cortisol as the conveyor of circadian input to bone marrow stroma and mediator of the circadian leukocyte oscillation. In summary, we establish hematopoietic-extrinsic cues as causal for circadian redistribution of circulating mature/immature blood cells.
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Affiliation(s)
- Miriam Stenzinger
- Institute for Immunology, University Hospital Heidelberg and Institute for Clinical Transfusion Medicine and Cell Therapy, 69120 Heidelberg, Germany
- Institute for Transfusion Medicine and Immunohematology, Goethe University and German Red Cross Blood Service Baden-Württemberg-Hessen, Institute Frankfurt a. M.; 60528 Frankfurt a. M., Germany
| | - Darja Karpova
- Institute for Transfusion Medicine and Immunohematology, Goethe University and German Red Cross Blood Service Baden-Württemberg-Hessen, Institute Frankfurt a. M.; 60528 Frankfurt a. M., Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christian Unterrainer
- Institute for Immunology, University Hospital Heidelberg and Institute for Clinical Transfusion Medicine and Cell Therapy, 69120 Heidelberg, Germany
| | - Sabine Harenkamp
- Institute for Transfusion Medicine and Immunohematology, Goethe University and German Red Cross Blood Service Baden-Württemberg-Hessen, Institute Frankfurt a. M.; 60528 Frankfurt a. M., Germany
| | - Eliza Wiercinska
- Institute for Transfusion Medicine and Immunohematology, Goethe University and German Red Cross Blood Service Baden-Württemberg-Hessen, Institute Frankfurt a. M.; 60528 Frankfurt a. M., Germany
| | - Keven Hoerster
- Institute for Transfusion Medicine and Immunohematology, Goethe University and German Red Cross Blood Service Baden-Württemberg-Hessen, Institute Frankfurt a. M.; 60528 Frankfurt a. M., Germany
| | - Martina Pfeffer
- Institute for Anatomy II, Division of Medicine, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Erik Maronde
- Institute for Anatomy III, Goethe University, 60596 Frankfurt a. M., Germany
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, Goethe University and German Red Cross Blood Service Baden-Württemberg-Hessen, Institute Frankfurt a. M.; 60528 Frankfurt a. M., Germany.
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3
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Abstract
Background Oscillations of different origin, period and amplitude play an important role in the regulation of cellular processes. Most widely studied is the circadian or approximately daily variation in gene expression activity. Timing of gene expression is controlled by internal molecular clock keeping steady periodic expression. In this study, we shift attention towards a broad range of periodically expressed genes involved in multiple cellular functions which may or may not be under direct control of the intrinsic circadian clock. Are all molecular functions represented in expressed genes at all times? Alternatively, are different molecular functions performed at different times? Is there a pattern of succession for molecular processes and functions throughout their daily activity period? Results To answer these questions, we re-analyzed a number of mouse circadian gene expression data available from public sources. These data represent the normal function of metabolically active peripheral tissues (white adipose tissue, brown adipose tissue, liver). We applied novel methods for the estimation of confidence in phase assignment to identify groups of synchronous genes peaking at the same time regardless of the amplitude or the absolute intensity of expression. Each synchronous group has been annotated to identify Gene Ontology (GO) terms and molecular pathways. Our analysis identified molecular functions specific to a particular time of the day in different tissues. Conclusion Improved methodology for datamining allowed for the discovery of functions and biological pathways in groups of genes with synchronized peak expression time. In particular, such functions as oxidative phase of energy metabolism, DNA repair, mRNA processing, lipid biosynthesis and others are separated in time. This timewise compartmentalization is important for understanding the cellular circuitry and can be used to optimize the time of intervention with drug or genome medication. Electronic supplementary material The online version of this article (10.1186/s12920-018-0325-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Andrey Ptitsyn
- Sidra Medicine, PO Box 26999, Doha, Qatar. .,Present Address: Gloucester Marine Genomics Institute, 2 Blackburn Center, Gloucester, MA, 01930, USA.
