1
|
Wegener C, Amatobi KM, Ozbek-Unal AG, Fekete A. Circadian Control of Lipid Metabolism. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024. [PMID: 38874889 DOI: 10.1007/5584_2024_810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
To ensure optimum health and performance, lipid metabolism needs to be temporally aligned to other body processes and to daily changes in the environment. Central and peripheral circadian clocks and environmental signals such as light provide internal and external time cues to the body. Importantly, each of the key organs involved in insect lipid metabolism contains a molecular clockwork which ticks with a varying degree of autonomy from the central clock in the brain. In this chapter, we review our current knowledge about peripheral clocks in the insect fat body, gut and oenocytes, and light- and circadian-driven diel patterns in lipid metabolites and lipid-related transcripts. In addition, we highlight selected neuroendocrine signaling pathways that are or may be involved in the temporal coordination and control of lipid metabolism.
Collapse
Affiliation(s)
- Christian Wegener
- Neurobiology and Genetics, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany.
| | - Kelechi M Amatobi
- Neurobiology and Genetics, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Ayten Gizem Ozbek-Unal
- Pharmaceutical Biology, Julius-von-Sachs-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Agnes Fekete
- Pharmaceutical Biology, Julius-von-Sachs-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| |
Collapse
|
2
|
Luis JR, Palencia-Madrid L, Runfeldt G, Garcia-Bertrand R, Herrera RJ. Delineating the dispersal of Y-chromosome sub-haplogroup O2a2b-P164 among Austronesian-speaking populations. Sci Rep 2024; 14:2066. [PMID: 38267477 PMCID: PMC10808098 DOI: 10.1038/s41598-024-52293-z] [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: 08/12/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024] Open
Abstract
This article reports on an exploration of the Y-chromosome sub-haplogroup O2a2b-P164 in Austronesian-speaking populations. Moderate to high abundance of the P 164 mutation is seen in the West Pacific including the Amis of Formosa (36%) and the Filipinos of Mindanao (50%) as well as in the Kiritimati of Micronesia (70%), and Tonga and Samoa of West Polynesia (54% and 33%, respectively), and it drops to low frequencies in populations of East Polynesia. The communities of Polynesia and Micronesia exhibit considerable inter- and intra-population haplotype sharing suggesting extensive population affinity. The observed affinities, as well as the ages and diversity values within the P 164 sub-haplogroup among Austronesian-speaking populations signal an ancestral migration route and relationships that link the Amis of Taiwan with distant communities in West and East Polynesia, Micronesia, and the Maori of New Zealand. High resolution sequencing of the Austronesian Y chromosome indicate that the P 164 lineage originated about 19,000 ya and then split into three branches separating the Ami aborigines, Southeast Asian and Polynesian/Micronesian populations about 4700 ya, roughly coinciding with the initiation of the Austronesian diaspora. The Y-chromosomes of all the Polynesian and Micronesian population examined belong to the new FT 257096 haplogroup.
Collapse
Affiliation(s)
- Javier Rodriguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Campus Sur s/n, 15782, Santiago de Compostela, Spain
| | - Leire Palencia-Madrid
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006, Vitoria-Gasteiz, Spain
| | | | - Ralph Garcia-Bertrand
- Department of Molecular Biology, Colorado College, 14 East Cache La Poudre Street, Colorado Springs, CO, 80903-3294, USA
| | - Rene J Herrera
- Department of Molecular Biology, Colorado College, 14 East Cache La Poudre Street, Colorado Springs, CO, 80903-3294, USA.
| |
Collapse
|
3
|
Lee S, Hong CI. Organoids as Model Systems to Investigate Circadian Clock-Related Diseases and Treatments. Front Genet 2022; 13:874288. [PMID: 35559029 PMCID: PMC9086274 DOI: 10.3389/fgene.2022.874288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
Circadian rhythms exist in most cell types in mammals regulating temporal organization of numerous cellular and physiological processes ranging from cell cycle to metabolism. The master clock, suprachiasmatic nucleus (SCN) in the hypothalamus, processes light input and coordinates peripheral clocks optimizing organisms' survival and functions aligning with external conditions. Intriguingly, it was demonstrated that circadian rhythms in the mouse liver can be decoupled from the master clock under time-restricted feeding regimen when food was provided during their inactive phase. Furthermore, mouse liver showed clock-controlled gene expression even in the absence of the master clock demonstrating independent functions of peripheral clocks apart from the SCN. These findings suggest a dynamic relationship between the master and peripheral clocks and highlight potential functions of peripheral clocks independent of the master clock. Importantly, disruption of circadian rhythms correlates with numerous human ailments including cancer and metabolic diseases, suggesting that diseases may be exacerbated by disruption of circadian rhythms in the SCN and/or peripheral clocks. However, molecular mechanisms providing causative links between circadian rhythms and human diseases remain largely unknown. Recent technical advances highlighted PCS- and tissue-derived 3-dimensional organoids as in vitro organs that possess numerous applications ranging from disease modeling to drug screening. In this mini-review, we highlight recent findings on the importance and contributions of peripheral clocks and potential uses of 3D organoids investigating complex circadian clock-related diseases.
Collapse
Affiliation(s)
| | - Christian I. Hong
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| |
Collapse
|
4
|
Miozzo F, Valencia-Alarcón EP, Stickley L, Majcin Dorcikova M, Petrelli F, Tas D, Loncle N, Nikonenko I, Bou Dib P, Nagoshi E. Maintenance of mitochondrial integrity in midbrain dopaminergic neurons governed by a conserved developmental transcription factor. Nat Commun 2022; 13:1426. [PMID: 35301315 PMCID: PMC8931002 DOI: 10.1038/s41467-022-29075-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/25/2022] [Indexed: 12/21/2022] Open
Abstract
Progressive degeneration of dopaminergic (DA) neurons in the substantia nigra is a hallmark of Parkinson’s disease (PD). Dysregulation of developmental transcription factors is implicated in dopaminergic neurodegeneration, but the underlying molecular mechanisms remain largely unknown. Drosophila Fer2 is a prime example of a developmental transcription factor required for the birth and maintenance of midbrain DA neurons. Using an approach combining ChIP-seq, RNA-seq, and genetic epistasis experiments with PD-linked genes, here we demonstrate that Fer2 controls a transcriptional network to maintain mitochondrial structure and function, and thus confers dopaminergic neuroprotection against genetic and oxidative insults. We further show that conditional ablation of Nato3, a mouse homolog of Fer2, in differentiated DA neurons causes mitochondrial abnormalities and locomotor impairments in aged mice. Our results reveal the essential and conserved role of Fer2 homologs in the mitochondrial maintenance of midbrain DA neurons, opening new perspectives for modeling and treating PD. Mitochondrial dysfunction in dopaminergic neurons is a pathological hallmark of Parkinson’s disease. Here, the authors find a conserved mechanism by which a single transcription factor controls mitochondrial health in dopaminergic neurons during the aging process.
Collapse
Affiliation(s)
- Federico Miozzo
- Department of Genetics and Evolution and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211, Geneva 4, Switzerland.,Neuroscience Institute - CNR (IN-CNR), Milan, Italy
| | - Eva P Valencia-Alarcón
- Department of Genetics and Evolution and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211, Geneva 4, Switzerland
| | - Luca Stickley
- Department of Genetics and Evolution and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211, Geneva 4, Switzerland
| | - Michaëla Majcin Dorcikova
- Department of Genetics and Evolution and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211, Geneva 4, Switzerland
| | | | - Damla Tas
- Department of Genetics and Evolution and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211, Geneva 4, Switzerland.,The Janssen Pharmaceutical Companies of Johnson & Johnson, Bern, Switzerland
| | - Nicolas Loncle
- Department of Genetics and Evolution and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211, Geneva 4, Switzerland.,Puma Biotechnology, Inc., Berkeley, CA, USA
| | - Irina Nikonenko
- Department of Basic Neurosciences and the Center for Neuroscience, CMU, University of Geneva, CH-1211, Geneva 4, Switzerland
| | - Peter Bou Dib
- Institute of Cell Biology, University of Bern, CH-3012, Bern, Switzerland
| | - Emi Nagoshi
- Department of Genetics and Evolution and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211, Geneva 4, Switzerland.
| |
Collapse
|
5
|
Yildirim E, Curtis R, Hwangbo DS. Roles of peripheral clocks: lessons from the fly. FEBS Lett 2022; 596:263-293. [PMID: 34862983 PMCID: PMC8844272 DOI: 10.1002/1873-3468.14251] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 02/03/2023]
Abstract
To adapt to and anticipate rhythmic changes in the environment such as daily light-dark and temperature cycles, internal timekeeping mechanisms called biological clocks evolved in a diverse set of organisms, from unicellular bacteria to humans. These biological clocks play critical roles in organisms' fitness and survival by temporally aligning physiological and behavioral processes to the external cues. The central clock is located in a small subset of neurons in the brain and drives daily activity rhythms, whereas most peripheral tissues harbor their own clock systems, which generate metabolic and physiological rhythms. Since the discovery of Drosophila melanogaster clock mutants in the early 1970s, the fruit fly has become an extensively studied model organism to investigate the mechanism and functions of circadian clocks. In this review, we primarily focus on D. melanogaster to survey key discoveries and progresses made over the past two decades in our understanding of peripheral clocks. We discuss physiological roles and molecular mechanisms of peripheral clocks in several different peripheral tissues of the fly.
