1
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Anyetei-Anum CS, Leatham-Jensen MP, Fox GC, Smith BR, Krajewski K, Strahl BD, Dowen JM, Matera AG, Duronio RJ, McKay DJ. Dual roles of histone H3 lysine-4 in antagonizing Polycomb group function and promoting target gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600669. [PMID: 38979215 PMCID: PMC11230394 DOI: 10.1101/2024.06.25.600669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Tight control over cell identity gene expression is necessary for proper adult form and function. The opposing activities of Polycomb and trithorax complexes determine the ON/OFF state of targets like the Hox genes. Trithorax encodes a methyltransferase specific to histone H3 lysine-4 (H3K4). However, there is no direct evidence that H3K4 regulates Polycomb group target genes in vivo . Here, we demonstrate two key roles for replication-dependent histone H3.2K4 in target control. We find that H3.2K4 antagonizes Polycomb group catalytic activity and that it is required for proper target gene activation. We conclude that H3.2K4 directly regulates expression of Polycomb targets.
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2
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Ahmed-de-Prado S, Estella C, Baonza A. Temporal dynamics of apoptosis-induced proliferation in pupal wing development: implications for regenerative ability. BMC Biol 2024; 22:98. [PMID: 38679694 PMCID: PMC11057159 DOI: 10.1186/s12915-024-01894-1] [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: 07/29/2023] [Accepted: 04/17/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND The ability of animals to regenerate damaged tissue is a complex process that involves various cellular mechanisms. As animals age, they lose their regenerative abilities, making it essential to understand the underlying mechanisms that limit regenerative ability during aging. Drosophila melanogaster wing imaginal discs are epithelial structures that can regenerate after tissue injury. While significant research has focused on investigating regenerative responses during larval stages our comprehension of the regenerative potential of pupal wings and the underlying mechanisms contributing to the decline of regenerative responses remains limited. RESULTS Here, we explore the temporal dynamics during pupal development of the proliferative response triggered by the induction of cell death, a typical regenerative response. Our results indicate that the apoptosis-induced proliferative response can continue until 34 h after puparium formation (APF), beyond this point cell death alone is not sufficient to induce a regenerative response. Under normal circumstances, cell proliferation ceases around 24 h APF. Interestingly, the failure of reinitiating the cell cycle beyond this time point is not attributed to an incapacity to activate the JNK pathway. Instead, our results suggest that the function of the ecdysone-responsive transcription factor E93 is involved in limiting the apoptosis-induced proliferative response during pupal development. CONCLUSIONS Our study shows that apoptosis can prolong the proliferative period of cells in the wing during pupal development as late as 34 h APF, at least 10 h longer than during normal development. After this time point, the regenerative response is diminished, a process mediated in part by the ecdysone-responsive transcription factor E93.
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Affiliation(s)
| | - Carlos Estella
- Centro de Biología Molecular Severo Ochoa (CSIC/UAM), C/Nicolás Cabrera 1, Madrid, 28049, Spain
| | - Antonio Baonza
- Centro de Biología Molecular Severo Ochoa (CSIC/UAM), C/Nicolás Cabrera 1, Madrid, 28049, Spain.
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3
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Morrow H, Mirth CK. Timing Drosophila development through steroid hormone action. Curr Opin Genet Dev 2024; 84:102148. [PMID: 38271845 DOI: 10.1016/j.gde.2023.102148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024]
Abstract
Specifically timed pulses of the moulting hormone ecdysone are necessary for developmental progression in insects, guiding development through important milestones such as larval moults, pupation and metamorphosis. It also coordinates the acquisition of cell identities, known as cell patterning, and growth in a tissue-specific manner. In the absence of ecdysone, the ecdysone receptor heterodimer Ecdysone Receptor and Ultraspiracle represses expression of target primary response genes, which become de-repressed as the ecdysone titre rises. However, ecdysone signalling elicits both repressive and activating responses in a temporal and tissue-specific manner. To understand how ecdysone achieves such specificity, this review explores the layers of gene regulation involved in stage-appropriate ecdysone responses in Drosophila fruit flies.
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Affiliation(s)
- Hannah Morrow
- School of Biological Sciences, Monash University, Clayton, Victoria 3000, Australia.
| | - Christen K Mirth
- School of Biological Sciences, Monash University, Clayton, Victoria 3000, Australia
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4
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Oliveira AC, Homem CCF. Opposing effects of ecdysone signaling regulate neuroblast proliferation to ensure coordination of brain and organism development. Dev Biol 2023; 503:53-67. [PMID: 37549863 DOI: 10.1016/j.ydbio.2023.08.001] [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: 01/13/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Growth regulation must be robust to ensure correct final size, but also adaptative to adjust to less favorable environmental conditions. Developmental coordination between whole-organism and the brain is particularly important, as the brain is a critical organ with little adaptability. Brain growth mainly depends on neural stem cell (NSC) proliferation to generate differentiated neural cells, it is however unclear how organism developmental progression is coordinated with NSCs. Here we demonstrate that the steroid hormone ecdysone plays a multi-step, stage specific role in regulating Drosophila NSCs, the neuroblasts. We used animals that are unable to synthesize ecdysone, to show that the developmental milestone called "critical weight peak", the peak that informs the body has reached minimum viable weight to survive metamorphosis, acts a checkpoint necessary to set neuroblast cell cycle pace during larval neurogenesis. The peaks of ecdysone that occur post-critical weight are no longer required to maintain neuroblast division rate. We additionally show that in a second stage, at the onset of pupariation, ecdysone is instead required to trigger neuroblast's proliferation exit and consequently the end of neurogenesis. We demonstrate that, without this signal from ecdysone, neuroblasts lose their ability to exit proliferation. Interestingly, although these neuroblasts proliferate for a longer period, the number of differentiated neurons is smaller compared to wild-type brains, suggesting a role for ecdysone in neuron maintenance. Our study provides insights into how neural stem cells coordinate their division rate with the pace of body growth, identifying a novel coordination mechanism between animal development and NSC proliferation.
