1
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Clément AE, Merdrignac C, Puiggros SR, Sévère D, Brionne A, Lafond T, Nguyen T, Montfort J, Guyomar C, Dauvé A, Herpin A, Jabaudon D, Colson V, Murat F, Bobe J. Parent-of-origin regulation by maternal auts2 shapes neurodevelopment and behavior in fish. Genome Biol 2025; 26:125. [PMID: 40346605 PMCID: PMC12063280 DOI: 10.1186/s13059-025-03600-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Accepted: 04/29/2025] [Indexed: 05/11/2025] Open
Abstract
BACKGROUND Parental experience can influence progeny behavior through gamete-mediated non-genetic inheritance, that is, mechanisms that do not involve changes in inherited DNA sequence. However, underlying mechanisms remain poorly understood in vertebrates, especially for maternal effects. Here, we use the medaka, a model fish species, to investigate the role of auts2a, the ortholog of human AUTS2, a gene repressed in the fish oocyte following maternal stress and associated with neurodevelopmental disorders. RESULTS We show that auts2a expression in the oocyte influences long-term progeny behavior, including anxiety-like behavior and environment recognition capabilities. Using single-nuclei RNA-sequencing, we reveal that maternal auts2a influences gene expression in neural cell populations during neurodevelopment. We also show that maternal auts2a knock-out triggers differences in maternally inherited factors, including early embryonic transcriptional and post-transcriptional regulators. CONCLUSIONS Together, our results reveal the unsuspected role of an autism-related gene expressed in the mother's oocyte in shaping progeny neurodevelopment and behavior. Finally, we report that auts2a/AUTS2 is part of a group of evolutionarily conserved genes associated with human neurodevelopmental disorders and expressed in oocytes across species, from fish to mammals. These findings raise important questions about their potential role in the non-genetic regulation of progeny neurodevelopment and behavior in vertebrates.
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Affiliation(s)
| | | | - Sergi Roig Puiggros
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Dorine Sévère
- INRAE, LPGP UR1037, Fish Physiology and Genomics Institute, Rennes, France
| | - Aurélien Brionne
- INRAE, LPGP UR1037, Fish Physiology and Genomics Institute, Rennes, France
| | - Thomas Lafond
- INRAE, LPGP UR1037, Fish Physiology and Genomics Institute, Rennes, France
| | - Thaovi Nguyen
- INRAE, LPGP UR1037, Fish Physiology and Genomics Institute, Rennes, France
| | - Jérôme Montfort
- INRAE, LPGP UR1037, Fish Physiology and Genomics Institute, Rennes, France
| | - Cervin Guyomar
- Sigenae, GenPhySE, INRAE, ENVT, Université de Toulouse, Toulouse, Castanet Tolosan, France
| | - Alexandra Dauvé
- MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Amaury Herpin
- INRAE, LPGP UR1037, Fish Physiology and Genomics Institute, Rennes, France
| | - Denis Jabaudon
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Violaine Colson
- INRAE, LPGP UR1037, Fish Physiology and Genomics Institute, Rennes, France
| | - Florent Murat
- INRAE, LPGP UR1037, Fish Physiology and Genomics Institute, Rennes, France
| | - Julien Bobe
- INRAE, LPGP UR1037, Fish Physiology and Genomics Institute, Rennes, France.
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2
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Ishorst N, Hölzel S, Greve C, Yilmaz Ö, Lindenberg T, Lambertz J, Drichel D, Zametica B, Mingardo E, Kalanithy JC, Channab K, Kibris D, Henne S, Degenhardt F, Siewert A, Dixon M, Kruse T, Ongkosuwito E, Girisha KM, Pande S, Nowak S, Hagelueken G, Geyer M, Carels C, van Rooij IALM, Ludwig KU, Odermatt B, Mangold E. Role of ZFHX4 in orofacial clefting based on human genetic data and zebrafish models. Eur J Hum Genet 2025; 33:595-606. [PMID: 39702590 PMCID: PMC7617551 DOI: 10.1038/s41431-024-01775-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 12/03/2024] [Accepted: 12/10/2024] [Indexed: 12/21/2024] Open
Abstract
Orofacial clefting (OFC) is a frequent congenital anomaly and can occur either in the context of underlying syndromes or in isolation (nonsyndromic). The two common OFC phenotypes are cleft lip with/without cleft palate (CL/P) and cleft palate only (CPO). In this study, we searched for penetrant CL/P genes, by evaluating de novo copy number variants (CNV) from an exome sequencing dataset of 50 nonsyndromic patient-parent trios. We detected a heterozygous 86 kb de novo deletion affecting exons 4-11 of ZFHX4, a gene previously associated with OFC. Genetic and phenotypic data from our in-house and the AGORA cohort (710 and 229 individuals with nonsyndromic CL/P) together with literature and database reviews demonstrate that ZFHX4 variants can lead to both nonsyndromic and syndromic forms not only of CL/P but also CPO. Expression analysis in published single-cell RNA-sequencing data (mouse embryo, zebrafish larva) at relevant time-points support an important role of Zfhx4/zfhx4 in craniofacial development. To characterize the role of zfhx4 in zebrafish craniofacial development, we knocked out/down the zebrafish orthologue. Cartilage staining of the zfhx4 CRISPR F0 knockout and morpholino knockdown at 4 days post-fertilization showed an underdeveloped and abnormally shaped ethmoid plate and cartilaginous jaw (resembling micrognathia). While there is evidence for the dominant inheritance of ZFHX4 variants in OFC, we here present a patient with a possible recessive inheritance. In conclusion, ZFHX4 has a highly heterogeneous phenotypic spectrum and variable mode of inheritance. Our data highlight that ZFHX4 should be considered in genetic testing in patients with nonsyndromic clefting.
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Affiliation(s)
- Nina Ishorst
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.
- Institute of Anatomy, Division of Neuroanatomy, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.
| | - Selina Hölzel
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
- Institute of Anatomy and Cell Biology, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Carola Greve
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Öznur Yilmaz
- Institute of Anatomy, Division of Neuroanatomy, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Tobias Lindenberg
- Institute of Anatomy, Division of Neuroanatomy, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Jessica Lambertz
- Institute of Anatomy, Division of Neuroanatomy, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Dmitriy Drichel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Berina Zametica
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Enrico Mingardo
- Institute of Anatomy and Cell Biology, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
- Faculty of Life Science, Nutritional Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Jeshurun C Kalanithy
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
- Institute of Anatomy, Division of Neuroanatomy, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Khadija Channab
- Institute of Anatomy and Cell Biology, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Duygu Kibris
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
- Institute of Anatomy, Division of Neuroanatomy, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Sabrina Henne
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Duisburg, Germany
| | - Anna Siewert
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Michael Dixon
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, M13 9PL, UK
| | - Teresa Kruse
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Orthodontics, Cologne, Germany
| | - Edwin Ongkosuwito
- Department of Dentistry, Section of Orthodontics and Craniofacial Biology, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stefanie Nowak
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | | | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Carine Carels
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Iris A L M van Rooij
- IQ Health Science Department, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Benjamin Odermatt
- Institute of Anatomy, Division of Neuroanatomy, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.
- Institute of Anatomy and Cell Biology, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.
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3
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Phelps WA, Ayers TN, Lee MT. Ribosomal RNA Depletion for Poly(A)-Tail-Independent Quantification of Genome Activation. Methods Mol Biol 2025; 2923:163-180. [PMID: 40418449 DOI: 10.1007/978-1-0716-4522-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2025]
Abstract
High-throughput RNA sequencing (RNA-seq) is commonly used to quantify gene expression transcriptome-wide. While usually paired with polyadenylate (poly(A)) selection to enrich for messenger RNA (mRNA) to the exclusion of highly abundant ribosomal RNA (rRNA) in the cell, this strategy will under-quantify mRNA with short or absent poly(A) tails and can conflate changes in poly(A) tail length with changes in RNA level. This is notably an issue during early development, when cytoplasmic polyadenylation of maternal mRNA over time can be mistaken for genome activation in poly(A) + RNA-seq time courses. Here, we present a method to perform total RNA-seq using a streamlined rRNA depletion strategy customizable to any taxon. Antisense DNA oligos are designed with the aid of our Oligo-ASST web tool to sparsely tile the length of the rRNA, which are used with thermostable RNaseH to digest rRNA from a total RNA sample. After column cleanup, the mRNA-enriched sample is ready for sequencing library construction.
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Affiliation(s)
- Wesley A Phelps
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Taylor N Ayers
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Miler T Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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4
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Reimão-Pinto MM, Behrens A, Forcelloni S, Fröhlich K, Kaya S, Nedialkova DD. The dynamics and functional impact of tRNA repertoires during early embryogenesis in zebrafish. EMBO J 2024; 43:5747-5779. [PMID: 39402326 PMCID: PMC11574265 DOI: 10.1038/s44318-024-00265-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 09/23/2024] [Accepted: 09/27/2024] [Indexed: 11/20/2024] Open
Abstract
Embryogenesis entails dramatic shifts in mRNA translation and turnover that reprogram gene expression during cellular proliferation and differentiation. Codon identity modulates mRNA stability during early vertebrate embryogenesis, but how the composition of tRNA pools is matched to translational demand is unknown. By quantitative profiling of tRNA repertoires in zebrafish embryos during the maternal-to-zygotic transition, we show that zygotic tRNA repertoires are established after the onset of gastrulation, succeeding the major wave of zygotic mRNA transcription. Maternal and zygotic tRNA pools are distinct, but their reprogramming does not result in a better match to the codon content of the zygotic transcriptome. Instead, we find that an increase in global translation at gastrulation sensitizes decoding rates to tRNA supply, thus destabilizing maternal mRNAs enriched in slowly translated codons. Translational activation and zygotic tRNA expression temporally coincide with an increase of TORC1 activity at gastrulation, which phosphorylates and inactivates the RNA polymerase III repressor Maf1a/b. Our data indicate that a switch in global translation, rather than tRNA reprogramming, determines the onset of codon-dependent maternal mRNA decay during zebrafish embryogenesis.
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Affiliation(s)
| | - Andrew Behrens
- Mechanisms of Protein Biogenesis Laboratory, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Sergio Forcelloni
- Mechanisms of Protein Biogenesis Laboratory, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | | | - Selay Kaya
- Mechanisms of Protein Biogenesis Laboratory, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Danny D Nedialkova
- Mechanisms of Protein Biogenesis Laboratory, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, 85748, Garching, Germany.
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5
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da Silva Pescador G, Baia Amaral D, Varberg JM, Zhang Y, Hao Y, Florens L, Bazzini AA. Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. Cell Rep 2024; 43:114769. [PMID: 39302832 PMCID: PMC11544563 DOI: 10.1016/j.celrep.2024.114769] [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: 04/12/2024] [Revised: 07/22/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024] Open
Abstract
The maternal-to-zygotic transition is crucial in embryonic development, marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However, the changes occurring at the protein level during this transition remain unclear. Here, we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry, integrating transcriptomics and translatomics datasets. Our data show that, unlike RNA changes, protein changes are less dynamic. Further, increases in protein levels correlate with mRNA translation, whereas declines in protein levels do not, suggesting active protein degradation processes. Interestingly, proteins from pure zygotic genes are present at fertilization, challenging existing mRNA-based gene classifications. As a proof of concept, we utilized CRISPR-Cas13d to target znf281b mRNA, a gene whose protein significantly accumulates within the first 2 h post-fertilization, demonstrating its crucial role in development. Consequently, our protein profiling, coupled with CRISPR-Cas13d, offers a complementary approach to unraveling maternal factor function during embryonic development.
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Affiliation(s)
| | | | - Joseph M Varberg
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Yan Hao
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas School of Medicine, Kansas City, KS 66160, USA.