Collapse
Affiliation(s)
| | - Rachel Curtis
- Department of Biology, University of Louisville, Louisville, KY, USA
| | - Dae-Sung Hwangbo
- Department of Biology, University of Louisville, Louisville, KY, USA
| |
Collapse
|
6
|
Jauregui-Lozano J, Hall H, Stanhope SC, Bakhle K, Marlin MM, Weake VM. The Clock:Cycle complex is a major transcriptional regulator of Drosophila photoreceptors that protects the eye from retinal degeneration and oxidative stress. PLoS Genet 2022; 18:e1010021. [PMID: 35100266 PMCID: PMC8830735 DOI: 10.1371/journal.pgen.1010021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/10/2022] [Accepted: 01/08/2022] [Indexed: 12/28/2022] Open
Abstract
The aging eye experiences physiological changes that include decreased visual function and increased risk of retinal degeneration. Although there are transcriptomic signatures in the aging retina that correlate with these physiological changes, the gene regulatory mechanisms that contribute to cellular homeostasis during aging remain to be determined. Here, we integrated ATAC-seq and RNA-seq data to identify 57 transcription factors that showed differential activity in aging Drosophila photoreceptors. These 57 age-regulated transcription factors include two circadian regulators, Clock and Cycle, that showed sustained increased activity during aging. When we disrupted the Clock:Cycle complex by expressing a dominant negative version of Clock (ClkDN) in adult photoreceptors, we observed changes in expression of 15-20% of genes including key components of the phototransduction machinery and many eye-specific transcription factors. Using ATAC-seq, we showed that expression of ClkDN in photoreceptors leads to changes in activity of 37 transcription factors and causes a progressive decrease in global levels of chromatin accessibility in photoreceptors. Supporting a key role for Clock-dependent transcription in the eye, expression of ClkDN in photoreceptors also induced light-dependent retinal degeneration and increased oxidative stress, independent of light exposure. Together, our data suggests that the circadian regulators Clock and Cycle act as neuroprotective factors in the aging eye by directing gene regulatory networks that maintain expression of the phototransduction machinery and counteract oxidative stress.
Collapse
Affiliation(s)
- Juan Jauregui-Lozano
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Hana Hall
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana, United States of America
| | - Sarah C. Stanhope
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Kimaya Bakhle
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Makayla M. Marlin
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Vikki M. Weake
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana, United States of America
- Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, United States of America
| |
Collapse
|
7
|
Straat ME, Hogenboom R, Boon MR, Rensen PCN, Kooijman S. Circadian control of brown adipose tissue. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158961. [PMID: 33933649 DOI: 10.1016/j.bbalip.2021.158961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023]
Abstract
Disruption of circadian (~24 h) rhythms is associated with an increased risk of cardiometabolic diseases. Therefore, unravelling how circadian rhythms are regulated in different metabolic tissues has become a prominent research focus. Of particular interest is brown adipose tissue (BAT), which combusts triglyceride-derived fatty acids and glucose into heat and displays a circannual and diurnal rhythm in its thermogenic activity. In this review, the genetic, neuronal and endocrine generation of these rhythms in BAT is discussed. In addition, the potential risks of disruption or attenuation of these rhythms in BAT, and possible factors influencing these rhythms, are addressed.
Collapse
Affiliation(s)
- Maaike E Straat
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Rick Hogenboom
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Mariëtte R Boon
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Patrick C N Rensen
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Sander Kooijman
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands.
| |
Collapse
|
8
|
Abstract
Circadian clocks are biochemical time-keeping machines that synchronize animal behavior and physiology with planetary rhythms. In Drosophila, the core components of the clock comprise a transcription/translation feedback loop and are expressed in seven neuronal clusters in the brain. Although it is increasingly evident that the clocks in each of the neuronal clusters are regulated differently, how these clocks communicate with each other across the circadian neuronal network is less clear. Here, we review the latest evidence that describes the physical connectivity of the circadian neuronal network . Using small ventral lateral neurons as a starting point, we summarize how one clock may communicate with another, highlighting the signaling pathways that are both upstream and downstream of these clocks. We propose that additional efforts are required to understand how temporal information generated in each circadian neuron is integrated across a neuronal circuit to regulate rhythmic behavior.
Collapse
Affiliation(s)
- Myra Ahmad
- Department of Pediatrics, Division of Medical Genetics, Dalhousie University, Halifax, NS, Canada
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Wanhe Li
- Laboratory of Genetics, The Rockefeller University, New York, NY, USA
| | - Deniz Top
- Department of Pediatrics, Division of Medical Genetics, Dalhousie University, Halifax, NS, Canada
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| |
Collapse
|
9
|
Ma D, Przybylski D, Abruzzi KC, Schlichting M, Li Q, Long X, Rosbash M. A transcriptomic taxonomy of Drosophila circadian neurons around the clock. eLife 2021; 10:63056. [PMID: 33438579 PMCID: PMC7837698 DOI: 10.7554/elife.63056] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 01/11/2021] [Indexed: 01/19/2023] Open
Abstract
Many different functions are regulated by circadian rhythms, including those orchestrated by discrete clock neurons within animal brains. To comprehensively characterize and assign cell identity to the 75 pairs of Drosophila circadian neurons, we optimized a single-cell RNA sequencing method and assayed clock neuron gene expression at different times of day. The data identify at least 17 clock neuron categories with striking spatial regulation of gene expression. Transcription factor regulation is prominent and likely contributes to the robust circadian oscillation of many transcripts, including those that encode cell-surface proteins previously shown to be important for cell recognition and synapse formation during development. The many other clock-regulated genes also constitute an important resource for future mechanistic and functional studies between clock neurons and/or for temporal signaling to circuits elsewhere in the fly brain.
Collapse
Affiliation(s)
- Dingbang Ma
- Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Dariusz Przybylski
- Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Katharine C Abruzzi
- Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | | | - Qunlong Li
- Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Xi Long
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Michael Rosbash
- Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| |
Collapse
|
10
|
Litovchenko M, Meireles-Filho ACA, Frochaux MV, Bevers RPJ, Prunotto A, Anduaga AM, Hollis B, Gardeux V, Braman VS, Russeil JMC, Kadener S, Dal Peraro M, Deplancke B. Extensive tissue-specific expression variation and novel regulators underlying circadian behavior. SCIENCE ADVANCES 2021; 7:eabc3781. [PMID: 33514540 PMCID: PMC7846174 DOI: 10.1126/sciadv.abc3781] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/10/2020] [Indexed: 05/10/2023]
Abstract
Natural genetic variation affects circadian rhythms across the evolutionary tree, but the underlying molecular mechanisms are poorly understood. We investigated population-level, molecular circadian clock variation by generating >700 tissue-specific transcriptomes of Drosophila melanogaster (w1118 ) and 141 Drosophila Genetic Reference Panel (DGRP) lines. This comprehensive circadian gene expression atlas contains >1700 cycling genes including previously unknown central circadian clock components and tissue-specific regulators. Furthermore, >30% of DGRP lines exhibited aberrant circadian gene expression, revealing abundant genetic variation-mediated, intertissue circadian expression desynchrony. Genetic analysis of one line with the strongest deviating circadian expression uncovered a novel cry mutation that, as shown by protein structural modeling and brain immunohistochemistry, disrupts the light-driven flavin adenine dinucleotide cofactor photoreduction, providing in vivo support for the importance of this conserved photoentrainment mechanism. Together, our study revealed pervasive tissue-specific circadian expression variation with genetic variants acting upon tissue-specific regulatory networks to generate local gene expression oscillations.
Collapse
Affiliation(s)
- Maria Litovchenko
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Antonio C A Meireles-Filho
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Michael V Frochaux
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Roel P J Bevers
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Alessio Prunotto
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | | | - Brian Hollis
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Vincent Gardeux
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Virginie S Braman
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Julie M C Russeil
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | | | - Matteo Dal Peraro
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| | - Bart Deplancke
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Vaud, Switzerland
| |
Collapse
|
11
|
Abstract
The identification and characterization of rhythmically expressed mRNAs have been an active area of research over the past 20 years, as these mRNAs are believed to produce the daily rhythms in a wide range of biological processes. Circadian transcriptome studies have used mature mRNA as a primary readout and focused largely on rhythmic RNA synthesis as a regulatory mechanism underlying rhythmic mRNA expression. However, RNA synthesis, RNA degradation, or a combination of both must be rhythmic to drive rhythmic RNA profiles, and it is still unclear to what extent rhythmic synthesis leads to rhythmic RNA profiles. In addition, circadian RNA expression is also often tissue specific. Although a handful of genes cycle in all or most tissues, others are rhythmic only in certain tissues, even though the same core clock mechanism is believed to control the rhythmic RNA profiles in all tissues. This review focuses on the dynamics of rhythmic RNA synthesis and degradation and discusses how these steps collectively determine the rhythmicity, phase, and amplitude of RNA accumulation. In particular, we highlight a possible role of RNA degradation in driving tissue-specific RNA rhythms. By unifying findings from experimental and theoretical studies, we will provide a comprehensive overview of how rhythmic gene expression can be achieved and how each regulatory step contributes to tissue-specific circadian transcriptome output in mammals.
