1
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Musaev D, Abdelmessih M, Vejnar CE, Yartseva V, Weiss LA, Strayer EC, Takacs CM, Giraldez AJ. UPF1 regulates mRNA stability by sensing poorly translated coding sequences. Cell Rep 2024; 43:114074. [PMID: 38625794 DOI: 10.1016/j.celrep.2024.114074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/07/2024] [Accepted: 03/21/2024] [Indexed: 04/18/2024] Open
Abstract
Post-transcriptional mRNA regulation shapes gene expression, yet how cis-elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that the strength of translation initiation, upstream open reading frame (uORF) content, codon optimality, AU-rich elements, microRNA binding sites, and open reading frame (ORF) length function combinatorially to regulate mRNA stability. Machine-learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs, which are associated with a higher decay rate, including mRNAs with uORFs and those with exposed ORFs after stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated, such as mRNAs with long ORFs, ORF-like 3' UTRs, and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an exon-junction complex (EJC)-independent nonsense-mediated decay (NMD) pathway that we term ORF-mediated decay (OMD).
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Affiliation(s)
- Damir Musaev
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Mario Abdelmessih
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; AstraZeneca, Waltham, MA 02451, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Kenai Therapeutics, San Diego, CA, USA
| | - Linnea A Weiss
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ethan C Strayer
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Carter M Takacs
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; University of New Haven, West Haven, CT 06516, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
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2
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Pownall ME, Miao L, Vejnar CE, M’Saad O, Sherrard A, Frederick MA, Benitez MD, Boswell CW, Zaret KS, Bewersdorf J, Giraldez AJ. Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin. Science 2023; 381:92-100. [PMID: 37410825 PMCID: PMC10372697 DOI: 10.1126/science.ade5308] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/17/2023] [Indexed: 07/08/2023]
Abstract
Nanoscale chromatin organization regulates gene expression. Although chromatin is notably reprogrammed during zygotic genome activation (ZGA), the organization of chromatin regulatory factors during this universal process remains unclear. In this work, we developed chromatin expansion microscopy (ChromExM) to visualize chromatin, transcription, and transcription factors in vivo. ChromExM of embryos during ZGA revealed how the pioneer factor Nanog interacts with nucleosomes and RNA polymerase II (Pol II), providing direct visualization of transcriptional elongation as string-like nanostructures. Blocking elongation led to more Pol II particles clustered around Nanog, with Pol II stalled at promoters and Nanog-bound enhancers. This led to a new model termed "kiss and kick", in which enhancer-promoter contacts are transient and released by transcriptional elongation. Our results demonstrate that ChromExM is broadly applicable to study nanoscale nuclear organization.
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Affiliation(s)
- Mark E. Pownall
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Liyun Miao
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Charles E. Vejnar
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Ons M’Saad
- Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University; New Haven, CT 06510, USA
| | - Alice Sherrard
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Megan A. Frederick
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria D.J. Benitez
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Curtis W. Boswell
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Kenneth S. Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale University School of Medicine; New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University; New Haven, CT 06510, USA
- Department of Physics, Yale University; New Haven, CT 06510, USA
- Nanobiology Institute, Yale University; West Haven, CT 06477, USA
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Cancer Center, Yale University School of Medicine; New Haven, CT 06510, USA
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3
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Hendry C, Giraldez AJ. The scientific director: A complimentary model for academic leadership. Cell 2023; 186:2951-2955. [PMID: 37419083 DOI: 10.1016/j.cell.2023.05.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/16/2023] [Accepted: 05/24/2023] [Indexed: 07/09/2023]
Abstract
The current model for academic leadership places unique demands on scientists with highly active research programs. A complimentary model with a dedicated scientific director could remove this strain and allow a greater institutional investment in the community via a partnership. This article explores the rationale and framework of this model.
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Affiliation(s)
- Caroline Hendry
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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4
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Tornini VA, Miao L, Lee HJ, Gerson T, Dube SE, Schmidt V, Kroll F, Tang Y, Du K, Kuchroo M, Vejnar CE, Bazzini AA, Krishnaswamy S, Rihel J, Giraldez AJ. linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells. eLife 2023; 12:e82249. [PMID: 37191016 PMCID: PMC10188112 DOI: 10.7554/elife.82249] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Thousands of long intergenic non-coding RNAs (lincRNAs) are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open-reading frames and are speculated to encode micropeptides. However, systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here, we show that two putative lincRNAs (linc-mipep, also called lnc-rps25, and linc-wrb) encode micropeptides with homology to the vertebrate-specific chromatin architectural protein, Hmgn1, and demonstrate that they are required for development of vertebrate-specific brain cell types. Specifically, we show that NMDA receptor-mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes - evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions, with implications for neurodevelopmental disorders and disease.
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Affiliation(s)
| | - Liyun Miao
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Ho-Joon Lee
- Department of Genetics, Yale UniversityNew HavenUnited States
- Yale Center for Genome Analysis, Yale UniversityNew HavenUnited States
| | - Timothy Gerson
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Sarah E Dube
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Valeria Schmidt
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - François Kroll
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Yin Tang
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Katherine Du
- Department of Genetics, Yale UniversityNew HavenUnited States
- Department of Computer Science, Yale UniversityNew HavenUnited States
| | - Manik Kuchroo
- Department of Genetics, Yale UniversityNew HavenUnited States
- Department of Computer Science, Yale UniversityNew HavenUnited States
| | | | - Ariel Alejandro Bazzini
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Molecular & Integrative Physiology, University of Kansas School of MedicineKansas CityUnited States
| | - Smita Krishnaswamy
- Department of Genetics, Yale UniversityNew HavenUnited States
- Department of Computer Science, Yale UniversityNew HavenUnited States
| | - Jason Rihel
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Antonio J Giraldez
- Department of Genetics, Yale UniversityNew HavenUnited States
- Yale Stem Cell Center, Yale University School of MedicineNew HavenUnited States
- Yale Cancer Center, Yale University School of MedicineNew HavenUnited States
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5
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Begik O, Diensthuber G, Liu H, Delgado-Tejedor A, Kontur C, Niazi AM, Valen E, Giraldez AJ, Beaudoin JD, Mattick JS, Novoa EM. Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing. Nat Methods 2023; 20:75-85. [PMID: 36536091 PMCID: PMC9834059 DOI: 10.1038/s41592-022-01714-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/03/2022] [Indexed: 12/24/2022]
Abstract
RNA polyadenylation plays a central role in RNA maturation, fate, and stability. In response to developmental cues, polyA tail lengths can vary, affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore 3' end-capture sequencing (Nano3P-seq), a method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance, tail composition, and tail length dynamics at per-read resolution. By employing a template-switching-based sequencing protocol, Nano3P-seq can sequence RNA molecule from its 3' end, regardless of its polyadenylation status, without the need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P-seq provides quantitative estimates of RNA abundance and tail lengths, and captures a wide diversity of RNA biotypes. We find that, in addition to mRNA and long non-coding RNA, polyA tails can be identified in 16S mitochondrial ribosomal RNA in both mouse and zebrafish models. Moreover, we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform-specific level, correlating with mRNA decay. Finally, we demonstrate the ability of Nano3P-seq in capturing non-A bases within polyA tails of various lengths, and reveal their distribution during vertebrate embryogenesis. Overall, Nano3P-seq is a simple and robust method for accurately estimating transcript levels, tail lengths, and tail composition heterogeneity in individual reads, with minimal library preparation biases, both in the coding and non-coding transcriptome.
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Affiliation(s)
- Oguzhan Begik
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Gregor Diensthuber
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Huanle Liu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Delgado-Tejedor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Adnan Muhammad Niazi
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | | | - Jean-Denis Beaudoin
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA
| | - John S Mattick
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
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6
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Greco V, Politi K, Eisenbarth S, Colón-Ramos D, Giraldez AJ, Bewersdorf J, Berg DN. A group approach to growing as a principal investigator. Curr Biol 2022; 32:R498-R504. [PMID: 35671717 DOI: 10.1016/j.cub.2022.04.082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Greco et al. describe their experience learning to be more effective and humane PIs. The key to their growth was regular and consistent work with a diverse group of their peers aided by the guidance of an organizational psychologist.
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Affiliation(s)
- Valentina Greco
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Cell Biology, Yale School of Medicine, New Haven, CT 06510, USA; Department of Dermatology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, New Haven, CT 06510, USA; Yale Cancer Center, New Haven, CT 06510, USA.
| | - Katerina Politi
- Yale Cancer Center, New Haven, CT 06510, USA; Departments of Pathology and Internal Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, CT 06510, USA.
| | - Stephanie Eisenbarth
- Department of Immunology and Lab Medicine, Yale School of Medicine, New Haven, CT 06510, USA; The Department of Medicine, Division of Allergy and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
| | - Daniel Colón-Ramos
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Wu Tsai Institute, Yale University, New Haven, CT, USA.
| | - Antonio J Giraldez
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA; Nanobiology Institute, Yale University, West Haven, CT, USA; Department of Physics, Yale University, New Haven, CT, USA.
| | - David N Berg
- Department of Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA.