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Affiliation(s)
- Andreia C Oliveira
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Catarina C F Homem
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
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5
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Perez-Mockus G, Cocconi L, Alexandre C, Aerne B, Salbreux G, Vincent JP. The Drosophila ecdysone receptor promotes or suppresses proliferation according to ligand level. Dev Cell 2023; 58:2128-2139.e4. [PMID: 37769663 PMCID: PMC7615657 DOI: 10.1016/j.devcel.2023.08.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/20/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023]
Abstract
The steroid hormone 20-hydroxy-ecdysone (20E) promotes proliferation in Drosophila wing precursors at low titer but triggers proliferation arrest at high doses. Remarkably, wing precursors proliferate normally in the complete absence of the 20E receptor, suggesting that low-level 20E promotes proliferation by overriding the default anti-proliferative activity of the receptor. By contrast, 20E needs its receptor to arrest proliferation. Dose-response RNA sequencing (RNA-seq) analysis of ex vivo cultured wing precursors identifies genes that are quantitatively activated by 20E across the physiological range, likely comprising positive modulators of proliferation and other genes that are only activated at high doses. We suggest that some of these "high-threshold" genes dominantly suppress the activity of the pro-proliferation genes. We then show mathematically and with synthetic reporters that combinations of basic regulatory elements can recapitulate the behavior of both types of target genes. Thus, a relatively simple genetic circuit can account for the bimodal activity of this hormone.
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Affiliation(s)
| | - Luca Cocconi
- The Francis Crick Institute, London NW1 1AT, UK.
| | | | | | - Guillaume Salbreux
- The Francis Crick Institute, London NW1 1AT, UK; Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1205 Geneva, Switzerland.
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6
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Opportunistic binding of EcR to open chromatin drives tissue-specific developmental responses. Proc Natl Acad Sci U S A 2022; 119:e2208935119. [PMID: 36161884 DOI: 10.1073/pnas.2208935119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Steroid hormones perform diverse biological functions in developing and adult animals. However, the mechanistic basis for their tissue specificity remains unclear. In Drosophila, the ecdysone steroid hormone is essential for coordinating developmental timing across physically separated tissues. Ecdysone directly impacts genome function through its nuclear receptor, a heterodimer of the EcR and ultraspiracle proteins. Ligand binding to EcR triggers a transcriptional cascade, including activation of a set of primary response transcription factors. The hierarchical organization of this pathway has left the direct role of EcR in mediating ecdysone responses obscured. Here, we investigate the role of EcR in controlling tissue-specific ecdysone responses, focusing on two tissues that diverge in their response to rising ecdysone titers: the larval salivary gland, which undergoes programmed destruction, and the wing imaginal disc, which initiates morphogenesis. We find that EcR functions bimodally, with both gene repressive and activating functions, even at the same developmental stage. EcR DNA binding profiles are highly tissue-specific, and transgenic reporter analyses demonstrate that EcR plays a direct role in controlling enhancer activity. Finally, despite a strong correlation between tissue-specific EcR binding and tissue-specific open chromatin, we find that EcR does not control chromatin accessibility at genomic targets. We conclude that EcR contributes extensively to tissue-specific ecdysone responses. However, control over access to its binding sites is subordinated to other transcription factors.
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7
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Blanco-Obregon D, El Marzkioui K, Brutscher F, Kapoor V, Valzania L, Andersen DS, Colombani J, Narasimha S, McCusker D, Léopold P, Boulan L. A Dilp8-dependent time window ensures tissue size adjustment in Drosophila. Nat Commun 2022; 13:5629. [PMID: 36163439 PMCID: PMC9512784 DOI: 10.1038/s41467-022-33387-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
The control of organ size mainly relies on precise autonomous growth programs. However, organ development is subject to random variations, called developmental noise, best revealed by the fluctuating asymmetry observed between bilateral organs. The developmental mechanisms ensuring bilateral symmetry in organ size are mostly unknown. In Drosophila, null mutations for the relaxin-like hormone Dilp8 increase wing fluctuating asymmetry, suggesting that Dilp8 plays a role in buffering developmental noise. Here we show that size adjustment of the wing primordia involves a peak of dilp8 expression that takes place sharply at the end of juvenile growth. Wing size adjustment relies on a cross-organ communication involving the epidermis as the source of Dilp8. We identify ecdysone signaling as both the trigger for epidermal dilp8 expression and its downstream target in the wing primordia, thereby establishing reciprocal hormonal feedback as a systemic mechanism, which controls organ size and bilateral symmetry in a narrow developmental time window. Mechanisms ensuring developmental precision are poorly understood. Here Blanco-Obregon et al. report reciprocal feedback between Dilp8 and Ecdysone, two hormones required during a precise time window of Drosophila development for organ size adjustment.
