1
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Zuo F, Jiang L, Su N, Zhang Y, Bao B, Wang L, Shi Y, Yang H, Huang X, Li R, Zeng Q, Chen Z, Lin Q, Zhuang Y, Zhao Y, Chen X, Zhu L, Yang Y. Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA. Nat Chem Biol 2024:10.1038/s41589-024-01629-x. [PMID: 38783134 DOI: 10.1038/s41589-024-01629-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Fluorescent RNAs (FRs) provide an attractive approach to visualizing RNAs in live cells. Although the color palette of FRs has been greatly expanded recently, a green FR with high cellular brightness and photostability is still highly desired. Here we develop a fluorogenic RNA aptamer, termed Okra, that can bind and activate the fluorophore ligand ACE to emit bright green fluorescence. Okra has an order of magnitude enhanced cellular brightness than currently available green FRs, allowing the robust imaging of messenger RNA in both live bacterial and mammalian cells. We further demonstrate the usefulness of Okra for time-resolved measurements of ACTB mRNA trafficking to stress granules, as well as live-cell dual-color superresolution imaging of RNA in combination with Pepper620, revealing nonuniform and distinct distributions of different RNAs throughout the granules. The favorable properties of Okra make it a versatile tool for the study of RNA dynamics and subcellular localization.
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Affiliation(s)
- Fangting Zuo
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Li Jiang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ni Su
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yaqiang Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Bingkun Bao
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Limei Wang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yajie Shi
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Huimin Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xinyi Huang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ruilong Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Qingmei Zeng
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengda Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qiuning Lin
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yingping Zhuang
- School of Bioengineering, East China University of Science and Technology, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China.
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
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2
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Yang L, Zhang Z, Jiang P, Kong D, Yu Z, Shi D, Han Y, Chen E, Zheng W, Sun J, Zhao Y, Luo Y, Shi J, Yao H, Huang H, Qian P. Phase separation-competent FBL promotes early pre-rRNA processing and translation in acute myeloid leukaemia. Nat Cell Biol 2024:10.1038/s41556-024-01420-z. [PMID: 38745030 DOI: 10.1038/s41556-024-01420-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
RNA-binding proteins (RBPs) are pivotal in acute myeloid leukaemia (AML), a lethal disease. Although specific phase separation-competent RBPs are recognized in AML, the effect of their condensate formation on AML leukaemogenesis, and the therapeutic potential of inhibition of phase separation are underexplored. In our in vivo CRISPR RBP screen, fibrillarin (FBL) emerges as a crucial nucleolar protein that regulates AML cell survival, primarily through its phase separation domains rather than methyltransferase or acetylation domains. These phase separation domains, with specific features, coordinately drive nucleoli formation and early processing of pre-rRNA (including efflux, cleavage and methylation), eventually enhancing the translation of oncogenes such as MYC. Targeting the phase separation capability of FBL with CGX-635 leads to elimination of AML cells, suggesting an additional mechanism of action for CGX-635 that complements its established therapeutic effects. We highlight the potential of PS modulation of critical proteins as a possible therapeutic strategy for AML.
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Affiliation(s)
- Lin Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Zhaoru Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Penglei Jiang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Delin Kong
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Zebin Yu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Danrong Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yingli Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Ertuo Chen
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Weiyan Zheng
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Sun
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanmin Zhao
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Luo
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jimin Shi
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - He Huang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China.
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Pengxu Qian
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China.
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3
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Almansour F, Keikhosravi A, Pegoraro G, Misteli T. Allele-level visualization of transcription and chromatin by high-throughput imaging. Histochem Cell Biol 2024:10.1007/s00418-024-02289-7. [PMID: 38724854 DOI: 10.1007/s00418-024-02289-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2024] [Indexed: 05/21/2024]
Abstract
The spatial arrangement of the genome within the nucleus is a pivotal aspect of cellular organization and function with implications for gene expression and regulation. While all genome organization features, such as loops, domains, and radial positioning, are nonrandom, they are characterized by a high degree of single-cell variability. Imaging approaches are ideally suited to visualize, measure, and study single-cell heterogeneity in genome organization. Here, we describe two methods for the detection of DNA and RNA of individual gene alleles by fluorescence in situ hybridization (FISH) in a high-throughput format. We have optimized combined DNA/RNA FISH approaches either using simultaneous or sequential detection of DNA and nascent RNA. These optimized DNA and RNA FISH protocols were implemented in a 384-well plate format alongside automated image and data analysis and enable accurate detection of individual gene alleles and their gene expression status across a large cell population. We successfully visualized MYC and EGFR DNA and nascent RNA with allele-level resolution in multiple cell types, and we determined the radial position of active and inactive MYC and EGFR alleles. These optimized DNA/RNA detection approaches are versatile and sensitive tools for mapping of chromatin features and gene activity at the single-allele level and at high throughput.