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6
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Wang Y, Wang X, Wang W, Cao Z, Zhang Y, Liu G. Screening of functional maternal-specific chromatin regulators in early embryonic development of zebrafish. Commun Biol 2024; 7:1354. [PMID: 39427068 PMCID: PMC11490497 DOI: 10.1038/s42003-024-06983-z] [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: 04/13/2023] [Accepted: 09/28/2024] [Indexed: 10/21/2024] Open
Abstract
The early stages of embryonic development rely on maternal products for proper regulation. However, screening for functional maternal-specific factors is challenging due to the time- and labor-intensive nature of traditional approaches. Here, we combine a computational pipeline and F0 null mutant technology to screen for functional maternal-specific chromatin regulators in zebrafish embryogenesis and identify Mcm3l, Mcm6l, and Npm2a as playing essential roles in DNA replication and cell division. Our results contribute to understanding the molecular mechanisms underlying early embryo development and highlight the importance of maternal-specific chromatin regulators in this critical stage.
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Affiliation(s)
- Yiman Wang
- State Key Laboratory of Cardiovascular Diseases and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Xiangxiu Wang
- State Key Laboratory of Cardiovascular Diseases and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Key Laboratory of Biorheological and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Modern Life Science Experiment Teaching Center at Bioengineering College of Chongqing University, Chongqing, 400030, China
| | - Wen Wang
- State Key Laboratory of Cardiovascular Diseases and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Zheng Cao
- State Key Laboratory of Cardiovascular Diseases and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yong Zhang
- State Key Laboratory of Cardiovascular Diseases and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Guifen Liu
- State Key Laboratory of Cardiovascular Diseases and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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7
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Hurton MD, Miller JM, Lee MT. H3K4me2 distinguishes a distinct class of enhancers during the maternal-to-zygotic transition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.26.609713. [PMID: 39253505 PMCID: PMC11383010 DOI: 10.1101/2024.08.26.609713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
After egg fertilization, an initially silent embryonic genome is transcriptionally activated during the maternal-to-zygotic transition. In zebrafish, maternal vertebrate pluripotency factors Nanog, Pou5f3 (OCT4 homolog), and Sox19b (SOX2 homolog) (NPS) play essential roles in orchestrating embryonic genome activation, acting as "pioneers" that open condensed chromatin and mediate acquisition of activating histone modifications. However, some embryonic gene transcription still occurs in the absence of these factors, suggesting the existence of other mechanisms regulating genome activation. To identify chromatin signatures of these unknown pathways, we profiled the histone modification landscape of zebrafish embryos using CUT&RUN. Our regulatory map revealed two subclasses of enhancers distinguished by presence or absence of H3K4me2. Enhancers lacking H3K4me2 tend to require NPS factors for de novo activation, while enhancers bearing H3K4me2 are epigenetically bookmarked by DNA hypomethylation to recapitulate gamete activity in the embryo, independent of NPS pioneering. Thus, parallel enhancer activation pathways combine to induce transcriptional reprogramming to pluripotency in the early embryo.
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Affiliation(s)
- Matthew D Hurton
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15213 U.S.A
| | - Jennifer M Miller
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15213 U.S.A
| | - Miler T Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15213 U.S.A
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8
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Fang F, Chen D, Basharat AR, Poulos W, Wang Q, Cibelli JB, Liu X, Sun L. Quantitative proteomics reveals the dynamic proteome landscape of zebrafish embryos during the maternal-to-zygotic transition. iScience 2024; 27:109944. [PMID: 38784018 PMCID: PMC11111832 DOI: 10.1016/j.isci.2024.109944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 08/23/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Maternal-to-zygotic transition (MZT) is central to early embryogenesis. However, its underlying molecular mechanisms are still not well described. Here, we revealed the expression dynamics of 5,000 proteins across four stages of zebrafish embryos during MZT, representing one of the most systematic surveys of proteome landscape of the zebrafish embryos during MZT. Nearly 700 proteins were differentially expressed and were divided into six clusters according to their expression patterns. The proteome expression profiles accurately reflect the main events that happen during the MZT, i.e., zygotic genome activation (ZGA), clearance of maternal mRNAs, and initiation of cellular differentiation and organogenesis. MZT is modulated by many proteins at multiple levels in a collaborative fashion, i.e., transcription factors, histones, histone-modifying enzymes, RNA helicases, and P-body proteins. Significant discrepancies were discovered between zebrafish proteome and transcriptome profiles during the MZT. The proteome dynamics database will be a valuable resource for bettering our understanding of MZT.
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Affiliation(s)
- Fei Fang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Abdul Rehman Basharat
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - William Poulos
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Jose B. Cibelli
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, 1441 Canal Street, New Orleans, LA 70112, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
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9
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Fishman L, Modak A, Nechooshtan G, Razin T, Erhard F, Regev A, Farrell JA, Rabani M. Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq. Nat Commun 2024; 15:3104. [PMID: 38600066 PMCID: PMC11006943 DOI: 10.1038/s41467-024-47290-9] [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: 04/12/2023] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the relative contributions of mRNA transcription and degradation to shaping those profiles remains challenging, especially within embryos with diverse cellular identities. Here, we combine single-cell RNA-Seq and metabolic labeling to capture temporal cellular transcriptomes of zebrafish embryos where newly-transcribed (zygotic) and pre-existing (maternal) mRNA can be distinguished. We introduce kinetic models to quantify mRNA transcription and degradation rates within individual cell types during their specification. These models reveal highly varied regulatory rates across thousands of genes, coordinated transcription and destruction rates for many transcripts, and link differences in degradation to specific sequence elements. They also identify cell-type-specific differences in degradation, namely selective retention of maternal transcripts within primordial germ cells and enveloping layer cells, two of the earliest specified cell types. Our study provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.
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Affiliation(s)
- Lior Fishman
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Avani Modak
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA
| | - Gal Nechooshtan
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Talya Razin
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
- Chair of Computational Immunology, University of Regensburg, Regensburg, Germany
| | - Aviv Regev
- Department of Biology, MIT, Cambridge, MA, 02139, USA
- Klarman Cell Observatory Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, 02142, USA
| | - Jeffrey A Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA.
| | - Michal Rabani
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel.
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10
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Karas BF, Terez KR, Mowla S, Battula N, Flannery KP, Gural BM, Aboussleman G, Mubin N, Manzini MC. Removal of pomt1 in zebrafish leads to loss of α-dystroglycan glycosylation and dystroglycanopathy phenotypes. Hum Mol Genet 2024; 33:709-723. [PMID: 38272461 PMCID: PMC11000664 DOI: 10.1093/hmg/ddae006] [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: 07/11/2023] [Revised: 11/28/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Biallelic mutations in Protein O-mannosyltransferase 1 (POMT1) are among the most common causes of a severe group of congenital muscular dystrophies (CMDs) known as dystroglycanopathies. POMT1 is a glycosyltransferase responsible for the attachment of a functional glycan mediating interactions between the transmembrane glycoprotein dystroglycan and its binding partners in the extracellular matrix (ECM). Disruptions in these cell-ECM interactions lead to multiple developmental defects causing brain and eye malformations in addition to CMD. Removing Pomt1 in the mouse leads to early embryonic death due to the essential role of dystroglycan during placental formation in rodents. Here, we characterized and validated a model of pomt1 loss of function in the zebrafish showing that developmental defects found in individuals affected by dystroglycanopathies can be recapitulated in the fish. We also discovered that pomt1 mRNA provided by the mother in the oocyte supports dystroglycan glycosylation during the first few weeks of development. Muscle disease, retinal synapse formation deficits, and axon guidance defects can only be uncovered during the first week post fertilization by generating knock-out embryos from knock-out mothers. Conversely, maternal pomt1 from heterozygous mothers was sufficient to sustain muscle, eye, and brain development only leading to loss of photoreceptor synapses at 30 days post fertilization. Our findings show that it is important to define the contribution of maternal mRNA while developing zebrafish models of dystroglycanopathies and that offspring generated from heterozygous and knock-out mothers can be used to differentiate the role of dystroglycan glycosylation in tissue formation and maintenance.
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Affiliation(s)
- Brittany F Karas
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Kristin R Terez
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Shorbon Mowla
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Namarata Battula
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Kyle P Flannery
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Brian M Gural
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Grace Aboussleman
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Numa Mubin
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - M Chiara Manzini
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
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11
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Baia Amaral D, Egidy R, Perera A, Bazzini AA. miR-430 regulates zygotic mRNA during zebrafish embryogenesis. Genome Biol 2024; 25:74. [PMID: 38504288 PMCID: PMC10949700 DOI: 10.1186/s13059-024-03197-8] [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: 07/05/2023] [Accepted: 02/15/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs, it has been challenging to study their expression dynamics separately. RESULTS By employing SLAM-seq, a nascent mRNA labeling transcriptomic approach, in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal-zygotic genes, emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional activation events and follow nascent mRNA trajectories, finding that most de novo transcriptional events are stable throughout this period. Additionally, by blocking microRNA-430 function, a key post transcriptional regulator during zebrafish embryogenesis, we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal-zygotic genes. This unveils a novel miR-430 function during embryogenesis, fine-tuning zygotic gene expression. CONCLUSION These insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post-transcriptional regulators in zygotic genome activation. The findings pave the way for future investigations into the coordinated interplay between transcriptional and post-transcriptional landscapes required for the establishment of animal cell identities and functions.
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Affiliation(s)
- Danielson Baia Amaral
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Rhonda Egidy
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA.
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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12
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Tucker SK, Ghosal R, Swartz ME, Zhang S, Eberhart JK. Zebrafish raptor mutation inhibits the activity of mTORC1, inducing craniofacial defects due to autophagy-induced neural crest cell death. Development 2024; 151:dev202216. [PMID: 38512806 PMCID: PMC11006402 DOI: 10.1242/dev.202216] [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: 07/25/2023] [Accepted: 01/26/2024] [Indexed: 03/23/2024]
Abstract
The mechanistic target of rapamycin (mTOR) coordinates metabolism and cell growth with environmental inputs. mTOR forms two functional complexes: mTORC1 and mTORC2. Proper development requires both complexes but mTORC1 has unique roles in numerous cellular processes, including cell growth, survival and autophagy. Here, we investigate the function of mTORC1 in craniofacial development. We created a zebrafish raptor mutant via CRISPR/Cas9, to specifically disrupt mTORC1. The entire craniofacial skeleton and eyes were reduced in size in mutants; however, overall body length and developmental timing were not affected. The craniofacial phenotype associates with decreased chondrocyte size and increased neural crest cell death. We found that autophagy is elevated in raptor mutants. Chemical inhibition of autophagy reduced cell death and improved craniofacial phenotypes in raptor mutants. Genetic inhibition of autophagy, via mutation of the autophagy gene atg7, improved facial phenotypes in atg7;raptor double mutants, relative to raptor single mutants. We conclude that finely regulated levels of autophagy, via mTORC1, are crucial for craniofacial development.