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Affiliation(s)
- D Blanco-Obregon
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, 26 Rue d'Ulm, 75005, Paris, France
| | - K El Marzkioui
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, 26 Rue d'Ulm, 75005, Paris, France
| | - F Brutscher
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - V Kapoor
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, 26 Rue d'Ulm, 75005, Paris, France
| | - L Valzania
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, 26 Rue d'Ulm, 75005, Paris, France
| | - D S Andersen
- Depatment of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Stem Cell Research, Faculty of Health and Medical Science, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - J Colombani
- Depatment of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Stem Cell Research, Faculty of Health and Medical Science, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - S Narasimha
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, 26 Rue d'Ulm, 75005, Paris, France
| | - D McCusker
- University of Michigan, Ann Arbor, MI, USA
| | - P Léopold
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, 26 Rue d'Ulm, 75005, Paris, France
| | - L Boulan
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, 26 Rue d'Ulm, 75005, Paris, France.
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8
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Strassburger K, Lutz M, Müller S, Teleman AA. Ecdysone regulates Drosophila wing disc size via a TORC1 dependent mechanism. Nat Commun 2021; 12:6684. [PMID: 34795214 PMCID: PMC8602387 DOI: 10.1038/s41467-021-26780-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/15/2021] [Indexed: 11/09/2022] Open
Abstract
Most cells in a developing organ stop proliferating when the organ reaches a correct, final size. The underlying molecular mechanisms are not understood. We find that in Drosophila the hormone ecdysone controls wing disc size. To study how ecdysone affects wing size, we inhibit endogenous ecdysone synthesis and feed larvae exogenous ecdysone in a dose-controlled manner. For any given ecdysone dose, discs stop proliferating at a particular size, with higher doses enabling discs to reach larger sizes. Termination of proliferation coincides with a drop in TORC1, but not Dpp or Yki signaling. Reactivating TORC1 bypasses the termination of proliferation, indicating that TORC1 is a main downstream effector causing proliferation termination at the maximal ecdysone-dependent size. Experimental manipulation of Dpp or Yki signaling can bypass proliferation termination in hinge and notum regions, but not the pouch, suggesting that the mechanisms regulating proliferation termination may be distinct in different disc regions.
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Affiliation(s)
- Katrin Strassburger
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373CellNetworks - Cluster of Excellence, Heidelberg University, Heidelberg, Germany ,grid.4488.00000 0001 2111 7257Present Address: Technische Universität Dresden, 01217 Dresden, Germany
| | - Marilena Lutz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373CellNetworks - Cluster of Excellence, Heidelberg University, Heidelberg, Germany
| | - Sandra Müller
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373CellNetworks - Cluster of Excellence, Heidelberg University, Heidelberg, Germany
| | - Aurelio A. Teleman
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373CellNetworks - Cluster of Excellence, Heidelberg University, Heidelberg, Germany
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9
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Bai Y, Caussinus E, Leo S, Bosshardt F, Myachina F, Rot G, Robinson MD, Lehner CF. A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells. BMC Genomics 2021; 22:771. [PMID: 34711176 PMCID: PMC8555087 DOI: 10.1186/s12864-021-08057-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 10/06/2021] [Indexed: 02/06/2023] Open
Abstract
Background Temperature change affects the myriad of concurrent cellular processes in a non-uniform, disruptive manner. While endothermic organisms minimize the challenge of ambient temperature variation by keeping the core body temperature constant, cells of many ectothermic species maintain homeostatic function within a considerable temperature range. The cellular mechanisms enabling temperature acclimation in ectotherms are still poorly understood. At the transcriptional level, the heat shock response has been analyzed extensively. The opposite, the response to sub-optimal temperature, has received lesser attention in particular in animal species. The tissue specificity of transcriptional responses to cool temperature has not been addressed and it is not clear whether a prominent general response occurs. Cis-regulatory elements (CREs), which mediate increased transcription at cool temperature, and responsible transcription factors are largely unknown. Results The ectotherm Drosophila melanogaster with a presumed temperature optimum around 25 °C was used for transcriptomic analyses of effects of temperatures at the lower end of the readily tolerated range (14–29 °C). Comparative analyses with adult flies and cell culture lines indicated a striking degree of cell-type specificity in the transcriptional response to cool. To identify potential cis-regulatory elements (CREs) for transcriptional upregulation at cool temperature, we analyzed temperature effects on DNA accessibility in chromatin of S2R+ cells. Candidate cis-regulatory elements (CREs) were evaluated with a novel reporter assay for accurate assessment of their temperature-dependency. Robust transcriptional upregulation at low temperature could be demonstrated for a fragment from the pastrel gene, which expresses more transcript and protein at reduced temperatures. This CRE is controlled by the JAK/STAT signaling pathway and antagonizing activities of the transcription factors Pointed and Ets97D. Conclusion Beyond a rich data resource for future analyses of transcriptional control within the readily tolerated range of an ectothermic animal, a novel reporter assay permitting quantitative characterization of CRE temperature dependence was developed. Our identification and functional dissection of the pst_E1 enhancer demonstrate the utility of resources and assay. The functional characterization of this CoolUp enhancer provides initial mechanistic insights into transcriptional upregulation induced by a shift to temperatures at the lower end of the readily tolerated range. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08057-4.
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Affiliation(s)
- Yu Bai
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Emmanuel Caussinus
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Stefano Leo
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Fritz Bosshardt
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Faina Myachina
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Gregor Rot
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Christian F Lehner
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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10
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Niederhuber MJ, McKay DJ. Mechanisms underlying the control of dynamic regulatory element activity and chromatin accessibility during metamorphosis. CURRENT OPINION IN INSECT SCIENCE 2021; 43:21-28. [PMID: 32979530 PMCID: PMC7985040 DOI: 10.1016/j.cois.2020.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/25/2020] [Indexed: 05/10/2023]
Abstract
Cis-regulatory modules of metazoan genomes determine the when and where of gene expression during development. Here we discuss insights into the genetic and molecular mechanisms behind cis-regulatory module usage that have come from recent application of genomics assays to insect metamorphosis. Assays including FAIRE-seq, ATAC-seq, and CUT&RUN indicate that sequential changes in chromatin accessibility play a key role in mediating stage-specific cis-regulatory module activity and gene expression. We review the current understanding of what controls precisely coordinated changes in chromatin accessibility during metamorphosis and describe evidence that points to systemic hormone signaling as a primary signal to trigger genome-wide shifts in accessibility patterns and cis-regulatory module usage.