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Affiliation(s)
- Faisal Almansour
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical School, Washington, DC, 20057, USA
| | - Adib Keikhosravi
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA.
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4
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Almansour F, Keikhosravi A, Pegoraro G, Misteli T. Allele-level visualization of transcription and chromatin by high-throughput imaging. RESEARCH SQUARE 2024:rs.3.rs-3970096. [PMID: 38464289 PMCID: PMC10925428 DOI: 10.21203/rs.3.rs-3970096/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The spatial arrangement of the genome within the nucleus is a pivotal aspect of cellular organization and function with implications for gene expression and regulation. While all genome organization features, such as loops, domains, and radial positioning, are non-random, they are characterized by a high degree of single-cell variability. Imaging approaches are ideally suited to visualize, measure, and study single-cell heterogeneity in genome organization. Here, we describe two methods for the detection of DNA and RNA of individual gene alleles by fluorescence in situ hybridization (FISH) in a high-throughput format. We have optimized combined DNA/RNA FISH approaches either using simultaneous or sequential detection. These optimized DNA and RNA FISH protocols, implemented in a 384-well plate format alongside automated image and data analysis, enable accurate detection of chromatin loci and their gene expression status across a large cell population with allele-level resolution. We successfully visualized MYC and EGFR DNA and RNA in multiple cell types, and we determined the radial position of active and inactive MYC and EGFR alleles. These optimized DNA/RNA detection approaches are versatile and sensitive tools for mapping of chromatin features and gene activity at the single-allele level and at high throughput.
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Affiliation(s)
| | | | | | - Tom Misteli
- National Cancer Institute, National Institute of Health
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5
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Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG. The contribution of mRNA targeting to spatial protein localization in bacteria. FEBS J 2024. [PMID: 38226707 DOI: 10.1111/febs.17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.
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Affiliation(s)
- Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | | | - Andreea Mihaela Mlesnita
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
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6
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Palumbo RJ, Yang Y, Feigon J, Hanes SD. Catalytic activity of the Bin3/MePCE methyltransferase domain is dispensable for 7SK snRNP function in Drosophila melanogaster. Genetics 2024; 226:iyad203. [PMID: 37982586 PMCID: PMC10763541 DOI: 10.1093/genetics/iyad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023] Open
Abstract
Methylphosphate Capping Enzyme (MePCE) monomethylates the gamma phosphate at the 5' end of the 7SK noncoding RNA, a modification thought to protect 7SK from degradation. 7SK serves as a scaffold for assembly of a snRNP complex that inhibits transcription by sequestering the positive elongation factor P-TEFb. While much is known about the biochemical activity of MePCE in vitro, little is known about its functions in vivo, or what roles-if any-there are for regions outside the conserved methyltransferase domain. Here, we investigated the role of Bin3, the Drosophila ortholog of MePCE, and its conserved functional domains in Drosophila development. We found that bin3 mutant females had strongly reduced rates of egg-laying, which was rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 promotes fecundity by repressing P-TEFb. bin3 mutants also exhibited neuromuscular defects, analogous to a patient with MePCE haploinsufficiency. These defects were also rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 and MePCE have conserved roles in promoting neuromuscular function by repressing P-TEFb. Unexpectedly, we found that a Bin3 catalytic mutant (Bin3Y795A) could still bind and stabilize 7SK and rescue all bin3 mutant phenotypes, indicating that Bin3 catalytic activity is dispensable for 7SK stability and snRNP function in vivo. Finally, we identified a metazoan-specific motif (MSM) outside of the methyltransferase domain and generated mutant flies lacking this motif (Bin3ΔMSM). Bin3ΔMSM mutant flies exhibited some-but not all-bin3 mutant phenotypes, suggesting that the MSM is required for a 7SK-independent, tissue-specific function of Bin3.