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4
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Ptitsyna N, Boughorbel S, El Anbari M, Ptitsyn A. The role of alternative Polyadenylation in regulation of rhythmic gene expression. BMC Genomics 2017; 18:576. [PMID: 28778154 PMCID: PMC5544998 DOI: 10.1186/s12864-017-3958-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/25/2017] [Indexed: 01/11/2023] Open
Abstract
Background Alternative transcription is common in eukaryotic cells and plays important role in regulation of cellular processes. Alternative polyadenylation results from ambiguous PolyA signals in 3′ untranslated region (UTR) of a gene. Such alternative transcripts share the same coding part, but differ by a stretch of UTR that may contain important functional sites. Methods The methodoogy of this study is based on mathematical modeling, analytical solution, and subsequent validation by datamining in multiple independent experimental data from previously published studies. Results In this study we propose a mathematical model that describes the population dynamics of alternatively polyadenylated transcripts in conjunction with rhythmic expression such as transcription oscillation driven by circadian or metabolic oscillators. Analysis of the model shows that alternative transcripts with different turnover rates acquire a phase shift if the transcript decay rate is different. Difference in decay rate is one of the consequences of alternative polyadenylation. Phase shift can reach values equal to half the period of oscillation, which makes alternative transcripts oscillate in abundance in counter-phase to each other. Since counter-phased transcripts share the coding part, the rate of translation becomes constant. We have analyzed a few data sets collected in circadian timeline for the occurrence of transcript behavior that fits the mathematical model. Conclusion Alternative transcripts with different turnover rate create the effect of rectifier. This “molecular diode” moderates or completely eliminates oscillation of individual transcripts and stabilizes overall protein production rate. In our observation this phenomenon is very common in different tissues in plants, mice, and humans. The occurrence of counter-phased alternative transcripts is also tissue-specific and affects functions of multiple biological pathways. Accounting for this mechanism is important for understanding the natural and engineering the synthetic cellular circuits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3958-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natalia Ptitsyna
- Embry-Riddle Aeronautical University, Daytona Beach, FL, 32114, USA
| | | | | | - Andrey Ptitsyn
- Sidra Medical and Research Center, P.O. box 26999, Doha, Qatar. .,Present affiliation: Gloucester Marine Genomics Institute, Gloucester, MA, 01930, USA.
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Durgan DJ, Crossland RF, Bryan RM. The rat cerebral vasculature exhibits time-of-day-dependent oscillations in circadian clock genes and vascular function that are attenuated following obstructive sleep apnea. J Cereb Blood Flow Metab 2017; 37:2806-2819. [PMID: 27798273 PMCID: PMC5536790 DOI: 10.1177/0271678x16675879] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Circadian clock components oscillate in cells of the cardiovascular system. Disruption of these oscillations has been observed in cardiovascular diseases. We hypothesized that obstructive sleep apnea, which is associated with cerebrovascular diseases, disrupts the cerebrovascular circadian clock and rhythms in vascular function. Apneas were produced in rats during sleep. Following two weeks of sham or obstructive sleep apnea, cerebral arteries were isolated over 24 h for mRNA and functional analysis. mRNA expression of clock genes exhibited 24-h rhythms in cerebral arteries of sham rats (p < 0.05). Interestingly, peak expression of clock genes was significantly lower following obstructive sleep apnea (p < 0.05). Obstructive sleep apnea did not alter clock genes in the heart, or rhythms in locomotor activity. Isolated posterior cerebral arteries from sham rats exhibited a diurnal rhythm in sensitivity to luminally applied ATP, being most responsive at the beginning of the active phase (p < 0.05). This rhythm was absent in arteries from obstructive sleep apnea rats (p < 0.05). Rhythms in ATP sensitivity in sham vessels were absent, and not different from obstructive sleep apnea, following treatment with L-NAME and indomethacin. We conclude that cerebral arteries possess a functional circadian clock and exhibit a diurnal rhythm in vasoreactivity to ATP. Obstructive sleep apnea attenuates these rhythms in cerebral arteries, potentially contributing to obstructive sleep apnea-associated cerebrovascular disease.