Collapse
Affiliation(s)
| | - Shihoko Kojima
- To whom all correspondence should be addressed: Shihoko Kojima, Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA, 24061, USA; .
| |
Collapse
|
12
|
Shokri L, Inukai S, Hafner A, Weinand K, Hens K, Vedenko A, Gisselbrecht SS, Dainese R, Bischof J, Furger E, Feuz JD, Basler K, Deplancke B, Bulyk ML. A Comprehensive Drosophila melanogaster Transcription Factor Interactome. Cell Rep 2020; 27:955-970.e7. [PMID: 30995488 PMCID: PMC6485956 DOI: 10.1016/j.celrep.2019.03.071] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/04/2019] [Accepted: 03/18/2019] [Indexed: 12/14/2022] Open
Abstract
Combinatorial interactions among transcription factors (TFs) play essential roles in generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid (Y2H) assays on nearly all sequence-specific Drosophila TFs, we identified 1,983 protein-protein interactions (PPIs), more than doubling the number of currently known PPIs among Drosophila TFs. For quality assessment, we validated a subset of our interactions using MITOMI and bimolecular fluorescence complementation assays. We combined our interactome with prior PPI data to generate an integrated Drosophila TF-TF binary interaction network. Our analysis of ChIP-seq data, integrating PPI and gene expression information, uncovered different modes by which interacting TFs are recruited to DNA. We further demonstrate the utility of our Drosophila interactome in shedding light on human TF-TF interactions. This study reveals how TFs interact to bind regulatory elements in vivo and serves as a resource of Drosophila TF-TF binary PPIs for understanding tissue-specific gene regulation. Combinatorial regulation by transcription factors (TFs) is one mechanism for achieving condition and tissue-specific gene regulation. Shokri et al. mapped TF-TF interactions between most Drosophila TFs, reporting a comprehensive TF-TF network integrated with previously known interactions. They used this network to discern distinct TF-DNA binding modes.
Collapse
Affiliation(s)
- Leila Shokri
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sachi Inukai
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Antonina Hafner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Systems Biology Graduate Program, Harvard University, Cambridge, MA 02138, USA; Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Kathryn Weinand
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Bioinformatics and Integrative Genomics Ph.D. Program, Harvard University, Cambridge, MA 02138, USA
| | - Korneel Hens
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Anastasia Vedenko
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Stephen S Gisselbrecht
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Riccardo Dainese
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Johannes Bischof
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Edy Furger
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Jean-Daniel Feuz
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Martha L Bulyk
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Systems Biology Graduate Program, Harvard University, Cambridge, MA 02138, USA; Bioinformatics and Integrative Genomics Ph.D. Program, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
13
|
Wang C, Shui K, Ma S, Lin S, Zhang Y, Wen B, Deng W, Xu H, Hu H, Guo A, Xue Y, Zhang L. Integrated omics in Drosophila uncover a circadian kinome. Nat Commun 2020; 11:2710. [PMID: 32483184 PMCID: PMC7264355 DOI: 10.1038/s41467-020-16514-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/06/2020] [Indexed: 02/06/2023] Open
Abstract
Most organisms on the earth exhibit circadian rhythms in behavior and physiology, which are driven by endogenous clocks. Phosphorylation plays a central role in timing the clock, but how this contributes to overt rhythms is unclear. Here we conduct phosphoproteomics in conjunction with transcriptomic and proteomic profiling using fly heads. By developing a pipeline for integrating multi-omics data, we identify 789 (~17%) phosphorylation sites with circadian oscillations. We predict 27 potential circadian kinases to participate in phosphorylating these sites, including 7 previously known to function in the clock. We screen the remaining 20 kinases for effects on circadian rhythms and find an additional 3 to be involved in regulating locomotor rhythm. We re-construct a signal web that includes the 10 circadian kinases and identify GASKET as a potentially important regulator. Taken together, we uncover a circadian kinome that potentially shapes the temporal pattern of the entire circadian molecular landscapes. Phosphorylation plays an important role in the regulation of molecular circadian clocks. Here the authors utilize multi-omics data from flies to describe the circadian kinome and identify GASKET as a potentially important regulator within the circadian kinase network.
Collapse
Affiliation(s)
- Chenwei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Ke Shui
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Shanshan Ma
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Shaofeng Lin
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Ying Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Bo Wen
- Department of Molecular and Human Genetics, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wankun Deng
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Haodong Xu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Hui Hu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Anyuan Guo
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China. .,Institute of Brain Research, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
| | - Luoying Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China. .,Institute of Brain Research, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
| |
Collapse
|
14
|
Greenwood M, Locke JC. The circadian clock coordinates plant development through specificity at the tissue and cellular level. CURRENT OPINION IN PLANT BIOLOGY 2020; 53:65-72. [PMID: 31783323 DOI: 10.1016/j.pbi.2019.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 05/27/2023]
Abstract
The circadian clock is a genetic circuit that allows organisms to anticipate daily events caused by the rotation of the Earth. The plant clock regulates physiology at multiple scales, from cell division to ecosystem-scale interactions. It is becoming clear that rather than being a single perfectly synchronised timer throughout the plant, the clock can be sensitive to different cues, run at different speeds, and drive distinct processes in different cell types and tissues. This flexibility may help the plant clock to regulate such a range of developmental and physiological processes. In this review, using examples from the literature, we describe how the clock regulates development at multiple scales and discuss how the clock might allow local flexibility in regulation whilst remaining coordinated across the plant.
Collapse
Affiliation(s)
- Mark Greenwood
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, UK; Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, UK
| | - James Cw Locke
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, UK.
| |
Collapse
|
15
|
Beytebiere JR, Greenwell BJ, Sahasrabudhe A, Menet JS. Clock-controlled rhythmic transcription: is the clock enough and how does it work? Transcription 2019; 10:212-221. [PMID: 31595813 DOI: 10.1080/21541264.2019.1673636] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Circadian clocks regulate the rhythmic expression of thousands of genes underlying the daily oscillations of biological functions. Here, we discuss recent findings showing that circadian clock rhythmic transcriptional outputs rely on additional mechanisms than just clock gene DNA binding, which may ultimately contribute to the plasticity of circadian transcriptional programs.
Collapse
Affiliation(s)
- Joshua R Beytebiere
- Department of Biology, Center for Biological Clock Research, Texas A&M University, TX, USA
| | - Ben J Greenwell
- Department of Biology, Center for Biological Clock Research, Texas A&M University, TX, USA.,Program of Genetics, Texas A&M University, College Station, TX, USA
| | - Aishwarya Sahasrabudhe
- Department of Biology, Center for Biological Clock Research, Texas A&M University, TX, USA
| | - Jerome S Menet
- Department of Biology, Center for Biological Clock Research, Texas A&M University, TX, USA.,Program of Genetics, Texas A&M University, College Station, TX, USA
| |
Collapse
|
16
|
Kozak GM, Wadsworth CB, Kahne SC, Bogdanowicz SM, Harrison RG, Coates BS, Dopman EB. Genomic Basis of Circannual Rhythm in the European Corn Borer Moth. Curr Biol 2019; 29:3501-3509.e5. [DOI: 10.1016/j.cub.2019.08.053] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 12/15/2022]
|
17
|
Zamudio AV, Dall'Agnese A, Henninger JE, Manteiga JC, Afeyan LK, Hannett NM, Coffey EL, Li CH, Oksuz O, Sabari BR, Boija A, Klein IA, Hawken SW, Spille JH, Decker TM, Cisse II, Abraham BJ, Lee TI, Taatjes DJ, Schuijers J, Young RA. Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes. Mol Cell 2019; 76:753-766.e6. [PMID: 31563432 DOI: 10.1016/j.molcel.2019.08.016] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/14/2019] [Accepted: 08/16/2019] [Indexed: 01/09/2023]
Abstract
The gene expression programs that define the identity of each cell are controlled by master transcription factors (TFs) that bind cell-type-specific enhancers, as well as signaling factors, which bring extracellular stimuli to these enhancers. Recent studies have revealed that master TFs form phase-separated condensates with the Mediator coactivator at super-enhancers. Here, we present evidence that signaling factors for the WNT, TGF-β, and JAK/STAT pathways use their intrinsically disordered regions (IDRs) to enter and concentrate in Mediator condensates at super-enhancers. We show that the WNT coactivator β-catenin interacts both with components of condensates and DNA-binding factors to selectively occupy super-enhancer-associated genes. We propose that the cell-type specificity of the response to signaling is mediated in part by the IDRs of the signaling factors, which cause these factors to partition into condensates established by the master TFs and Mediator at genes with prominent roles in cell identity.
Collapse
Affiliation(s)
- Alicia V Zamudio
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - John C Manteiga
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lena K Afeyan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Eliot L Coffey
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ozgur Oksuz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Benjamin R Sabari
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ann Boija
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Susana W Hawken
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jan-Hendrik Spille
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tim-Michael Decker
- Department of Biochemistry, University of Colorado, Boulder, Boulder, CO 80303, USA
| | - Ibrahim I Cisse
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Tong I Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, Boulder, CO 80303, USA
| | - Jurian Schuijers
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
18
|
Krachun C, Lurz R, Mahovetz LM, Hopkins WD. Mirror self-recognition and its relationship to social cognition in chimpanzees. Anim Cogn 2019; 22:1171-1183. [PMID: 31542841 DOI: 10.1007/s10071-019-01309-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 09/03/2019] [Accepted: 09/13/2019] [Indexed: 12/23/2022]
Abstract
Chimpanzees and humans are capable of recognizing their own reflection in mirrors. Little is understood about the selective pressures that led to this evolved trait and about the mechanisms that underlie it. Here, we investigated the hypothesis that mirror self-recognition in chimpanzees is the byproduct of a developed form of self-awareness that was naturally selected for its adaptive use in social cognitive behaviors. We present here the first direct attempt to assess the social cognition hypothesis by analyzing the association between mirror self-recognition in chimpanzees, as measured by a mirror-mark test, and their performance on a variety of social cognition tests. Consistent with the social cognition hypothesis, chimpanzees who showed evidence of mirror self-recognition in the mark test tended to perform significantly better on the social cognition tasks than those who failed the mark test. Additionally, the data as a whole fit the social cognition hypothesis better than the main competing hypothesis of mirror self-recognition in great apes, the secondary representation hypothesis. Our findings strongly suggest that the evolutionary origins of great apes' and humans' capacity to understand ourselves, as revealed by our capacity to recognize ourselves in mirrors, are intimately linked to our ability to understand others.
