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Baron F, Zhang M, Archer N, Bellows E, Knight HM, Welham S, Rutland CS, Mongan NP, Hayes CJ, Fray RG, Bodi Z. The importance of m 6A topology in chicken embryo mRNA: a precise mapping of m 6A at the conserved chicken β-actin zipcode. RNA (NEW YORK, N.Y.) 2023; 29:777-789. [PMID: 36810234 PMCID: PMC10187669 DOI: 10.1261/rna.079615.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 05/18/2023]
Abstract
N6-methyladenosine (m6A) in mRNA regulates almost every stage in the mRNA life cycle, and the development of methodologies for the high-throughput detection of methylated sites in mRNA using m6A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIPSeq) or m6A individual-nucleotide-resolution cross-linking and immunoprecipitation (miCLIP) have revolutionized the m6A research field. Both of these methods are based on immunoprecipitation of fragmented mRNA. However, it is well documented that antibodies often have nonspecific activities, thus verification of identified m6A sites using an antibody-independent method would be highly desirable. We mapped and quantified the m6A site in the chicken β-actin zipcode based on the data from chicken embryo MeRIPSeq results and our RNA-Epimodification Detection and Base-Recognition (RedBaron) antibody-independent assay. We also demonstrated that methylation of this site in the β-actin zipcode enhances ZBP1 binding in vitro, while methylation of a nearby adenosine abolishes binding. This suggests that m6A may play a role in regulating localized translation of β-actin mRNA, and the ability of m6A to enhance or inhibit a reader protein's RNA binding highlights the importance of m6A detection at nucleotide resolution.
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Affiliation(s)
- Francis Baron
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
- School of Chemistry, The University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Mi Zhang
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Nathan Archer
- School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Eleanor Bellows
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Helen M Knight
- Faculty of Medicine and Health Sciences, Queen's Medical Center, Nottingham NG7 2UH, United Kingdom
| | - Simon Welham
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Catrin S Rutland
- School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Nigel P Mongan
- School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Christopher J Hayes
- School of Chemistry, The University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Rupert G Fray
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Zsuzsa Bodi
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
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Anillin governs mitotic rounding during early epidermal development. BMC Biol 2022; 20:145. [PMID: 35710398 PMCID: PMC9205045 DOI: 10.1186/s12915-022-01345-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/07/2022] [Indexed: 11/18/2022] Open
Abstract
Background The establishment of tissue architecture requires coordination between distinct processes including basement membrane assembly, cell adhesion, and polarity; however, the underlying mechanisms remain poorly understood. The actin cytoskeleton is ideally situated to orchestrate tissue morphogenesis due to its roles in mechanical, structural, and regulatory processes. However, the function of many pivotal actin-binding proteins in mammalian development is poorly understood. Results Here, we identify a crucial role for anillin (ANLN), an actin-binding protein, in orchestrating epidermal morphogenesis. In utero RNAi-mediated silencing of Anln in mouse embryos disrupted epidermal architecture marked by adhesion, polarity, and basement membrane defects. Unexpectedly, these defects cannot explain the profoundly perturbed epidermis of Anln-depleted embryos. Indeed, even before these defects emerge, Anln-depleted epidermis exhibits abnormalities in mitotic rounding and its associated processes: chromosome segregation, spindle orientation, and mitotic progression, though not in cytokinesis that was disrupted only in Anln-depleted cultured keratinocytes. We further show that ANLN localizes to the cell cortex during mitotic rounding, where it regulates the distribution of active RhoA and the levels, activity, and structural organization of the cortical actomyosin proteins. Conclusions Our results demonstrate that ANLN is a major regulator of epidermal morphogenesis and identify a novel role for ANLN in mitotic rounding, a near-universal process that governs cell shape, fate, and tissue morphogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01345-9.
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Padmanabhan K, Grobe H, Cohen J, Soffer A, Mahly A, Adir O, Zaidel-Bar R, Luxenburg C. Thymosin β4 is essential for adherens junction stability and epidermal planar cell polarity. Development 2020; 147:dev.193425. [PMID: 33310787 PMCID: PMC7758630 DOI: 10.1242/dev.193425] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/27/2020] [Indexed: 01/19/2023]
Abstract
Planar cell polarity (PCP) is essential for tissue morphogenesis and homeostasis; however, the mechanisms that orchestrate the cell shape and packing dynamics required to establish PCP are poorly understood. Here, we identified a major role for the globular (G)-actin-binding protein thymosin-β4 (TMSB4X) in PCP establishment and cell adhesion in the developing epidermis. Depletion of Tmsb4x in mouse embryos hindered eyelid closure and hair-follicle angling owing to PCP defects. Tmsb4x depletion did not preclude epidermal cell adhesion in vivo or in vitro; however, it resulted in abnormal structural organization and stability of adherens junction (AJ) due to defects in filamentous (F)-actin and G-actin distribution. In cultured keratinocytes, TMSB4X depletion increased the perijunctional G/F-actin ratio and decreased G-actin incorporation into junctional actin networks, but it did not change the overall actin expression level or cellular F-actin content. A pharmacological treatment that increased the G/F-actin ratio and decreased actin polymerization mimicked the effects of Tmsb4x depletion on both AJs and PCP. Our results provide insights into the regulation of the actin pool and its involvement in AJ function and PCP establishment. Highlighted Article: By regulating actin pool distribution and incorporation into junctional actin networks, thymosin β4 regulates cell–cell adhesion, planar cell polarity and epidermal morphogenesis.
