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Buono L, Annona G, Magri MS, Negueruela S, Sepe RM, Caccavale F, Maeso I, Arnone MI, D’Aniello S. Conservation of cis-Regulatory Syntax Underlying Deuterostome Gastrulation. Cells 2024; 13:1121. [PMID: 38994973 PMCID: PMC11240583 DOI: 10.3390/cells13131121] [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: 05/15/2024] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024] Open
Abstract
Throughout embryonic development, the shaping of the functional and morphological characteristics of embryos is orchestrated by an intricate interaction between transcription factors and cis-regulatory elements. In this study, we conducted a comprehensive analysis of deuterostome cis-regulatory landscapes during gastrulation, focusing on four paradigmatic species: the echinoderm Strongylocentrotus purpuratus, the cephalochordate Branchiostoma lanceolatum, the urochordate Ciona intestinalis, and the vertebrate Danio rerio. Our approach involved comparative computational analysis of ATAC-seq datasets to explore the genome-wide blueprint of conserved transcription factor binding motifs underlying gastrulation. We identified a core set of conserved DNA binding motifs associated with 62 known transcription factors, indicating the remarkable conservation of the gastrulation regulatory landscape across deuterostomes. Our findings offer valuable insights into the evolutionary molecular dynamics of embryonic development, shedding light on conserved regulatory subprograms and providing a comprehensive perspective on the conservation and divergence of gene regulation underlying the gastrulation process.
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Affiliation(s)
- Lorena Buono
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
| | - Giovanni Annona
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
- Department of Research Infrastructure for Marine Biological Resources (RIMAR), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Marta Silvia Magri
- Centro Andaluz de Biología del Desarollo (CABD), Universidad Pablo de Olavide, 41013 Sevilla, Spain;
| | | | - Rosa Maria Sepe
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton, 80133 Naples, Italy
| | - Filomena Caccavale
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
| | - Ignacio Maeso
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona (UB), 08028 Barcelona, Spain;
- Institut de Recerca de la Biodiversitat (IRBio), University of Barcelona (UB), 08028 Barcelona, Spain
| | - Maria Ina Arnone
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
| | - Salvatore D’Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
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Harvey-Carroll J, Stevenson TJ, Spencer KA. Maternal developmental history alters transfer of circadian clock genes to offspring in Japanese quail (Coturnix japonica). J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2024; 210:399-413. [PMID: 37589732 PMCID: PMC11106187 DOI: 10.1007/s00359-023-01666-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/25/2023] [Accepted: 08/02/2023] [Indexed: 08/18/2023]
Abstract
Maternal signals shape embryonic development, and in turn post-natal phenotypes. RNA deposition is one such method of maternal signalling and circadian rhythms are one trait thought to be maternally inherited, through this mechanism. These maternal circadian gene transcripts aid development of a functioning circadian system. There is increasing evidence that maternal signals can be modified, depending on prevailing environmental conditions to optimise offspring fitness. However, currently, it is unknown if maternal circadian gene transcripts, and consequently early embryonic gene transcription, are altered by maternal developmental conditions. Here, using avian mothers who experienced either pre-natal corticosterone exposure, and/or post-natal stress as juveniles we were able to determine the effects of the timing of stress on downstream circadian RNA deposition in offspring. We demonstrated that maternal developmental history does indeed affect transfer of offspring circadian genes, but the timing of stress was important. Avian mothers who experienced stress during the first 2 weeks of post-natal life increased maternally deposited transcript levels of two core circadian clock genes, BMAL1 and PER2. These differences in transcript levels were transient and disappeared at the point of embryonic genome transcription. Pre-natal maternal stress alone was found to elicit delayed changes in circadian gene expression. After activation of the embryonic genome, both BMAL1 and PER2 expression were significantly decreased. If both pre-natal and post-natal stress occurred, then initial maternal transcript levels of BMAL1 were significantly increased. Taken together, these results suggest that developmental stress differentially produces persistent transgenerational effects on offspring circadian genes.
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Affiliation(s)
- Jessica Harvey-Carroll
- School of Psychology and Neuroscience, University of St Andrews, South Street, St Andrews, KY16 9JP, UK.
- Department of Biological and Environmental Sciences, University of Gothenburg, Medicinaregatan 18A, 413 90, Gothenburg, Sweden.
| | - Tyler J Stevenson
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G36 1QH, UK
| | - Karen A Spencer
- School of Psychology and Neuroscience, University of St Andrews, South Street, St Andrews, KY16 9JP, UK
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Parasram K, Zuccato A, Shin M, Willms R, DeVeale B, Foley E, Karpowicz P. The emergence of circadian timekeeping in the intestine. Nat Commun 2024; 15:1788. [PMID: 38413599 PMCID: PMC10899604 DOI: 10.1038/s41467-024-45942-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
The circadian clock is a molecular timekeeper, present from cyanobacteria to mammals, that coordinates internal physiology with the external environment. The clock has a 24-h period however development proceeds with its own timing, raising the question of how these interact. Using the intestine of Drosophila melanogaster as a model for organ development, we track how and when the circadian clock emerges in specific cell types. We find that the circadian clock begins abruptly in the adult intestine and gradually synchronizes to the environment after intestinal development is complete. This delayed start occurs because individual cells at earlier stages lack the complete circadian clock gene network. As the intestine develops, the circadian clock is first consolidated in intestinal stem cells with changes in Ecdysone and Hnf4 signalling influencing the transcriptional activity of Clk/cyc to drive the expression of tim, Pdp1, and vri. In the mature intestine, stem cell lineage commitment transiently disrupts clock activity in differentiating progeny, mirroring early developmental clock-less transitions. Our data show that clock function and differentiation are incompatible and provide a paradigm for studying circadian clocks in development and stem cell lineages.