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Affiliation(s)
- Ryan J Palumbo
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Yuan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Steven D Hanes
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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7
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Xu C, Wang A, Ebraham L, Sullivan L, Tasker C, Pizutelli V, Couret J, Hernandez C, Kolli P, Deb PQ, Fritzky L, Subbian S, Gao N, Lo Y, Salvatore M, Rivera A, Lemenze A, Fitzgerald-Bocarsly P, Tyagi S, Lu W, Beaulieu A, Chang TL. Interferon ɛ restricts Zika virus infection in the female reproductive tract. PNAS NEXUS 2023; 2:pgad350. [PMID: 37954158 PMCID: PMC10639110 DOI: 10.1093/pnasnexus/pgad350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/13/2023] [Indexed: 11/14/2023]
Abstract
Interferon ɛ (IFNɛ) is a unique type I IFN that has been implicated in host defense against sexually transmitted infections. Zika virus (ZIKV), an emerging pathogen, can infect the female reproductive tract (FRT) and cause devastating diseases, particularly in pregnant women. How IFNɛ contributes to protection against ZIKV infection in vivo is unknown. In this study, we show that IFNɛ plays a critical role in host protection against vaginal ZIKV infection in mice. We found that IFNɛ was expressed not only by epithelial cells in the FRT but also by immune and stromal cells at baseline or after exposure to viruses or specific Toll-like receptor (TLR) agonists. IFNɛ-deficient mice exhibited abnormalities in the epithelial border and underlying tissue in the cervicovaginal tract, and these defects were associated with increased susceptibility to vaginal but not subcutaneous ZIKV infection. IFNɛ deficiency resulted in an increase in magnitude, duration, and depth of ZIKV infection in the FRT. Critically, intravaginal administration of recombinant IFNɛ protected Ifnɛ-/- mice and highly susceptible Ifnar1-/- mice against vaginal ZIKV infection, indicating that IFNɛ was sufficient to provide protection even in the absence of signals from other type I IFNs and in an IFNAR1-independent manner. Our findings reveal a potentially critical role for IFNɛ in mediating protection against the transmission of ZIKV in the context of sexual contact.
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Affiliation(s)
- Chuan Xu
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Annie Wang
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Laith Ebraham
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Liam Sullivan
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Carley Tasker
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Vanessa Pizutelli
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Jennifer Couret
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Cyril Hernandez
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Priyanka Kolli
- Graduate School of Biological Sciences, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Pratik Q Deb
- Department of Pathology and Laboratory Medicine, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Luke Fritzky
- Department of Pathology and Laboratory Medicine, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Selvakumar Subbian
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Nan Gao
- Department of Cell Biology, Rutgers, School of Art and Science-Newark, Newark, NJ 07103, USA
| | - Yungtai Lo
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Mirella Salvatore
- Departmentof Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Amariliz Rivera
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Alexander Lemenze
- Department of Pathology and Laboratory Medicine, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | | | - Sanjay Tyagi
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Wuyuan Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, and Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai 200032, China
| | - Aimee Beaulieu
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Theresa L Chang
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
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8
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Venkei ZG, Gainetdinov I, Bagci A, Starostik MR, Choi CP, Fingerhut JM, Chen P, Balsara C, Whitfield TW, Bell GW, Feng S, Jacobsen SE, Aravin AA, Kim JK, Zamore PD, Yamashita YM. A maternally programmed intergenerational mechanism enables male offspring to make piRNAs from Y-linked precursor RNAs in Drosophila. Nat Cell Biol 2023; 25:1495-1505. [PMID: 37723298 PMCID: PMC10567549 DOI: 10.1038/s41556-023-01227-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 08/09/2023] [Indexed: 09/20/2023]
Abstract
In animals, PIWI-interacting RNAs (piRNAs) direct PIWI proteins to silence complementary targets such as transposons. In Drosophila and other species with a maternally specified germline, piRNAs deposited in the egg initiate piRNA biogenesis in the progeny. However, Y chromosome loci cannot participate in such a chain of intergenerational inheritance. How then can the biogenesis of Y-linked piRNAs be initiated? Here, using Suppressor of Stellate (Su(Ste)), a Y-linked Drosophila melanogaster piRNA locus as a model, we show that Su(Ste) piRNAs are made in the early male germline via 5'-to-3' phased piRNA biogenesis initiated by maternally deposited 1360/Hoppel transposon piRNAs. Notably, deposition of Su(Ste) piRNAs from XXY mothers obviates the need for phased piRNA biogenesis in sons. Together, our study uncovers a developmentally programmed, intergenerational mechanism that allows fly mothers to protect their sons using a Y-linked piRNA locus.