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7
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Bogoch Y, Jamieson-Lucy A, Vejnar CE, Levy K, Giraldez AJ, Mullins MC, Elkouby YM. Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis. Front Cell Dev Biol 2022; 10:826892. [PMID: 35733854 PMCID: PMC9207522 DOI: 10.3389/fcell.2022.826892] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/11/2022] [Indexed: 01/21/2023] Open
Abstract
Oogenesis produces functional eggs and is essential for fertility, embryonic development, and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates, and recent studies have identified multiple regulators in oocyte development through forward genetic screens, as well as reverse genetics by CRISPR mutagenesis. However, many developmental steps in oogenesis, in zebrafish and other species, remain poorly understood, and their underlying mechanisms are unknown. Here, we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis, from the onset of oocyte differentiation through Stage III, which precedes oocyte maturation. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis, as well as their expression in pair-wise comparisons between stages. We determined their functionally enriched terms, identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish, which we deposit online as a resource for the community. Further, the presence of multiple gene paralogs in zebrafish, and the exclusive curation by many bioinformatic tools of the single paralogs present in humans, challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether, our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.
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Affiliation(s)
- Yoel Bogoch
- Department of Developmental Biology and Cancer Research, Hebrew University of Jerusalem Faculty of Medicine, Jerusalem, Israel
- Institute for Biomedical Research, Israel-Canada, Jerusalem, Israel
| | - Allison Jamieson-Lucy
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | | | - Karine Levy
- Department of Developmental Biology and Cancer Research, Hebrew University of Jerusalem Faculty of Medicine, Jerusalem, Israel
- Institute for Biomedical Research, Israel-Canada, Jerusalem, Israel
| | | | - Mary C. Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Yaniv M. Elkouby
- Department of Developmental Biology and Cancer Research, Hebrew University of Jerusalem Faculty of Medicine, Jerusalem, Israel
- Institute for Biomedical Research, Israel-Canada, Jerusalem, Israel
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8
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Miao L, Tang Y, Bonneau AR, Chan SH, Kojima ML, Pownall ME, Vejnar CE, Gao F, Krishnaswamy S, Hendry CE, Giraldez AJ. The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation. Mol Cell 2022; 82:986-1002.e9. [PMID: 35182480 PMCID: PMC9327391 DOI: 10.1016/j.molcel.2022.01.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 10/19/2022]
Abstract
Upon fertilization, embryos undergo chromatin reprogramming and genome activation; however, the mechanisms that regulate these processes are poorly understood. Here, we generated a triple mutant for Nanog, Pou5f3, and Sox19b (NPS) in zebrafish and found that NPS pioneer chromatin opening at >50% of active enhancers. NPS regulate acetylation across core histones at enhancers and promoters, and their function in gene activation can be bypassed by recruiting histone acetyltransferase to individual genes. NPS pioneer chromatin opening individually, redundantly, or additively depending on sequence context, and we show that high nucleosome occupancy facilitates NPS pioneering activity. Nucleosome position varies based on the input of different transcription factors (TFs), providing a flexible platform to modulate pioneering activity. Altogether, our results illuminate the sequence of events during genome activation and offer a conceptual framework to understand how pioneer factors interpret the genome and integrate different TF inputs across cell types and developmental transitions.
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Affiliation(s)
- Liyun Miao
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
| | - Yin Tang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510.,These authors contributed equally
| | - Ashley R. Bonneau
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510
| | - Shun Hang Chan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510
| | - Mina L. Kojima
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510
| | - Mark E. Pownall
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510
| | - Charles E. Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510
| | - Feng Gao
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510
| | - Smita Krishnaswamy
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510.,Department of Computer Science, Yale University School of Medicine, New Haven, CT 06510
| | - Caroline E. Hendry
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510.,Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510.,Lead Contact
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9
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Jamieson-Lucy AH, Kobayashi M, James Aykit Y, Elkouby YM, Escobar-Aguirre M, Vejnar CE, Giraldez AJ, Mullins MC. A proteomics approach identifies novel resident zebrafish Balbiani body proteins Cirbpa and Cirbpb. Dev Biol 2022; 484:1-11. [PMID: 35065906 PMCID: PMC8967276 DOI: 10.1016/j.ydbio.2022.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 01/17/2023]
Abstract
The Balbiani body (Bb) is the first marker of polarity in vertebrate oocytes. The Bb is a conserved structure found in diverse animals including insects, fish, amphibians, and mammals. During early zebrafish oogenesis, the Bb assembles as a transient aggregate of mRNA, proteins, and membrane-bound organelles at the presumptive vegetal side of the oocyte. As the early oocyte develops, the Bb appears to grow slowly, until at the end of stage I of oogenesis it disassembles and deposits its cargo of localized mRNAs and proteins. In fish and frogs, this cargo includes the germ plasm as well as gene products required to specify dorsal tissues of the future embryo. We demonstrate that the Bb is a stable, solid structure that forms a size exclusion barrier similar to other biological hydrogels. Despite its central role in oocyte polarity, little is known about the mechanism behind the Bb's action. Analysis of the few known protein components of the Bb is insufficient to explain how the Bb assembles, translocates, and disassembles. We isolated Bbs from zebrafish oocytes and performed mass spectrometry to define the Bb proteome. We successfully identified 77 proteins associated with the Bb sample, including known Bb proteins and novel RNA-binding proteins. In particular, we identified Cirbpa and Cirbpb, which have both an RNA-binding domain and a predicted self-aggregation domain. In stage I oocytes, Cirbpa and Cirbpb localize to the Bb rather than the nucleus (as in somatic cells), indicating that they may have a specialized function in the germ line. Both the RNA-binding domain and the self-aggregation domain are sufficient to localize to the Bb, suggesting that Cirbpa and Cirbpb interact with more than just their mRNA targets within the Bb. We propose that Cirbp proteins crosslink mRNA cargo and proteinaceous components of the Bb as it grows. Beyond Cirbpa and Cirbpb, our proteomics dataset presents many candidates for further study, making it a valuable resource for building a comprehensive mechanism for Bb function at a protein level.
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Affiliation(s)
- Allison H Jamieson-Lucy
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Manami Kobayashi
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Y James Aykit
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yaniv M Elkouby
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Matias Escobar-Aguirre
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Mary C Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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10
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Strayer EC, Tornini VA, Giraldez AJ. Giving translation a hand. Dev Cell 2021; 56:2921-2923. [PMID: 34752744 PMCID: PMC10519192 DOI: 10.1016/j.devcel.2021.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
A cell's identity is commonly regarded as its transcriptomic profile. In this issue of Developmental Cell, Fujii et al. (2021) show that a global translation factor subunit acts differentially on transcripts to modulate morphogen signaling levels, revealing a global mechanism of transcript-specific translational control in development.
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Affiliation(s)
- Ethan C Strayer
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Valerie A Tornini
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
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11
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Maerker M, Getwan M, Dowdle ME, McSheene JC, Gonzalez V, Pelliccia JL, Hamilton DS, Yartseva V, Vejnar C, Tingler M, Minegishi K, Vick P, Giraldez AJ, Hamada H, Burdine RD, Sheets MD, Blum M, Schweickert A. Bicc1 and Dicer regulate left-right patterning through post-transcriptional control of the Nodal inhibitor Dand5. Nat Commun 2021; 12:5482. [PMID: 34531379 PMCID: PMC8446035 DOI: 10.1038/s41467-021-25464-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 08/11/2021] [Indexed: 12/12/2022] Open
Abstract
Rotating cilia at the vertebrate left-right organizer (LRO) generate an asymmetric leftward flow, which is sensed by cells at the left LRO margin. Ciliary activity of the calcium channel Pkd2 is crucial for flow sensing. How this flow signal is further processed and relayed to the laterality-determining Nodal cascade in the left lateral plate mesoderm (LPM) is largely unknown. We previously showed that flow down-regulates mRNA expression of the Nodal inhibitor Dand5 in left sensory cells. De-repression of the co-expressed Nodal, complexed with the TGFß growth factor Gdf3, drives LPM Nodal cascade induction. Here, we show that post-transcriptional repression of dand5 is a central process in symmetry breaking of Xenopus, zebrafish and mouse. The RNA binding protein Bicc1 was identified as a post-transcriptional regulator of dand5 and gdf3 via their 3'-UTRs. Two distinct Bicc1 functions on dand5 mRNA were observed at pre- and post-flow stages, affecting mRNA stability or flow induced translational inhibition, respectively. To repress dand5, Bicc1 co-operates with Dicer1, placing both proteins in the process of flow sensing. Intriguingly, Bicc1 mediated translational repression of a dand5 3'-UTR mRNA reporter was responsive to pkd2, suggesting that a flow induced Pkd2 signal triggers Bicc1 mediated dand5 inhibition during symmetry breakage.
