1
|
Soto X, Burton J, Manning CS, Minchington T, Lea R, Lee J, Kursawe J, Rattray M, Papalopulu N. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. Development 2022; 149:276990. [PMID: 36189829 PMCID: PMC9641661 DOI: 10.1242/dev.200474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/26/2022] [Indexed: 11/06/2022]
Abstract
MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state.
Collapse
Affiliation(s)
- Ximena Soto
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK,Authors for correspondence (; )
| | - Joshua Burton
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Cerys S. Manning
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Thomas Minchington
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Robert Lea
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Jessica Lee
- Discovery Department, Medicines Discovery Catapult, Block 35, Mereside, Alderley Park, Alderley Edge, Cheshire, SK10 4TG, UK
| | - Jochen Kursawe
- School of Mathematics and Statistics, University of St Andrews, North Haugh, St Andrews, KY16 9SS, UK
| | - Magnus Rattray
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Nancy Papalopulu
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK,Authors for correspondence (; )
| |
Collapse
|
2
|
Soto X, Biga V, Kursawe J, Lea R, Doostdar P, Thomas R, Papalopulu N. Dynamic properties of noise and Her6 levels are optimized by miR-9, allowing the decoding of the Her6 oscillator. EMBO J 2020; 39:e103558. [PMID: 32395844 PMCID: PMC7298297 DOI: 10.15252/embj.2019103558] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 03/25/2020] [Accepted: 04/03/2020] [Indexed: 01/08/2023] Open
Abstract
Noise is prevalent in biology and has been widely quantified using snapshot measurements. This static view obscures our understanding of dynamic noise properties and how these affect gene expression and cell state transitions. Using a CRISPR/Cas9 Zebrafish her6::Venus reporter combined with mathematical and in vivo experimentation, we explore how noise affects the protein dynamics of Her6, a basic helix-loop-helix transcriptional repressor. During neurogenesis, Her6 expression transitions from fluctuating to oscillatory at single-cell level. We identify that absence of miR-9 input generates high-frequency noise in Her6 traces, inhibits the transition to oscillatory protein expression and prevents the downregulation of Her6. Together, these impair the upregulation of downstream targets and cells accumulate in a normally transitory state where progenitor and early differentiation markers are co-expressed. Computational modelling and double smFISH of her6 and the early neurogenesis marker, elavl3, suggest that the change in Her6 dynamics precedes the downregulation in Her6 levels. This sheds light onto the order of events at the moment of cell state transition and how this is influenced by the dynamic properties of noise. Our results suggest that Her/Hes oscillations, facilitated by dynamic noise optimization by miR-9, endow progenitor cells with the ability to make a cell state transition.
Collapse
Affiliation(s)
- Ximena Soto
- Faculty of Biology Medicine and HealthSchool of Medical SciencesThe University of ManchesterManchesterUK
| | - Veronica Biga
- Faculty of Biology Medicine and HealthSchool of Medical SciencesThe University of ManchesterManchesterUK
| | - Jochen Kursawe
- School of Mathematics and StatisticsUniversity of St AndrewsSt AndrewsUK
| | - Robert Lea
- Faculty of Biology Medicine and HealthSchool of Medical SciencesThe University of ManchesterManchesterUK
| | - Parnian Doostdar
- Faculty of Biology Medicine and HealthSchool of Medical SciencesThe University of ManchesterManchesterUK
| | - Riba Thomas
- Faculty of Biology Medicine and HealthSchool of Medical SciencesThe University of ManchesterManchesterUK
| | - Nancy Papalopulu
- Faculty of Biology Medicine and HealthSchool of Medical SciencesThe University of ManchesterManchesterUK
| |
Collapse
|
3
|