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Affiliation(s)
- Matthew J Niederhuber
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Daniel J McKay
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States.
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11
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Sun S, Gresham D. Cellular quiescence in budding yeast. Yeast 2021; 38:12-29. [PMID: 33350503 DOI: 10.1002/yea.3545] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 12/20/2022] Open
Abstract
Cellular quiescence, the temporary and reversible exit from proliferative growth, is the predominant state of all cells. However, our understanding of the biological processes and molecular mechanisms that underlie cell quiescence remains incomplete. As with the mitotic cell cycle, budding and fission yeast are preeminent model systems for studying cellular quiescence owing to their rich experimental toolboxes and the evolutionary conservation across eukaryotes of pathways and processes that control quiescence. Here, we review current knowledge of cell quiescence in budding yeast and how it pertains to cellular quiescence in other organisms, including multicellular animals. Quiescence entails large-scale remodeling of virtually every cellular process, organelle, gene expression, and metabolic state that is executed dynamically as cells undergo the initiation, maintenance, and exit from quiescence. We review these major transitions, our current understanding of their molecular bases, and highlight unresolved questions. We summarize the primary methods employed for quiescence studies in yeast and discuss their relative merits. Understanding cell quiescence has important consequences for human disease as quiescent single-celled microbes are notoriously difficult to kill and quiescent human cells play important roles in diseases such as cancer. We argue that research on cellular quiescence will be accelerated through the adoption of common criteria, and methods, for defining cell quiescence. An integrated approach to studying cell quiescence, and a focus on the behavior of individual cells, will yield new insights into the pathways and processes that underlie cell quiescence leading to a more complete understanding of the life cycle of cells. TAKE AWAY: Quiescent cells are viable cells that have reversibly exited the cell cycle Quiescence is induced in response to a variety of nutrient starvation signals Quiescence is executed dynamically through three phases: initiation, maintenance, and exit Quiescence entails large-scale remodeling of gene expression, organelles, and metabolism Single-cell approaches are required to address heterogeneity among quiescent cells.
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Affiliation(s)
- Siyu Sun
- Center for Genomics and Systems Biology, New York University, New York, New York, 10003, USA.,Department of Biology, New York University, New York, New York, 10003, USA
| | - David Gresham
- Center for Genomics and Systems Biology, New York University, New York, New York, 10003, USA.,Department of Biology, New York University, New York, New York, 10003, USA
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12
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Texada MJ, Koyama T, Rewitz K. Regulation of Body Size and Growth Control. Genetics 2020; 216:269-313. [PMID: 33023929 PMCID: PMC7536854 DOI: 10.1534/genetics.120.303095] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/29/2020] [Indexed: 12/20/2022] Open
Abstract
The control of body and organ growth is essential for the development of adults with proper size and proportions, which is important for survival and reproduction. In animals, adult body size is determined by the rate and duration of juvenile growth, which are influenced by the environment. In nutrient-scarce environments in which more time is needed for growth, the juvenile growth period can be extended by delaying maturation, whereas juvenile development is rapidly completed in nutrient-rich conditions. This flexibility requires the integration of environmental cues with developmental signals that govern internal checkpoints to ensure that maturation does not begin until sufficient tissue growth has occurred to reach a proper adult size. The Target of Rapamycin (TOR) pathway is the primary cell-autonomous nutrient sensor, while circulating hormones such as steroids and insulin-like growth factors are the main systemic regulators of growth and maturation in animals. We discuss recent findings in Drosophila melanogaster showing that cell-autonomous environment and growth-sensing mechanisms, involving TOR and other growth-regulatory pathways, that converge on insulin and steroid relay centers are responsible for adjusting systemic growth, and development, in response to external and internal conditions. In addition to this, proper organ growth is also monitored and coordinated with whole-body growth and the timing of maturation through modulation of steroid signaling. This coordination involves interorgan communication mediated by Drosophila insulin-like peptide 8 in response to tissue growth status. Together, these multiple nutritional and developmental cues feed into neuroendocrine hubs controlling insulin and steroid signaling, serving as checkpoints at which developmental progression toward maturation can be delayed. This review focuses on these mechanisms by which external and internal conditions can modulate developmental growth and ensure proper adult body size, and highlights the conserved architecture of this system, which has made Drosophila a prime model for understanding the coordination of growth and maturation in animals.