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Affiliation(s)
- David J Durgan
- Department of Anesthesiology, Baylor College of Medicine, Houston, USA
| | - Randy F Crossland
- Department of Anesthesiology, Baylor College of Medicine, Houston, USA
| | - Robert M Bryan
- Department of Anesthesiology, Baylor College of Medicine, Houston, USA
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6
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Zhang R, Podtelezhnikov AA, Hogenesch JB, Anafi RC. Discovering Biology in Periodic Data through Phase Set Enrichment Analysis (PSEA). J Biol Rhythms 2016; 31:244-57. [PMID: 26955841 DOI: 10.1177/0748730416631895] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Several tools use prior biological knowledge to interpret gene expression data. However, existing enrichment tools assume that variables are monotonic and incorrectly measure the distance between periodic phases. As a result, these tools are poorly suited for the analysis of the cell cycle, circadian clock, or other periodic systems. Here, we develop Phase Set Enrichment Analysis (PSEA) to incorporate prior knowledge into the analysis of periodic data. PSEA identifies biologically related gene sets showing temporally coordinated expression. Using synthetic gene sets of various sizes generated from von Mises (circular normal) distributions, we benchmarked PSEA alongside existing methods. PSEA offered enhanced sensitivity over a broad range of von Mises distributions and gene set sizes. Importantly, and unlike existing tools, the sensitivity of PSEA is independent of the mean expression phase of the set. We applied PSEA to 4 published datasets. Application of PSEA to the mouse circadian atlas revealed that several pathways, including those regulating immune and cell-cycle function, demonstrate temporal orchestration across multiple tissues. We then applied PSEA to the phase shifts following a restricted feeding paradigm. We found that this perturbation disrupts intraorgan metabolic synchrony in the liver, altering the timing between anabolic and catabolic pathways. Reanalysis of expression data using custom gene sets derived from recent ChIP-seq results revealed circadian transcriptional targets bound exclusively by CLOCK, independently of BMAL1, differ from other exclusive circadian output genes and have well-synchronized phases. Finally, we used PSEA to compare 2 cell-cycle datasets. PSEA increased the apparent biological overlap while also revealing evidence of cell-cycle dysregulation in these cancer cells. To encourage its use by the community, we have implemented PSEA as a Java application. In sum, PSEA offers a powerful new tool to investigate large-scale, periodic data for biological insight.
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Affiliation(s)
- Ray Zhang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Alexei A Podtelezhnikov
- Department of Genetics and Pharmacogenomics, Merck Research Laboratories, West Point, Pennsylvania
| | - John B Hogenesch
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, Ohio
| | - Ron C Anafi
- Department of Medicine and Center for Sleep and Circadian Neurobiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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7
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Montenegro-Montero A, Larrondo LF. In the Driver's Seat: The Case for Transcriptional Regulation and Coupling as Relevant Determinants of the Circadian Transcriptome and Proteome in Eukaryotes. J Biol Rhythms 2015; 31:37-47. [PMID: 26446874 DOI: 10.1177/0748730415607321] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Circadian clocks drive daily oscillations in a variety of biological processes through the coordinate orchestration of precise gene expression programs. Global expression profiling experiments have suggested that a significant fraction of the transcriptome and proteome is under circadian control, and such output rhythms have historically been assumed to rely on the rhythmic transcription of these genes. Recent genome-wide studies, however, have challenged this long-held view and pointed to a major contribution of posttranscriptional regulation in driving oscillations at the messenger RNA (mRNA) level, while others have highlighted extensive clock translational regulation, regardless of mRNA rhythms. There are various examples of genes that are uniformly transcribed throughout the day but that exhibit rhythmic mRNA levels, and of flat mRNAs, with oscillating protein levels, and such observations have largely been considered to result from independent regulation at each step. These studies have thereby obviated any connections, or coupling, that might exist between the different steps of gene expression and the impact that any of them could have on subsequent ones. Here, we argue that due to both biological and technical reasons, the jury is still out on the determination of the relative contributions of each of the different stages of gene expression in regulating output molecular rhythms. In addition, we propose that through a variety of coupling mechanisms, gene transcription (even when apparently arrhythmic) might play a much relevant role in determining oscillations in gene expression than currently estimated, regulating rhythms at downstream steps. Furthermore, we posit that eukaryotic genomes regulate daily RNA polymerase II (RNAPII) recruitment and histone modifications genome-wide, setting the stage for global nascent transcription, but that tissue-specific mechanisms locally specify the different processes under clock control.
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Affiliation(s)
- Alejandro Montenegro-Montero
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis F Larrondo
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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8
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El Anbari M, Fadda A, Ptitsyn A. Confidence in Phase Definition for Periodicity in Genes Expression Time Series. PLoS One 2015; 10:e0131111. [PMID: 26161537 PMCID: PMC4498625 DOI: 10.1371/journal.pone.0131111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/28/2015] [Indexed: 11/24/2022] Open
Abstract
Circadian oscillation in baseline gene expression plays an important role in the regulation of multiple cellular processes. Most of the knowledge of circadian gene expression is based on studies measuring gene expression over time. Our ability to dissect molecular events in time is determined by the sampling frequency of such experiments. However, the real peaks of gene activity can be at any time on or between the time points at which samples are collected. Thus, some genes with a peak activity near the observation point have their phase of oscillation detected with better precision then those which peak between observation time points. Separating genes for which we can confidently identify peak activity from ambiguous genes can improve the analysis of time series gene expression. In this study we propose a new statistical method to quantify the phase confidence of circadian genes. The numerical performance of the proposed method has been tested using three real gene expression data sets.