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Affiliation(s)
- Markus Maerker
- University of Hohenheim, Institute of Biology, Department of Zoology, Stuttgart, Germany
| | - Maike Getwan
- University of Zurich, Institute of Anatomy, Zurich, Switzerland
| | - Megan E Dowdle
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI, USA
| | - Jason C McSheene
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Vanessa Gonzalez
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - José L Pelliccia
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Charles Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Melanie Tingler
- University of Hohenheim, Institute of Biology, Department of Zoology, Stuttgart, Germany
| | - Katsura Minegishi
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
| | - Philipp Vick
- University of Hohenheim, Institute of Biology, Department of Zoology, Stuttgart, Germany
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Hiroshi Hamada
- Laboratory for Organismal Patterning, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
| | - Rebecca D Burdine
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael D Sheets
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI, USA
| | - Martin Blum
- University of Hohenheim, Institute of Biology, Department of Zoology, Stuttgart, Germany
| | - Axel Schweickert
- University of Hohenheim, Institute of Biology, Department of Zoology, Stuttgart, Germany.
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12
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Burkhardt DB, Stanley JS, Tong A, Perdigoto AL, Gigante SA, Herold KC, Wolf G, Giraldez AJ, van Dijk D, Krishnaswamy S. Quantifying the effect of experimental perturbations at single-cell resolution. Nat Biotechnol 2021; 39:619-629. [PMID: 33558698 PMCID: PMC8122059 DOI: 10.1038/s41587-020-00803-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/11/2020] [Indexed: 01/30/2023]
Abstract
Current methods for comparing single-cell RNA sequencing datasets collected in multiple conditions focus on discrete regions of the transcriptional state space, such as clusters of cells. Here we quantify the effects of perturbations at the single-cell level using a continuous measure of the effect of a perturbation across the transcriptomic space. We describe this space as a manifold and develop a relative likelihood estimate of observing each cell in each of the experimental conditions using graph signal processing. This likelihood estimate can be used to identify cell populations specifically affected by a perturbation. We also develop vertex frequency clustering to extract populations of affected cells at the level of granularity that matches the perturbation response. The accuracy of our algorithm at identifying clusters of cells that are enriched or depleted in each condition is, on average, 57% higher than the next-best-performing algorithm tested. Gene signatures derived from these clusters are more accurate than those of six alternative algorithms in ground truth comparisons.
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Affiliation(s)
| | - Jay S Stanley
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Alexander Tong
- Department of Computer Science, Yale University, New Haven, CT, USA
| | | | - Scott A Gigante
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Kevan C Herold
- Department of Immunobiology, Yale University, New Haven, CT, USA
| | - Guy Wolf
- Department of Mathematics and Statistics, Université de Montréal, Montreal, QC, Canada
- Mila - Quebec AI Institute, Montreal, QC, Canada
| | | | - David van Dijk
- Department of Internal Medicine (Cardiology), Yale University, New Haven, CT, USA.
| | - Smita Krishnaswamy
- Department of Genetics, Yale University, New Haven, CT, USA.
- Department of Computer Science, Yale University, New Haven, CT, USA.
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13
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Vejnar CE, Giraldez AJ. LabxDB: versatile databases for genomic sequencing and lab management. Bioinformatics 2021; 36:4530-4531. [PMID: 32502232 DOI: 10.1093/bioinformatics/btaa557] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 12/18/2022] Open
Abstract
SUMMARY Experimental laboratory management and data-driven science require centralized software for sharing information, such as lab collections or genomic sequencing datasets. Although database servers such as PostgreSQL can store such information with multiple-user access, they lack user-friendly graphical and programmatic interfaces for easy data access and inputting. We developed LabxDB, a versatile open-source solution for organizing and sharing structured data. We provide several out-of-the-box databases for deployment in the cloud including simple mutant or plasmid collections and purchase-tracking databases. We also developed a high-throughput sequencing (HTS) database, LabxDB seq, dedicated to storage of hierarchical sample annotations. Scientists can import their own or publicly available HTS data into LabxDB seq to manage them from production to publication. Using LabxDB's programmatic access (REST API), annotations can be easily integrated into bioinformatics pipelines. LabxDB is modular, offering a flexible framework that scientists can leverage to build new database interfaces adapted to their needs. AVAILABILITY AND IMPLEMENTATION LabxDB is available at https://gitlab.com/vejnar/labxdb and https://labxdb.vejnar.org for documentation. LabxDB is licensed under the terms of the Mozilla Public License 2.0. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Antonio J Giraldez
- Department of Genetics.,Yale Stem Cell Center.,Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA
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14
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Kontur C, Jeong M, Cifuentes D, Giraldez AJ. Ythdf m 6A Readers Function Redundantly during Zebrafish Development. Cell Rep 2020; 33:108598. [PMID: 33378672 DOI: 10.1016/j.celrep.2020.108598] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/09/2020] [Accepted: 12/14/2020] [Indexed: 12/19/2022] Open
Abstract
During the maternal-to-zygotic transition (MZT), multiple mechanisms precisely control massive decay of maternal mRNAs. N6-methyladenosine (m6A) is known to regulate mRNA decay, yet how this modification promotes maternal transcript degradation remains unclear. Here, we find that m6A promotes maternal mRNA deadenylation. Yet, genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance, zygotic genome activation, or the onset of gastrulation, challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development, as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally, we show that the microRNA miR-430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.
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Affiliation(s)
- Cassandra Kontur
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
| | - Minsun Jeong
- Chey Institute for Advanced Studies, Seoul 06141, Republic of Korea
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
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15
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Chan SH, Tang Y, Miao L, Darwich-Codore H, Vejnar CE, Beaudoin JD, Musaev D, Fernandez JP, Benitez MDJ, Bazzini AA, Moreno-Mateos MA, Giraldez AJ. Brd4 and P300 Confer Transcriptional Competency during Zygotic Genome Activation. Dev Cell 2020; 49:867-881.e8. [PMID: 31211993 DOI: 10.1016/j.devcel.2019.05.037] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/10/2019] [Accepted: 05/21/2019] [Indexed: 12/28/2022]
Abstract
The awakening of the genome after fertilization is a cornerstone of animal development. However, the mechanisms that activate the silent genome after fertilization are poorly understood. Here, we show that transcriptional competency is regulated by Brd4- and P300-dependent histone acetylation in zebrafish. Live imaging of transcription revealed that genome activation, beginning at the miR-430 locus, is gradual and stochastic. We show that genome activation does not require slowdown of the cell cycle and is regulated through the translation of maternally inherited mRNAs. Among these, the enhancer regulators P300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked, whereas inhibition of histone acetylation blocks genome activation. We conclude that P300 and Brd4 are sufficient to trigger genome-wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical for initiating zygotic development and developmental reprogramming.
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Affiliation(s)
- Shun Hang Chan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yin Tang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Liyun Miao
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Hiba Darwich-Codore
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Jean-Denis Beaudoin
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Damir Musaev
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Juan P Fernandez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Maria D J Benitez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ariel A Bazzini
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | | | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
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16
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Vejnar CE, Abdel Messih M, Takacs CM, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee MT, Beaudoin JD, Musaev D, Darwich-Codore H, Walther TC, Tavazoie S, Cifuentes D, Giraldez AJ. Genome wide analysis of 3' UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. Genome Res 2019; 29:1100-1114. [PMID: 31227602 PMCID: PMC6633259 DOI: 10.1101/gr.245159.118] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 06/07/2019] [Indexed: 12/16/2022]
Abstract
Posttranscriptional regulation plays a crucial role in shaping gene expression. During the maternal-to-zygotic transition (MZT), thousands of maternal transcripts are regulated. However, how different cis-elements and trans-factors are integrated to determine mRNA stability remains poorly understood. Here, we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. By using a massively parallel reporter assay, we identified cis-regulatory sequences in the 3′ UTR, including U-rich motifs that are associated with increased mRNA stability. In contrast, miR-430 target sequences, UAUUUAUU AU-rich elements (ARE), CCUC, and CUGC elements emerged as destabilizing motifs, with miR-430 and AREs causing mRNA deadenylation upon genome activation. We identified trans-factors by profiling RNA–protein interactions and found that poly(U)-binding proteins are preferentially associated with 3′ UTR sequences and stabilizing motifs. We show that this activity is antagonized by C-rich motifs and correlated with protein binding. Finally, we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.