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Affiliation(s)
| | - Takashi Koyama
- Department of Biology, University of Copenhagen, 2100, Denmark
| | - Kim Rewitz
- Department of Biology, University of Copenhagen, 2100, Denmark
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13
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Tattikota SG, Cho B, Liu Y, Hu Y, Barrera V, Steinbaugh MJ, Yoon SH, Comjean A, Li F, Dervis F, Hung RJ, Nam JW, Ho Sui S, Shim J, Perrimon N. A single-cell survey of Drosophila blood. eLife 2020; 9:e54818. [PMID: 32396065 PMCID: PMC7237219 DOI: 10.7554/elife.54818] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/08/2020] [Indexed: 12/30/2022] Open
Abstract
Drosophila blood cells, called hemocytes, are classified into plasmatocytes, crystal cells, and lamellocytes based on the expression of a few marker genes and cell morphologies, which are inadequate to classify the complete hemocyte repertoire. Here, we used single-cell RNA sequencing (scRNA-seq) to map hemocytes across different inflammatory conditions in larvae. We resolved plasmatocytes into different states based on the expression of genes involved in cell cycle, antimicrobial response, and metabolism together with the identification of intermediate states. Further, we discovered rare subsets within crystal cells and lamellocytes that express fibroblast growth factor (FGF) ligand branchless and receptor breathless, respectively. We demonstrate that these FGF components are required for mediating effective immune responses against parasitoid wasp eggs, highlighting a novel role for FGF signaling in inter-hemocyte crosstalk. Our scRNA-seq analysis reveals the diversity of hemocytes and provides a rich resource of gene expression profiles for a systems-level understanding of their functions.
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Affiliation(s)
| | - Bumsik Cho
- Department of Life Science, Hanyang UniversitySeoulRepublic of Korea
| | - Yifang Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | | | | | - Sang-Ho Yoon
- Department of Life Science, Hanyang UniversitySeoulRepublic of Korea
| | - Aram Comjean
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Fangge Li
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Franz Dervis
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Ruei-Jiun Hung
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Jin-Wu Nam
- Department of Life Science, Hanyang UniversitySeoulRepublic of Korea
| | | | - Jiwon Shim
- Department of Life Science, Hanyang UniversitySeoulRepublic of Korea
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
- Howard Hughes Medical InstituteBostonUnited States
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14
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Nystrom SL, Niederhuber MJ, McKay DJ. Expression of E93 provides an instructive cue to control dynamic enhancer activity and chromatin accessibility during development. Development 2020; 147:dev181909. [PMID: 32094114 PMCID: PMC7097197 DOI: 10.1242/dev.181909] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 02/10/2020] [Indexed: 12/14/2022]
Abstract
How temporal cues combine with spatial inputs to control gene expression during development is poorly understood. Here, we test the hypothesis that the Drosophila transcription factor E93 controls temporal gene expression by regulating chromatin accessibility. Precocious expression of E93 early in wing development reveals that it can simultaneously activate and deactivate different target enhancers. Notably, the precocious patterns of enhancer activity resemble the wild-type patterns that occur later in development, suggesting that expression of E93 alters the competence of enhancers to respond to spatial cues. Genomic profiling reveals that precocious E93 expression is sufficient to regulate chromatin accessibility at a subset of its targets. These accessibility changes mimic those that normally occur later in development, indicating that precocious E93 accelerates the wild-type developmental program. Further, we find that target enhancers that do not respond to precocious E93 in early wings become responsive after a developmental transition, suggesting that parallel temporal pathways work alongside E93. These findings support a model wherein E93 expression functions as an instructive cue that defines a broad window of developmental time through control of chromatin accessibility.
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Affiliation(s)
- Spencer L Nystrom
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew J Niederhuber
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel J McKay
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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15
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Zhou Y, Yang Y, Huang Y, Wang H, Wang S, Luo H. Broad Promotes Neuroepithelial Stem Cell Differentiation in the Drosophila Optic Lobe. Genetics 2019; 213:941-951. [PMID: 31530575 PMCID: PMC6827381 DOI: 10.1534/genetics.119.302421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/08/2019] [Indexed: 11/18/2022] Open
Abstract
Brain development requires the generation of the right number, and type, of neurons and glial cells at the right time. The Drosophila optic lobe, like mammalian brains, develops from simple neuroepithelia; they first divide symmetrically to expand the progenitor pool and then differentiate into neuroblasts, which divide asymmetrically to generate neurons and glial cells. Here, we investigate the mechanisms that control neuroepithelial growth and differentiation in the optic lobe. We find that the Broad/Tramtrack/Bric a brac-zinc finger protein Broad, which is dynamically expressed in the optic lobe neuroepithelia, promotes the transition of neuroepithelial cells to medulla neuroblasts. Loss of Broad function causes neuroepithelial cells to remain highly proliferative and delays neuroepithelial cell differentiation into neuroblasts, which leads to defective lamina and medulla. Conversely, Broad overexpression induces neuroepithelial cells to prematurely transform into medulla neuroblasts. We find that the ecdysone receptor is required for neuroepithelial maintenance and growth, and that Broad expression in neuroepithelial cells is repressed by the ecdysone receptor. Our studies identify Broad as an important cell-intrinsic transcription factor that promotes the neuroepithelial-cell-to-neuroblast transition.