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Affiliation(s)
- Mohammed El Anbari
- Division of Biomedical Informatics, Sidra Medical and Research Center, Doha, Qatar
- * E-mail:
| | - Abeer Fadda
- Division of Biomedical Informatics, Sidra Medical and Research Center, Doha, Qatar
| | - Andrey Ptitsyn
- Division of Biomedical Informatics, Sidra Medical and Research Center, Doha, Qatar
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9
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Luna A, McFadden GB, Aladjem MI, Kohn KW. Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response. PLoS Comput Biol 2015; 11:e1004144. [PMID: 26020938 PMCID: PMC4462596 DOI: 10.1371/journal.pcbi.1004144] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 01/20/2015] [Indexed: 02/06/2023] Open
Abstract
The circadian clock is a set of regulatory steps that oscillate with a period of approximately 24 hours influencing many biological processes. These oscillations are robust to external stresses, and in the case of genotoxic stress (i.e. DNA damage), the circadian clock responds through phase shifting with primarily phase advancements. The effect of DNA damage on the circadian clock and the mechanism through which this effect operates remains to be thoroughly investigated. Here we build an in silico model to examine damage-induced circadian phase shifts by investigating a possible mechanism linking circadian rhythms to metabolism. The proposed model involves two DNA damage response proteins, SIRT1 and PARP1, that are each consumers of nicotinamide adenine dinucleotide (NAD), a metabolite involved in oxidation-reduction reactions and in ATP synthesis. This model builds on two key findings: 1) that SIRT1 (a protein deacetylase) is involved in both the positive (i.e. transcriptional activation) and negative (i.e. transcriptional repression) arms of the circadian regulation and 2) that PARP1 is a major consumer of NAD during the DNA damage response. In our simulations, we observe that increased PARP1 activity may be able to trigger SIRT1-induced circadian phase advancements by decreasing SIRT1 activity through competition for NAD supplies. We show how this competitive inhibition may operate through protein acetylation in conjunction with phosphorylation, consistent with reported observations. These findings suggest a possible mechanism through which multiple perturbations, each dominant during different points of the circadian cycle, may result in the phase advancement of the circadian clock seen during DNA damage. Many physiological processes are regulated by the circadian clock, and we are continuing to learn about the role of the circadian clock in disease. Research in recent years has begun to shed light on the feedback mechanisms that exist between circadian regulation and other processes, including metabolism and the response to DNA damage. A challenge has been to understand the dynamic nature of the protein interactions of these processes, which often involve protein modification as a means of communicating cellular states, such as damaged DNA. Here we have devised a model that simulates an alteration of the circadian clock that is observed during DNA damage response. A novel aspect of this model is the inclusion of SIRT1, a protein that regulates core circadian proteins through modification and helps to repress gene expression. SIRT1 is dependent on a metabolite regulated by the circadian clock and is depleted during DNA damage. In conjunction with a second form of protein modification, our results suggest that multiple forms of protein modification may contribute to the experimentally observed alterations to circadian function.
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Affiliation(s)
- Augustin Luna
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
- Department of Bioinformatics, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
| | - Geoffrey B. McFadden
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
| | - Mirit I. Aladjem
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Kurt W. Kohn
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
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10
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Wu G, Zhu J, Yu J, Zhou L, Huang JZ, Zhang Z. Evaluation of five methods for genome-wide circadian gene identification. J Biol Rhythms 2015; 29:231-42. [PMID: 25238853 DOI: 10.1177/0748730414537788] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Identification of circadian-regulated genes based on temporal transcriptome data is important for studying the regulation mechanism of the circadian system. However, various computational methods adopting different strategies for the identification of cycling transcripts usually yield inconsistent results even for the same dataset, making it challenging to choose the optimal method for a specific circadian study. To address this challenge, we evaluate 5 popular methods, including ARSER (ARS), COSOPT (COS), Fisher's G test (FIS), HAYSTACK (HAY), and JTK_CYCLE (JTK), based on both simulated and empirical datasets. Our results show that increasing the number of total samples (through improving sampling frequency or lengthening the sampling time window) is beneficial for computational methods to accurately identify circadian transcripts and measure circadian phase. For a given number of total samples, higher sampling frequency is more important for HAY and JTK, and the longer sampling time window is more crucial for ARS and COS, as testified on simulated and empirical datasets from which circadian signals are computationally identified. In addition, the preference of higher sampling frequency or the longer sampling time window is also obvious for JTK, ARS, and COS in estimating circadian phases of simulated periodic profiles. Our results also indicate that attention should be paid to the significance threshold that is used for each method in selecting circadian genes, especially when analyzing the same empirical dataset with 2 or more methods. To summarize, for any study involving genome-wide identification of circadian genes from transcriptome data, our evaluation results provide suggestions for the selection of an optimal method based on specific goal and experimental design.