Collapse
Affiliation(s)
- Carla Krachun
- Department of Psychology, University of Saskatchewan, 9 Campus Drive, Saskatoon, SK, Canada.
| | - Robert Lurz
- Department of Philosophy, Brooklyn College, CUNY, 2900 Bedford Avenue, Brooklyn, NY, USA
| | - Lindsay M Mahovetz
- Department of Psychology, University of North Florida, 1 UNF Drive, Jacksonville, FL, USA
| | - William D Hopkins
- Department of Comparative Medicine, University of Texas MD Anderson Cancer Center, Bastrop, TX, USA
| |
Collapse
|
19
|
Buchberger E, Reis M, Lu TH, Posnien N. Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies. Genes (Basel) 2019; 10:E492. [PMID: 31261769 PMCID: PMC6678813 DOI: 10.3390/genes10070492] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Accepted: 06/26/2019] [Indexed: 12/20/2022] Open
Abstract
Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic evolution. An exceptional contribution of cis-regulatory divergence has been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and stage-specific expression. We argue that the regulatory context must be considered in comparative expression studies.
Collapse
Affiliation(s)
- Elisa Buchberger
- University Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Dpt. of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
| | - Micael Reis
- University Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Dpt. of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
| | - Ting-Hsuan Lu
- University Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Dpt. of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
- International Max Planck Research School for Genome Science, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Nico Posnien
- University Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Dpt. of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
| |
Collapse
|
20
|
Abstract
In mammals, genetic influences of circadian rhythms occur at many levels. A set of core "clock genes" have been identified that form a feedback loop of gene transcription and translation. The core genetic clockwork generates circadian rhythms in cells throughout the body. Polymorphisms in both core clock genes and interacting genes contribute to individual differences in the expression and properties of circadian rhythms. The circadian clock profoundly influences the patterns of gene expression and cellular functions, providing a mechanistic basis for the impact of the genetic circadian system on normal physiological processes as well as the development of diseases.
Collapse
Affiliation(s)
- Martha Hotz Vitaterna
- Center for Sleep and Circadian Biology; Department of Neurobiology, Weinberg College of Arts and Sciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA.
| | - Kazuhiro Shimomura
- Center for Sleep and Circadian Biology; Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, 420 East Superior Street, Chicago, IL 60611, USA
| | - Peng Jiang
- Center for Sleep and Circadian Biology; Department of Neurobiology, Weinberg College of Arts and Sciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| |
Collapse
|
21
|
Abstract
The circadian clock in the suprachiasmatic nucleus (SCN) of mammals drives 24-h rhythms of sleep/wake cycles. Peripheral clocks present in other organs coordinate local and global physiology according to rhythmic signals from the SCN and via metabolic cues. The core circadian clockwork is identical in all cells. However, there is only a small amount of overlap of the circadian transcriptomes in different organs and tissues. A novel study by Beytebiere and colleagues (pp. 294-309) indicates that the regulation of tissue-specific rhythmic gene expression involves the cooperation of the circadian transcription factor (TF) BMAL1:CLOCK with tissue-specific TFs (ts-TFs) and correlates with the potential of BMAL1:CLOCK to facilitate rhythmic enhancer-enhancer interactions.
Collapse
Affiliation(s)
- Anton Shostak
- Heidelberg University Biochemistry Center, Heidelberg D-69120, Germany
| | - Michael Brunner
- Heidelberg University Biochemistry Center, Heidelberg D-69120, Germany
| |
Collapse
|
22
|
Beytebiere JR, Trott AJ, Greenwell BJ, Osborne CA, Vitet H, Spence J, Yoo SH, Chen Z, Takahashi JS, Ghaffari N, Menet JS. Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer-enhancer interactions. Genes Dev 2019; 33:294-309. [PMID: 30804225 PMCID: PMC6411008 DOI: 10.1101/gad.322198.118] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/02/2019] [Indexed: 12/31/2022]
Abstract
The mammalian circadian clock relies on the transcription factor CLOCK:BMAL1 to coordinate the rhythmic expression of thousands of genes. Consistent with the various biological functions under clock control, rhythmic gene expression is tissue-specific despite an identical clockwork mechanism in every cell. Here we show that BMAL1 DNA binding is largely tissue-specific, likely because of differences in chromatin accessibility between tissues and cobinding of tissue-specific transcription factors. Our results also indicate that BMAL1 ability to drive tissue-specific rhythmic transcription is associated with not only the activity of BMAL1-bound enhancers but also the activity of neighboring enhancers. Characterization of physical interactions between BMAL1 enhancers and other cis-regulatory regions by RNA polymerase II chromatin interaction analysis by paired-end tag (ChIA-PET) reveals that rhythmic BMAL1 target gene expression correlates with rhythmic chromatin interactions. These data thus support that much of BMAL1 target gene transcription depends on BMAL1 capacity to rhythmically regulate a network of enhancers.
Collapse
Affiliation(s)
- Joshua R Beytebiere
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
| | - Alexandra J Trott
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
- Program of Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Ben J Greenwell
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
- Program of Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Collin A Osborne
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
- Program of Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Helene Vitet
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
| | - Jessica Spence
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Joseph S Takahashi
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Noushin Ghaffari
- Center for Bioinformatics and Genomic Systems Engineering (CBGSE), Texas A&M AgriLife Research, College Station, Texas 77845, USA
- AgriLife Genomics and Bioinformatics, Texas A&M AgriLife Research, College Station, Texas 77845, USA
| | - Jerome S Menet
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
- Program of Genetics, Texas A&M University, College Station, Texas 77843, USA
| |
Collapse
|
23
|
Inoue K, Araki T, Endo M. Oscillator networks with tissue-specific circadian clocks in plants. Semin Cell Dev Biol 2018; 83:78-85. [DOI: 10.1016/j.semcdb.2017.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 12/31/2022]
|
24
|
Vesicle-based secretion in schistosomes: Analysis of protein and microRNA (miRNA) content of exosome-like vesicles derived from Schistosoma mansoni. Sci Rep 2018; 8:3286. [PMID: 29459722 PMCID: PMC5818524 DOI: 10.1038/s41598-018-21587-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/07/2018] [Indexed: 01/16/2023] Open
Abstract
Exosomes are small vesicles of endocytic origin, which are released into the extracellular environment and mediate a variety of physiological and pathological conditions. Here we show that Schistosoma mansoni releases exosome-like vesicles in vitro. Vesicles were purified from culture medium by sucrose gradient fractionation and fractions containing vesicles verified by western blot analyses and electron microscopy. Proteomic analyses of exosomal contents unveiled 130 schistosome proteins. Among these proteins are common exosomal markers such as heat shock proteins, energy-generating enzymes, cytoskeletal proteins, and others. In addition, the schistosome extracellular vesicles contain proteins of potential importance for host-parasite interaction, notably peptidases, signaling proteins, cell adhesion proteins (e.g., integrins) and previously described vaccine candidates, including glutathione-S-transferase (GST), tetraspanin (TSP-2) and calpain. S. mansoni exosomes also contain 143 microRNAs (miRNA), of which 25 are present at high levels, including miRNAs detected in sera of infected hosts. Quantitative PCR analysis confirmed the presence of schistosome-derived miRNAs in exosomes purified from infected mouse sera. The results provide evidence of vesicle-mediated secretion in these parasites and suggest that schistosome-derived exosomes could play important roles in host-parasite interactions and could be a useful tool in the development of vaccines and therapeutics.
Collapse
|
25
|
Hursh DA, Stultz BG. Odd-Paired: The Drosophila Zic Gene. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:41-58. [PMID: 29442316 DOI: 10.1007/978-981-10-7311-3_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Zinc finger in the cerebellum (Zic) proteins are a family of transcription factors with multiple roles during development, particularly in neural tissues. The founding member of the Zic family is the Drosophila odd-paired (opa) gene. The Opa protein has a DNA binding domain containing five Cys2His2-type zinc fingers and has been shown to act as a sequence-specific DNA binding protein. Opa has significant homology to mammalian Zic1, Zic2, and Zic3 within the zinc finger domain and in two other conserved regions outside that domain. opa was initially identified as a pair-rule gene, part of the hierarchy of genes that establish the segmental body plan of the early Drosophila embryo. However, its wide expression pattern during embryogenesis indicates it plays additional roles. Embryos deficient in opa die before hatching with aberrant segmentation but also with defects in larval midgut formation. Post-embryonically, opa plays important roles in adult head development and circadian rhythm. Based on extensive neural expression, opa is predicted to be involved in many aspects of neural development and behavior, like other proteins of the Zic family. Consensus DNA binding sites have been identified for Opa and have been shown to activate transcription in vivo. However, there is evidence Opa may serve as a transcriptional regulator in the absence of direct DNA binding, as has been seen for other Zic proteins.
Collapse
Affiliation(s)
- Deborah A Hursh
- Division of Cell and Gene Therapy, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
| | - Brian G Stultz
- Division of Cell and Gene Therapy, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| |
Collapse
|
26
|
Abstract
The brain is a network of neurons, one that generates behaviour, and knowing the former is crucial to understanding the latter. Identifying the exact network of synaptic connections, or connectome, of the fly's central nervous system is now a major objective in Drosophila neurobiology, one that has been initiated in several laboratories, especially the Janelia Research Campus of the Howard Hughes Medical Institute. Progress is most advanced in the optic neuropiles of the visual system. The effort to derive a connectome from these and other neuropile regions is proceeding by various methods of electron microscopy, especially focused-ion beam milling scanning electron microscopy, and relies upon - but is to be carefully distinguished from - published light microscopic methods that reveal the projections of genetically labelled cell types. The latter reveal those neurons that come into close proximity and are therefore candidate synaptic partners. Synaptic partnerships are not in fact reliably revealed by such candidate pairs, anatomical connections often revealing unexpected pathways. Synaptic partnerships identified from ultrastructural features provide a strong heuristic basis to interpret not only functional interactions between identified neurons, but also a powerful means to predict such interactions, and suggest functional pathways not readily predicted from existing experimental evidence. The analysis of circuit function may proceed cell by cell, by examining the behavioural outcome of either interrupting or restoring function to any one element in an anatomically defined circuit, but can be foiled by degeneracy in pathway elements. Circuit information can also be used to identify and analyse circuit motifs, and their role in higher-order network properties. These attempts in Drosophila anticipate parallel attempts in other systems, notably the inner plexiform layer of the vertebrate retina, and augment the one complete connectome already available to us, that available for 30 years in the nematode Caenorhabditis elegans.