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Affiliation(s)
- Kathyani Parasram
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Amy Zuccato
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Minjeong Shin
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Reegan Willms
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Brian DeVeale
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Edan Foley
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Phillip Karpowicz
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada.
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Price KH, Dziema H, Aten S, Loeser J, Norona FE, Hoyt K, Obrietan K. Modulation of learning and memory by the targeted deletion of the circadian clock gene Bmal1 in forebrain circuits. Behav Brain Res 2016; 308:222-35. [PMID: 27091299 PMCID: PMC5344043 DOI: 10.1016/j.bbr.2016.04.027] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 03/27/2016] [Accepted: 04/14/2016] [Indexed: 02/06/2023]
Abstract
A large body of literature has shown that the disruption of circadian clock timing has profound effects on mood, memory and complex thinking. Central to this time keeping process is the master circadian pacemaker located within the suprachiasmatic nucleus (SCN). Of note, within the central nervous system, clock timing is not exclusive to the SCN, but rather, ancillary oscillatory capacity has been detected in a wide range of cell types and brain regions, including forebrain circuits that underlie complex cognitive processes. These observations raise questions about the hierarchical and functional relationship between the SCN and forebrain oscillators, and, relatedly, about the underlying clock-gated synaptic circuitry that modulates cognition. Here, we utilized a clock knockout strategy in which the essential circadian timing gene Bmal1 was selectively deleted from excitatory forebrain neurons, whilst the SCN clock remained intact, to test the role of forebrain clock timing in learning, memory, anxiety, and behavioral despair. With this model system, we observed numerous effects on hippocampus-dependent measures of cognition. Mice lacking forebrain Bmal1 exhibited deficits in both acquisition and recall on the Barnes maze. Notably, loss of forebrain Bmal1 abrogated time-of-day dependent novel object location memory. However, the loss of Bmal1 did not alter performance on the elevated plus maze, open field assay, and tail suspension test, indicating that this phenotype specifically impairs cognition but not affect. Together, these data suggest that forebrain clock timing plays a critical role in shaping the efficiency of learning and memory retrieval over the circadian day.
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Affiliation(s)
- Kaiden H Price
- Department of Neuroscience, Ohio State University, Columbus, OH, USA
| | - Heather Dziema
- Department of Neuroscience, Ohio State University, Columbus, OH, USA
| | - Sydney Aten
- Department of Neuroscience, Ohio State University, Columbus, OH, USA
| | - Jacob Loeser
- Department of Neuroscience, Ohio State University, Columbus, OH, USA
| | - Frances E Norona
- Department of Neuroscience, Ohio State University, Columbus, OH, USA
| | - Kari Hoyt
- Division of Pharmacology, Ohio State University, Columbus, OH, USA
| | - Karl Obrietan
- Department of Neuroscience, Ohio State University, Columbus, OH, USA.
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Gouveia A, Marcelino HM, Gonçalves L, Palmeirim I, Andrade RP. Patterning in time and space: HoxB cluster gene expression in the developing chick embryo. Cell Cycle 2015; 14:135-45. [PMID: 25602523 DOI: 10.4161/15384101.2014.972868] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The developing embryo is a paradigmatic model to study molecular mechanisms of time control in Biology. Hox genes are key players in the specification of tissue identity during embryo development and their expression is under strict temporal regulation. However, the molecular mechanisms underlying timely Hox activation in the early embryo remain unknown. This is hindered by the lack of a rigorous temporal framework of sequential Hox expression within a single cluster. Herein, a thorough characterization of HoxB cluster gene expression was performed over time and space in the early chick embryo. Clear temporal collinearity of HoxB cluster gene expression activation was observed. Spatial collinearity of HoxB expression was evidenced in different stages of development and in multiple tissues. Using embryo explant cultures we showed that HoxB2 is cyclically expressed in the rostral presomitic mesoderm with the same periodicity as somite formation, suggesting a link between timely tissue specification and somite formation. We foresee that the molecular framework herein provided will facilitate experimental approaches aimed at identifying the regulatory mechanisms underlying Hox expression in Time and Space.
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Affiliation(s)
- Analuce Gouveia
- a Life and Health Sciences Research Institute (ICVS); School of Health Sciences , University of Minho ; Braga , Portugal
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Liu X, Liu L, Zhang M, Yang N, Qi Y, Sun Y, Li X. Messenger RNA expression of chicken CLOCK gene in the response to Campylobacter jejuni inoculation. Poult Sci 2015. [DOI: 10.3382/ps/pev203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Brown SA. Circadian clock-mediated control of stem cell division and differentiation: beyond night and day. Development 2014; 141:3105-11. [DOI: 10.1242/dev.104851] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A biological ‘circadian’ clock conveys diurnal regulation upon nearly all aspects of behavior and physiology to optimize them within the framework of the solar day. From digestion to cardiac function and sleep, both cellular and systemic processes show circadian variations that coincide with diurnal need. However, recent research has shown that this same timekeeping mechanism might have been co-opted to optimize other aspects of development and physiology that have no obvious link to the 24 h day. For example, clocks have been suggested to underlie heterogeneity in stem cell populations, to optimize cycles of cell division during wound healing, and to alter immune progenitor differentiation and migration. Here, I review these circadian mechanisms and propose that they could serve as metronomes for a surprising variety of physiologically and medically important functions that far exceed the daily timekeeping roles for which they probably evolved.
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Affiliation(s)
- Steven A. Brown
- Institute of Pharmacology and Toxicology, University of Zürich, 190 Winterthurerstrasse, Zürich 8057, Switzerland
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