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Affiliation(s)
- Yanna Zhou
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuqin Yang
- College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Yanyi Huang
- College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Hui Wang
- College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Shengyu Wang
- College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Hong Luo
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Biology, Hunan University, Changsha, Hunan 410082, China
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16
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Ma Y, McKay DJ, Buttitta L. Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cells. PLoS Biol 2019; 17:e3000378. [PMID: 31479438 PMCID: PMC6743789 DOI: 10.1371/journal.pbio.3000378] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 09/13/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
During terminal differentiation, most cells exit the cell cycle and enter into a prolonged or permanent G0 in which they are refractory to mitogenic signals. Entry into G0 is usually initiated through the repression of cell cycle gene expression by formation of a transcriptional repressor complex called dimerization partner (DP), retinoblastoma (RB)-like, E2F and MuvB (DREAM). However, when DREAM repressive function is compromised during terminal differentiation, additional unknown mechanisms act to stably repress cycling and ensure robust cell cycle exit. Here, we provide evidence that developmentally programmed, temporal changes in chromatin accessibility at a small subset of critical cell cycle genes act to enforce cell cycle exit during terminal differentiation in the Drosophila melanogaster wing. We show that during terminal differentiation, chromatin closes at a set of pupal wing enhancers for the key rate-limiting cell cycle regulators Cyclin E (cycE), E2F transcription factor 1 (e2f1), and string (stg). This closing coincides with wing cells entering a robust postmitotic state that is strongly refractory to cell cycle reactivation, and the regions that close contain known binding sites for effectors of mitogenic signaling pathways such as Yorkie and Notch. When cell cycle exit is genetically disrupted, chromatin accessibility at cell cycle genes remains unaffected, and the closing of distal enhancers at cycE, e2f1, and stg proceeds independent of the cell cycling status. Instead, disruption of cell cycle exit leads to changes in accessibility and expression of a subset of hormone-induced transcription factors involved in the progression of terminal differentiation. Our results uncover a mechanism that acts as a cell cycle–independent timer to limit the response to mitogenic signaling and aberrant cycling in terminally differentiating tissues. In addition, we provide a new molecular description of the cross talk between cell cycle exit and terminal differentiation during metamorphosis. The longer a cell remains in G0, the more refractory it becomes to re-entering the cell cycle. This study shows that in terminally differentiated cells in vivo, regulatory elements at genes encoding just three key cell cycle regulators (cycE, e2f1 and stg) become inaccessible, limiting their aberrant activation and maintaining a prolonged, robust G0.
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Affiliation(s)
- Yiqin Ma
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Daniel J McKay
- Department of Biology, Department of Genetics, Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Laura Buttitta
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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17
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Wang W, Peng J, Li Z, Wang P, Guo M, Zhang T, Qian W, Xia Q, Cheng D. Transcription factor E93 regulates wing development by directly promoting Dpp signaling in Drosophila. Biochem Biophys Res Commun 2019; 513:280-286. [DOI: 10.1016/j.bbrc.2019.03.100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/16/2019] [Indexed: 12/21/2022]
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18
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Direct and widespread role for the nuclear receptor EcR in mediating the response to ecdysone in Drosophila. Proc Natl Acad Sci U S A 2019; 116:9893-9902. [PMID: 31019084 PMCID: PMC6525475 DOI: 10.1073/pnas.1900343116] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ecdysone pathway was among the first experimental systems employed to study the impact of steroid hormones on the genome. In Drosophila and other insects, ecdysone coordinates developmental transitions, including wholesale transformation of the larva into the adult during metamorphosis. Like other hormones, ecdysone controls gene expression through a nuclear receptor, which functions as a ligand-dependent transcription factor. Although it is clear that ecdysone elicits distinct transcriptional responses within its different target tissues, the role of its receptor, EcR, in regulating target gene expression is incompletely understood. In particular, EcR initiates a cascade of transcription factor expression in response to ecdysone, making it unclear which ecdysone-responsive genes are direct EcR targets. Here, we use the larval-to-prepupal transition of developing wings to examine the role of EcR in gene regulation. Genome-wide DNA binding profiles reveal that EcR exhibits widespread binding across the genome, including at many canonical ecdysone response genes. However, the majority of its binding sites reside at genes with wing-specific functions. We also find that EcR binding is temporally dynamic, with thousands of binding sites changing over time. RNA-seq reveals that EcR acts as both a temporal gate to block precocious entry to the next developmental stage as well as a temporal trigger to promote the subsequent program. Finally, transgenic reporter analysis indicates that EcR regulates not only temporal changes in target enhancer activity but also spatial patterns. Together, these studies define EcR as a multipurpose, direct regulator of gene expression, greatly expanding its role in coordinating developmental transitions.
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19
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Mirth CK, Shingleton AW. Coordinating Development: How Do Animals Integrate Plastic and Robust Developmental Processes? Front Cell Dev Biol 2019; 7:8. [PMID: 30788342 PMCID: PMC6372504 DOI: 10.3389/fcell.2019.00008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/16/2019] [Indexed: 02/02/2023] Open
Abstract
Our developmental environment significantly affects myriad aspects of our biology, including key life history traits, morphology, physiology, and our susceptibility to disease. This environmentally-induced variation in phenotype is known as plasticity. In many cases, plasticity results from alterations in the rate of synthesis of important developmental hormones. However, while developmental processes like organ growth are sensitive to environmental conditions, others like patterning - the process that generates distinct cell identities - remain robust to perturbation. This is particularly surprising given that the same hormones that regulate organ growth also regulate organ patterning. In this review, we revisit the current approaches that address how organs coordinate their growth and pattern, and outline our hypotheses for understanding how organs achieve correct pattern across a range of sizes.
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Affiliation(s)
- Christen K Mirth
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Alexander W Shingleton
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
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20
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Edwards SS, Delgado MG, Nader GPDF, Piel M, Bellaïche Y, Lennon-Duménil AM, Glavic Á. An in vitro method for studying subcellular rearrangements during cell polarization in Drosophila melanogaster hemocytes. Mech Dev 2018; 154:277-286. [PMID: 30096416 DOI: 10.1016/j.mod.2018.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/04/2018] [Accepted: 08/06/2018] [Indexed: 12/13/2022]
Abstract
Thanks to the power of Drosophila genetics, this animal model has been a precious tool for scientists to uncover key processes associated to innate immunity. The fly immune system relies on a population of macrophage-like cells, also referred to as hemocytes, which are highly migratory and phagocytic, and can easily be followed in vivo. These cells have shown to play important roles in fly development, both at the embryonic and pupal stages. However, there is no robust assay for the study of hemocyte migration in vitro, which limits our understanding of the molecular mechanisms involved. Here, we contribute to fill this gap by showing that hemocytes adopt a polarized morphology upon ecdysone stimulation, allowing the study of the cytoskeleton rearrangements and organelle reorganization that take place during the first step of cell locomotion.