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Affiliation(s)
- Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Mario Abdel Messih
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Carter M Takacs
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,University of New Haven, West Haven, Connecticut 06516, USA
| | - Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Department of Neuroscience, Genentech, Incorporated, South San Francisco, California 94080, USA
| | - Panos Oikonomou
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
| | - Romain Christiano
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Marlon Stoeckius
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,New York Genome Center, New York, New York 10013, USA
| | - Stephanie Lau
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Miler T Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Jean-Denis Beaudoin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Damir Musaev
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Hiba Darwich-Codore
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Tobias C Walther
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02124, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Saeed Tavazoie
- Department of Biochemistry and Molecular Biophysics, and Department of Systems Biology, Columbia University, New York, New York 10032, USA
| | - Daniel Cifuentes
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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17
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Fernandez JP, Vejnar CE, Giraldez AJ, Rouet R, Moreno-Mateos MA. Optimized CRISPR-Cpf1 system for genome editing in zebrafish. Methods 2018; 150:11-18. [PMID: 29964176 PMCID: PMC7098853 DOI: 10.1016/j.ymeth.2018.06.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 06/15/2018] [Accepted: 06/26/2018] [Indexed: 12/26/2022] Open
Abstract
The impact of the CRISPR-Cas biotechnological systems has recently broadened the genome editing toolbox available to different model organisms further with the addition of new efficient RNA-guided endonucleases. We have recently optimized CRISPR-Cpf1 (renamed Cas12a) system in zebrafish. We showed that (i) in the absence of Cpf1 protein, crRNAs are unstable and degraded in vivo, and CRISPR-Cpf1 RNP complexes efficiently mutagenize the zebrafish genome; and (ii) temperature modulates Cpf1 activity especially affecting AsCpf1, which experiences a reduced performance below 37 °C. Here, we describe a step-by-step protocol on how to easily design and generate crRNAs in vitro, purify recombinant Cpf1 proteins, and assemble ribonucleoprotein complexes to carry out efficient mutagenesis in zebrafish in a constitutive and temperature-controlled manner. Finally, we explain how to induce Cpf1-mediated homology-directed repair using single-stranded DNA oligonucleotides. In summary, this protocol includes the steps to efficiently modify the zebrafish genome and other ectothermic organisms using the CRISPR-Cpf1 system.
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Affiliation(s)
- Juan P Fernandez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
| | - Romain Rouet
- Garvan Institute of Medical Research, Sydney, NSW, Australia.
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18
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Fernandez JP, Moreno-Mateos MA, Gohr A, Miao L, Chan SH, Irimia M, Giraldez AJ. RES complex is associated with intron definition and required for zebrafish early embryogenesis. PLoS Genet 2018; 14:e1007473. [PMID: 29969449 PMCID: PMC6047831 DOI: 10.1371/journal.pgen.1007473] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 07/16/2018] [Accepted: 06/06/2018] [Indexed: 12/16/2022] Open
Abstract
Pre-mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome-wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA-binding proteins. The retention and splicing (RES) complex is formed by three different proteins (Bud13p, Pml1p and Snu17p) and is involved in splicing in yeast. However, the importance of the RES complex for vertebrate splicing, the intronic features associated with its activity, and its role in development are unknown. In this study, we have generated loss-of-function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13, snip1 (pml1) and rbmx2 (snu17) mutants revealed a global defect in intron splicing, with strong mis-splicing of a subset of introns. We found these RES-dependent introns were short, rich in GC and flanked by GC depleted exons, all of which are features associated with intron definition. Using these features, we developed and validated a predictive model that classifies RES dependent introns. Altogether, our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.
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Affiliation(s)
- Juan Pablo Fernandez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
| | | | - Andre Gohr
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Liyun Miao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
| | - Shun Hang Chan
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, United States of America
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, United States of America
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19
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Yartseva V, Takacs CM, Vejnar CE, Lee MT, Giraldez AJ. RESA identifies mRNA-regulatory sequences at high resolution. Nat Methods 2016; 14:201-207. [PMID: 28024160 PMCID: PMC5423094 DOI: 10.1038/nmeth.4121] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/02/2016] [Indexed: 11/22/2022]
Abstract
Gene expression is regulated extensively at the level of mRNA stability, localization, and translation. However, decoding functional RNA regulatory features remains a limitation to understanding post-transcriptional regulation in vivo. Here, we developed RNA Element Selection Assay (RESA), a method that selects RNA elements based on their activity in vivo and uses high-throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements, we developed a bisulfite-mediated nucleotide conversion strategy for large-scale mutational analysis (RESA-bisulfite). Finally, we used the versatile RESA platform to map candidate protein-RNA interactions in vivo (RESA-CLIP). The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.
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Affiliation(s)
- Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Carter M Takacs
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Miler T Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA.,Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
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20
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Vejnar CE, Moreno-Mateos MA, Cifuentes D, Bazzini AA, Giraldez AJ. Optimization Strategies for the CRISPR-Cas9 Genome-Editing System. Cold Spring Harb Protoc 2016; 2016:2016/10/pdb.top090894. [PMID: 27698246 DOI: 10.1101/pdb.top090894] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The CRISPR-Cas9 system uncovered in bacteria has emerged as a powerful genome-editing technology in eukaryotic cells. It consists of two components-a single guide RNA (sgRNA) that directs the Cas9 endonuclease to a complementary DNA target site. Efficient targeting of individual genes requires highly active sgRNAs. Recent efforts have made significant progress in understanding the sequence features that increase sgRNA activity. In this introduction, we highlight advancements in the field of CRISPR-Cas9 targeting and discuss our web tool CRISPRscan, which predicts the targeting activity of sgRNAs and improves the efficiency of the CRISPR-Cas9 system for in vivo genome engineering.
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Affiliation(s)
- Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Miguel A Moreno-Mateos
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Daniel Cifuentes
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Ariel A Bazzini
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510 Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut 06520
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21
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Vejnar CE, Moreno-Mateos MA, Cifuentes D, Bazzini AA, Giraldez AJ. Optimized CRISPR-Cas9 System for Genome Editing in Zebrafish. Cold Spring Harb Protoc 2016; 2016:2016/10/pdb.prot086850. [PMID: 27698232 DOI: 10.1101/pdb.prot086850] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This protocol describes how to generate and genotype mutants using an optimized CRISPR-Cas9 genome-editing system in zebrafish (CRISPRscan). Because single guide RNAs (sgRNAs) have variable efficiency when targeting specific loci, our protocol starts by explaining how to use the web tool CRISPRscan to design highly efficient sgRNAs. The CRISPRscan algorithm is based on the results of an integrated analysis of more than 1000 sgRNAs in zebrafish, which uncovered highly predictive factors that influence Cas9 activity. Next, we describe how to easily generate sgRNAs in vitro, which can then be injected in vivo to target specific loci. The use of highly efficient sgRNAs can lead to biallelic mutations in the injected embryos, causing lethality. We explain how targeting Cas9 to the germline increases viability by reducing somatic mutations. Finally, we combine two methods to identify F1 heterozygous fish carrying the desired mutations: (i) Mut-Seq, a method based on high-throughput sequencing to detect F0 founder fish; and (ii) a polymerase chain reaction-based fragment analysis method that identifies F1 heterozygous fish characterized by Mut-Seq. In summary, this protocol includes the steps to generate and characterize mutant zebrafish lines using the CRISPR-Cas9 genome engineering system.
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Affiliation(s)
- Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Miguel A Moreno-Mateos
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Daniel Cifuentes
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Ariel A Bazzini
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510; Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut 06520
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22
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Reischauer S, Stone OA, Villasenor A, Chi N, Jin SW, Martin M, Lee MT, Fukuda N, Marass M, Witty A, Fiddes I, Kuo T, Chung WS, Salek S, Lerrigo R, Alsiö J, Luo S, Tworus D, Augustine SM, Mucenieks S, Nystedt B, Giraldez AJ, Schroth GP, Andersson O, Stainier DYR. Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification. Nature 2016; 535:294-8. [PMID: 27411634 DOI: 10.1038/nature18614] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 05/25/2016] [Indexed: 12/15/2022]
Abstract
Vascular and haematopoietic cells organize into specialized tissues during early embryogenesis to supply essential nutrients to all organs and thus play critical roles in development and disease. At the top of the haemato-vascular specification cascade lies cloche, a gene that when mutated in zebrafish leads to the striking phenotype of loss of most endothelial and haematopoietic cells and a significant increase in cardiomyocyte numbers. Although this mutant has been analysed extensively to investigate mesoderm diversification and differentiation and continues to be broadly used as a unique avascular model, the isolation of the cloche gene has been challenging due to its telomeric location. Here we used a deletion allele of cloche to identify several new cloche candidate genes within this genomic region, and systematically genome-edited each candidate. Through this comprehensive interrogation, we succeeded in isolating the cloche gene and discovered that it encodes a PAS-domain-containing bHLH transcription factor, and that it is expressed in a highly specific spatiotemporal pattern starting during late gastrulation. Gain-of-function experiments show that it can potently induce endothelial gene expression. Epistasis experiments reveal that it functions upstream of etv2 and tal1, the earliest expressed endothelial and haematopoietic transcription factor genes identified to date. A mammalian cloche orthologue can also rescue blood vessel formation in zebrafish cloche mutants, indicating a highly conserved role in vertebrate vasculogenesis and haematopoiesis. The identification of this master regulator of endothelial and haematopoietic fate enhances our understanding of early mesoderm diversification and may lead to improved protocols for the generation of endothelial and haematopoietic cells in vivo and in vitro.