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Affiliation(s)
- Gang Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jiang Zhu
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Lan Zhou
- Department of Statistics, Texas A&M University, College Station, Texas, USA
| | - Jianhua Z Huang
- Department of Statistics, Texas A&M University, College Station, Texas, USA
| | - Zhang Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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11
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Prevalence of cycling genes and drug targets calls for prospective chronotherapeutics. Proc Natl Acad Sci U S A 2014; 111:15869-70. [PMID: 25368193 DOI: 10.1073/pnas.1418570111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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12
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A circadian gene expression atlas in mammals: implications for biology and medicine. Proc Natl Acad Sci U S A 2014; 111:16219-24. [PMID: 25349387 DOI: 10.1073/pnas.1408886111] [Citation(s) in RCA: 1476] [Impact Index Per Article: 147.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
To characterize the role of the circadian clock in mouse physiology and behavior, we used RNA-seq and DNA arrays to quantify the transcriptomes of 12 mouse organs over time. We found 43% of all protein coding genes showed circadian rhythms in transcription somewhere in the body, largely in an organ-specific manner. In most organs, we noticed the expression of many oscillating genes peaked during transcriptional "rush hours" preceding dawn and dusk. Looking at the genomic landscape of rhythmic genes, we saw that they clustered together, were longer, and had more spliceforms than nonoscillating genes. Systems-level analysis revealed intricate rhythmic orchestration of gene pathways throughout the body. We also found oscillations in the expression of more than 1,000 known and novel noncoding RNAs (ncRNAs). Supporting their potential role in mediating clock function, ncRNAs conserved between mouse and human showed rhythmic expression in similar proportions as protein coding genes. Importantly, we also found that the majority of best-selling drugs and World Health Organization essential medicines directly target the products of rhythmic genes. Many of these drugs have short half-lives and may benefit from timed dosage. In sum, this study highlights critical, systemic, and surprising roles of the mammalian circadian clock and provides a blueprint for advancement in chronotherapy.
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Wu G, Zhu J, He F, Wang W, Hu S, Yu J. Gene and genome parameters of mammalian liver circadian genes (LCGs). PLoS One 2012; 7:e46961. [PMID: 23071677 PMCID: PMC3468600 DOI: 10.1371/journal.pone.0046961] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/07/2012] [Indexed: 11/19/2022] Open
Abstract
The mammalian circadian system controls various physiology processes and behavior responses by regulating thousands of circadian genes with rhythmic expressions. In this study, we redefined circadian-regulated genes based on published results in the mouse liver and compared them with other gene groups defined relative to circadian regulations, especially the non-circadian-regulated genes expressed in liver at multiple molecular levels from gene position to protein expression based on integrative analyses of different datasets from the literature. Based on the intra-tissue analysis, the liver circadian genes or LCGs show unique features when compared to other gene groups. First, LCGs in general have less neighboring genes and larger in both genomic and 3'-UTR lengths but shorter in CDS (coding sequence) lengths. Second, LCGs have higher mRNA and protein abundance, higher temporal expression variations, and shorter mRNA half-life. Third, more than 60% of LCGs form major co-expression clusters centered in four temporal windows: dawn, day, dusk, and night. In addition, larger and smaller LCGs are found mainly expressed in the day and night temporal windows, respectively, and we believe that LCGs are well-partitioned into the gene expression regulatory network that takes advantage of gene size, expression constraint, and chromosomal architecture. Based on inter-tissue analysis, more than half of LCGs are ubiquitously expressed in multiple tissues but only show rhythmical expression in one or limited number of tissues. LCGs show at least three-fold lower expression variations across the temporal windows than those among different tissues, and this observation suggests that temporal expression variations regulated by the circadian system is relatively subtle as compared with the tissue expression variations formed during development. Taken together, we suggest that the circadian system selects gene parameters in a cost effective way to improve tissue-specific functions by adapting temporal variations from the environment over evolutionary time scales.