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Affiliation(s)
- Krishnanand Padmanabhan
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Hanna Grobe
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Jonathan Cohen
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Arad Soffer
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Adnan Mahly
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Orit Adir
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Ronen Zaidel-Bar
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
| | - Chen Luxenburg
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
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Cohen J, Raviv S, Adir O, Padmanabhan K, Soffer A, Luxenburg C. The Wave complex controls epidermal morphogenesis and proliferation by suppressing Wnt-Sox9 signaling. J Cell Biol 2019; 218:1390-1406. [PMID: 30867227 PMCID: PMC6446834 DOI: 10.1083/jcb.201807216] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/11/2018] [Accepted: 02/01/2019] [Indexed: 02/08/2023] Open
Abstract
The Wave complex promotes Arp2/3-mediated actin polymerization. Cohen et al. show that Wave complex activity regulates epidermal shape and growth. Without Wave complex activity, F-actin content is down-regulated and ectopic activity of the Wnt/β-catenin–SOX9 pathway is triggered. This activity induces epidermal hyperproliferation and disrupts tissue architecture. Development of the skin epidermis requires tight spatiotemporal control over the activity of several signaling pathways; however, the mechanisms that orchestrate these events remain poorly understood. Here, we identify a key role for the Wave complex proteins ABI1 and Wave2 in regulating signals that control epidermal shape and growth. In utero RNAi-mediated silencing of Abi1 or Wasf2 induced cellular hyperproliferation and defects in architecture of the interfollicular epidermis (IFE) and delayed hair follicle growth. Unexpectedly, SOX9, a hair follicle growth regulator, was aberrantly expressed throughout the IFE of the mutant embryos, and its forced overexpression mimicked the Wave complex loss-of-function phenotype. Moreover, Wnt signaling, which regulates SOX9+ cell specification, was up-regulated in Wave complex loss-of-function IFE. Importantly, we show that the Wave complex regulates filamentous actin content and that a decrease in actin levels is sufficient to elevate Wnt/β-catenin signaling. Our results identify a novel role for Wave complex– and actin-regulated signaling via Wnt and SOX9 in skin development.
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Affiliation(s)
- Jonathan Cohen
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shaul Raviv
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orit Adir
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Krishnanand Padmanabhan
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Arad Soffer
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chen Luxenburg
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Tharp KM, Weaver VM. Modeling Tissue Polarity in Context. J Mol Biol 2018; 430:3613-3628. [PMID: 30055167 DOI: 10.1016/j.jmb.2018.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/27/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022]
Abstract
Polarity is critical for development and tissue-specific function. However, the acquisition and maintenance of tissue polarity is context dependent. Thus, cell and tissue polarity depend on cell adhesion which is regulated by the cytoskeleton and influenced by the biochemical composition of the extracellular microenvironment and modified by biomechanical cues within the tissue. These biomechanical cues include fluid flow induced shear stresses, cell-density and confinement-mediated compression, and cellular actomyosin tension intrinsic to the tissue or induced in response to morphogens or extracellular matrix stiffness. Here, we discuss how extracellular matrix stiffness and fluid flow influence cell-cell and cell-extracellular matrix adhesion and alter cytoskeletal organization to modulate cell and tissue polarity. We describe model systems that when combined with state of the art molecular screens and high-resolution imaging can be used to investigate how force modulates cell and tissue polarity.
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Affiliation(s)
- Kevin M Tharp
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Department of Radiation Oncology, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA.
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Vedula P, Kashina A. The makings of the 'actin code': regulation of actin's biological function at the amino acid and nucleotide level. J Cell Sci 2018; 131:131/9/jcs215509. [PMID: 29739859 DOI: 10.1242/jcs.215509] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The actin cytoskeleton plays key roles in every eukaryotic cell and is essential for cell adhesion, migration, mechanosensing, and contractility in muscle and non-muscle tissues. In higher vertebrates, from birds through to mammals, actin is represented by a family of six conserved genes. Although these genes have evolved independently for more than 100 million years, they encode proteins with ≥94% sequence identity, which are differentially expressed in different tissues, and tightly regulated throughout embryogenesis and adulthood. It has been previously suggested that the existence of such similar actin genes is a fail-safe mechanism to preserve the essential function of actin through redundancy. However, knockout studies in mice and other organisms demonstrate that the different actins have distinct biological roles. The mechanisms maintaining this distinction have been debated in the literature for decades. This Review summarizes data on the functional regulation of different actin isoforms, and the mechanisms that lead to their different biological roles in vivo We focus here on recent studies demonstrating that at least some actin functions are regulated beyond the amino acid level at the level of the actin nucleotide sequence.
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Affiliation(s)
- Pavan Vedula
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
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