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Affiliation(s)
- Scott K. Tucker
- Department of Molecular Biosciences, Waggoner Center for Alcohol and Addiction Research and Institute for Neuroscience, University of Texas, Austin, TX 78712, USA
| | - Ritika Ghosal
- Department of Molecular Biosciences, Waggoner Center for Alcohol and Addiction Research and Institute for Neuroscience, University of Texas, Austin, TX 78712, USA
| | - Mary E. Swartz
- Department of Molecular Biosciences, Waggoner Center for Alcohol and Addiction Research and Institute for Neuroscience, University of Texas, Austin, TX 78712, USA
| | - Stephanie Zhang
- Department of Molecular Biosciences, Waggoner Center for Alcohol and Addiction Research and Institute for Neuroscience, University of Texas, Austin, TX 78712, USA
| | - Johann K. Eberhart
- Department of Molecular Biosciences, Waggoner Center for Alcohol and Addiction Research and Institute for Neuroscience, University of Texas, Austin, TX 78712, USA
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13
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Camacho-Macorra C, Tabanera N, Sánchez-Bustamante E, Bovolenta P, Cardozo MJ. Maternal vgll4a regulates zebrafish epiboly through Yap1 activity. Front Cell Dev Biol 2024; 12:1362695. [PMID: 38444829 PMCID: PMC10912589 DOI: 10.3389/fcell.2024.1362695] [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: 12/28/2023] [Accepted: 02/01/2024] [Indexed: 03/07/2024] Open
Abstract
Gastrulation in zebrafish embryos commences with the morphogenetic rearrangement of blastodermal cells, which undergo a coordinated spreading from the animal pole to wrap around the egg at the vegetal pole. This rearrangement, known as epiboly, relies on the orchestrated activity of maternal transcripts present in the egg, compensating for the gradual activation of the zygotic genome. Epiboly involves the mechano-transducer activity of yap1 but what are the regulators of yap1 activity and whether these are maternally or zygotically derived remain elusive. Our study reveals the crucial role of maternal vgll4a, a proposed Yap1 competitor, during zebrafish epiboly. In embryos lacking maternal/zygotic vgll4a (MZvgll4a), the progression of epiboly and blastopore closure is delayed. This delay is associated with the ruffled appearance of the sliding epithelial cells, decreased expression of yap1-downstream targets and transient impairment of the actomyosin ring at the syncytial layer. Our study also shows that, rather than competing with yap1, vgll4a modulates the levels of the E-cadherin/β-catenin adhesion complex at the blastomeres' plasma membrane and hence their actin cortex distribution. Taking these results together, we propose that maternal vgll4a acts at epiboly initiation upstream of yap1 and the E-cadherin/β-catenin adhesion complex, contributing to a proper balance between tissue tension/cohesion and contractility, thereby promoting a timely epiboly progression.
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Affiliation(s)
- Carlos Camacho-Macorra
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Noemí Tabanera
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Elena Sánchez-Bustamante
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Paola Bovolenta
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Marcos J Cardozo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
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14
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Hotez PJ, Bottazzi ME, Islam NY, Lee J, Pollet J, Poveda C, Strych U, Thimmiraju SR, Uzcategui NL, Versteeg L, Gorelick D. The zebrafish as a potential model for vaccine and adjuvant development. Expert Rev Vaccines 2024; 23:535-545. [PMID: 38664959 DOI: 10.1080/14760584.2024.2345685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/17/2024] [Indexed: 04/30/2024]
Abstract
INTRODUCTION Zebrafishes represent a proven model for human diseases and systems biology, exhibiting physiological and genetic similarities and having innate and adaptive immune systems. However, they are underexplored for human vaccinology, vaccine development, and testing. Here we summarize gaps and challenges. AREAS COVERED Zebrafish models have four potential applications: 1) Vaccine safety: The past successes in using zebrafishes to test xenobiotics could extend to vaccine and adjuvant formulations for general safety or target organs due to the zebrafish embryos' optical transparency. 2) Innate immunity: The zebrafish offers refined ways to examine vaccine effects through signaling via Toll-like or NOD-like receptors in zebrafish myeloid cells. 3) Adaptive immunity: Zebrafishes produce IgM, IgD,and two IgZ immunoglobulins, but these are understudied, due to a lack of immunological reagents for challenge studies. 4) Systems vaccinology: Due to the availability of a well-referenced zebrafish genome, transcriptome, proteome, and epigenome, this model offers potential here. EXPERT OPINION It remains unproven whether zebrafishes can be employed for testing and developing human vaccines. We are still at the hypothesis-generating stage, although it is possible to begin outlining experiments for this purpose. Through transgenic manipulation, zebrafish models could offer new paths for shaping animal models and systems vaccinology.
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Affiliation(s)
- Peter J Hotez
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Maria Elena Bottazzi
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Nelufa Yesmin Islam
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jungsoon Lee
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jeroen Pollet
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Cristina Poveda
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Ulrich Strych
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Syamala Rani Thimmiraju
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Nestor L Uzcategui
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Leroy Versteeg
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Daniel Gorelick
- Center for Precision Environmental Health, Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
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15
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Takada Y, Fierro L, Sato K, Sanada T, Ishii A, Yamamoto T, Kotani T. Mature mRNA processing that deletes 3' end sequences directs translational activation and embryonic development. SCIENCE ADVANCES 2023; 9:eadg6532. [PMID: 38000026 PMCID: PMC10672166 DOI: 10.1126/sciadv.adg6532] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023]
Abstract
Eggs accumulate thousands of translationally repressed mRNAs that are translated into proteins after fertilization to direct diverse developmental processes. However, molecular mechanisms underlying the translation of stored mRNAs after fertilization remain unclear. Here, we report a previously unknown RNA processing of 3' end sequences of mature mRNAs that activates the translation of stored mRNAs. Specifically, 9 to 72 nucleotides at the 3' ends of zebrafish pou5f3 and mouse Pou5f1 mRNAs were deleted in the early stages of development. Reporter assays illustrated the effective translation of the truncated forms of mRNAs. Moreover, promotion and inhibition of the shortening of 3' ends accelerated and attenuated Pou5f3 accumulation, respectively, resulting in defective development. Identification of proteins binding to unprocessed and/or processed mRNAs revealed that mRNA shortening acts as molecular switches. Comprehensive analysis revealed that >250 mRNAs underwent this processing. Therefore, our results provide a molecular principle that triggers the translational activation and directs development.
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Affiliation(s)
- Yuki Takada
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Ludivine Fierro
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Keisuke Sato
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takahiro Sanada
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Anna Ishii
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takehiro Yamamoto
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tomoya Kotani
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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16
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Rao A, Lyu B, Jahan I, Lubertozzi A, Zhou G, Tedeschi F, Jankowsky E, Kang J, Carstens B, Poss KD, Baskin K, Goldman JA. The translation initiation factor homolog eif4e1c regulates cardiomyocyte metabolism and proliferation during heart regeneration. Development 2023; 150:dev201376. [PMID: 37306388 PMCID: PMC10281269 DOI: 10.1242/dev.201376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/28/2023] [Indexed: 05/25/2023]
Abstract
The eIF4E family of translation initiation factors bind 5' methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability, yet other related eIF4E families exist and are utilized in specific contexts or tissues. Here, we describe a family called Eif4e1c, for which we find roles during heart development and regeneration in zebrafish. The Eif4e1c family is present in all aquatic vertebrates but is lost in all terrestrial species. A core group of amino acids shared over 500 million years of evolution forms an interface along the protein surface, suggesting that Eif4e1c functions in a novel pathway. Deletion of eif4e1c in zebrafish caused growth deficits and impaired survival in juveniles. Mutants surviving to adulthood had fewer cardiomyocytes and reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although eif4e1c is broadly expressed, its disruption had most notable impact on the heart and at juvenile stages. Our findings reveal context-dependent requirements for translation initiation regulators during heart regeneration.
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Affiliation(s)
- Anupama Rao
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Baken Lyu
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Ishrat Jahan
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Anna Lubertozzi
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Gao Zhou
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Frank Tedeschi
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Bryan Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kenneth D. Poss
- Department of Cell Biology, Duke Regeneration Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kedryn Baskin
- Department of Cell Biology and Physiology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Joseph Aaron Goldman
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
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17
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Phelps WA, Hurton MD, Ayers TN, Carlson AE, Rosenbaum JC, Lee MT. Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis. eLife 2023; 12:e83952. [PMID: 37787392 PMCID: PMC10569791 DOI: 10.7554/elife.83952] [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: 10/04/2022] [Accepted: 10/02/2023] [Indexed: 10/04/2023] Open
Abstract
After fertilization, maternally contributed factors to the egg initiate the transition to pluripotency to give rise to embryonic stem cells, in large part by activating de novo transcription from the embryonic genome. Diverse mechanisms coordinate this transition across animals, suggesting that pervasive regulatory remodeling has shaped the earliest stages of development. Here, we show that maternal homologs of mammalian pluripotency reprogramming factors OCT4 and SOX2 divergently activate the two subgenomes of Xenopus laevis, an allotetraploid that arose from hybridization of two diploid species ~18 million years ago. Although most genes have been retained as two homeologous copies, we find that a majority of them undergo asymmetric activation in the early embryo. Chromatin accessibility profiling and CUT&RUN for modified histones and transcription factor binding reveal extensive differences in predicted enhancer architecture between the subgenomes, which likely arose through genomic disruptions as a consequence of allotetraploidy. However, comparison with diploid X. tropicalis and zebrafish shows broad conservation of embryonic gene expression levels when divergent homeolog contributions are combined, implying strong selection to maintain dosage in the core vertebrate pluripotency transcriptional program, amid genomic instability following hybridization.
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Affiliation(s)
- Wesley A Phelps
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Matthew D Hurton
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Taylor N Ayers
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Anne E Carlson
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Joel C Rosenbaum
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Miler T Lee
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
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18
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Fishman L, Nechooshtan G, Erhard F, Regev A, Farrell JA, Rabani M. Single-cell temporal dynamics reveals the relative contributions of transcription and degradation to cell-type specific gene expression in zebrafish embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.537620. [PMID: 37131717 PMCID: PMC10153228 DOI: 10.1101/2023.04.20.537620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the underlying regulation of mRNA transcription and degradation remains a challenge, especially within whole embryos with diverse cellular identities. Here, we collect temporal cellular transcriptomes of zebrafish embryos, and decompose them into their newly-transcribed (zygotic) and pre-existing (maternal) mRNA components by combining single-cell RNA-Seq and metabolic labeling. We introduce kinetic models capable of quantifying regulatory rates of mRNA transcription and degradation within individual cell types during their specification. These reveal different regulatory rates between thousands of genes, and sometimes between cell types, that shape spatio-temporal expression patterns. Transcription drives most cell-type restricted gene expression. However, selective retention of maternal transcripts helps to define the gene expression profiles of germ cells and enveloping layer cells, two of the earliest specified cell-types. Coordination between transcription and degradation restricts expression of maternal-zygotic genes to specific cell types or times, and allows the emergence of spatio-temporal patterns when overall mRNA levels are held relatively constant. Sequence-based analysis links differences in degradation to specific sequence motifs. Our study reveals mRNA transcription and degradation events that control embryonic gene expression, and provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.
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Affiliation(s)
- Lior Fishman
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Gal Nechooshtan
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Aviv Regev
- Department of Biology, MIT, Cambridge MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jeffrey A. Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA
| | - Michal Rabani
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
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19
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Harry ND, Zakas C. Maternal patterns of inheritance alter transcript expression in eggs. BMC Genomics 2023; 24:191. [PMID: 37038099 PMCID: PMC10084599 DOI: 10.1186/s12864-023-09291-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/01/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Modifications to early development can lead to evolutionary diversification. The early stages of development are under maternal control, as mothers produce eggs loaded with nutrients, proteins and mRNAs that direct early embryogenesis. Maternally provided mRNAs are the only expressed genes in initial stages of development and are tightly regulated. Differences in maternal mRNA provisioning could lead to phenotypic changes in embryogenesis and ultimately evolutionary changes in development. However, the extent that maternal mRNA expression in eggs can vary is unknown for most developmental models. Here, we use a species with dimorphic development- where females make eggs and larvae of different sizes and life-history modes-to investigate the extent of variation in maternal mRNA provisioning to the egg. RESULTS We find that there is significant variation in gene expression across eggs of different development modes, and that there are both qualitative and quantitative differences in mRNA expression. We separate parental effects from allelic effects, and find that both mechanisms contribute to mRNA expression differences. We also find that offspring of intraspecific crosses differentially provision their eggs based on the parental cross direction (a parental effect), which has not been previously demonstrated in reproductive traits like oogenesis. CONCLUSION We find that maternally controlled initiation of development is functionally distinct between eggs of different sizes and maternal genotypes. Both allele-specific effects and parent-of-origin effects contribute to gene expression differences in eggs. The latter indicates an intergenerational effect where a parent's genotype can affect gene expression in an egg made by the next generation.