Functional characterization of the mucus barrier on the Xenopus tropicalis skin surface. Proc Natl Acad Sci U S A 2018; 115:726-731. [PMID: 29311327 PMCID: PMC5789918 DOI: 10.1073/pnas.1713539115] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The production of mucus helps to trap pathogens, preventing their entry into the body, while it also acts as an interface for many important physiological events (e.g., gas and nutrient exchange). In mammalian models, a detailed study of mucus and its component parts is hindered by the difficulty in accessing these internally located tissues. The Xenopus tropicalis tadpole skin offers a complementary nonmammalian model system to study mucosal epithelia. Using this, we identify a mucin, similar to human mucins, that protects against infection. This system offers an experimentally tractable approach to study mucins and the mucus barrier and their role in conferring protection at mucosal surfaces. Mucosal surfaces represent critical routes for entry and exit of pathogens. As such, animals have evolved strategies to combat infection at these sites, in particular the production of mucus to prevent attachment and to promote subsequent movement of the mucus/microbe away from the underlying epithelial surface. Using biochemical, biophysical, and infection studies, we have investigated the host protective properties of the skin mucus barrier of the Xenopus tropicalis tadpole. Specifically, we have characterized the major structural component of the barrier and shown that it is a mucin glycoprotein (Otogelin-like or Otogl) with similar sequence, domain organization, and structural properties to human gel-forming mucins. This mucin forms the structural basis of a surface barrier (∼6 μm thick), which is depleted through knockdown of Otogl. Crucially, Otogl knockdown leads to susceptibility to infection by the opportunistic pathogen Aeromonas hydrophila. To more accurately reflect its structure, tissue localization, and function, we have renamed Otogl as Xenopus Skin Mucin, or MucXS. Our findings characterize an accessible and tractable model system to define mucus barrier function and host–microbe interactions.
Collapse
|
4
|
Dubaissi E, Rousseau K, Lea R, Soto X, Nardeosingh S, Schweickert A, Amaya E, Thornton DJ, Papalopulu N. A secretory cell type develops alongside multiciliated cells, ionocytes and goblet cells, and provides a protective, anti-infective function in the frog embryonic mucociliary epidermis. Development 2014; 141:1514-25. [PMID: 24598166 PMCID: PMC3957375 DOI: 10.1242/dev.102426] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 02/02/2014] [Indexed: 02/05/2023]
Abstract
The larval epidermis of Xenopus is a bilayered epithelium, which is an excellent model system for the study of the development and function of mucosal and mucociliary epithelia. Goblet cells develop in the outer layer while multiciliated cells and ionocytes sequentially intercalate from the inner to the outer layer. Here, we identify and characterise a fourth cell type, the small secretory cell (SSC). We show that the development of these cells is controlled by the transcription factor Foxa1 and that they intercalate into the outer layer of the epidermis relatively late, at the same time as embryonic hatching. Ultrastructural and molecular characterisation shows that these cells have an abundance of large apical secretory vesicles, which contain highly glycosylated material, positive for binding of the lectin, peanut agglutinin, and an antibody to the carbohydrate epitope, HNK-1. By specifically depleting SSCs, we show that these cells are crucial for protecting the embryo against bacterial infection. Mass spectrometry studies show that SSCs secrete a glycoprotein similar to Otogelin, which may form the structural component of a mucus-like protective layer, over the surface of the embryo, and several potential antimicrobial substances. Our study completes the characterisation of all the epidermal cell types in the early tadpole epidermis and reinforces the suitability of this system for the in vivo study of complex epithelia, including investigation of innate immune defences.
Collapse
Affiliation(s)
- Eamon Dubaissi
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Karine Rousseau
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Wellcome Trust Centre for Cell Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Robert Lea
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- The Healing Foundation Centre, University of Manchester, Manchester M13 9PT, UK
| | - Ximena Soto
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Siddarth Nardeosingh
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Axel Schweickert
- University of Hohenheim, Institute of Zoology, Garbenstrasse 30, D-70593 Stuttgart, Germany
| | - Enrique Amaya
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- The Healing Foundation Centre, University of Manchester, Manchester M13 9PT, UK
| | - David J. Thornton
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Wellcome Trust Centre for Cell Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Nancy Papalopulu
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| |
Collapse
|