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Affiliation(s)
- Zsolt G Venkei
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ayca Bagci
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Charlotte P Choi
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jaclyn M Fingerhut
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peiwei Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chiraag Balsara
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Troy W Whitfield
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George W Bell
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
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9
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Ebraham L, Xu C, Wang A, Hernandez C, Siclari N, Rajah D, Walter L, Marras SAE, Tyagi S, Fine DH, Daep CA, Chang TL. Oral Epithelial Cells Expressing Low or Undetectable Levels of Human Angiotensin-Converting Enzyme 2 Are Susceptible to SARS-CoV-2 Virus Infection In Vitro. Pathogens 2023; 12:843. [PMID: 37375533 DOI: 10.3390/pathogens12060843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
The oral cavity is thought to be one of the portals for SARS-CoV-2 entry, although there is limited evidence of active oral infection by SARS-CoV-2 viruses. We assessed the capacity of SARS-CoV-2 to infect and replicate in oral epithelial cells. Oral gingival epithelial cells (hTERT TIGKs), salivary gland epithelial cells (A-253), and oral buccal epithelial cells (TR146), which occupy different regions of the oral cavity, were challenged with replication-competent SARS-CoV-2 viruses and with pseudo-typed viruses expressing SARS-CoV-2 spike proteins. All oral epithelial cells expressing undetectable or low levels of human angiotensin-converting enzyme 2 (hACE2) but high levels of the alternative receptor CD147 were susceptible to SARS-CoV-2 infection. Distinct viral dynamics were seen in hTERT TIGKs compared to A-253 and TR146 cells. For example, levels of viral transcripts were sustained in hTERT TIGKs but were significantly decreased in A-253 and TR146 cells on day 3 after infection. Analysis of oral epithelial cells infected by replication-competent SARS-CoV-2 viruses expressing GFP showed that the GFP signal and SARS-CoV-2 mRNAs were not evenly distributed. Furthermore, we found cumulative SARS-CoV-2 RNAs from released viruses in the media from oral epithelial cells on day 1 and day 2 after infection, indicating productive viral infection. Taken together, our results demonstrated that oral epithelial cells were susceptible to SARS-CoV-2 viruses despite low or undetectable levels of hACE2, suggesting that alternative receptors contribute to SARS-CoV-2 infection and may be considered for the development of future vaccines and therapeutics.