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Affiliation(s)
- Nathan D Harry
- Department of Biological Sciences, North Carolina State University, 112 Derieux Place, Raleigh, NC, 27607, USA
| | - Christina Zakas
- Department of Biological Sciences, North Carolina State University, 112 Derieux Place, Raleigh, NC, 27607, USA.
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20
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Bhat P, Cabrera-Quio LE, Herzog VA, Fasching N, Pauli A, Ameres SL. SLAMseq resolves the kinetics of maternal and zygotic gene expression during early zebrafish embryogenesis. Cell Rep 2023; 42:112070. [PMID: 36757845 DOI: 10.1016/j.celrep.2023.112070] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/27/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
The maternal-to-zygotic transition (MZT) is a key developmental process in metazoan embryos that involves the activation of zygotic transcription (ZGA) and degradation of maternal transcripts. We employed metabolic mRNA sequencing (SLAMseq) to deconvolute the compound embryonic transcriptome in zebrafish. While mitochondrial zygotic transcripts prevail prior to MZT, we uncover the spurious transcription of hundreds of short and intron-poor genes as early as the 2-cell stage. Upon ZGA, most zygotic transcripts originate from thousands of maternal-zygotic (MZ) genes that are transcribed at rates comparable to those of hundreds of purely zygotic genes and replenish maternal mRNAs at distinct timescales. Rapid replacement of MZ transcripts involves transcript decay features unrelated to major maternal degradation pathways and promotes de novo synthesis of the core gene expression machinery by increasing poly(A)-tail length and translation efficiency. SLAMseq hence provides insights into the timescales, molecular features, and regulation of MZT during zebrafish embryogenesis.
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Affiliation(s)
- Pooja Bhat
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Luis E Cabrera-Quio
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria; Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Veronika A Herzog
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Nina Fasching
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
| | - Stefan L Ameres
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), 1030 Vienna, Austria.
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21
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Kuznetsova K, Chabot NM, Ugolini M, Wu E, Lalit M, Oda H, Sato Y, Kimura H, Jug F, Vastenhouw NL. Nanog organizes transcription bodies. Curr Biol 2023; 33:164-173.e5. [PMID: 36476751 DOI: 10.1016/j.cub.2022.11.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/21/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
Abstract
The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells.1-3 How proteins of the transcriptional machinery come together to form such bodies, however, is unclear. Here, we take advantage of two large, isolated, and long-lived transcription bodies that reproducibly form during early zebrafish embryogenesis to characterize the dynamics of transcription body formation. Once formed, these transcription bodies are enriched for initiating and elongating RNA polymerase II, as well as the transcription factors Nanog and Sox19b. Analyzing the events leading up to transcription, we find that Nanog and Sox19b cluster prior to transcription. The clustering of transcription factors is sequential; Nanog clusters first, and this is required for the clustering of Sox19b and the initiation of transcription. Mutant analysis revealed that both the DNA-binding domain as well as one of the two intrinsically disordered regions of Nanog are required to organize the two bodies of transcriptional activity. Taken together, our data suggest that the clustering of transcription factors dictates the formation of transcription bodies.
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Affiliation(s)
- Ksenia Kuznetsova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Noémie M Chabot
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Integrative Genomics, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Martino Ugolini
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Integrative Genomics, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Edlyn Wu
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Integrative Genomics, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Manan Lalit
- Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Yuko Sato
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Florian Jug
- Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Fondazione Human Technopole, Viale Rita Levi-Montalcini 1, Area MIND, 20157 Milano, Italy
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Integrative Genomics, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland.
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22
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Hagadorn MA, Hunter FK, DeLory T, Johnson MM, Pitts-Singer TL, Kapheim KM. Maternal body condition and season influence RNA deposition in the oocytes of alfalfa leafcutting bees ( Megachile rotundata). Front Genet 2023; 13:1064332. [PMID: 36685934 PMCID: PMC9845908 DOI: 10.3389/fgene.2022.1064332] [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: 10/08/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023] Open
Abstract
Maternal effects are an important source of phenotypic variance, whereby females influence offspring developmental trajectory beyond direct genetic contributions, often in response to changing environmental conditions. However, relatively little is known about the mechanisms by which maternal experience is translated into molecular signals that shape offspring development. One such signal may be maternal RNA transcripts (mRNAs and miRNAs) deposited into maturing oocytes. These regulate the earliest stages of development of all animals, but are understudied in most insects. Here we investigated the effects of female internal (body condition) and external (time of season) environmental conditions on maternal RNA in the maturing oocytes and 24-h-old eggs (24-h eggs) of alfalfa leafcutting bees. Using gene expression and WGCNA analysis, we found that females adjust the quantity of mRNAs related to protein phosphorylation, transcriptional regulation, and nuclease activity deposited into maturing oocytes in response to both poor body condition and shorter day lengths that accompany the late season. However, the magnitude of these changes was higher for time of season. Females also adjusted miRNA deposition in response to seasonal changes, but not body condition. We did not observe significant changes in maternal RNAs in response to either body condition or time of season in 24-h eggs, which were past the maternal-to-zygotic transition. Our results suggest that females adjust the RNA transcripts they provide for offspring to regulate development in response to both internal and external environmental cues. Variation in maternal RNAs may, therefore, be important for regulating offspring phenotype in response to environmental change.
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Affiliation(s)
- Mallory A. Hagadorn
- Department of Biology, Department of Biology, Utah State University, Logan, UT, United States
| | - Frances K. Hunter
- Department of Biology, Department of Biology, Utah State University, Logan, UT, United States
| | - Tim DeLory
- Department of Biology, Department of Biology, Utah State University, Logan, UT, United States
| | - Makenna M. Johnson
- Department of Biology, Department of Biology, Utah State University, Logan, UT, United States,United States Department of Agriculture, Agricultural Research Service, Pollinating Insects Research Unit, Logan, UT, United States
| | - Theresa L. Pitts-Singer
- United States Department of Agriculture, Agricultural Research Service, Pollinating Insects Research Unit, Logan, UT, United States
| | - Karen M. Kapheim
- Department of Biology, Department of Biology, Utah State University, Logan, UT, United States,*Correspondence: Karen M. Kapheim ,
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23
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Xiong Y, Wang DY, Guo W, Gong G, Chen ZX, Tang Q, Mei J. Sexually Dimorphic Gene Expression in X and Y Sperms Instructs Sexual Dimorphism of Embryonic Genome Activation in Yellow Catfish ( Pelteobagrus fulvidraco). BIOLOGY 2022; 11:1818. [PMID: 36552327 PMCID: PMC9775105 DOI: 10.3390/biology11121818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/02/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022]
Abstract
Paternal factors play an important role in embryonic morphogenesis and contribute to sexual dimorphism in development. To assess the effect of paternal DNA on sexual dimorphism of embryonic genome activation, we compared X and Y sperm and different sexes of embryos before sex determination. Through transcriptome sequencing (RNA-seq) and whole-genome bisulfite sequencing (WGBS) of X and Y sperm, we found a big proportion of upregulated genes in Y sperm, supported by the observation that genome-wide DNA methylation level is slightly lower than in X sperm. Cytokine-cytokine receptor interaction, TGF-beta, and toll-like receptor pathways play important roles in spermatogenesis. Through whole-genome re-sequencing (WGRS) of parental fish and RNA-seq of five early embryonic stages, we found the low-blastocyst time point is a key to maternal transcriptome degradation and zygotic genome activation. Generally, sexual differences emerged from the bud stage. Moreover, through integrated analysis of paternal SNPs and gene expression, we evaluated the influence of paternal inheritance on sexual dimorphism of genome activation. Besides, we screened out gata6 and ddx5 as potential instructors for early sex determination and gonad development in yellow catfish. This work is meaningful for revealing the molecular mechanisms of sex determination and sexual dimorphism of fish species.
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Affiliation(s)
- Yang Xiong
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan-Yang Wang
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenjie Guo
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Gaorui Gong
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhen-Xia Chen
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Qin Tang
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Mei
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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24
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Chau TCY, Keyser MS, Da Silva JA, Morris EK, Yordanov TE, Duscyz KP, Paterson S, Yap AS, Hogan BM, Lagendijk AK. Dynamically regulated focal adhesions coordinate endothelial cell remodelling in developing vasculature. Development 2022; 149:285926. [PMID: 36314606 DOI: 10.1242/dev.200454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 10/20/2022] [Indexed: 12/13/2022]
Abstract
The assembly of a mature vascular network involves coordinated endothelial cell (EC) shape changes, including the process of EC elongation. How EC elongation is dynamically regulated in vivo is not fully understood. Here, we have generated a zebrafish mutant that is deficient for the integrin adaptor protein Talin 1 (Tln1). Using a new focal adhesion (FA) marker line expressing endothelial Vinculinb-eGFP, we demonstrate that EC FAs function dynamically and are lost in our tln1 mutants, allowing us to uncouple the primary roles of FAs in EC morphogenesis from the secondary effects that occur due to systemic vessel failure or loss of blood flow. Tln1 loss led to compromised F-actin rearrangements, perturbed EC elongation and disrupted cell-cell junction linearisation in vessel remodelling. Finally, chemical induction of actin polymerisation restored actin dynamics and EC elongation during vascular morphogenesis. Together, we identify that FAs are essential for EC elongation and junction linearisation in flow-pressured vessels and that they influence actin polymerisation in cellular morphogenesis. These observations can explain the severely compromised vessel beds and vascular leakage observed in mutant models that lack integrin signalling. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Tevin C Y Chau
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mikaela S Keyser
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Jason A Da Silva
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Elysse K Morris
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Teodor E Yordanov
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Kinga P Duscyz
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Scott Paterson
- Organogenesis and Cancer Program, Peter MacCallum Cancer Centre and The PeterMac Callum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Alpha S Yap
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Benjamin M Hogan
- Organogenesis and Cancer Program, Peter MacCallum Cancer Centre and The PeterMac Callum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3000, Australia.,Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Anne Karine Lagendijk
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.,School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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25
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Xiao J, Wang WX. Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish. J Mol Biol 2022; 434:167821. [PMID: 36087778 DOI: 10.1016/j.jmb.2022.167821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 10/31/2022]
Abstract
Many vertebrate genes generate multiple transcript variants that may encode functionally distinct protein isoforms, but the transcriptomes of various developmental stages are poorly defined. Identifying the transcriptome and its regulation during the normal developmental process is the key to deciphering the developmental stage-specific functions of genes. Here we presented a systematic assessment of the temporal alternative splicing (AS) events during the critical development stages to capture the dynamic gene expression changes and AS in zebrafish. An unexpected transcriptome complexity generated by AS was observed during zebrafish development. The patterns of AS events varied substantially among developmental stages despite the similarities in the total proportion of AS genes. We further found that AS afforded substantial functional diversification of genes through the generation of stage-specific AS events from broadly protein-coding genes as an essential developmental regulatory mechanism. Skipped exon (SE) showed the strongest signals among developmental AS (devAS), suggesting that devAS events generated by SE may be necessary for the normal development of zebrafish. Most developmental genes regulated by AS mechanisms were not modulated in terms of their overall expression levels, indicating that AS shaped the transcriptome independently from transcriptional regulation during development. 128-cell stage was a critical stage for gene transcription during embryonic development. Splicing factors as an essential developmental regulator underwent AS in the potential autoregulatory feedback loop and expressed multiple isoforms. Thus, zebrafish development was shaped by an interplay of programs controlling gene expression levels and AS. Overall, we provided a global view of developmental patterns of AS during zebrafish development and revealed that AS transitions were the crucial regulatory component of zebrafish embryonic development.
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Affiliation(s)
- Jie Xiao
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Wen-Xiong Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China.