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Affiliation(s)
- Sven Reischauer
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.,Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
| | - Oliver A Stone
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.,Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
| | - Alethia Villasenor
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.,Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
| | - Neil Chi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.,Department of Medicine, Division of Cardiology, Institute of Genomic Medicine, University of California San Diego, La Jolla, California 92037, USA
| | - Suk-Won Jin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Marcel Martin
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna 17121, Sweden
| | - Miler T Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Nana Fukuda
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
| | - Michele Marass
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
| | - Alec Witty
- Department of Medicine, Division of Cardiology, Institute of Genomic Medicine, University of California San Diego, La Jolla, California 92037, USA
| | - Ian Fiddes
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Taiyi Kuo
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Won-Suk Chung
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Sherveen Salek
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Robert Lerrigo
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Jessica Alsiö
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Shujun Luo
- Illumina, San Diego, California 92122, USA
| | - Dominika Tworus
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Sruthy M Augustine
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
| | - Sophie Mucenieks
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
| | - Björn Nystedt
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | | | - Olov Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Didier Y R Stainier
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.,Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
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23
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Bazzini AA, Del Viso F, Moreno-Mateos MA, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ. Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition. EMBO J 2016; 35:2087-2103. [PMID: 27436874 DOI: 10.15252/embj.201694699] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/16/2016] [Indexed: 12/26/2022] Open
Abstract
Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal-to-zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by post-transcriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs, this pathway does not fully explain mRNA clearance. We investigated how codon identity and translation affect mRNA stability during development and homeostasis. We show that the codon triplet contains translation-dependent regulatory information that influences transcript decay. Codon composition shapes maternal mRNA clearance during the maternal-to-zygotic transition in zebrafish, Xenopus, mouse, and Drosophila, and gene expression during homeostasis across human tissues. Some synonymous codons show consistent stabilizing or destabilizing effects, suggesting that amino acid composition influences mRNA stability. Codon composition affects both polyadenylation status and translation efficiency. Thus, the ribosome interprets two codes within the mRNA: the genetic code which specifies the amino acid sequence and a conserved "codon optimality code" that shapes mRNA stability and translation efficiency across vertebrates.
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Affiliation(s)
- Ariel A Bazzini
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Florencia Del Viso
- Departments of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | | | - Timothy G Johnstone
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Yidan Qin
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Jun Yao
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Mustafa K Khokha
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA Departments of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
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Johnstone TG, Bazzini AA, Giraldez AJ. Upstream ORFs are prevalent translational repressors in vertebrates. EMBO J 2016; 35:706-23. [PMID: 26896445 DOI: 10.15252/embj.201592759] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 01/08/2016] [Indexed: 12/20/2022] Open
Abstract
Regulation of gene expression is fundamental in establishing cellular diversity and a target of natural selection. Untranslated mRNA regions (UTRs) are key mediators of post-transcriptional regulation. Previous studies have predicted thousands of ORFs in 5'UTRs, the vast majority of which have unknown function. Here, we present a systematic analysis of the translation and function of upstream open reading frames (uORFs) across vertebrates. Using high-resolution ribosome footprinting, we find that (i)uORFs are prevalent within vertebrate transcriptomes, (ii) the majority show signatures of active translation, and (iii)uORFs act as potent regulators of translation and RNA levels, with a similar magnitude to miRNAs. Reporter experiments reveal clear repression of downstream translation by uORFs/oORFs. uORF number, intercistronic distance, overlap with the CDS, and initiation context most strongly influence translation. Evolution has targeted these features to favor uORFs amenable to regulation over constitutively repressive uORFs/oORFs. Finally, we observe that the regulatory potential of uORFs on individual genes is conserved across species. These results provide insight into the regulatory code within mRNA leader sequences and their capacity to modulate translation across vertebrates.
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Affiliation(s)
- Timothy G Johnstone
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Ariel A Bazzini
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
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25
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Hoffman EJ, Turner KJ, Fernandez JM, Cifuentes D, Ghosh M, Ijaz S, Jain RA, Kubo F, Bill BR, Baier H, Granato M, Barresi MJF, Wilson SW, Rihel J, State MW, Giraldez AJ. Estrogens Suppress a Behavioral Phenotype in Zebrafish Mutants of the Autism Risk Gene, CNTNAP2. Neuron 2016; 89:725-33. [PMID: 26833134 DOI: 10.1016/j.neuron.2015.12.039] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/16/2015] [Accepted: 12/21/2015] [Indexed: 12/20/2022]
Abstract
Autism spectrum disorders (ASDs) are a group of devastating neurodevelopmental syndromes that affect up to 1 in 68 children. Despite advances in the identification of ASD risk genes, the mechanisms underlying ASDs remain unknown. Homozygous loss-of-function mutations in Contactin Associated Protein-like 2 (CNTNAP2) are strongly linked to ASDs. Here we investigate the function of Cntnap2 and undertake pharmacological screens to identify phenotypic suppressors. We find that zebrafish cntnap2 mutants display GABAergic deficits, particularly in the forebrain, and sensitivity to drug-induced seizures. High-throughput behavioral profiling identifies nighttime hyperactivity in cntnap2 mutants, while pharmacological testing reveals dysregulation of GABAergic and glutamatergic systems. Finally, we find that estrogen receptor agonists elicit a behavioral fingerprint anti-correlative to that of cntnap2 mutants and show that the phytoestrogen biochanin A specifically reverses the mutant behavioral phenotype. These results identify estrogenic compounds as phenotypic suppressors and illuminate novel pharmacological pathways with relevance to autism.
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Affiliation(s)
- Ellen J Hoffman
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Katherine J Turner
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Joseph M Fernandez
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Daniel Cifuentes
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Marcus Ghosh
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Sundas Ijaz
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Roshan A Jain
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Biology, Haverford College, Haverford, PA 19041, USA
| | - Fumi Kubo
- Department Genes - Circuits - Behavior, Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Brent R Bill
- Center for Autism Research and Treatment, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biology, The University of Texas at Tyler, Tyler, TX 75799, USA
| | - Herwig Baier
- Department Genes - Circuits - Behavior, Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Michael Granato
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michael J F Barresi
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Jason Rihel
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
| | - Matthew W State
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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26
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Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods 2015; 12:982-8. [PMID: 26322839 PMCID: PMC4589495 DOI: 10.1038/nmeth.3543] [Citation(s) in RCA: 774] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/12/2015] [Indexed: 12/24/2022]
Abstract
CRISPR-Cas9 technology provides a powerful system for genome engineering. However, variable activity across different single guide RNAs (sgRNAs) remains a significant limitation. We analyzed the molecular features that influence sgRNA stability, activity and loading into Cas9 in vivo. We observed that guanine enrichment and adenine depletion increased sgRNA stability and activity, whereas differential sgRNA loading, nucleosome positioning and Cas9 off-target binding were not major determinants. We also identified sgRNAs truncated by one or two nucleotides and containing 5' mismatches as efficient alternatives to canonical sgRNAs. On the basis of these results, we created a predictive sgRNA-scoring algorithm, CRISPRscan, that effectively captures the sequence features affecting the activity of CRISPR-Cas9 in vivo. Finally, we show that targeting Cas9 to the germ line using a Cas9-nanos 3' UTR led to the generation of maternal-zygotic mutants, as well as increased viability and decreased somatic mutations. These results identify determinants that influence Cas9 activity and provide a framework for the design of highly efficient sgRNAs for genome targeting in vivo.
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Affiliation(s)
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jean-Denis Beaudoin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Juan P Fernandez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Emily K Mis
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mustafa K Khokha
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
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27
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Abstract
Cellular transitions occur at all stages of organismal life from conception to adult regeneration. Changing cellular state involves three main features: activating gene expression necessary to install the new cellular state, modifying the chromatin status to stabilize the new gene expression program, and removing existing gene products to clear out the previous cellular program. The maternal-to-zygotic transition (MZT) is one of the most profound changes in the life of an organism. It involves gene expression remodeling at all levels, including the active clearance of the maternal oocyte program to adopt the embryonic totipotency. In this chapter, we provide an overview of molecular mechanisms driving maternal mRNA clearance during the MZT, describe the developmental consequences of losing components of this gene regulation, and illustrate how remodeling of gene expression during the MZT is common to other cellular transitions with parallels to cellular reprogramming.
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Affiliation(s)
- Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA.
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28
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Lee M, Choi Y, Kim K, Jin H, Lim J, Nguyen TA, Yang J, Jeong M, Giraldez AJ, Yang H, Patel DJ, Kim VN. Adenylation of maternally inherited microRNAs by Wispy. Mol Cell 2014; 56:696-707. [PMID: 25454948 DOI: 10.1016/j.molcel.2014.10.011] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/03/2014] [Accepted: 10/10/2014] [Indexed: 12/31/2022]
Abstract
Early development depends heavily on accurate control of maternally inherited mRNAs, and yet it remains unknown how maternal microRNAs are regulated during maternal-to-zygotic transition (MZT). We here find that maternal microRNAs are highly adenylated at their 3' ends in mature oocytes and early embryos. Maternal microRNA adenylation is widely conserved in fly, sea urchin, and mouse. We identify Wispy, a noncanonical poly(A) polymerase, as the enzyme responsible for microRNA adenylation in flies. Knockout of wispy abrogates adenylation and results in microRNA accumulation in eggs, whereas overexpression of Wispy increases adenylation and reduces microRNA levels in S2 cells. Wispy interacts with Ago1 through protein-protein interaction, which may allow the effective and selective adenylation of microRNAs. Thus, adenylation may contribute to the clearance of maternally deposited microRNAs during MZT. Our work provides mechanistic insights into the regulation of maternal microRNAs and illustrates the importance of RNA tailing in development.