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Affiliation(s)
- Laith Ebraham
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Chuan Xu
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Annie Wang
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Cyril Hernandez
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Nicholas Siclari
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Divino Rajah
- Global Technology Center, Colgate-Palmolive Company, Piscataway, NJ 08855, USA
| | - Lewins Walter
- Global Technology Center, Colgate-Palmolive Company, Piscataway, NJ 08855, USA
| | - Salvatore A E Marras
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Daniel H Fine
- Department of Oral Biology, School of Dental Medicine, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Carlo Amorin Daep
- Global Technology Center, Colgate-Palmolive Company, Piscataway, NJ 08855, USA
| | - Theresa L Chang
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
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10
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Palumbo RJ, Hanes SD. Catalytic activity of the Bin3/MEPCE methyltransferase domain is dispensable for 7SK snRNP function in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543302. [PMID: 37333392 PMCID: PMC10274667 DOI: 10.1101/2023.06.01.543302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Methylphosphate Capping Enzyme (MEPCE) monomethylates the gamma phosphate at the 5' end of the 7SK noncoding RNA, a modification thought to protect 7SK from degradation. 7SK serves as a scaffold for assembly of a snRNP complex that inhibits transcription by sequestering the positive elongation factor P-TEFb. While much is known about the biochemical activity of MEPCE in vitro, little is known about its functions in vivo, or what roles- if any-there are for regions outside the conserved methyltransferase domain. Here, we investigated the role of Bin3, the Drosophila ortholog of MEPCE, and its conserved functional domains in Drosophila development. We found that bin3 mutant females had strongly reduced rates of egg-laying, which was rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 promotes fecundity by repressing P-TEFb. bin3 mutants also exhibited neuromuscular defects, analogous to a patient with MEPCE haploinsufficiency. These defects were also rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 and MEPCE have conserved roles in promoting neuromuscular function by repressing P-TEFb. Unexpectedly, we found that a Bin3 catalytic mutant (Bin3Y795A) could still bind and stabilize 7SK and rescue all bin3 mutant phenotypes, indicating that Bin3 catalytic activity is dispensable for 7SK stability and snRNP function in vivo. Finally, we identified a metazoan-specific motif (MSM) outside of the methyltransferase domain and generated mutant flies lacking this motif (Bin3ΔMSM). Bin3ΔMSM mutant flies exhibited some-but not all-bin3 mutant phenotypes, suggesting that the MSM is required for a 7SK-independent, tissue-specific function of Bin3.
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Affiliation(s)
- Ryan J Palumbo
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, 4283 Weiskotten Hall, Syracuse, New York, 13210
| | - Steven D Hanes
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, 4283 Weiskotten Hall, Syracuse, New York, 13210
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11
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Afzal Z, Lange JJ, Nolte C, McKinney S, Wood C, Paulson A, De Kumar B, Unruh J, Slaughter BD, Krumlauf R. Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube. Development 2023; 150:dev201259. [PMID: 37102683 PMCID: PMC10233718 DOI: 10.1242/dev.201259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
Signaling pathways regulate the patterns of Hox gene expression that underlie their functions in the specification of axial identity. Little is known about the properties of cis-regulatory elements and underlying transcriptional mechanisms that integrate graded signaling inputs to coordinately control Hox expression. Here, we optimized a single molecule fluorescent in situ hybridization (smFISH) technique with probes spanning introns to evaluate how three shared retinoic acid response element (RARE)-dependent enhancers in the Hoxb cluster regulate patterns of nascent transcription in vivo at the level of single cells in wild-type and mutant embryos. We predominately detect nascent transcription of only a single Hoxb gene in each cell, with no evidence for simultaneous co-transcriptional coupling of all or specific subsets of genes. Single and/or compound RARE mutations indicate that each enhancer differentially impacts global and local patterns of nascent transcription, suggesting that selectivity and competitive interactions between these enhancers is important to robustly maintain the proper levels and patterns of nascent Hoxb transcription. This implies that rapid and dynamic regulatory interactions potentiate transcription of genes through combined inputs from these enhancers in coordinating the retinoic acid response.
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Affiliation(s)
- Zainab Afzal
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christof Nolte
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christopher Wood
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
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12
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Xu C, Wang A, Ebraham L, Sullivan L, Tasker C, Pizutelli V, Couret J, Hernandez C, Deb PQ, Fritzky L, Subbian S, Gao N, Lo Y, Salvatore M, Rivera A, Lemenze A, Fitzgerald-Bocarsly P, Tyagi S, Lu W, Beaulieu A, Chang TL. Interferon ε restricts Zika virus infection in the female reproductive tract. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535968. [PMID: 37066223 PMCID: PMC10104157 DOI: 10.1101/2023.04.06.535968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Interferon ε (IFNε) is a unique type I IFN that has been implicated in host defense against sexually transmitted infections (STIs). Zika virus (ZIKV), an emerging pathogen, can infect the female reproductive tract (FRT) and cause devastating diseases, particularly in pregnant women. How IFNε contributes to protection against ZIKV infection in vivo is unknown. Here, we show that IFNε plays a critical role in host protection against vaginal ZIKV infection in mice. We found that IFNε was expressed not only by epithelial cells in the FRT, but also by certain immune and other cells at baseline or after exposure to viruses or specific TLR agonists. IFNε-deficient mice exhibited abnormalities in the epithelial border and underlying tissue in the cervicovaginal tract, and these defects were associated with increased susceptibility to vaginal, but not subcutaneous ZIKV infection. IFNε-deficiency resulted in an increase in magnitude, duration, and depth of ZIKV infection in the FRT. Critically, intravaginal administration of recombinant IFNε protected Ifnε-/- mice and highly susceptible Ifnar1-/- mice against vaginal ZIKV infection, indicating that IFNε was sufficient to provide protection even in the absence of signals from other type I IFNs and in an IFNAR1-independent manner. Our findings reveal a potentially critical role for IFNε in mediating protection against transmission of ZIKV in the context of sexual contact.