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26
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Dynamic Transcriptional Landscape of Grass Carp (Ctenopharyngodon idella) Reveals Key Transcriptional Features Involved in Fish Development. Int J Mol Sci 2022; 23:ijms231911547. [PMID: 36232849 PMCID: PMC9569805 DOI: 10.3390/ijms231911547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
A high-quality baseline transcriptome is a valuable resource for developmental research as well as a useful reference for other studies. We gathered 41 samples representing 11 tissues/organs from 22 important developmental time points within 197 days of fertilization of grass carp eggs in order to systematically examine the role of lncRNAs and alternative splicing in fish development. We created a high-quality grass carp baseline transcriptome with a completeness of up to 93.98 percent by combining strand-specific RNA sequencing and single-molecule real-time RNA sequencing technologies, and we obtained temporal expression profiles of 33,055 genes and 77,582 transcripts during development and tissue differentiation. A family of short interspersed elements was preferentially expressed at the early stage of zygotic activation in grass carp, and its possible regulatory components were discovered through analysis. Additionally, after thoroughly analyzing alternative splicing events, we discovered that retained intron (RI) alternative splicing events change significantly in both zygotic activation and tissue differentiation. During zygotic activation, we also revealed the precise regulatory characteristics of the underlying functional RI events.
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27
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Zou Z, Zhang C, Wang Q, Hou Z, Xiong Z, Kong F, Wang Q, Song J, Liu B, Liu B, Wang L, Lai F, Fan Q, Tao W, Zhao S, Ma X, Li M, Wu K, Zhao H, Chen ZJ, Xie W. Translatome and transcriptome co-profiling reveals a role of TPRXs in human zygotic genome activation. Science 2022; 378:abo7923. [PMID: 36074823 DOI: 10.1126/science.abo7923] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Translational regulation plays a critical role during the oocyte-to-embryo transition (OET) and zygotic genome activation (ZGA). Here, we integrated ultra-low-input Ribo-seq with mRNA-seq to co-profile the translatome and transcriptome in human oocytes and early embryos. Comparison with mouse counterparts identified widespread differentially translated genes functioning in epigenetic reprogramming, transposon defense, and small RNA biogenesis, in part driven by species-specific regulatory elements in 3' untranslated regions. Moreover, PRD-like homeobox transcription factors, including TPRXL, TPRX1, and TPRX2, are highly translated around ZGA. TPRX1/2/L knockdown leads to defective ZGA and preimplantation development. Ectopically expressed TPRXs bind and activate key ZGA genes in human embryonic stem cells. These data reveal the conservation and divergence of translation landscapes during OET and identify critical regulators of human ZGA.
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Affiliation(s)
- Zhuoning Zou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chuanxin Zhang
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Qiuyan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhenzhen Hou
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Zhuqing Xiong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jinzhu Song
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Boyang Liu
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Bofeng Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lijuan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fangnong Lai
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenrong Tao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Shuai Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Xiaonan Ma
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Miao Li
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Keliang Wu
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Han Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China.,Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
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28
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Liu Z, Wang W, Li X, Zhao X, Zhao H, Yang W, Zuo Y, Cai L, Xing Y. Temporal Dynamic Analysis of Alternative Splicing During Embryonic Development in Zebrafish. Front Cell Dev Biol 2022; 10:879795. [PMID: 35874832 PMCID: PMC9304896 DOI: 10.3389/fcell.2022.879795] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing is pervasive in mammalian genomes and involved in embryo development, whereas research on crosstalk of alternative splicing and embryo development was largely restricted to mouse and human and the alternative splicing regulation during embryogenesis in zebrafish remained unclear. We constructed the alternative splicing atlas at 18 time-course stages covering maternal-to-zygotic transition, gastrulation, somitogenesis, pharyngula stages, and post-fertilization in zebrafish. The differential alternative splicing events between different developmental stages were detected. The results indicated that abundance alternative splicing and differential alternative splicing events are dynamically changed and remarkably abundant during the maternal-to-zygotic transition process. Based on gene expression profiles, we found splicing factors are expressed with specificity of developmental stage and largely expressed during the maternal-to-zygotic transition process. The better performance of cluster analysis was achieved based on the inclusion level of alternative splicing. The biological function analysis uncovered the important roles of alternative splicing during embryogenesis. The identification of isoform switches of alternative splicing provided a new insight into mining the regulated mechanism of transcript isoforms, which always is hidden by gene expression. In conclusion, we inferred that alternative splicing activation is synchronized with zygotic genome activation and discovered that alternative splicing is coupled with transcription during embryo development in zebrafish. We also unveiled that the temporal expression dynamics of splicing factors during embryo development, especially co-orthologous splicing factors. Furthermore, we proposed that the inclusion level of alternative splicing events can be employed for cluster analysis as a novel parameter. This work will provide a deeper insight into the regulation of alternative splicing during embryogenesis in zebrafish.
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Affiliation(s)
- Zhe Liu
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Wei Wang
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Xinru Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
- Digital College, Inner Mongolia Intelligent Union Big Data Academy, Inner Mongolia Wesure Date Technology Co., Ltd., Hohhot, China
| | - Xiujuan Zhao
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hongyu Zhao
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Wuritu Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
- Hohhot Science and Technology Bureau, Hohhot, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
- Digital College, Inner Mongolia Intelligent Union Big Data Academy, Inner Mongolia Wesure Date Technology Co., Ltd., Hohhot, China
| | - Lu Cai
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Yongqiang Xing
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
- *Correspondence: Yongqiang Xing,
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Sato K, Sakai M, Ishii A, Maehata K, Takada Y, Yasuda K, Kotani T. Identification of embryonic RNA granules that act as sites of mRNA translation after changing their physical properties. iScience 2022; 25:104344. [PMID: 35620421 PMCID: PMC9127168 DOI: 10.1016/j.isci.2022.104344] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/16/2022] [Accepted: 04/27/2022] [Indexed: 11/08/2022] Open
Abstract
Fertilized eggs begin to translate mRNAs at appropriate times and placements to control development, but how the translation is regulated remains unclear. Here, we found that pou5f3 mRNA encoding a transcriptional factor essential for development formed granules in a dormant state in zebrafish oocytes. Although the number of pou5f3 granules remained constant, Pou5f3 protein accumulated after fertilization. Intriguingly, signals of newly synthesized peptides and a ribosomal protein became colocalized with pou5f3 granules after fertilization and, moreover, nascent Pou5f3 was shown to be synthesized in the granules. This functional change was accompanied by changes in the state and internal structure of granules. Dissolution of the granules reduced the rate of protein synthesis. Similarly, nanog and sox19b mRNAs in zebrafish and Pou5f1/Oct4 mRNA in mouse assembled into granules. Our results reveal that subcellular compartments, termed embryonic RNA granules, function as activation sites of translation after changing physical properties for directing vertebrate development.
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Affiliation(s)
- Keisuke Sato
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Moeko Sakai
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Anna Ishii
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kaori Maehata
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yuki Takada
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kyota Yasuda
- Department of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8526, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Hiroshima 739-8526, Japan
| | - Tomoya Kotani
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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30
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Pluripotency factors determine gene expression repertoire at zygotic genome activation. Nat Commun 2022; 13:788. [PMID: 35145080 PMCID: PMC8831532 DOI: 10.1038/s41467-022-28434-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 01/24/2022] [Indexed: 12/28/2022] Open
Abstract
Awakening of zygotic transcription in animal embryos relies on maternal pioneer transcription factors. The interplay of global and specific functions of these proteins remains poorly understood. Here, we analyze chromatin accessibility and time-resolved transcription in single and double mutant zebrafish embryos lacking pluripotency factors Pou5f3 and Sox19b. We show that two factors modify chromatin in a largely independent manner. We distinguish four types of direct enhancers by differential requirements for Pou5f3 or Sox19b. We demonstrate that changes in chromatin accessibility of enhancers underlie the changes in zygotic expression repertoire in the double mutants. Pou5f3 or Sox19b promote chromatin accessibility of enhancers linked to the genes involved in gastrulation and ventral fate specification. The genes regulating mesendodermal and dorsal fates are primed for activation independently of Pou5f3 and Sox19b. Strikingly, simultaneous loss of Pou5f3 and Sox19b leads to premature expression of genes, involved in regulation of organogenesis and differentiation. Zygotic genome activation in zebrafish relies on pluripotency transcription factors Pou5f3 and Sox19b. Here the authors investigate how these factors interact in vivo by analyzing the changes in chromatin state and time-resolved transcription in Pou5f3 and Sox19b single and double mutant embryos.
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31
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Kouprianov VA, Selmek AA, Ferguson JL, Mo X, Shive HR. brca2-mutant zebrafish exhibit context- and tissue-dependent alterations in cell phenotypes and response to injury. Sci Rep 2022; 12:883. [PMID: 35042909 PMCID: PMC8766490 DOI: 10.1038/s41598-022-04878-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/20/2021] [Indexed: 11/29/2022] Open
Abstract
Cancer cells frequently co-opt molecular programs that are normally activated in specific contexts, such as embryonic development and the response to injury. Determining the impact of cancer-associated mutations on cellular phenotypes within these discrete contexts can provide new insight into how such mutations lead to dysregulated cell behaviors and subsequent cancer onset. Here we assess the impact of heritable BRCA2 mutation on embryonic development and the injury response using a zebrafish model (Danio rerio). Unlike most mouse models for BRCA2 mutation, brca2-mutant zebrafish are fully viable and thus provide a unique tool for assessing both embryonic and adult phenotypes. We find that maternally provided brca2 is critical for normal oocyte development and embryonic survival in zebrafish, suggesting that embryonic lethality associated with BRCA2 mutation is likely to reflect defects in both meiotic and embryonic developmental programs. On the other hand, we find that adult brca2-mutant zebrafish exhibit aberrant proliferation of several cell types under basal conditions and in response to injury in tissues at high risk for cancer development. These divergent effects exemplify the often-paradoxical outcomes that occur in embryos (embryonic lethality) versus adult animals (cancer predisposition) with mutations in cancer susceptibility genes such as BRCA2. The altered cell behaviors identified in brca2-mutant embryonic and adult tissues, particularly in adult tissues at high risk for cancer, indicate that the effects of BRCA2 mutation on cellular phenotypes are both context- and tissue-dependent.
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Affiliation(s)
| | - Aubrie A Selmek
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jordan L Ferguson
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Xiaokui Mo
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Heather R Shive
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
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32
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Chille E, Strand E, Neder M, Schmidt V, Sherman M, Mass T, Putnam H. Developmental series of gene expression clarifies maternal mRNA provisioning and maternal-to-zygotic transition in a reef-building coral. BMC Genomics 2021; 22:815. [PMID: 34763678 PMCID: PMC8588723 DOI: 10.1186/s12864-021-08114-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Maternal mRNA provisioning of oocytes regulates early embryogenesis. Maternal transcripts are degraded as zygotic genome activation (ZGA) intensifies, a phenomenon known as the maternal-to-zygotic transition (MZT). Here, we examine gene expression over nine developmental stages in the Pacific rice coral, Montipora capitata, from eggs and embryos at 1, 4, 9, 14, 22, and 36 h-post-fertilization (hpf), as well as swimming larvae (9d), and adult colonies. RESULTS Weighted Gene Coexpression Network Analysis revealed four expression peaks, identifying the maternal complement, two waves of the MZT, and adult expression. Gene ontology enrichment revealed maternal mRNAs are dominated by cell division, methylation, biosynthesis, metabolism, and protein/RNA processing and transport functions. The first MZT wave occurs from ~4-14 hpf and is enriched in terms related to biosynthesis, methylation, cell division, and transcription. In contrast, functional enrichment in the second MZT wave, or ZGA, from 22 hpf-9dpf, includes ion/peptide transport and cell signaling. Finally, adult expression is enriched for functions related to signaling, metabolism, and ion/peptide transport. Our proposed MZT timing is further supported by expression of enzymes involved in zygotic transcriptional repression (Kaiso) and activation (Sox2), which peak at 14 hpf and 22 hpf, respectively. Further, DNA methylation writing (DNMT3a) and removing (TET1) enzymes peak and remain stable past ~4 hpf, suggesting that methylome programming occurs before 4 hpf. CONCLUSIONS Our high-resolution insight into the coral maternal mRNA and MZT provides essential baseline information to understand parental carryover effects and the sensitivity of developmental success under increasing environmental stress.