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Affiliation(s)
- Mihye Lee
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Yeon Choi
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Kijun Kim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Hua Jin
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Jaechul Lim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Tuan Anh Nguyen
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Jihye Yang
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Minsun Jeong
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hui Yang
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea.
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29
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Abstract
Embryogenesis depends on a highly coordinated cascade of genetically encoded events. In animals, maternal factors contributed by the egg cytoplasm initially control development, whereas the zygotic nuclear genome is quiescent. Subsequently, the genome is activated, embryonic gene products are mobilized, and maternal factors are cleared. This transfer of developmental control is called the maternal-to-zygotic transition (MZT). In this review, we discuss recent advances toward understanding the scope, timing, and mechanisms that underlie zygotic genome activation at the MZT in animals. We describe high-throughput techniques to measure the embryonic transcriptome and explore how regulation of the cell cycle, chromatin, and transcription factors together elicits specific patterns of embryonic gene expression. Finally, we illustrate the interplay between zygotic transcription and maternal clearance and show how these two activities combine to reprogram two terminally differentiated gametes into a totipotent embryo.
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Affiliation(s)
- Miler T Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520; ,
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30
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Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J 2014; 33:981-93. [PMID: 24705786 DOI: 10.1002/embj.201488411] [Citation(s) in RCA: 459] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptide-encoding genes in vertebrates, providing an entry point to define their function in vivo.
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Affiliation(s)
- Ariel A Bazzini
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
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31
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Staton AA, Knaut H, Giraldez AJ. Reply to: "On the robustness of germ cell migration and microRNA-mediated regulation of chemokine signaling". Nat Genet 2014; 45:1266-7. [PMID: 24165725 DOI: 10.1038/ng.2812] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alison A Staton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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32
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Yoda M, Cifuentes D, Izumi N, Sakaguchi Y, Suzuki T, Giraldez AJ, Tomari Y. Poly(A)-specific ribonuclease mediates 3'-end trimming of Argonaute2-cleaved precursor microRNAs. Cell Rep 2013; 5:715-26. [PMID: 24209750 DOI: 10.1016/j.celrep.2013.09.029] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/14/2013] [Accepted: 09/23/2013] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are typically generated as ~22-nucleotide double-stranded RNAs via the processing of precursor hairpins by the ribonuclease III enzyme Dicer, after which they are loaded into Argonaute (Ago) proteins to form an RNA-induced silencing complex (RISC). However, the biogenesis of miR-451, an erythropoietic miRNA conserved in vertebrates, occurs independently of Dicer and instead requires cleavage of the 3' arm of the pre-miR-451 precursor hairpin by Ago2. The 3' end of the Ago2-cleaved pre-miR-451 intermediate is then trimmed to the mature length by an unknown nuclease. Here, using a classical chromatographic approach, we identified poly(A)-specific ribonuclease (PARN) as the enzyme responsible for the 3'-5' exonucleolytic trimming of Ago2-cleaved pre-miR-451. Surprisingly, our data show that trimming of Ago2-cleaved precursor miRNAs is not essential for target silencing, indicating that RISC is functional with miRNAs longer than the mature length. Our findings define the maturation step in the miRNA biogenesis pathway that depends on Ago2-mediated cleavage.
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Affiliation(s)
- Mayuko Yoda
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Medical Genome Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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33
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Lee MT, Bonneau AR, Takacs CM, Bazzini AA, DiVito KR, Fleming ES, Giraldez AJ. Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. Nature 2013; 503:360-4. [PMID: 24056933 PMCID: PMC3925760 DOI: 10.1038/nature12632] [Citation(s) in RCA: 313] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 09/04/2013] [Indexed: 12/21/2022]
Abstract
Upon fertilization, maternal factors direct development and trigger zygotic genome activation (ZGA) at the maternal-to-zygotic transition (MZT). In zebrafish, ZGA is required for gastrulation and clearance of maternal mRNAs, which is in part regulated by the conserved microRNA miR-430. However, the factors that activate the zygotic program in vertebrates are unknown. Here, we show that Nanog, Pou5f1 and SoxB1 regulate zygotic gene activation in zebrafish. We identified several hundred genes directly activated by maternal factors, constituting the first wave of zygotic transcription. Ribosome profiling revealed that nanog, sox19b and pou5f1 are the most highly translated transcription factors pre-MZT. Combined loss of these factors resulted in developmental arrest prior to gastrulation and a failure to activate >75% of zygotic genes, including miR-430. Our results demonstrate that maternal Nanog, Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and induce clearance of the maternal program by activating miR-430 expression.
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Affiliation(s)
- Miler T Lee
- 1] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA [2]
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Stahlhut C, Suárez Y, Lu J, Mishima Y, Giraldez AJ. miR-1 and miR-206 regulate angiogenesis by modulating VegfA expression in zebrafish. Development 2013; 139:4356-64. [PMID: 23132244 DOI: 10.1242/dev.083774] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cellular communication across tissues is an essential process during embryonic development. Secreted factors with potent morphogenetic activity are key elements of this cross-talk, and precise regulation of their expression is required to elicit appropriate physiological responses. MicroRNAs (miRNAs) are versatile post-transcriptional modulators of gene expression. However, the large number of putative targets for each miRNA hinders the identification of physiologically relevant miRNA-target interactions. Here we show that miR-1 and miR-206 negatively regulate angiogenesis during zebrafish development. Using target protectors, our results indicate that miR-1/206 directly regulate the levels of Vascular endothelial growth factor A (VegfA) in muscle, controlling the strength of angiogenic signaling to the endothelium. Conversely, reducing the levels of VegfAa, but not VegfAb, rescued the increase in angiogenesis observed when miR-1/206 were knocked down. These findings uncover a novel function for miR-1/206 in the control of developmental angiogenesis through the regulation of VegfA, and identify a key role for miRNAs as regulators of cross-tissue signaling.
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Affiliation(s)
- Carlos Stahlhut
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
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Abstract
MicroRNAs regulate gene expression through deadenylation, repression, and messenger RNA (mRNA) decay. However, the contribution of each mechanism in non-steady-state situations remains unclear. We monitored the impact of miR-430 on ribosome occupancy of endogenous mRNAs in wild-type and dicer mutant zebrafish embryos and found that miR-430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. Translational repression occurs before complete deadenylation, and disrupting deadenylation with use of an internal polyadenylate tail did not block target repression. Lastly, we observed that ribosome density along the length of the message remains constant, suggesting that translational repression occurs by reducing the rate of initiation rather than affecting elongation or causing ribosomal drop-off. These results show that miR-430 regulates translation initiation before inducing mRNA decay during zebrafish development.
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Affiliation(s)
- Ariel A Bazzini
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
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36
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Abstract
MicroRNAs (miRNAs) regulate gene expression by pairing with complementary sequences in the 3' untranslated regions (UTRs) of transcripts. Although the molecular mechanism underlying miRNA biogenesis and activity is becoming better understood, determining the physiological role of the interaction of an miRNA with its target remains a challenge. A number of methods have been developed to inhibit individual miRNAs, but it can be difficult to determine which specific targets are responsible for any observed phenotypes. To address this problem, we use target protector (TP) morpholinos that interfere with a single miRNA-mRNA pair by binding specifically to the miRNA target sequence in the 3' UTR. In this protocol, we detail the steps for identifying miRNA targets, validating their regulation and using TPs to interrogate their function in zebrafish. Depending on the biological context, this set of experiments can be completed in 6-8 weeks.
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Affiliation(s)
- Alison A Staton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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37
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Zhu C, Smith T, McNulty J, Rayla AL, Lakshmanan A, Siekmann AF, Buffardi M, Meng X, Shin J, Padmanabhan A, Cifuentes D, Giraldez AJ, Look AT, Epstein JA, Lawson ND, Wolfe SA. Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish. Development 2011; 138:4555-64. [PMID: 21937602 PMCID: PMC3177320 DOI: 10.1242/dev.066779] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2011] [Indexed: 12/20/2022]
Abstract
Zinc-finger nucleases (ZFNs) allow targeted gene inactivation in a wide range of model organisms. However, construction of target-specific ZFNs is technically challenging. Here, we evaluate a straightforward modular assembly-based approach for ZFN construction and gene inactivation in zebrafish. From an archive of 27 different zinc-finger modules, we assembled more than 70 different zinc-finger cassettes and evaluated their specificity using a bacterial one-hybrid assay. In parallel, we constructed ZFNs from these cassettes and tested their ability to induce lesions in zebrafish embryos. We found that the majority of zinc-finger proteins assembled from these modules have favorable specificities and nearly one-third of modular ZFNs generated lesions at their targets in the zebrafish genome. To facilitate the application of ZFNs within the zebrafish community we constructed a public database of sites in the zebrafish genome that can be targeted using this archive. Importantly, we generated new germline mutations in eight different genes, confirming that this is a viable platform for heritable gene inactivation in vertebrates. Characterization of one of these mutants, gata2a, revealed an unexpected role for this transcription factor in vascular development. This work provides a resource to allow targeted germline gene inactivation in zebrafish and highlights the benefit of a definitive reverse genetic strategy to reveal gene function.