Collapse
Affiliation(s)
- Ian A Meinertzhagen
- a Department of Psychology and Neuroscience, Life Sciences Centre , Dalhousie University , Halifax , Canada ;,b Janelia Research Campus of Howard Hughes Medical Institute , Ashburn , VA , USA
| |
Collapse
|
27
|
Adewoye AB, Nuzhdin SV, Tauber E. Mapping Quantitative Trait Loci Underlying Circadian Light Sensitivity in Drosophila. J Biol Rhythms 2017; 32:394-405. [PMID: 28990443 DOI: 10.1177/0748730417731863] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Despite the significant advance in our understanding of the molecular basis of light entrainment of the circadian clock in Drosophila, the underlying genetic architecture is still largely unknown. The aim of this study was to identify loci associated with variation in circadian photosensitivity, which are important for the evolution of this trait. We have used complementary approaches that combined quantitative trait loci (QTL) mapping, complementation testing, and transcriptome profiling to dissect this variation. We identified a major QTL on chromosome 2, which was subsequently fine mapped using deficiency complementation mapping into 2 smaller regions spanning 139 genes, some of which are known to be involved in functions that have been previously implicated in light entrainment. Two genes implicated with the clock and located within that interval, timeless and cycle, failed to complement the QTL, indicating that alleles of these genes contribute to the variation in light response. Specifically, we find that the timeless s/ ls polymorphism that has been previously shown to constitute a latitudinal cline in Europe is also segregating in our recombinant inbred lines and is contributing to the phenotypic variation in light sensitivity. We also profiled gene expression in 2 recombinant inbred strains that differ significantly in their photosensitivity and identified a total of 368 transcripts that showed differential expression (false discovery rate < 0.1). Of 131 transcripts that showed a significant recombinant inbred line by treatment interaction (i.e., putative expression QTL), 4 are located within QTL2.
Collapse
Affiliation(s)
- Adeolu B Adewoye
- Department of Genetics, University of Leicester, Leicester, UK.,1 Wolfson School of Mechanical and Manufacturing Engineering, Centre for Biological Engineering, Loughborough University Loughborough, UK
| | - Sergey V Nuzhdin
- Program in Molecular and Computation Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California, USA
| | - Eran Tauber
- Department of Genetics, University of Leicester, Leicester, UK.,Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, Haifa, Israel
| |
Collapse
|
28
|
Bazalova O, Dolezel D. Daily Activity of the Housefly, Musca domestica, Is Influenced by Temperature Independent of 3' UTR period Gene Splicing. G3 (BETHESDA, MD.) 2017; 7:2637-2649. [PMID: 28620087 PMCID: PMC5555469 DOI: 10.1534/g3.117.042374] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/06/2017] [Indexed: 12/19/2022]
Abstract
Circadian clocks orchestrate daily activity patterns and free running periods of locomotor activity under constant conditions. While the first often depends on temperature, the latter is temperature-compensated over a physiologically relevant range. Here, we explored the locomotor activity of the temperate housefly Musca domestica Under low temperatures, activity was centered round a major and broad afternoon peak, while high temperatures resulted in activity throughout the photophase with a mild midday depression, which was especially pronounced in males exposed to long photoperiods. While period (per) mRNA peaked earlier under low temperatures, no temperature-dependent splicing of the last per 3' end intron was identified. The expression of timeless, vrille, and Par domain protein 1 was also influenced by temperature, each in a different manner. Our data indicated that comparable behavioral trends in daily activity distribution have evolved in Drosophila melanogaster and M. domestica, yet the behaviors of these two species are orchestrated by different molecular mechanisms.
Collapse
Affiliation(s)
- Olga Bazalova
- Biology Center, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
- Department of Molecular Biology, Faculty of Sciences, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - David Dolezel
- Biology Center, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
- Department of Molecular Biology, Faculty of Sciences, University of South Bohemia, 37005 České Budějovice, Czech Republic
| |
Collapse
|
29
|
Agrawal P, Houl JH, Gunawardhana KL, Liu T, Zhou J, Zoran MJ, Hardin PE. Drosophila CRY Entrains Clocks in Body Tissues to Light and Maintains Passive Membrane Properties in a Non-clock Body Tissue Independent of Light. Curr Biol 2017; 27:2431-2441.e3. [PMID: 28781048 DOI: 10.1016/j.cub.2017.06.064] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/24/2017] [Accepted: 06/26/2017] [Indexed: 12/20/2022]
Abstract
Circadian (∼24 hr) clocks regulate daily rhythms in physiology, metabolism, and behavior via cell-autonomous transcriptional feedback loops. In Drosophila, the blue-light photoreceptor CRYPTOCHROME (CRY) synchronizes these feedback loops to light:dark cycles by binding to and degrading TIMELESS (TIM) protein. CRY also acts independently of TIM in Drosophila to alter potassium channel conductance in arousal neurons after light exposure, and in many animals CRY acts independently of light to repress rhythmic transcription. CRY expression has been characterized in the Drosophila brain and eyes, but not in peripheral clock and non-clock tissues in the body. To investigate CRY expression and function in body tissues, we generated a GFP-tagged-cry transgene that rescues light-induced behavioral phase resetting in cry03 mutant flies and sensitively reports GFP-CRY expression. In bodies, CRY is detected in clock-containing tissues including Malpighian tubules, where it mediates both light-dependent TIM degradation and clock function. In larval salivary glands, which lack clock function but are amenable to electrophysiological recording, CRY prevents membrane input resistance from falling to low levels in a light-independent manner. The ability of CRY to maintain high input resistance in these non-excitable cells also requires the K+ channel subunits Hyperkinetic, Shaker, and ether-a-go-go. These findings for the first time define CRY expression in Drosophila peripheral tissues and reveal that CRY acts together with K+ channels to maintain passive membrane properties in a non-clock-containing peripheral tissue independent of light.
Collapse
Affiliation(s)
- Parul Agrawal
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA
| | - Jerry H Houl
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA
| | - Kushan L Gunawardhana
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA
| | - Tianxin Liu
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA
| | - Jian Zhou
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA
| | - Mark J Zoran
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA
| | - Paul E Hardin
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA.
| |
Collapse
|
30
|
Zhao X, Karpac J. Muscle Directs Diurnal Energy Homeostasis through a Myokine-Dependent Hormone Module in Drosophila. Curr Biol 2017; 27:1941-1955.e6. [PMID: 28669758 DOI: 10.1016/j.cub.2017.06.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/26/2017] [Accepted: 06/01/2017] [Indexed: 02/04/2023]
Abstract
Inter-tissue communication is critical to control organismal energy homeostasis in response to temporal changes in feeding and activity or external challenges. Muscle is emerging as a key mediator of this homeostatic control through consumption of lipids, carbohydrates, and amino acids, as well as governing systemic signaling networks. However, it remains less clear how energy substrate usage tissues, such as muscle, communicate with energy substrate storage tissues in order to adapt with diurnal changes in energy supply and demand. Using Drosophila, we show here that muscle plays a crucial physiological role in promoting systemic synthesis and accumulation of lipids in fat storage tissues, which subsequently impacts diurnal changes in circulating lipid levels. Our data reveal that the metabolic transcription factor Foxo governs expression of the cytokine unpaired 2 (Upd2) in skeletal muscle, which acts as a myokine to control glucagon-like adipokinetic hormone (AKH) secretion from specialized neuroendocrine cells. Circulating AKH levels in turn regulate lipid homeostasis in fat body/adipose and the intestine. Our data also reveal that this novel myokine-dependent hormone module is critical to maintain diurnal rhythms in circulating lipids. This tissue crosstalk provides a putative mechanism that allows muscle to integrate autonomous energy demand with systemic energy storage and turnover. Together, these findings reveal a diurnal inter-tissue signaling network between muscle and fat storage tissues that constitutes an ancestral mechanism governing systemic energy homeostasis.