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Affiliation(s)
- Sandra Sofía Edwards
- Centro de Regulación del Genoma, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
| | - María Graciela Delgado
- Institut Curie, PSL Research University, INSERM U932 Immunité et Cancer, F-75248 Paris Cedex 05, France.
| | - Guilherme Pedreira de Freitas Nader
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France; Institut Pierre-Gilles de Gennes, PSL Research University, F-75005 Paris, France.
| | - Matthieu Piel
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France; Institut Pierre-Gilles de Gennes, PSL Research University, F-75005 Paris, France.
| | - Yohanns Bellaïche
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, France; Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 3215, INSERM U934, F-75005, France.
| | - Ana María Lennon-Duménil
- Institut Curie, PSL Research University, INSERM U932 Immunité et Cancer, F-75248 Paris Cedex 05, France.
| | - Álvaro Glavic
- Centro de Regulación del Genoma, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
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21
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Diaz-de-la-Loza MDC, Ray RP, Ganguly PS, Alt S, Davis JR, Hoppe A, Tapon N, Salbreux G, Thompson BJ. Apical and Basal Matrix Remodeling Control Epithelial Morphogenesis. Dev Cell 2018; 46:23-39.e5. [PMID: 29974861 PMCID: PMC6035286 DOI: 10.1016/j.devcel.2018.06.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 04/04/2018] [Accepted: 06/07/2018] [Indexed: 01/28/2023]
Abstract
Epithelial tissues can elongate in two dimensions by polarized cell intercalation, oriented cell division, or cell shape change, owing to local or global actomyosin contractile forces acting in the plane of the tissue. In addition, epithelia can undergo morphogenetic change in three dimensions. We show that elongation of the wings and legs of Drosophila involves a columnar-to-cuboidal cell shape change that reduces cell height and expands cell width. Remodeling of the apical extracellular matrix by the Stubble protease and basal matrix by MMP1/2 proteases induces wing and leg elongation. Matrix remodeling does not occur in the haltere, a limb that fails to elongate. Limb elongation is made anisotropic by planar polarized Myosin-II, which drives convergent extension along the proximal-distal axis. Subsequently, Myosin-II relocalizes to lateral membranes to accelerate columnar-to-cuboidal transition and isotropic tissue expansion. Thus, matrix remodeling induces dynamic changes in actomyosin contractility to drive epithelial morphogenesis in three dimensions.
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Affiliation(s)
| | - Robert P Ray
- HHMI Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Poulami S Ganguly
- Theoretical Physics of Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Silvanus Alt
- Theoretical Physics of Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, Berlin-Buch 13125, Germany
| | - John R Davis
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andreas Hoppe
- Kingston University, Penrhyn Road, Kingston upon Thames, London KT1 2EE, UK
| | - Nic Tapon
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Guillaume Salbreux
- Theoretical Physics of Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Barry J Thompson
- Epithelial Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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22
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Lim DH, Lee S, Han JY, Choi MS, Hong JS, Seong Y, Kwon YS, Lee YS. Ecdysone-responsive microRNA-252-5p controls the cell cycle by targeting Abi in Drosophila. FASEB J 2018. [PMID: 29543534 DOI: 10.1096/fj.201701185rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The steroid hormone ecdysone has a central role in the developmental transitions of insects through its control of responsive protein-coding and microRNA (miRNA) gene expression. However, the complete regulatory network controlling the expression of these genes remains to be elucidated. In this study, we performed cross-linking immunoprecipitation coupled with deep sequencing of endogenous Argonaute 1 (Ago1) protein, the core effector of the miRNA pathway, in Drosophila S2 cells. We found that regulatory interactions between miRNAs and their cognate targets were substantially altered by Ago1 in response to ecdysone signaling. Additionally, during the larva-to-adult metamorphosis, miR-252-5p was up-regulated via the canonical ecdysone-signaling pathway. Moreover, we provide evidence that miR-252-5p targets Abelson interacting protein ( Abi) to decrease the protein levels of cyclins A and B, controlling the cell cycle. Overall, our data suggest a potential role for the ecdysone/miR-252-5p/Abi regulatory axis partly in cell-cycle control during metamorphosis in Drosophila.-Lim, D.-H., Lee, S., Han, J. Y., Choi, M.-S., Hong, J.-S., Seong, Y., Kwon, Y.-S., Lee, Y. S. Ecdysone-responsive microR-252-5p controls the cell cycle by targeting Abi in Drosophila.