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Affiliation(s)
- Erin Chille
- Department of Biological Sciences, University of Rhode Island, Rhode Island, USA.
| | - Emma Strand
- Department of Biological Sciences, University of Rhode Island, Rhode Island, USA
| | - Mayaan Neder
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- The Interuniversity Institute of Marine Science, 88103, Eilat, Israel
| | | | - Madeleine Sherman
- Department of Biological Sciences, University of Rhode Island, Rhode Island, USA
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Hollie Putnam
- Department of Biological Sciences, University of Rhode Island, Rhode Island, USA
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33
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Creighton JH, Jessen JR. Core pathway proteins and the molecular basis of planar polarity in the zebrafish gastrula. Semin Cell Dev Biol 2021; 125:17-25. [PMID: 34635444 DOI: 10.1016/j.semcdb.2021.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/22/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022]
Abstract
The planar polarization of cells and subcellular structures is critical for embryonic development. Coordination of this polarity can provide cells a sense of direction in relation to the anterior-posterior and dorsal-ventral body axes. Fly epithelia use a core pathway comprised of transmembrane (Van Gogh/Strabismus, Frizzled, and Flamingo/Starry night) and cytoplasmic (Prickle or Spiny-legs, Dishevelled, and Diego) proteins to communicate directional information between cells and thereby promote the uniform orientation of structures such as hairs. In the zebrafish gastrula, planar polarity underlies complex cellular processes, including directed migration and intercalation, that are required to shape the embryo body. Like other vertebrates, the zebrafish genome encodes homologs of each core protein, and it is well-established that polarized gastrula cell behaviors are regulated by some of them. However, it is unknown whether a conserved six-member core protein pathway regulates planar polarity during zebrafish gastrulation. Here, we review our current understanding of core protein function as it relates to two specific examples of planar polarity, the dorsal convergence of lateral gastrula cells and the mediolateral intercalation of midline cells. We consider the hallmarks of fly planar polarity and discuss data regarding asymmetric protein localization and function, and the intercellular communication of polarity information.
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Affiliation(s)
- Joy H Creighton
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Jason R Jessen
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA.
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34
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Hansen CL, Chamberlain TJ, Trevena RL, Kurek JE, Pelegri F. Conserved germ plasm characteristics across the Danio and Devario lineages. Genesis 2021; 59:e23452. [PMID: 34617657 DOI: 10.1002/dvg.23452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/26/2021] [Accepted: 08/29/2021] [Indexed: 11/06/2022]
Abstract
In many animal species, germ cell specification requires the inheritance of germ plasm, a biomolecular condensate containing maternally derived RNAs and proteins. Most studies of germ plasm composition and function have been performed in widely evolutionarily divergent model organisms, such as Caenorhabditis elegans, Drosophila, Xenopus laevis, and Danio rerio (zebrafish). In zebrafish, 12 RNAs localize to germ plasm at the furrows of the early embryo. Here, we tested for the presence of these RNAs in three additional species within the Danionin clade: Danio kyathit, Danio albolineatus, and Devario aequipinnatus. By visualizing nanos RNA, we find that germ plasm segregation patterns during early embryogenesis are conserved across these species. Ten additional germ plasm RNAs exhibit localization at the furrows of early embryos in all three non-zebrafish Danionin species, consistent with germ plasm localization. One component of zebrafish germ plasm, ca15b, lacked specific localization in embryos of the more distantly related D. aequipinnatus. Our findings show that within a subset of closely related Danionin species, the vast majority of germ plasm RNA components are conserved. At the same time, the lack of ca15b localization in D. aequipinnatus germ plasm highlights the potential for the divergence of germ plasm composition across a restricted phylogenetic space.
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Affiliation(s)
- Christina L Hansen
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Trevor J Chamberlain
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Ryan L Trevena
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Jacob E Kurek
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Francisco Pelegri
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, Wisconsin, USA
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35
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Vandestadt C, Vanwalleghem GC, Khabooshan MA, Douek AM, Castillo HA, Li M, Schulze K, Don E, Stamatis SA, Ratnadiwakara M, Änkö ML, Scott EK, Kaslin J. RNA-induced inflammation and migration of precursor neurons initiates neuronal circuit regeneration in zebrafish. Dev Cell 2021; 56:2364-2380.e8. [PMID: 34428400 DOI: 10.1016/j.devcel.2021.07.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 06/18/2021] [Accepted: 07/27/2021] [Indexed: 11/29/2022]
Abstract
Tissue regeneration and functional restoration after injury are considered as stem- and progenitor-cell-driven processes. In the central nervous system, stem cell-driven repair is slow and problematic because function needs to be restored rapidly for vital tasks. In highly regenerative vertebrates, such as zebrafish, functional recovery is rapid, suggesting a capability for fast cell production and functional integration. Surprisingly, we found that migration of dormant "precursor neurons" to the injury site pioneers functional circuit regeneration after spinal cord injury and controls the subsequent stem-cell-driven repair response. Thus, the precursor neurons make do before the stem cells make new. Furthermore, RNA released from the dying or damaged cells at the site of injury acts as a signal to attract precursor neurons for repair. Taken together, our data demonstrate an unanticipated role of neuronal migration and RNA as drivers of neural repair.
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Affiliation(s)
- Celia Vandestadt
- Australian Regenerative Medicine Institute, Monash University, Clayton VIC, 3800, Australia
| | - Gilles C Vanwalleghem
- The Queensland Brain Institute, the University of Queensland, St. Lucia, QLD, Australia
| | - Mitra Amiri Khabooshan
- Australian Regenerative Medicine Institute, Monash University, Clayton VIC, 3800, Australia
| | - Alon M Douek
- Australian Regenerative Medicine Institute, Monash University, Clayton VIC, 3800, Australia
| | - Hozana Andrade Castillo
- Australian Regenerative Medicine Institute, Monash University, Clayton VIC, 3800, Australia; Brazilian Biosciences National Laboratory, Brazilian Centre for Research in Energy and Materials, Campinas CEP 13083-100, Brazil
| | - Mei Li
- Australian Regenerative Medicine Institute, Monash University, Clayton VIC, 3800, Australia
| | - Keith Schulze
- Monash Micro Imaging, Monash University, Monash University, Clayton, VIC 3800, Australia
| | - Emily Don
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | | | - Madara Ratnadiwakara
- Centre for Reproductive Health and Center for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Minna-Liisa Änkö
- Centre for Reproductive Health and Center for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Ethan K Scott
- The Queensland Brain Institute, the University of Queensland, St. Lucia, QLD, Australia
| | - Jan Kaslin
- Australian Regenerative Medicine Institute, Monash University, Clayton VIC, 3800, Australia.
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36
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Pottie L, Van Gool W, Vanhooydonck M, Hanisch FG, Goeminne G, Rajkovic A, Coucke P, Sips P, Callewaert B. Loss of zebrafish atp6v1e1b, encoding a subunit of vacuolar ATPase, recapitulates human ARCL type 2C syndrome and identifies multiple pathobiological signatures. PLoS Genet 2021; 17:e1009603. [PMID: 34143769 PMCID: PMC8244898 DOI: 10.1371/journal.pgen.1009603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 06/30/2021] [Accepted: 05/17/2021] [Indexed: 11/27/2022] Open
Abstract
The inability to maintain a strictly regulated endo(lyso)somal acidic pH through the proton-pumping action of the vacuolar-ATPases (v-ATPases) has been associated with various human diseases including heritable connective tissue disorders. Autosomal recessive (AR) cutis laxa (CL) type 2C syndrome is associated with genetic defects in the ATP6V1E1 gene and is characterized by skin wrinkles or loose redundant skin folds with pleiotropic systemic manifestations. The underlying pathological mechanisms leading to the clinical presentations remain largely unknown. Here, we show that loss of atp6v1e1b in zebrafish leads to early mortality, associated with craniofacial dysmorphisms, vascular anomalies, cardiac dysfunction, N-glycosylation defects, hypotonia, and epidermal structural defects. These features are reminiscent of the phenotypic manifestations in ARCL type 2C patients. Our data demonstrates that loss of atp6v1e1b alters endo(lyso)somal protein levels, and interferes with non-canonical v-ATPase pathways in vivo. In order to gain further insights into the processes affected by loss of atp6v1e1b, we performed an untargeted analysis of the transcriptome, metabolome, and lipidome in early atp6v1e1b-deficient larvae. We report multiple affected pathways including but not limited to oxidative phosphorylation, sphingolipid, fatty acid, and energy metabolism together with profound defects on mitochondrial respiration. Taken together, our results identify complex pathobiological effects due to loss of atp6v1e1b in vivo. Cutis laxa syndromes are pleiotropic disorders of the connective tissue, characterized by skin redundancy and variable systemic manifestations. Cutis laxa syndromes are caused by pathogenic variants in genes encoding structural and regulatory components of the extracellular matrix or in genes encoding components of cellular trafficking, metabolism, and mitochondrial function. Pathogenic variants in genes coding for vacuolar-ATPases, a multisubunit complex responsible for the acidification of multiple intracellular vesicles, cause type 2 cutis laxa syndromes, a group of cutis laxa subtypes further characterized by neurological, skeletal, and rarely cardiopulmonary manifestations. To investigate the pathomechanisms of vacuolar-ATPase dysfunction, we generated zebrafish models that lack a crucial subunit of the vacuolar-ATPases. The mutant zebrafish models show morphological and functional features reminiscent of the phenotypic manifestations in cutis laxa patients carrying pathogenic variants in ATP6V1E1. In-depth analysis at multiple -omic levels identified biological signatures that indicate impairment of signaling pathways, lipid metabolism, and mitochondrial respiration. We anticipate that these data will contribute to a better understanding of the pathogenesis of cutis laxa syndromes and other disorders involving defective v-ATPase function, which may eventually improve patient treatment and management.
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Affiliation(s)
- Lore Pottie
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Wouter Van Gool
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Michiel Vanhooydonck
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Franz-Georg Hanisch
- Institute of Biochemistry II, Medical Faculty, University of Cologne, Cologne, Germany
| | - Geert Goeminne
- VIB Metabolomics Core Ghent, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Andreja Rajkovic
- Department of Food technology, Safety and Health, Faculty of Bioscience Engineering, University of Ghent, Ghent, Belgium
| | - Paul Coucke
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Patrick Sips
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- * E-mail:
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37
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Bayega A, Oikonomopoulos S, Gregoriou ME, Tsoumani KT, Giakountis A, Wang YC, Mathiopoulos KD, Ragoussis J. Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest. Sci Rep 2021; 11:7878. [PMID: 33846393 PMCID: PMC8042104 DOI: 10.1038/s41598-021-86753-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 03/10/2021] [Indexed: 11/21/2022] Open
Abstract
The olive fruit fly, Bactrocera oleae, is the most important pest for the olive fruit but lacks adequate transcriptomic characterization that could aid in molecular control approaches. We apply nanopore long-read RNA-seq with internal RNA standards allowing absolute transcript quantification to analyze transcription dynamics during early embryo development for the first time in this organism. Sequencing on the MinION platform generated over 31 million reads. Over 50% of the expressed genes had at least one read covering its entire length validating our full-length approach. We generated a de novo transcriptome assembly and identified 1768 new genes and a total of 79,810 isoforms; a fourfold increase in transcriptome diversity compared to the current NCBI predicted transcriptome. Absolute transcript quantification per embryo allowed an insight into the dramatic re-organization of maternal transcripts. We further identified Zelda as a possible regulator of early zygotic genome activation in B. oleae and provide further insights into the maternal-to-zygotic transition. These data show the utility of long-read RNA in improving characterization of non-model organisms that lack a fully annotated genome, provide potential targets for sterile insect technic approaches, and provide the first insight into the transcriptome landscape of the developing olive fruit fly embryo.