Collapse
Affiliation(s)
- Xiao Zhao
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Jason Karpac
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA.
| |
Collapse
|
31
|
Castelo-Szekely V, Arpat AB, Janich P, Gatfield D. Translational contributions to tissue specificity in rhythmic and constitutive gene expression. Genome Biol 2017. [PMID: 28622766 PMCID: PMC5473967 DOI: 10.1186/s13059-017-1222-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background The daily gene expression oscillations that underlie mammalian circadian rhythms show striking differences between tissues and involve post-transcriptional regulation. Both aspects remain poorly understood. We have used ribosome profiling to explore the contribution of translation efficiency to temporal gene expression in kidney and contrasted our findings with liver data available from the same mice. Results Rhythmic translation of constantly abundant messenger RNAs (mRNAs) affects largely non-overlapping transcript sets with distinct phase clustering in the two organs. Moreover, tissue differences in translation efficiency modulate the timing and amount of protein biosynthesis from rhythmic mRNAs, consistent with organ specificity in clock output gene repertoires and rhythmicity parameters. Our comprehensive datasets provided insights into translational control beyond temporal regulation. Between tissues, many transcripts show differences in translation efficiency, which are, however, of markedly smaller scale than mRNA abundance differences. Tissue-specific changes in translation efficiency are associated with specific transcript features and, intriguingly, globally counteracted and compensated transcript abundance variations, leading to higher similarity at the level of protein biosynthesis between both tissues. Conclusions We show that tissue specificity in rhythmic gene expression extends to the translatome and contributes to define the identities, the phases and the expression levels of rhythmic protein biosynthesis. Moreover, translational compensation of transcript abundance divergence leads to overall higher similarity at the level of protein production across organs. The unique resources provided through our study will serve to address fundamental questions of post-transcriptional control and differential gene expression in vivo. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1222-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Violeta Castelo-Szekely
- Center for Integrative Genomics, University of Lausanne, Génopode, 1015, Lausanne, Switzerland
| | - Alaaddin Bulak Arpat
- Center for Integrative Genomics, University of Lausanne, Génopode, 1015, Lausanne, Switzerland.,Vital-IT, Swiss Institute of Bioinformatics, Génopode, 1015, Lausanne, Switzerland
| | - Peggy Janich
- Center for Integrative Genomics, University of Lausanne, Génopode, 1015, Lausanne, Switzerland
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Génopode, 1015, Lausanne, Switzerland.
| |
Collapse
|
32
|
Chahad-Ehlers S, Arthur LP, Lima ALA, Gesto JSM, Torres FR, Peixoto AA, de Brito RA. Expanding the view of Clock and cycle gene evolution in Diptera. INSECT MOLECULAR BIOLOGY 2017; 26:317-331. [PMID: 28234413 DOI: 10.1111/imb.12296] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We expanded the view of Clock (Clk) and cycle (cyc) gene evolution in Diptera by studying the fruit fly Anastrepha fraterculus (Afra), a Brachycera. Despite the high conservation of clock genes amongst insect groups, striking structural and functional differences of some clocks have appeared throughout evolution. Clk and cyc nucleotide sequences and corresponding proteins were characterized, along with their mRNA expression data, to provide an evolutionary overview in the two major groups of Diptera: Lower Diptera and Higher Brachycera. We found that AfraCYC lacks the BMAL (Brain and muscle ARNT-like) C-terminus region (BCTR) domain and is constitutively expressed, suggesting that AfraCLK has the main transactivation function, which is corroborated by the presence of poly-Q repeats and an oscillatory pattern. Our analysis suggests that the loss of BCTR in CYC is not exclusive of drosophilids, as it also occurs in other Acalyptratae flies such as tephritids and drosophilids, however, but it is also present in some Calyptratae, such as Muscidae, Calliphoridae and Sarcophagidae. This indicates that BCTR is missing from CYC of all higher-level Brachycera and that it was lost during the evolution of Lower Brachycera. Thus, we can infer that CLK protein may play the main role in the CLK\CYC transcription complex in these flies, like in its Drosophila orthologues.
Collapse
Affiliation(s)
- S Chahad-Ehlers
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - L P Arthur
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - A L A Lima
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - J S M Gesto
- Laboratório de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - F R Torres
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - A A Peixoto
- Laboratório de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - R A de Brito
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| |
Collapse
|
33
|
Cao Y, Wang RH. Associations among Metabolism, Circadian Rhythm and Age-Associated Diseases. Aging Dis 2017; 8:314-333. [PMID: 28580187 PMCID: PMC5440111 DOI: 10.14336/ad.2016.1101] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/01/2016] [Indexed: 12/12/2022] Open
Abstract
Accumulating epidemiological studies have implicated a strong link between age associated metabolic diseases and cancer, though direct and irrefutable evidence is missing. In this review, we discuss the connection between Warburg effects and tumorigenesis, as well as adaptive responses to environment such as circadian rhythms on molecular pathways involved in metabolism. We also review the central role of the sirtuin family of proteins in physiological modulation of cellular processes and age-associated metabolic diseases. We also provide a macroscopic view of how the circadian rhythm affects metabolism and may be involved in cell metabolism reprogramming and cancer pathogenesis. The aberrations in metabolism and the circadian system may lead to age-associated diseases directly or through intermediates. These intermediates may be either mutated or reprogrammed, thus becoming responsible for chromatin modification and oncogene transcription. Integration of circadian rhythm and metabolic reprogramming in the holistic understanding of metabolic diseases and cancer may provide additional insights into human diseases.
Collapse
Affiliation(s)
- Yiwei Cao
- Faculty of Health Science, University of Macau, Macau, China
| | - Rui-Hong Wang
- Faculty of Health Science, University of Macau, Macau, China
| |
Collapse
|
34
|
Abstract
Candida albicans is an important etiological agent of superficial and life-threatening infections in individuals with compromised immune systems. To date, we know of several overlapping genetic networks that govern virulence attributes in this fungal pathogen. Classical use of deletion mutants has led to the discovery of numerous virulence factors over the years, and genome-wide functional analysis has propelled gene discovery at an even faster pace. Indeed, a number of recent studies using large-scale genetic screens followed by genome-wide functional analysis has allowed for the unbiased discovery of many new genes involved in C. albicans biology. Here we share our perspectives on the role of these studies in analyzing fundamental aspects of C. albicans virulence properties.
Collapse
Affiliation(s)
- Thabiso E Motaung
- a Agricultural Research Council - Small Grain Institute , Bethlehem , South Africa
| | - Ruan Ells
- b University of the Free Sate , Bloemfontein , South Africa
| | | | | | - Toi J Tsilo
- a Agricultural Research Council - Small Grain Institute , Bethlehem , South Africa.,c Department of Life and Consumer Sciences , University of South Africa , Pretoria , South Africa
| |
Collapse
|
35
|
Achilles is a circadian clock-controlled gene that regulates immune function in Drosophila. Brain Behav Immun 2017; 61:127-136. [PMID: 27856350 PMCID: PMC5316375 DOI: 10.1016/j.bbi.2016.11.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/02/2016] [Accepted: 11/12/2016] [Indexed: 02/06/2023] Open
Abstract
The circadian clock is a transcriptional/translational feedback loop that drives the rhythmic expression of downstream mRNAs. Termed "clock-controlled genes," these molecular outputs of the circadian clock orchestrate cellular, metabolic, and behavioral rhythms. As part of our on-going work to characterize key upstream regulators of circadian mRNA expression, we have identified a novel clock-controlled gene in Drosophila melanogaster, Achilles (Achl), which is rhythmic at the mRNA level in the brain and which represses expression of antimicrobial peptides in the immune system. Achilles knock-down in neurons dramatically elevates expression of crucial immune response genes, including IM1 (Immune induced molecule 1), Mtk (Metchnikowin), and Drs (Drosomysin). As a result, flies with knocked-down Achilles expression are resistant to bacterial challenges. Meanwhile, no significant change in core clock gene expression and locomotor activity is observed, suggesting that Achilles influences rhythmic mRNA outputs rather than directly regulating the core timekeeping mechanism. Notably, Achilles knock-down in the absence of immune challenge significantly diminishes the fly's overall lifespan, indicating a behavioral or metabolic cost of constitutively activating this pathway. Together, our data demonstrate that (1) Achilles is a novel clock-controlled gene that (2) regulates the immune system, and (3) participates in signaling from neurons to immunological tissues.
Collapse
|
36
|
Abruzzi KC, Zadina A, Luo W, Wiyanto E, Rahman R, Guo F, Shafer O, Rosbash M. RNA-seq analysis of Drosophila clock and non-clock neurons reveals neuron-specific cycling and novel candidate neuropeptides. PLoS Genet 2017; 13:e1006613. [PMID: 28182648 PMCID: PMC5325595 DOI: 10.1371/journal.pgen.1006613] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/24/2017] [Accepted: 02/01/2017] [Indexed: 12/21/2022] Open
Abstract
Locomotor activity rhythms are controlled by a network of ~150 circadian neurons within the adult Drosophila brain. They are subdivided based on their anatomical locations and properties. We profiled transcripts “around the clock” from three key groups of circadian neurons with different functions. We also profiled a non-circadian outgroup, dopaminergic (TH) neurons. They have cycling transcripts but fewer than clock neurons as well as low expression and poor cycling of clock gene transcripts. This suggests that TH neurons do not have a canonical circadian clock and that their gene expression cycling is driven by brain systemic cues. The three circadian groups are surprisingly diverse in their cycling transcripts and overall gene expression patterns, which include known and putative novel neuropeptides. Even the overall phase distributions of cycling transcripts are distinct, indicating that different regulatory principles govern transcript oscillations. This surprising cell-type diversity parallels the functional heterogeneity of the different neurons. Organisms ranging from bacteria to humans contain circadian clocks. They keep internal time and also integrate environmental cues such as light to provide external time information for entrainment. In the fruit fly Drosophila melanogaster, ~150 brain neurons contain the circadian machinery and are critical for controlling behavior. Several subgroups of these clock neurons have been identified by their anatomical locations and specific functions. Our work aims to profile these neurons and to characterize their molecular contents: what to they contain and how do they differ? To this end, we have purified 3 important subgroups of clock neurons and identified their expressed genes at different times of day. Some are expressed at all times, whereas others are “cycling,” i.e., expressed more strongly at a particular time of day like the morning. Interestingly, each circadian subgroup is quite different. The data provide hints about what functions each group of neurons carries out and how they may work together to keep time. In addition, even a non-circadian group of neurons has cycling genes and has implications for the extent to which all cells have or do not have a functional circadian clock.