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Affiliation(s)
- Do-Hwan Lim
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
| | - Seungjae Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
| | - Jee Yun Han
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Min-Seok Choi
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
| | - Jae-Sang Hong
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
| | - Youngmo Seong
- Department of Bioscience and Biotechnology, Sejong University, Seoul, South Korea
| | - Young-Soo Kwon
- Department of Bioscience and Biotechnology, Sejong University, Seoul, South Korea
| | - Young Sik Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
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23
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Ma Y, Buttitta L. Chromatin organization changes during the establishment and maintenance of the postmitotic state. Epigenetics Chromatin 2017; 10:53. [PMID: 29126440 PMCID: PMC5681785 DOI: 10.1186/s13072-017-0159-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/30/2017] [Indexed: 02/06/2023] Open
Abstract
Background Genome organization changes during development as cells differentiate. Chromatin motion becomes increasingly constrained and heterochromatin clusters as cells become restricted in their developmental potential. These changes coincide with slowing of the cell cycle, which can also influence chromatin organization and dynamics. Terminal differentiation is often coupled with permanent exit from the cell cycle, and existing data suggest a close relationship between a repressive chromatin structure and silencing of the cell cycle in postmitotic cells. Heterochromatin clustering could also contribute to stable gene repression to maintain terminal differentiation or cell cycle exit, but whether clustering is initiated by differentiation, cell cycle changes, or both is unclear. Here we examine the relationship between chromatin organization, terminal differentiation and cell cycle exit. Results We focused our studies on the Drosophila wing, where epithelial cells transition from active proliferation to a postmitotic state in a temporally controlled manner. We find there are two stages of G0 in this tissue, a flexible G0 period where cells can be induced to reenter the cell cycle under specific genetic manipulations and a state we call “robust,” where cells become strongly refractory to cell cycle reentry. Compromising the flexible G0 by driving ectopic expression of cell cycle activators causes a global disruption of the clustering of heterochromatin-associated histone modifications such as H3K27 trimethylation and H3K9 trimethylation, as well as their associated repressors, Polycomb and heterochromatin protein 1 (HP1). However, this disruption is reversible. When cells enter a robust G0 state, even in the presence of ectopic cell cycle activity, clustering of heterochromatin-associated modifications is restored. If cell cycle exit is bypassed, cells in the wing continue to terminally differentiate, but heterochromatin clustering is severely disrupted. Heterochromatin-dependent gene silencing does not appear to be required for cell cycle exit, as compromising the H3K27 methyltransferase Enhancer of zeste, and/or HP1 cannot prevent the robust cell cycle exit, even in the face of normally oncogenic cell cycle activities. Conclusions Heterochromatin clustering during terminal differentiation is a consequence of cell cycle exit, rather than differentiation. Compromising heterochromatin-dependent gene silencing does not disrupt cell cycle exit. Electronic supplementary material The online version of this article (10.1186/s13072-017-0159-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yiqin Ma
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Laura Buttitta
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
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24
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Uyehara CM, Nystrom SL, Niederhuber MJ, Leatham-Jensen M, Ma Y, Buttitta LA, McKay DJ. Hormone-dependent control of developmental timing through regulation of chromatin accessibility. Genes Dev 2017; 31:862-875. [PMID: 28536147 PMCID: PMC5458754 DOI: 10.1101/gad.298182.117] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/26/2017] [Indexed: 11/24/2022]
Abstract
Uyehara et al. show that hormone-induced transcription factors control temporal gene expression by regulating accessibility of DNA regulatory elements. Using the Drosophila wing, they demonstrate that temporal changes in gene expression are accompanied by genome-wide changes in chromatin accessibility at temporal-specific enhancers. Specification of tissue identity during development requires precise coordination of gene expression in both space and time. Spatially, master regulatory transcription factors are required to control tissue-specific gene expression programs. However, the mechanisms controlling how tissue-specific gene expression changes over time are less well understood. Here, we show that hormone-induced transcription factors control temporal gene expression by regulating the accessibility of DNA regulatory elements. Using the Drosophila wing, we demonstrate that temporal changes in gene expression are accompanied by genome-wide changes in chromatin accessibility at temporal-specific enhancers. We also uncover a temporal cascade of transcription factors following a pulse of the steroid hormone ecdysone such that different times in wing development can be defined by distinct combinations of hormone-induced transcription factors. Finally, we show that the ecdysone-induced transcription factor E93 controls temporal identity by directly regulating chromatin accessibility across the genome. Notably, we found that E93 controls enhancer activity through three different modalities, including promoting accessibility of late-acting enhancers and decreasing accessibility of early-acting enhancers. Together, this work supports a model in which an extrinsic signal triggers an intrinsic transcription factor cascade that drives development forward in time through regulation of chromatin accessibility.
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Affiliation(s)
- Christopher M Uyehara
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Spencer L Nystrom
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Matthew J Niederhuber
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Mary Leatham-Jensen
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Yiqin Ma
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Laura A Buttitta
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Daniel J McKay
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
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Abstract
Most cells in nature are not actively dividing, yet are able to return to the cell cycle given the appropriate environmental signals. There is now ample evidence that quiescent G0 cells are not shut-down but still metabolically and transcriptionally active. Quiescent cells must maintain a basal transcriptional capacity to maintain transcripts and proteins necessary for survival. This implies a tight control over RNA polymerases: RNA pol II for mRNA transcription during G0, but especially RNA pol I and RNA pol III to maintain an appropriate level of structural RNAs, raising the possibility that specific transcriptional control mechanisms evolved in quiescent cells. In accordance with this, we recently discovered that RNA interference is necessary to control RNA polymerase I transcription during G0. While this mini-review focuses on yeast model organisms (Saccharomyces cerevisiae and Schizosaccharomyces pombe), parallels are drawn to other eukaryotes and mammalian systems, in particular stem cells.
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Affiliation(s)
- Benjamin Roche
- a Cold Spring Harbor Laboratory , Cold Spring Harbor , NY , USA
| | - Benoit Arcangioli
- b Genome Dynamics Unit , UMR 3525 CNRS, Institut Pasteur, 25-28 rue du Docteur Roux , Paris , France
| | - Robert Martienssen
- a Cold Spring Harbor Laboratory , Cold Spring Harbor , NY , USA.,c Howard Hughes Medical Institute-Gordon and Betty Moore Foundation (HHMI-GBM) Investigator , NY , USA
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