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Affiliation(s)
- Anthony Bayega
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Spyros Oikonomopoulos
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Maria-Eleni Gregoriou
- Laboratory of Molecular Biology and Genomics, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Konstantina T Tsoumani
- Laboratory of Molecular Biology and Genomics, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Antonis Giakountis
- Laboratory of Molecular Biology and Genomics, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Yu Chang Wang
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Kostas D Mathiopoulos
- Laboratory of Molecular Biology and Genomics, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
| | - Jiannis Ragoussis
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, Québec, Canada.
- Department of Bioengineering, McGill University, Montréal, Québec, Canada.
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38
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The adaptor protein Grb2b is an essential modulator for lympho-venous sprout formation in the zebrafish trunk. Angiogenesis 2021; 24:345-362. [PMID: 33677657 PMCID: PMC8205915 DOI: 10.1007/s10456-021-09774-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/12/2021] [Indexed: 12/13/2022]
Abstract
Vegfc/Vegfr3 signaling is critical for lymphangiogenesis, the sprouting of lymphatic vessels. In zebrafish, cells sprouting from the posterior cardinal vein can either form lymphatic precursor cells or contribute to intersegmental vein formation. Both, the Vegfc-dependent differential induction of Prox1a in sprouting cells as well as a Notch-mediated pre-pattern within intersegmental vessels have been associated with the regulation of secondary sprout behavior. However, how exactly a differential lymphatic versus venous sprout cell behavior is achieved is not fully understood. Here, we characterize a zebrafish mutant in the adaptor protein Grb2b, and demonstrate through genetic interaction studies that Grb2b acts within the Vegfr3 pathway. Mutant embryos exhibit phenotypes that are consistent with reduced Vegfr3 signaling outputs prior to the sprouting of endothelial cells from the vein. During secondary sprouting stages, loss of grb2b leads to defective cell behaviors resulting in a loss of parachordal lymphangioblasts, while only partially affecting the number of intersegmental veins. A second GRB2 zebrafish ortholog, grb2a, contributes to the development of lymphatic structures in the meninges and in the head, but not in the trunk. Our results illustrate an essential role of Grb2b in vivo for cell migration to the horizontal myoseptum and for the correct formation of the lymphatic vasculature, while being less critically required in intersegmental vein formation. Thus, there appear to be higher requirements for Grb2b and therefore Vegfr3 downstream signaling levels in lymphatic versus vein precursor-generating sprouts.
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D'Orazio FM, Balwierz PJ, González AJ, Guo Y, Hernández-Rodríguez B, Wheatley L, Jasiulewicz A, Hadzhiev Y, Vaquerizas JM, Cairns B, Lenhard B, Müller F. Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization. Dev Cell 2021; 56:641-656.e5. [PMID: 33651978 PMCID: PMC7957325 DOI: 10.1016/j.devcel.2021.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 10/25/2020] [Accepted: 02/03/2021] [Indexed: 02/09/2023]
Abstract
In many animal models, primordial germ cell (PGC) development depends on maternally deposited germ plasm, which prevents somatic cell fate. Here, we show that PGCs respond to regulatory information from the germ plasm in two distinct phases using two distinct mechanisms in zebrafish. We demonstrate that PGCs commence zygotic genome activation together with the somatic blastocysts with no demonstrable differences in transcriptional and chromatin opening. Unexpectedly, both PGC and somatic blastocysts activate germ-cell-specific genes, which are only stabilized in PGCs by cytoplasmic germ plasm determinants. Disaggregated perinuclear relocalization of germ plasm during PGC migration is regulated by the germ plasm determinant Tdrd7 and is coupled to dramatic divergence between PGC and somatic transcriptomes. This transcriptional divergence relies on PGC-specific cis-regulatory elements characterized by promoter-proximal distribution. We show that Tdrd7-dependent reconfiguration of chromatin accessibility is required for elaboration of PGC fate but not for PGC migration. No evidence for transcriptional activation delay in zebrafish PGCs Germ-plasm-associated post-transcriptional divergence during ZGA Epigenetic reprogramming marks onset of PGC migration Epigenetic reprogramming in PGCs relies on Tdrd7, coupled to germ plasm relocalization
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Affiliation(s)
- Fabio M D'Orazio
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, UK
| | - Piotr J Balwierz
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, UK
| | - Ada Jimenez González
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Yixuan Guo
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Lucy Wheatley
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Aleksandra Jasiulewicz
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Yavor Hadzhiev
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Juan M Vaquerizas
- MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK; Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, Muenster, Germany
| | - Bradley Cairns
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Boris Lenhard
- MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, UK.
| | - Ferenc Müller
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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40
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Phelps WA, Carlson AE, Lee MT. Optimized design of antisense oligomers for targeted rRNA depletion. Nucleic Acids Res 2021; 49:e5. [PMID: 33221877 PMCID: PMC7797071 DOI: 10.1093/nar/gkaa1072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/01/2020] [Accepted: 10/21/2020] [Indexed: 11/14/2022] Open
Abstract
RNA sequencing (RNA-seq) is extensively used to quantify gene expression transcriptome-wide. Although often paired with polyadenylate (poly(A)) selection to enrich for messenger RNA (mRNA), many applications require alternate approaches to counteract the high proportion of ribosomal RNA (rRNA) in total RNA. Recently, digestion using RNaseH and antisense DNA oligomers tiling target rRNAs has emerged as an alternative to commercial rRNA depletion kits. Here, we present a streamlined, more economical RNaseH-mediated rRNA depletion with substantially lower up-front costs, using shorter antisense oligos only sparsely tiled along the target RNA in a 5-min digestion reaction. We introduce a novel Web tool, Oligo-ASST, that simplifies oligo design to target regions with optimal thermodynamic properties, and additionally can generate compact, common oligo pools that simultaneously target divergent RNAs, e.g. across different species. We demonstrate the efficacy of these strategies by generating rRNA-depletion oligos for Xenopus laevis and for zebrafish, which expresses two distinct versions of rRNAs during embryogenesis. The resulting RNA-seq libraries reduce rRNA to <5% of aligned reads, on par with poly(A) selection, and also reveal expression of many non-adenylated RNA species. Oligo-ASST is freely available at https://mtleelab.pitt.edu/oligo to design antisense oligos for any taxon or to target any abundant RNA for depletion.
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Affiliation(s)
- Wesley A Phelps
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Anne E Carlson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Miler T Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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41
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Trivellin G, Tirosh A, Hernández-Ramírez LC, Gupta T, Tsai-Morris CH, Faucz FR, Burgess HA, Feldman B, Stratakis CA. The X-linked acrogigantism-associated gene gpr101 is a regulator of early embryonic development and growth in zebrafish. Mol Cell Endocrinol 2021; 520:111091. [PMID: 33248229 PMCID: PMC8771005 DOI: 10.1016/j.mce.2020.111091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 12/28/2022]
Abstract
We recently described X-linked acrogigantism (X-LAG), a condition of early childhood-onset pituitary gigantism associated with microduplications of the GPR101 receptor. The expression of GPR101 in hyperplastic pituitary regions and tumors in X-LAG patients, and GPR101's normally transient pituitary expression during fetal development, suggest a role in the regulation of growth. Nevertheless, little is still known about GPR101's physiological functions, especially during development. By using zebrafish models, we investigated the role of gpr101 during embryonic development and somatic growth. Transient ectopic gpr101 expression perturbed the embryonic body plan but did not affect growth. Loss of gpr101 led to a significant reduction in body size that was even more pronounced in the absence of maternal transcripts, as well as subfertility. These changes were accompanied by gastrulation and hypothalamic defects. In conclusion, both gpr101 loss- and gain-of-function affect, in different ways, fertility, embryonic patterning, growth and brain development.
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Affiliation(s)
- Giampaolo Trivellin
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA; Laboratory of Cellular and Molecular Endocrinology and Laboratory of Pharmacology and Brain Pathology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Mi, Italy.
| | - Amit Tirosh
- NET Service and Endocrine Oncology Bioinformatics Lab, Sheba Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Ramat Gan, Israel
| | - Laura C Hernández-Ramírez
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Tripti Gupta
- Division of Developmental Biology, NICHD, NIH, Bethesda, MD, USA
| | | | - Fabio R Faucz
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Harold A Burgess
- Division of Developmental Biology, NICHD, NIH, Bethesda, MD, USA
| | - Benjamin Feldman
- Division of Developmental Biology, NICHD, NIH, Bethesda, MD, USA
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
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Shi DL. Decoding Dishevelled-Mediated Wnt Signaling in Vertebrate Early Development. Front Cell Dev Biol 2020; 8:588370. [PMID: 33102490 PMCID: PMC7554312 DOI: 10.3389/fcell.2020.588370] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/15/2020] [Indexed: 12/22/2022] Open
Abstract
Dishevelled proteins are key players of Wnt signaling pathways. They transduce Wnt signals and perform cellular functions through distinct conserved domains. Due to the presence of multiple paralogs, the abundant accumulation of maternal transcripts, and the activation of distinct Wnt pathways, their regulatory roles during vertebrate early development and the mechanism by which they dictate the pathway specificity have been enigmatic and attracted much attention in the past decades. Extensive studies in different animal models have provided significant insights into the structure-function relationship of conserved Dishevelled domains in Wnt signaling and the implications of Dishevelled isoforms in early developmental processes. Notably, intra- and inter-molecular interactions and Dishevelled dosage may be important in modulating the specificity of Wnt signaling. There are also distinct and redundant functions among Dishevelled isoforms in development and disease, which may result from differential spatiotemporal expression patterns and biochemical properties and post-translational modifications. This review presents the advances and perspectives in understanding Dishevelled-mediated Wnt signaling during gastrulation and neurulation in vertebrate early embryos.
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Affiliation(s)
- De-Li Shi
- Developmental Biology Laboratory, CNRS-UMR 7622, IBPS, Sorbonne University, Paris, France
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43
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De la Paz JF, Anguita-Salinas C, Díaz-Celis C, Chávez FP, Allende ML. The Zebrafish Perivitelline Fluid Provides Maternally-Inherited Defensive Immunity. Biomolecules 2020; 10:biom10091274. [PMID: 32899417 PMCID: PMC7564447 DOI: 10.3390/biom10091274] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 11/25/2022] Open
Abstract
In the teleost egg, the embryo is immersed in an extraembryonic fluid that fills the space between the embryo and the chorion and partially isolates it from the external environment, called the perivitelline fluid (PVF). The exact composition of the PVF remains unknown in vertebrate animals. The PVF allows the embryo to avoid dehydration, to maintain a safe osmotic balance and provides mechanical protection; however, its potential defensive properties against bacterial pathogens has not been reported. In this work, we determined the global proteomic profile of PVF in zebrafish eggs and embryos, and the maternal or zygotic origin of the identified proteins was studied. In silico analysis of PVF protein composition revealed an enrichment of protein classes associated with non-specific humoral innate immunity. We found lectins, protease inhibitors, transferrin, and glucosidases present from early embryogenesis until hatching. Finally, in vitro and in vivo experiments done with this fluid demonstrated that the PVF possessed a strong agglutinating capacity on bacterial cells and protected the embryos when challenged with the pathogenic bacteria Edwardsiella tarda. Our results suggest that the PVF is a primitive inherited immune extraembryonic system that protects the embryos from external biological threats prior to hatching.
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Affiliation(s)
- Javiera F. De la Paz
- FONDAP Center for Genome Regulation, Faculty of Sciences, University of Chile, RM 7800003 Santiago, Chile; (J.F.D.l.P.); (C.A.-S.)
- Laboratory of Systems Microbiology, Faculty of Sciences, University of Chile, RM 7800003 Santiago, Chile;
- Danio Biotechnologies SpA, RM 7800003 Santiago, Chile
| | - Consuelo Anguita-Salinas
- FONDAP Center for Genome Regulation, Faculty of Sciences, University of Chile, RM 7800003 Santiago, Chile; (J.F.D.l.P.); (C.A.-S.)