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Affiliation(s)
- Cong Zhu
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Tom Smith
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Joseph McNulty
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Amy L. Rayla
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Abirami Lakshmanan
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Arndt F. Siekmann
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Matthew Buffardi
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Xiangdong Meng
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jimann Shin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Arun Padmanabhan
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Daniel Cifuentes
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan A. Epstein
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Nathan D. Lawson
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Scot A. Wolfe
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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38
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Staton AA, Knaut H, Giraldez AJ. miRNA regulation of Sdf1 chemokine signaling provides genetic robustness to germ cell migration. Nat Genet 2011; 43:204-11. [PMID: 21258340 PMCID: PMC3071589 DOI: 10.1038/ng.758] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 12/14/2010] [Indexed: 02/03/2023]
Abstract
microRNAs function as genetic rheostats to control gene output. Based on their role as modulators, it has been postulated that microRNAs canalize development and provide genetic robustness. Here, we uncover a novel regulatory layer of chemokine signaling by microRNAs that confers genetic robustness on primordial-germ-cell (PGC) migration. In zebrafish, PGCs are guided to the gonad by the ligand Sdf1a, which is regulated by sequestration receptor Cxcr7b. We find that miR-430 regulates sdf1a- and cxcr7-mRNAs. Using Target Protectors, we demonstrate that miR-430-mediated regulation of endogenous sdf1a and cxcr7b (i) facilitates dynamic expression of sdf1a by clearing its mRNA from previous expression domains, (ii) modulates the levels of the decoy receptor Cxcr7b to avoid excessive depletion of Sdf1a and (iii) buffers against variation in gene dosage of chemokine signaling components to ensure accurate PGC migration. Our results indicate that losing microRNA-mediated regulation can expose otherwise buffered genetic lesions leading to developmental defects.
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Affiliation(s)
- Alison A Staton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y, Pierick CJ, Hoffman E, Maeder ML, Khayter C, Reyon D, Dobbs D, Langenau DM, Stupar RM, Giraldez AJ, Voytas DF, Peterson RT, Yeh JRJ, Joung JK. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods 2011; 8:67-9. [PMID: 21151135 PMCID: PMC3018472 DOI: 10.1038/nmeth.1542] [Citation(s) in RCA: 359] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 11/16/2010] [Indexed: 11/30/2022]
Abstract
Engineered zinc-finger nucleases (ZFNs) enable targeted genome modification. Here we describe context-dependent assembly (CoDA), a platform for engineering ZFNs using only standard cloning techniques or custom DNA synthesis. Using CoDA-generated ZFNs, we rapidly altered 20 genes in Danio rerio, Arabidopsis thaliana and Glycine max. The simplicity and efficacy of CoDA will enable broad adoption of ZFN technology and make possible large-scale projects focused on multigene pathways or genome-wide alterations.
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Affiliation(s)
- Jeffry D. Sander
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115 USA
| | - Elizabeth J. Dahlborg
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129 USA
| | - Mathew J. Goodwin
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129 USA
| | - Lindsay Cade
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129 USA
| | - Feng Zhang
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Daniel Cifuentes
- Genetics Department, Yale University School of Medicine, New Haven, CT 06517 USA
| | - Shaun J. Curtin
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 USA
| | - Jessica S. Blackburn
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115 USA
| | - Stacey Thibodeau-Beganny
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129 USA
| | - Yiping Qi
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Christopher J. Pierick
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Ellen Hoffman
- Genetics Department, Yale University School of Medicine, New Haven, CT 06517 USA
| | - Morgan L. Maeder
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115 USA
| | - Cyd Khayter
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129 USA
| | - Deepak Reyon
- Department of Genetics, Development and Cell Biology and Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011 USA
| | - Drena Dobbs
- Department of Genetics, Development and Cell Biology and Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011 USA
| | - David M. Langenau
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115 USA
| | - Robert M. Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 USA
| | - Antonio J. Giraldez
- Genetics Department, Yale University School of Medicine, New Haven, CT 06517 USA
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Randall T. Peterson
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute, Cambridge, MA 02142 USA
| | - Jing-Ruey J. Yeh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115 USA
| | - J. Keith Joung
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129 USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115 USA
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115 USA
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40
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Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, Wolfe SA, Giraldez AJ. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science 2010; 328:1694-8. [PMID: 20448148 PMCID: PMC3093307 DOI: 10.1126/science.1190809] [Citation(s) in RCA: 619] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Dicer is a central enzyme in microRNA (miRNA) processing. We identified a Dicer-independent miRNA biogenesis pathway that uses Argonaute2 (Ago2) slicer catalytic activity. In contrast to other miRNAs, miR-451 levels were refractory to dicer loss of function but were reduced in MZago2 (maternal-zygotic) mutants. We found that pre-miR-451 processing requires Ago2 catalytic activity in vivo. MZago2 mutants showed delayed erythropoiesis that could be rescued by wild-type Ago2 or miR-451-duplex but not by catalytically dead Ago2. Changing the secondary structure of Dicer-dependent miRNAs to mimic that of pre-miR-451 restored miRNA function and rescued developmental defects in MZdicer mutants, indicating that the pre-miRNA secondary structure determines the processing pathway in vivo. We propose that Ago2-mediated cleavage of pre-miRNAs, followed by uridylation and trimming, generates functional miRNAs independently of Dicer.
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Affiliation(s)
- Daniel Cifuentes
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Huiling Xue
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - David W. Taylor
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Heather Patnode
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yuichiro Mishima
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodaicho Nadaku, Kobe 657-8501, Japan
| | - Sihem Cheloufi
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Enbo Ma
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Shrikant Mane
- Yale Center for Genome Analysis, Yale West Campus, Orange, CT 06477, USA
| | - Gregory J. Hannon
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Nathan D. Lawson
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Scot A. Wolfe
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
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41
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Giraldez AJ. microRNAs, the cell's Nepenthe: clearing the past during the maternal-to-zygotic transition and cellular reprogramming. Curr Opin Genet Dev 2010; 20:369-75. [PMID: 20452200 DOI: 10.1016/j.gde.2010.04.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 04/07/2010] [Accepted: 04/12/2010] [Indexed: 12/18/2022]
Abstract
The maternal-to-zygotic transition (MZT) is a universal step in animal development characterized by two major events: activation of zygotic transcription and degradation of maternally provided mRNAs. How zygotic gene products instruct the degradation of maternal messages remains a long-standing question in biology. MicroRNAs (miRNAs) have recently emerged as widespread regulators of gene expression. miRNAs control temporal and spatial gene expression by both accelerating the decay of mRNAs from previous developmental stages and modulating the levels of actively transcribed genes. In this review, I discuss recent studies of the roles of miRNAs during the maternal-to-zygotic transition and cellular reprogramming, where they reshape transcriptional landscapes to facilitate the establishment of novel cellular states.
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Affiliation(s)
- Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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42
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Abstract
microRNAs (miRNAs) encode small RNA molecules of approximately 22nts in length that regulate the deadenylation, translation, and decay of their target mRNAs. The identification of miRNAs in plants and animals has uncovered a new layer of gene regulation with important implications for development, cellular homeostasis and disease. Because each miRNA is predicted to regulate several hundred genes, a major challenge in the field remains to elucidate the precise roles for each miRNA and to understand the physiological relevance of individual miRNA-target interactions in vivo. Despite the wide variety of biological contexts where miRNAs function, a common theme emerges, whereby miRNAs shape gene expression within both spatial and temporal dimensions by removing messages from previous cellular states as well as modulating the levels of actively transcribed genes. This review will focus on the role that the teleost Danio rerio (zebrafish) has played in shaping our understanding of miRNA function in vertebrates.
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Affiliation(s)
- Carter M Takacs
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
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43
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Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ. Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes Dev 2009; 23:619-32. [PMID: 19240126 DOI: 10.1101/gad.1760209] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
microRNAs (miRNAs) represent approximately 4% of the genes in vertebrates, where they regulate deadenylation, translation, and decay of the target messenger RNAs (mRNAs). The integrated role of miRNAs to regulate gene expression and cell function remains largely unknown. Therefore, to identify the targets coordinately regulated by muscle miRNAs in vivo, we performed gene expression arrays on muscle cells sorted from wild type, dicer mutants, and single miRNA knockdown embryos. Our analysis reveals that two particular miRNAs, miR-1 and miR-133, influence gene expression patterns in the zebrafish embryo where they account for >54% of the miRNA-mediated regulation in the muscle. We also found that muscle miRNA targets (1) tend to be expressed at low levels in wild-type muscle but are more highly expressed in dicer mutant muscle, and (2) are enriched for actin-related and actin-binding proteins. Loss of dicer function or down-regulation of miR-1 and miR-133 alters muscle gene expression and disrupts actin organization during sarcomere assembly. These results suggest that miR-1 and miR-133 actively shape gene expression patterns in muscle tissue, where they regulate sarcomeric actin organization.