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Affiliation(s)
- Gang Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Jiang Zhu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Fuhong He
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Weiwei Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Chin SL, Marcus IM, Klevecz RR, Li CM. Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators. FEBS J 2012; 279:1119-30. [PMID: 22289124 DOI: 10.1111/j.1742-4658.2012.08508.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Genetic and environmental factors are well-studied influences on phenotype; however, time is a variable that is rarely considered when studying changes in cellular phenotype. Time-resolved microarray data revealed genome-wide transcriptional oscillation in a yeast continuous culture system with ∼ 2 and ∼ 4 h periods. We mapped the global patterns of transcriptional oscillations into a 3D map to represent different cellular phenotypes of redox cycles. This map shows the dynamic nature of gene expression in that transcripts are ordered and coupled to each other through time and concentration space. Although cells differed in oscillation periods, transcripts involved in certain processes were conserved in a deterministic way. When oscillation period lengthened, the peak to trough ratio of transcripts increased and the fraction of cells in the unbudded (G0/G1) phase of the cell division cycle increased. Decreasing the glucose level in the culture medium was one way to increase the redox cycle, possibly from changes in metabolic flux. The period may be responding to lower glucose levels by increasing the fraction of cells in G1 and reducing S-phase gating so that cells can spend more time in catabolic processes. Our results support that gene transcripts are coordinated with metabolic functions and the cell division cycle.
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Affiliation(s)
- Shwe L Chin
- Dynamic Systems Group, Division of Biology, City of Hope Beckman Research Institute, Duarte, CA, USA
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Abstract
What mechanisms control circadian rhythms in the gastrointestinal tract and how does this impact nutrient metabolism? The deadenylase and leucine zipper protein Nocturnin is now shown to play a central role.
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Affiliation(s)
- Jeffrey M Gimble
- Stem Cell Biology, Louisiana State University System, Baton Rouge, LA 70808, USA.
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Ptitsyn AA, Reyes-Solis G, Saavedra-Rodriguez K, Betz J, Suchman EL, Carlson JO, Black WC. Rhythms and synchronization patterns in gene expression in the Aedes aegypti mosquito. BMC Genomics 2011; 12:153. [PMID: 21414217 PMCID: PMC3072344 DOI: 10.1186/1471-2164-12-153] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 03/17/2011] [Indexed: 12/11/2022] Open
Abstract
Background Aedes aegypti is arguably the most studied of all mosquito species in the laboratory and is the primary vector of both Dengue and Yellow Fever flaviviruses in the field. A large number of transcriptional studies have been made in the species and these usually report transcript quantities observed at a certain age or stage of development. However, circadian oscillation is an important characteristic of gene expression in many animals and plants, modulating both their physiology and behavior. Circadian gene expression in mosquito species has been previously reported but for only a few genes directly involved in the function of the molecular clock. Results Herein we analyze the transcription profiles of 21,494 messenger RNAs using an Ae. aegypti Agilent® microarray. Transcripts were quantified in adult female heads at 24 hours and then again at 72 hours and eight subsequent time points spaced four hours apart. We document circadian rhythms in multiple molecular pathways essential for growth, development, immune response, detoxification/pesticide resistance. Circadian rhythms were also noted in ribosomal protein genes used for normalization in reverse transcribed PCR (RT-PCR) to determine transcript abundance. We report pervasive oscillations and intricate synchronization patterns relevant to all known biological pathways. Conclusion These results argue strongly that transcriptional analyses either need to be made over time periods rather than confining analyses to a single time point or development stage or exceptional care needs to be made to synchronize all mosquitoes to be analyzed and compared among treatment groups.
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Affiliation(s)
- Andrey A Ptitsyn
- Center for Bioinformatics, Colorado State University, Fort Collins, CO 80525, USA
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Bray MS, Young ME. Regulation of fatty acid metabolism by cell autonomous circadian clocks: time to fatten up on information? J Biol Chem 2011; 286:11883-9. [PMID: 21296875 DOI: 10.1074/jbc.r110.214643] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Molecular, cellular, and animal-based studies have recently exposed circadian clocks as critical regulators of energy balance. Invariably, mouse models of genetically manipulated circadian clock components display features indicative of altered lipid/fatty acid metabolism, including differential adiposity and circulating lipids. The purpose of this minireview is to provide a comprehensive summary of current knowledge regarding the regulation of fatty acid metabolism by distinct cell autonomous circadian clocks. The implications of these recent findings for cardiometabolic disease and human health are discussed.
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Affiliation(s)
- Molly S Bray
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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