- Danio Biotechnologies SpA, RM 7800003 Santiago, Chile
| | - César Díaz-Celis
- Laboratory of Systems Microbiology, Faculty of Sciences, University of Chile, RM 7800003 Santiago, Chile;
| | - Francisco P. Chávez
- Laboratory of Systems Microbiology, Faculty of Sciences, University of Chile, RM 7800003 Santiago, Chile;
- Correspondence: (F.P.C.); (M.L.A.)
| | - Miguel L. Allende
- FONDAP Center for Genome Regulation, Faculty of Sciences, University of Chile, RM 7800003 Santiago, Chile; (J.F.D.l.P.); (C.A.-S.)
- Correspondence: (F.P.C.); (M.L.A.)
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44
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Abstract
Gastrulation is a critical early morphogenetic process of animal development, during which the three germ layers; mesoderm, endoderm and ectoderm, are rearranged by internalization movements. Concurrent epiboly movements spread and thin the germ layers while convergence and extension movements shape them into an anteroposteriorly elongated body with head, trunk, tail and organ rudiments. In zebrafish, gastrulation follows the proliferative and inductive events that establish the embryonic and extraembryonic tissues and the embryonic axis. Specification of these tissues and embryonic axes are controlled by the maternal gene products deposited in the egg. These early maternally controlled processes need to generate sufficient cell numbers and establish the embryonic polarity to ensure normal gastrulation. Subsequently, after activation of the zygotic genome, the zygotic gene products govern mesoderm and endoderm induction and germ layer patterning. Gastrulation is initiated during the maternal-to-zygotic transition, a process that entails both activation of the zygotic genome and downregulation of the maternal transcripts. Genomic studies indicate that gastrulation is largely controlled by the zygotic genome. Nonetheless, genetic studies that investigate the relative contributions of maternal and zygotic gene function by comparing zygotic, maternal and maternal zygotic mutant phenotypes, reveal significant contribution of maternal gene products, transcripts and/or proteins, that persist through gastrulation, to the control of gastrulation movements. Therefore, in zebrafish, the maternally expressed gene products not only set the stage for, but they also actively participate in gastrulation morphogenesis.
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Affiliation(s)
- Lilianna Solnica-Krezel
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, United States.
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45
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Transcriptome Analysis of Maternal Gene Transcripts in Unfertilized Eggs of Misgurnus anguillicaudatus and Identification of Immune-Related Maternal Genes. Int J Mol Sci 2020; 21:ijms21113872. [PMID: 32485896 PMCID: PMC7312655 DOI: 10.3390/ijms21113872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022] Open
Abstract
Maternal genes are important in directing early development and determining egg quality in fish. We here report the de novo transcriptome from four tissue libraries of the cyprinid loach, Misgurnus anguillicaudatus, and for the first time identified maternal gene transcripts in unfertilized eggs and suggest their immune system involvement. Expression profiles and functional enrichment revealed a total 24,116 transcripts were expressed as maternal transcripts in unfertilized eggs, which were involved in a wide range of biological functions and pathways. Comparison expression profiles and analysis of tissue specificity revealed that the large numbers of maternal transcripts were stored in unfertilized eggs near the late phase of ovarian maturation and before ovulation. Functional classification showed a total of 279 maternal immune-related transcripts classified with immune system process GO term and immune system KEGG pathway. qPCR analysis showed that transcript levels of identified maternal immune-related candidate genes were dynamically modulated during development and early ontogeny of M. anguillicaudatus. Taken together, this study could not only provide knowledge on the protective roles of maternal immune-related genes during early life stage of M. anguillicaudatus but could also be a valuable transcriptomic/genomic resource for further analysis of maternally provisioned genes in M. anguillicaudatus and other related teleost fishes.
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46
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Varga M, Csályi K, Bertyák I, Menyhárd DK, Poole RJ, Cerveny KL, Kövesdi D, Barátki B, Rouse H, Vad Z, Hawkins TA, Stickney HL, Cavodeassi F, Schwarz Q, Young RM, Wilson SW. Tissue-Specific Requirement for the GINS Complex During Zebrafish Development. Front Cell Dev Biol 2020; 8:373. [PMID: 32548116 PMCID: PMC7270345 DOI: 10.3389/fcell.2020.00373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022] Open
Abstract
Efficient and accurate DNA replication is particularly critical in stem and progenitor cells for successful proliferation and survival. The replisome, an amalgam of protein complexes, is responsible for binding potential origins of replication, unwinding the double helix, and then synthesizing complimentary strands of DNA. According to current models, the initial steps of DNA unwinding and opening are facilitated by the CMG complex, which is composed of a GINS heterotetramer that connects Cdc45 with the mini-chromosome maintenance (Mcm) helicase. In this work, we provide evidence that in the absence of GINS function DNA replication is cell autonomously impaired, and we also show that gins1 and gins2 mutants exhibit elevated levels of apoptosis restricted to actively proliferating regions of the central nervous system (CNS). Intriguingly, our results also suggest that the rapid cell cycles during early embryonic development in zebrafish may not require the function of the canonical GINS complex as neither zygotic Gins1 nor Gins2 isoforms seem to be present during these stages.
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Affiliation(s)
- Máté Varga
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary.,Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Kitti Csályi
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - István Bertyák
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dóra K Menyhárd
- HAS-ELTE Protein Modeling Research Group and Laboratory of Structural Chemistry and Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Richard J Poole
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Kara L Cerveny
- Biology Department, Reed College, Portland, OR, United States
| | - Dorottya Kövesdi
- Office of Supported Research Groups of the Hungarian Academy of Sciences, Budapest, Hungary.,Department of Immunology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Balázs Barátki
- Department of Immunology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Hannah Rouse
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Zsuzsa Vad
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Thomas A Hawkins
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Heather L Stickney
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Florencia Cavodeassi
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom.,Institute of Medical and Biomedical Education, St. George's University of London, London, United Kingdom
| | - Quenten Schwarz
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Rodrigo M Young
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
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Shi B, Zhang J, Heng J, Gong J, Zhang T, Li P, Sun BF, Yang Y, Zhang N, Zhao YL, Wang HL, Liu F, Zhang QC, Yang YG. RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function. Genome Biol 2020; 21:120. [PMID: 32423473 PMCID: PMC7236375 DOI: 10.1186/s13059-020-02022-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 04/16/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structure have revealed its pervasive and crucial roles in RNA processing and functions, but whether and how RNA structure regulates the fate of the maternal transcriptome have yet to be determined. RESULTS Here we establish the global map of four nucleotide-based mRNA structures by icSHAPE during zebrafish early embryogenesis. Strikingly, we observe that RNA structurally variable regions are enriched in the 3' UTR and contain cis-regulatory elements important for maternal-to-zygotic transition (MZT). We find that the RNA-binding protein Elavl1a stabilizes maternal mRNAs by binding to the cis-elements. Conversely, RNA structure formation suppresses Elavl1a's binding leading to the decay of its maternal targets. CONCLUSIONS Our study finds that RNA structurally variable regions are enriched in mRNA 3' UTRs and contain cis-regulatory elements during zebrafish early embryogenesis. We reveal that Elavl1a regulates maternal RNA stability in an RNA structure-dependent fashion. Overall, our findings reveal a broad and fundamental role of RNA structure-based regulation in vertebrate early embryogenesis.
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Affiliation(s)
- Boyang Shi
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinsong Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian Heng
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Gong
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ting Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pan Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Bao-Fa Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ning Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yong-Liang Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hai-Lin Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Feng Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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48
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Akdogan-Ozdilek B, Duval KL, Goll MG. Chromatin dynamics at the maternal to zygotic transition: recent advances from the zebrafish model. F1000Res 2020; 9. [PMID: 32528656 PMCID: PMC7262572 DOI: 10.12688/f1000research.21809.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2020] [Indexed: 01/02/2023] Open
Abstract
Early animal development is characterized by intense reorganization of the embryonic genome, including large-scale changes in chromatin structure and in the DNA and histone modifications that help shape this structure. Particularly profound shifts in the chromatin landscape are associated with the maternal-to-zygotic transition, when the zygotic genome is first transcribed and maternally loaded transcripts are degraded. The accessibility of the early zebrafish embryo facilitates the interrogation of chromatin during this critical window of development, making it an important model for early chromatin regulation. Here, we review our current understanding of chromatin dynamics during early zebrafish development, highlighting new advances as well as similarities and differences between early chromatin regulation in zebrafish and other species.
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Affiliation(s)
| | | | - Mary G Goll
- Department of Genetics, University of Georgia, Athens, GA, USA
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Zhu Z, Liu Y, Xu W, Liu T, Xie Y, Sham KWY, Sha O, Cheng CHK. Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development. Front Genet 2020; 11:299. [PMID: 32296464 PMCID: PMC7136893 DOI: 10.3389/fgene.2020.00299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 03/13/2020] [Indexed: 12/25/2022] Open
Abstract
Dgcr8 is involved in the biogenesis of canonical miRNAs to process pri-miRNA into pre-miRNA. Previous studies have provided evidence that Dgcr8 plays an essential role in different biological processes. However, the function of maternal and zygotic Dgcr8 in early embryonic development remains largely unknown. Recently, we have reported a novel approach for generating germline-specific deletions in zebrafish. This germline knockout model offers an opportunity to investigate into the differential roles of maternal or zygotic Dgcr8. Although germline specific dgcr8 deletion has no influence on gonad development, maternal or zygotic dgcr8 is essential for embryonic development in the offspring. Both maternal dgcr8 (Mdgcr8) and maternal zygotic dgcr8 (MZdgcr8) mutants display multiple developmental defects and die within 1 week. Moreover, MZdcgr8 mutant displays more severe morphogenesis defects. However, when a miR-430 duplex (the most abundantly expressed miRNA in early embryonic stage) is used to rescue the maternal mutant phenotype, the Mdgcr8 embryos could be rescued successfully and grow into adulthood and achieve sexual maturation, whereas the MZdgcr8 embryos are only partially rescued and they all die within 1 week. The differential phenotypes between the Mdgcr8 and MZdgcr8 embryos provide us with an opportunity to study the roles of individual miRNAs during early development.
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Affiliation(s)
- Zeyao Zhu
- Department of Anatomy, Histology and Developmental Biology, School of Basic Medical Sciences, Shenzhen University, Shenzhen, China.,School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
| | - Wen Xu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Taian Liu
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yuxin Xie
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kathy W Y Sham
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ou Sha
- Department of Anatomy, Histology and Developmental Biology, School of Basic Medical Sciences, Shenzhen University, Shenzhen, China
| | - Christopher H K Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
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Rochon ER, Corti P. Globins and nitric oxide homeostasis in fish embryonic development. Mar Genomics 2020; 49:100721. [PMID: 31711848 DOI: 10.1016/j.margen.2019.100721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/07/2019] [Accepted: 10/18/2019] [Indexed: 11/30/2022]
Abstract
Since the discovery of new members of the globin superfamily such as Cytoglobin, Neuroglobin and Globin X, in addition to the most well-known members, Hemoglobin and Myoglobin, different hypotheses have been suggested about their function in vertebrates. Globins are ubiquitously found in living organisms and can carry out different functions based on their ability to bind ligands such as O2, and nitric oxide (NO) and to catalyze reactions scavenging NO or generating NO by reducing nitrite. NO is a highly diffusible molecule with a central role in signaling important for egg maturation, fertilization and early embryonic development. The globins ability to scavenge or generate NO makes these proteins ideal candidates in regulating NO homeostasis depending on the micro environment and tissue NO demands. Different amounts of various globins have been found in zebrafish eggs and developing embryos where it's unlikely that they function as respiratory proteins and instead could play a role in maintaining embryonic NO homeostasis. Here we summarize the current knowledge concerning the role of NO in adult fish in comparison to mammals and we discuss NO function during embryonic development with possible implications for globins in maintaining embryonic NO homeostasis.
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Affiliation(s)
- Elizabeth R Rochon
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Paola Corti
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA; Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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