Collapse
Affiliation(s)
- Katharine C. Abruzzi
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Abigail Zadina
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Weifei Luo
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Evelyn Wiyanto
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Reazur Rahman
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Fang Guo
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Orie Shafer
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Michael Rosbash
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
- * E-mail:
| |
Collapse
|
37
|
Shlyueva D, Meireles-Filho ACA, Pagani M, Stark A. Genome-Wide Ultrabithorax Binding Analysis Reveals Highly Targeted Genomic Loci at Developmental Regulators and a Potential Connection to Polycomb-Mediated Regulation. PLoS One 2016; 11:e0161997. [PMID: 27575958 PMCID: PMC5004984 DOI: 10.1371/journal.pone.0161997] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 08/16/2016] [Indexed: 12/22/2022] Open
Abstract
Hox homeodomain transcription factors are key regulators of animal development. They specify the identity of segments along the anterior-posterior body axis in metazoans by controlling the expression of diverse downstream targets, including transcription factors and signaling pathway components. The Drosophila melanogaster Hox factor Ultrabithorax (Ubx) directs the development of thoracic and abdominal segments and appendages, and loss of Ubx function can lead for example to the transformation of third thoracic segment appendages (e.g. halters) into second thoracic segment appendages (e.g. wings), resulting in a characteristic four-wing phenotype. Here we present a Drosophila melanogaster strain with a V5-epitope tagged Ubx allele, which we employed to obtain a high quality genome-wide map of Ubx binding sites using ChIP-seq. We confirm the sensitivity of the V5 ChIP-seq by recovering 7/8 of well-studied Ubx-dependent cis-regulatory regions. Moreover, we show that Ubx binding is predictive of enhancer activity as suggested by comparison with a genome-scale resource of in vivo tested enhancer candidates. We observed densely clustered Ubx binding sites at 12 extended genomic loci that included ANTP-C, BX-C, Polycomb complex genes, and other regulators and the clustered binding sites were frequently active enhancers. Furthermore, Ubx binding was detected at known Polycomb response elements (PREs) and was associated with significant enrichments of Pc and Pho ChIP signals in contrast to binding sites of other developmental TFs. Together, our results show that Ubx targets developmental regulators via strongly clustered binding sites and allow us to hypothesize that regulation by Ubx might involve Polycomb group proteins to maintain specific regulatory states in cooperative or mutually exclusive fashion, an attractive model that combines two groups of proteins with prominent gene regulatory roles during animal development.
Collapse
Affiliation(s)
- Daria Shlyueva
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | | | - Michaela Pagani
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- * E-mail:
| |
Collapse
|
38
|
Pacemaker-neuron-dependent disturbance of the molecular clockwork by a Drosophila CLOCK mutant homologous to the mouse Clock mutation. Proc Natl Acad Sci U S A 2016; 113:E4904-13. [PMID: 27489346 DOI: 10.1073/pnas.1523494113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Circadian clocks are composed of transcriptional/translational feedback loops (TTFLs) at the cellular level. In Drosophila TTFLs, the transcription factor dCLOCK (dCLK)/CYCLE (CYC) activates clock target gene expression, which is repressed by the physical interaction with PERIOD (PER). Here, we show that amino acids (AA) 657-707 of dCLK, a region that is homologous to the mouse Clock exon 19-encoded region, is crucial for PER binding and E-box-dependent transactivation in S2 cells. Consistently, in transgenic flies expressing dCLK with an AA657-707 deletion in the Clock (Clk(out)) genetic background (p{dClk-Δ};Clk(out)), oscillation of core clock genes' mRNAs displayed diminished amplitude compared with control flies, and the highly abundant dCLKΔ657-707 showed significantly decreased binding to PER. Behaviorally, the p{dClk-Δ};Clk(out) flies exhibited arrhythmic locomotor behavior in the photic entrainment condition but showed anticipatory activities of temperature transition and improved free-running rhythms in the temperature entrainment condition. Surprisingly, p{dClk-Δ};Clk(out) flies showed pacemaker-neuron-dependent alterations in molecular rhythms; the abundance of dCLK target clock proteins was reduced in ventral lateral neurons (LNvs) but not in dorsal neurons (DNs) in both entrainment conditions. In p{dClk-Δ};Clk(out) flies, however, strong but delayed molecular oscillations in temperature cycle-sensitive pacemaker neurons, such as DN1s and DN2s, were correlated with delayed anticipatory activities of temperature transition. Taken together, our study reveals that the LNv molecular clockwork is more sensitive than the clockwork of DNs to dysregulation of dCLK by AA657-707 deletion. Therefore, we propose that the dCLK/CYC-controlled TTFL operates differently in subsets of pacemaker neurons, which may contribute to their specific functions.
Collapse
|
39
|
Wang RH, Zhao T, Cui K, Hu G, Chen Q, Chen W, Wang XW, Soto-Gutierrez A, Zhao K, Deng CX. Negative reciprocal regulation between Sirt1 and Per2 modulates the circadian clock and aging. Sci Rep 2016; 6:28633. [PMID: 27346580 PMCID: PMC4922021 DOI: 10.1038/srep28633] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/06/2016] [Indexed: 12/13/2022] Open
Abstract
Sirtuin 1 (SIRT1) is involved in both aging and circadian-clock regulation, yet the link between the two processes in relation to SIRT1 function is not clear. Using Sirt1-deficient mice, we found that Sirt1 and Period 2 (Per2) constitute a reciprocal negative regulation loop that plays important roles in modulating hepatic circadian rhythmicity and aging. Sirt1-deficient mice exhibited profound premature aging and enhanced acetylation of histone H4 on lysine16 (H4K16) in the promoter of Per2, the latter of which leads to its overexpression; in turn, Per2 suppresses Sirt1 transcription through binding to the Sirt1 promoter at the Clock/Bmal1 site. This negative reciprocal relationship between SIRT1 and PER2 was also observed in human hepatocytes. We further demonstrated that the absence of Sirt1 or the ectopic overexpression of Per2 in the liver resulted in a dysregulated pace of the circadian rhythm. The similar circadian rhythm was also observed in aged wild type mice. The interplay between Sirt1 and Per2 modulates aging gene expression and circadian-clock maintenance.
Collapse
Affiliation(s)
- Rui-Hong Wang
- Faculty of Health Sciences, University of Macau, Macau SAR, China.,Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tingrui Zhao
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Gangqing Hu
- Systems Biology Center, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Qiang Chen
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Weiping Chen
- Genomic Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Xin-Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Chu-Xia Deng
- Faculty of Health Sciences, University of Macau, Macau SAR, China.,Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
40
|
Endo M. Tissue-specific circadian clocks in plants. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:44-9. [PMID: 26723003 DOI: 10.1016/j.pbi.2015.11.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/30/2015] [Accepted: 11/05/2015] [Indexed: 05/28/2023]
Abstract
Circadian clocks affect a large proportion of differentially expressed genes in many organisms. Tissue-specific hierarchies in circadian networks in mammals have been contentiously debated, whereas little attention has been devoted to the concept in plants, owing to technical difficulties. Recently, several studies have demonstrated tissue-specific circadian clocks and their coupling in plants, suggesting that plants possess a hierarchical network of circadian clocks. The following review summarizes recent studies describing the tissue-specific functions and properties of these circadian clocks and discusses the network structure and potential messengers that might share temporal information on such a network.
Collapse
Affiliation(s)
- Motomu Endo
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto 606-8501, Japan; Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan.
| |
Collapse
|
41
|
Rivas GBS, Bauzer LGSDR, Meireles-Filho ACA. "The Environment is Everything That Isn't Me": Molecular Mechanisms and Evolutionary Dynamics of Insect Clocks in Variable Surroundings. Front Physiol 2016; 6:400. [PMID: 26793115 PMCID: PMC4709423 DOI: 10.3389/fphys.2015.00400] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/07/2015] [Indexed: 12/24/2022] Open
Abstract
Circadian rhythms are oscillations in behavior, metabolism and physiology that have a period close to 24 h. These rhythms are controlled by an internal pacemaker that evolved under strong selective pressures imposed by environmental cyclical changes, mainly of light and temperature. The molecular nature of the circadian pacemaker was extensively studied in a number of organisms under controlled laboratory conditions. But although these studies were fundamental to our understanding of the circadian clock, most of the environmental conditions used resembled rather crudely the relatively constant situation at lower latitudes. At higher latitudes light-dark and temperature cycles vary considerably across different seasons, with summers having long and hot days and winters short and cold ones. Considering these differences and other external cues, such as moonlight, recent studies in more natural and semi-natural situations revealed unexpected features at both molecular and behavioral levels, highlighting the dramatic influence of multiple environmental variables in the molecular clockwork. This emphasizes the importance of studying the circadian clock in the wild, where seasonal environmental changes fine-tune the underlying circadian mechanism, affecting population dynamics and impacting the geographical variation in clock genes. Indeed, latitudinal clines in clock gene frequencies suggest that natural selection and demography shape the circadian clock over wide geographical ranges. In this review we will discuss the recent advances in understanding the molecular underpinnings of the circadian clock, how it resonates with the surrounding variables (both in the laboratory and in semi-natural conditions) and its impact on population dynamics and evolution. In addition, we will elaborate on how next-generation sequencing technologies will complement classical reductionist approaches by identifying causal variants in natural populations that will link genetic variation to circadian phenotypes, illuminating how the circadian clock functions in the real world.