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Affiliation(s)
- Yuichiro Mishima
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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44
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Choi PS, Zakhary L, Choi WY, Caron S, Alvarez-Saavedra E, Miska EA, McManus M, Harfe B, Giraldez AJ, Horvitz HR, Schier AF, Dulac C. Members of the miRNA-200 family regulate olfactory neurogenesis. Neuron 2008; 57:41-55. [PMID: 18184563 PMCID: PMC2204047 DOI: 10.1016/j.neuron.2007.11.018] [Citation(s) in RCA: 203] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 09/10/2007] [Accepted: 11/14/2007] [Indexed: 12/27/2022]
Abstract
MicroRNAs (miRNAs) are highly expressed in vertebrate neural tissues, but the contribution of specific miRNAs to the development and function of different neuronal populations is still largely unknown. We report that miRNAs are required for terminal differentiation of olfactory precursors in both mouse and zebrafish but are dispensable for proper function of mature olfactory neurons. The repertoire of miRNAs expressed in olfactory tissues contains over 100 distinct miRNAs. A subset, including the miR-200 family, shows high olfactory enrichment and expression patterns consistent with a role during olfactory neurogenesis. Loss of function of the miR-200 family phenocopies the terminal differentiation defect observed in absence of all miRNA activity in olfactory progenitors. Our data support the notion that vertebrate tissue differentiation is controlled by conserved subsets of organ-specific miRNAs in both mouse and zebrafish and provide insights into control mechanisms underlying olfactory differentiation in vertebrates.
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Affiliation(s)
- Philip S Choi
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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45
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Abstract
MicroRNAs (miRNAs) repress hundreds of target messenger RNAs (mRNAs), but the physiological roles of specific miRNA-mRNA interactions remain largely elusive. We report that zebrafish microRNA-430 (miR-430) dampens and balances the expression of the transforming growth factor-beta (TGF-beta) Nodal agonist squint and the TGF-beta Nodal antagonist lefty. To disrupt the interaction of specific miRNA-mRNA pairs, we developed target protector morpholinos complementary to miRNA binding sites in target mRNAs. Protection of squint or lefty mRNAs from miR-430 resulted in enhanced or reduced Nodal signaling, respectively. Simultaneous protection of squint and lefty or absence of miR-430 caused an imbalance and reduction in Nodal signaling. These findings establish an approach to analyze the in vivo roles of specific miRNA-mRNA pairs and reveal a requirement for miRNAs in dampening and balancing agonist/antagonist pairs.
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Affiliation(s)
- Wen-Yee Choi
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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46
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Abstract
Although many microRNAs (miRNAs) and their targets have been identified, the importance of miRNAs in vivo is still unclear. In this issue, Zhao et al. (2007) generate mice deficient in a cardiac-specific miRNA, miR-1-2, and reveal that this microRNA plays a crucial role in heart development and physiology.
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Affiliation(s)
- Yuichiro Mishima
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
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47
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Mishima Y, Giraldez AJ, Takeda Y, Fujiwara T, Sakamoto H, Schier AF, Inoue K. Differential regulation of germline mRNAs in soma and germ cells by zebrafish miR-430. Curr Biol 2007; 16:2135-42. [PMID: 17084698 PMCID: PMC1764209 DOI: 10.1016/j.cub.2006.08.086] [Citation(s) in RCA: 238] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 08/28/2006] [Accepted: 08/29/2006] [Indexed: 01/28/2023]
Abstract
Early in development, primordial germ cells (PGCs) are set aside from somatic cells and acquire a unique gene-expression program . The mechanisms underlying germline-specific gene expression are largely unknown. Nanos expression is required during germline development and is posttranscriptionally restricted to PGCs . Here we report that the microRNA miR-430 targets the 3' untranslated region (UTR) of nanos1 during zebrafish embryogenesis. A miR-430 target site within the nanos1 3' UTR reduces poly(A) tail length, mRNA stability, and translation. Repression is disrupted in maternal-zygotic dicer mutants (MZdicer), which lack mature miRNAs , and is restored by injection of processed miR-430. Although miR-430 represses other genes equally in germline and soma, specific regions in the nanos1 3' UTR compensate for microRNA-mediated repression in PGCs and allow germline-specific expression. We show that the 3' UTR of an additional PGC-specific gene, TDRD7, is also targeted by miR-430. These results indicate that miR-430 targets the 3' UTRs of germline genes and suggest that differential susceptibility to microRNAs contributes to tissue-specific gene expression.
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Affiliation(s)
- Yuichiro Mishima
- Department of Biology, Graduate School of Science and Technology, Kobe University, 1-1 Rokkodaicho, Nadaku, Kobe 657-8501, Japan
| | - Antonio J. Giraldez
- Developmental Genetics Program, Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, New York, NY 10016. USA
- Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Broad Institute, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138
| | - Yasuaki Takeda
- Department of Biology, Graduate School of Science and Technology, Kobe University, 1-1 Rokkodaicho, Nadaku, Kobe 657-8501, Japan
| | - Toshinobu Fujiwara
- Department of Biology, Graduate School of Science and Technology, Kobe University, 1-1 Rokkodaicho, Nadaku, Kobe 657-8501, Japan
| | - Hiroshi Sakamoto
- Department of Biology, Graduate School of Science and Technology, Kobe University, 1-1 Rokkodaicho, Nadaku, Kobe 657-8501, Japan
| | - Alexander F. Schier
- Developmental Genetics Program, Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, New York, NY 10016. USA
- Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Broad Institute, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138
- *To whom correspondence should be addressed. E-mail: Tel: +81-78-803-5725 Fax: +81-78-803-5720; Tel: +1-617-496-4835 Fax: +1-617-495-9300
| | - Kunio Inoue
- Department of Biology, Graduate School of Science and Technology, Kobe University, 1-1 Rokkodaicho, Nadaku, Kobe 657-8501, Japan
- *To whom correspondence should be addressed. E-mail: Tel: +81-78-803-5725 Fax: +81-78-803-5720; Tel: +1-617-496-4835 Fax: +1-617-495-9300
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Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, Enright AJ, Schier AF. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 2006; 312:75-9. [PMID: 16484454 DOI: 10.1126/science.1122689] [Citation(s) in RCA: 1152] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) comprise 1 to 3% of all vertebrate genes, but their in vivo functions and mechanisms of action remain largely unknown. Zebrafish miR-430 is expressed at the onset of zygotic transcription and regulates morphogenesis during early development. By using a microarray approach and in vivo target validation, we find that miR-430 directly regulates several hundred target messenger RNA molecules (mRNAs). Most targets are maternally expressed mRNAs that accumulate in the absence of miR-430. We also show that miR-430 accelerates the deadenylation of target mRNAs. These results suggest that miR-430 facilitates the deadenylation and clearance of maternal mRNAs during early embryogenesis.
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Affiliation(s)
- Antonio J Giraldez
- Developmental Genetics Program, Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.
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Abstract
MicroRNAs (miRNAs) are small RNAs that bind to the 3 UTR of mRNAs. We are using zebra fish as a model system to study the developmental roles of miRNAs and to determine the mechanisms by which miRNAs regulate target mRNAs. We generated zebra fish embryos that lack the miRNA-processing enzyme Dicer. Mutant embryos are devoid of mature miRNAs and have morphogenesis defects, but differentiate multiple cell types. Injection of miR-430 miRNAs, a miRNA family expressed at the onset of zygotic transcription, rescues the early morphogenesis defects in dicer mutants. miR-430 accelerates the decay of hundreds of maternal mRNAs and induces the deadenylation of target mRNAs. These studies suggest that miRNAs are not obligatory components of all fate specification or signaling pathways but facilitate developmental transitions and induce the deadenylation and decay of hundreds of target mRNAs.
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Affiliation(s)
- A F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Le Good JA, Joubin K, Giraldez AJ, Ben-Haim N, Beck S, Chen Y, Schier AF, Constam DB. Nodal stability determines signaling range. Curr Biol 2005; 15:31-6. [PMID: 15649361 DOI: 10.1016/j.cub.2004.12.062] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Revised: 10/29/2004] [Accepted: 10/29/2004] [Indexed: 11/29/2022]
Abstract
Secreted TGFbeta proteins of the Nodal family pattern the vertebrate body axes and induce mesoderm and endoderm . Nodal proteins can act as morphogens , but the mechanisms regulating their activity and signaling range are poorly understood. In particular, it has been unclear how inefficient processing or rapid turnover of the Nodal protein influences autocrine and paracrine signaling properties . Here, we evaluate the role of Nodal processing and stability in tissue culture and zebrafish embryos. Removal of the pro domain potentiates autocrine signaling but reduces Nodal stability and signaling range. Insertion of an N-glycosylation site present in several related TGFbeta proteins increases the stability of mature Nodal. The stabilized form of Nodal acts at a longer range than the wild-type form. These results suggest that increased proteolytic maturation of Nodal potentiates autocrine signaling, whereas increased Nodal stability extends paracrine signaling.
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Affiliation(s)
- J Ann Le Good
- Swiss Institute for Experimental Cancer Research (ISREC), Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland
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