Collapse
Affiliation(s)
- Gustavo B. S. Rivas
- Laboratório de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo CruzRio de Janeiro, Brazil
| | - Luiz G. S. da R. Bauzer
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz, Fundação Oswaldo CruzRio de Janeiro, Brazil
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo CruzRio de Janeiro, Brazil
| | - Antonio C. A. Meireles-Filho
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, École Polytechnique Fédérale de LausanneLausanne, Switzerland
- Swiss Institute of BioinformaticsLausanne, Switzerland
| |
Collapse
|
42
|
Ommundsen A, Noever C, Glenner H. Caught in the act: phenotypic consequences of a recent shift in feeding strategy of the shark barnacle Anelasma squalicola (Lovén, 1844). ZOOMORPHOLOGY 2016; 135:51-65. [PMID: 26893532 PMCID: PMC4742507 DOI: 10.1007/s00435-015-0296-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 10/18/2015] [Accepted: 10/26/2015] [Indexed: 12/04/2022]
Abstract
Anelasma squalicola is a barnacle found attached to deep-water lantern sharks of the family Etmopteridae and is the only known cirriped on fish hosts. While A. squalicola is equipped with mouth and thoracic appendages (cirri), which are used for suspension feeding in conventional barnacles, its attachment device (peduncle) appears to have evolved into a feeding device, embedded into the tissue of its host. Here we demonstrate, through comparisons of the feeding apparatuses between A. squalicola and conventional suspension-feeding barnacles, that mouthparts and cirri of A. squalicola are highly reduced, and incapable of suspension-feeding activities. We show that in conventional suspension-feeding barnacles strong symmetries exist within these vital trophic structures. In A. squalicola strong asymmetries are widespread, indicating that those structures have been uncoupled from natural selection. The digestive tract is consistently empty, suggesting that feeding via cirri does not occur in A. squalicola. In addition, comparisons of stable isotope ratios (δ13C and δ15N) between A. squalicola, its shark host, and a conventional suspending feeding barnacle indicate that A. squalicola is taking nutrition directly from its host shark and not from the surrounding water. Our results strongly indicate that this barnacle has abandoned suspension feeding and now solely relies on obtaining nutrition from its host by a de novo evolved feeding mechanism.
Collapse
Affiliation(s)
| | | | - Henrik Glenner
- />Department of Biology, University of Bergen, Bergen, Norway
- />CMEC, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
43
|
Block DH, Shapira M. GATA transcription factors as tissue-specific master regulators for induced responses. WORM 2015; 4:e1118607. [PMID: 27123374 PMCID: PMC4826149 DOI: 10.1080/21624054.2015.1118607] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/03/2015] [Accepted: 11/05/2015] [Indexed: 01/15/2023]
Abstract
GATA transcription factors play important roles in directing developmental genetic programs and cell differentiation, and are conserved in animals, plants and fungi. C. elegans has 11 GATA-type transcription factors that orchestrate development of the gut, epidermis and vulva. However, the expression of certain GATA proteins persists into adulthood, where their function is less understood. Accumulating evidence demonstrates contributions of 2 terminal differentiation GATA transcription factors, ELT-2 and ELT-3, to epithelial immune responses in the adult intestine and epidermis (hypodermis), respectively. Involvement in other stress responses has also been documented. We recently showed that ELT-2 acted as a tissue-specific master regulator, cooperating with 2 transcription factors activated by the p38 pathway, ATF-7 and SKN-1, to control immune responses in the adult C. elegans intestine. Here, we discuss the broader implications of these findings for understanding the involvement of GATA transcription factors in adult stress responses, and draw parallels between ELT-2 and ELT-3 to speculate that the latter may fulfill similar tissue-specific functions in the epidermis.
Collapse
Affiliation(s)
- Dena Hs Block
- Department of Integrative Biology; University of California ; Berkeley, CA USA
| | - Michael Shapira
- Department of Integrative Biology; University of California; Berkeley, CA USA; Graduate Group in Microbiology; University of California; Berkeley, CA USA
| |
Collapse
|
44
|
Jolma A, Yin Y, Nitta KR, Dave K, Popov A, Taipale M, Enge M, Kivioja T, Morgunova E, Taipale J. DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature 2015; 527:384-8. [PMID: 26550823 DOI: 10.1038/nature15518] [Citation(s) in RCA: 380] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 08/24/2015] [Indexed: 12/28/2022]
|
45
|
Ubiquitin ligase Siah2 regulates RevErbα degradation and the mammalian circadian clock. Proc Natl Acad Sci U S A 2015; 112:12420-5. [PMID: 26392558 DOI: 10.1073/pnas.1501204112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Regulated degradation of proteins by the proteasome is often critical to their function in dynamic cellular pathways. The molecular clock underlying mammalian circadian rhythms relies on the rhythmic expression and degradation of its core components. However, because the tools available for identifying the mechanisms underlying the degradation of a specific protein are limited, the mechanisms regulating clock protein degradation are only beginning to be elucidated. Here we describe a cell-based functional screening approach designed to quickly identify the ubiquitin E3 ligases that induce the degradation of potentially any protein of interest. We screened the nuclear hormone receptor RevErbα (Nr1d1), a key constituent of the mammalian circadian clock, for E3 ligases that regulate its stability and found Seven in absentia2 (Siah2) to be a key regulator of RevErbα stability. Previously implicated in hypoxia signaling, Siah2 overexpression destabilizes RevErbα/β, and siRNA depletion of Siah2 stabilizes endogenous RevErbα. Moreover, Siah2 depletion delays circadian degradation of RevErbα and lengthens period length. These results demonstrate the utility of functional screening approaches for identifying regulators of protein stability and reveal Siah2 as a previously unidentified circadian clockwork regulator that mediates circadian RevErbα turnover.
Collapse
|
46
|
Abstract
Circadian rhythms are daily endogenous oscillations of behavior, metabolism, and physiology. At a molecular level, these oscillations are generated by transcriptional-translational feedback loops composed of core clock genes. In turn, core clock genes drive the rhythmic accumulation of downstream outputs-termed clock-controlled genes (CCGs)-whose rhythmic translation and function ultimately underlie daily oscillations at a cellular and organismal level. Given the circadian clock's profound influence on human health and behavior, considerable efforts have been made to systematically identify CCGs. The recent development of next-generation sequencing has dramatically expanded our ability to study the expression, processing, and stability of rhythmically expressed mRNAs. Nevertheless, like any new technology, there are many technical issues to be addressed. Here, we discuss considerations for studying circadian rhythms using genome scale transcriptional profiling, with a particular emphasis on RNA sequencing. We make a number of practical recommendations-including the choice of sampling density, read depth, alignment algorithms, read-depth normalization, and cycling detection algorithms-based on computational simulations and our experience from previous studies. We believe that these results will be of interest to the circadian field and help investigators design experiments to derive most values from these large and complex data sets.
Collapse
Affiliation(s)
- Jiajia Li
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Gregory R Grant
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John B Hogenesch
- Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael E Hughes
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, USA.
| |
Collapse
|
47
|
Endo M, Shimizu H, Nohales MA, Araki T, Kay SA. Tissue-specific clocks in Arabidopsis show asymmetric coupling. Nature 2014; 515:419-22. [PMID: 25363766 PMCID: PMC4270698 DOI: 10.1038/nature13919] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 09/30/2014] [Indexed: 12/19/2022]
Abstract
Many organisms rely on a circadian clock system to adapt to daily and seasonal environmental changes. The mammalian circadian clock consists of a central clock in the suprachiasmatic nucleus that has tightly coupled neurons and synchronizes other clocks in peripheral tissues. Plants also have a circadian clock, but plant circadian clock function has long been assumed to be uncoupled. Only a few studies have been able to show weak, local coupling among cells. Here, by implementing two novel techniques, we have performed a comprehensive tissue-specific analysis of leaf tissues, and show that the vasculature and mesophyll clocks asymmetrically regulate each other in Arabidopsis. The circadian clock in the vasculature has characteristics distinct from other tissues, cycles robustly without environmental cues, and affects circadian clock regulation in other tissues. Furthermore, we found that vasculature-enriched genes that are rhythmically expressed are preferentially expressed in the evening, whereas rhythmic mesophyll-enriched genes tend to be expressed in the morning. Our results set the stage for a deeper understanding of how the vasculature circadian clock in plants regulates key physiological responses such as flowering time.
Collapse
Affiliation(s)
- Motomu Endo
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto 606-8501, Japan
- Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Hanako Shimizu
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Maria A. Nohales
- University of Southern California Molecular and Computational Biology, Department of Biology Dana and David Dornsife College of Letters, Arts and Science, Los Angeles, CA 90089, United States
| | - Takashi Araki
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Steve A. Kay
- University of Southern California Molecular and Computational Biology, Department of Biology Dana and David Dornsife College of Letters, Arts and Science, Los Angeles, CA 90089, United States
| |
Collapse
|
48
|
Medullary bone-like tissue in the mandibular symphyses of a pterosaur suggests non-reproductive significance. Sci Rep 2014. [DOI: 10.1038/srep06253] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
|
49
|
Abstract
The circadian clock uses a widely expressed pair of clock activators to drive tissue-specific rhythms in target gene expression. A new study sheds light on this tissue specificity by showing that binding of clock activators and tissue-specific transcription factors to closely associated target sites enables cooperative activation of target genes in different tissues.
Collapse
Affiliation(s)
- Jerome S Menet
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843-3258, USA
| | - Paul E Hardin
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843-3258, USA.
| |
Collapse
|
50
|
Slattery M, Zhou T, Yang L, Dantas Machado AC, Gordân R, Rohs R. Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci 2014; 39:381-99. [PMID: 25129887 DOI: 10.1016/j.tibs.2014.07.002] [Citation(s) in RCA: 366] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/21/2022]
Abstract
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a genome. TFs recognize DNA in a specific manner; the mechanisms underlying this specificity have been identified for many TFs based on 3D structures of protein-DNA complexes. More recently, structural views have been complemented with data from high-throughput in vitro and in vivo explorations of the DNA-binding preferences of many TFs. Together, these approaches have greatly expanded our understanding of TF-DNA interactions. However, the mechanisms by which TFs select in vivo binding sites and alter gene expression remain unclear. Recent work has highlighted the many variables that influence TF-DNA binding, while demonstrating that a biophysical understanding of these many factors will be central to understanding TF function.
Collapse
Affiliation(s)
- Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Tianyin Zhou
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Lin Yang
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Ana Carolina Dantas Machado
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Departments of Biostatistics and Bioinformatics, Computer Science, and Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA.
| | - Remo Rohs
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|