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Affiliation(s)
- Chuan Xu
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Annie Wang
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Laith Ebraham
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Liam Sullivan
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Carley Tasker
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Vanessa Pizutelli
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Jennifer Couret
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Cyril Hernandez
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Pratik Q. Deb
- Department of Pathology and Laboratory Medicine, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Luke Fritzky
- Department of Pathology and Laboratory Medicine, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Selvakumar Subbian
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Nan Gao
- Department of Cell Biology, Rutgers, School of Art and Science-Newark, Newark, NJ 07103, USA
| | - Yungtai Lo
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY10461
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medical College, New York, NY, 10065
| | - Amariliz Rivera
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Alexander Lemenze
- Department of Pathology and Laboratory Medicine, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | | | - Sanjay Tyagi
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Wuyuan Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, and Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai 200032, China
| | - Aimee Beaulieu
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
| | - Theresa L. Chang
- Public Health Research Institute, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, New Jersey Medical School, Newark, NJ 07103, USA
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13
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Monné Rodríguez JM, Frisk AL, Kreutzer R, Lemarchand T, Lezmi S, Saravanan C, Stierstorfer B, Thuilliez C, Vezzali E, Wieczorek G, Yun SW, Schaudien D. European Society of Toxicologic Pathology (Pathology 2.0 Molecular Pathology Special Interest Group): Review of In Situ Hybridization Techniques for Drug Research and Development. Toxicol Pathol 2023; 51:92-111. [PMID: 37449403 PMCID: PMC10467011 DOI: 10.1177/01926233231178282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
In situ hybridization (ISH) is used for the localization of specific nucleic acid sequences in cells or tissues by complementary binding of a nucleotide probe to a specific target nucleic acid sequence. In the last years, the specificity and sensitivity of ISH assays were improved by innovative techniques like synthetic nucleic acids and tandem oligonucleotide probes combined with signal amplification methods like branched DNA, hybridization chain reaction and tyramide signal amplification. These improvements increased the application spectrum for ISH on formalin-fixed paraffin-embedded tissues. ISH is a powerful tool to investigate DNA, mRNA transcripts, regulatory noncoding RNA, and therapeutic oligonucleotides. ISH can be used to obtain spatial information of a cell type, subcellular localization, or expression levels of targets. Since immunohistochemistry and ISH share similar workflows, their combination can address simultaneous transcriptomics and proteomics questions. The goal of this review paper is to revisit the current state of the scientific approaches in ISH and its application in drug research and development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Seong-Wook Yun
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Dirk Schaudien
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
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14
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Kumar R, Kolloli A, Subbian S, Kaushal D, Shi L, Tyagi S. Imaging Architecture of Granulomas Induced by Mycobacterium tuberculosis Infections with Single-Molecule FISH. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526702. [PMID: 36778404 PMCID: PMC9915589 DOI: 10.1101/2023.02.02.526702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Granulomas are an important hallmark of Mycobacterium tuberculosis (Mtb) infection. They are organized and dynamic structures created by an assembly of immune cells around the sites of infection in the lungs to locally restrict the bacterial growth and the host's inflammatory responses. The cellular architecture of granulomas is traditionally studied by immunofluorescence labeling of phenotypic surface markers. However, very few antibodies are available for model animals used in tuberculosis research, such as non-human primates and rabbits; secreted immunological markers such as cytokines cannot be imaged in situ using antibodies; and traditional phenotypic surface markers do not provide sufficient resolution for the detection of many subtypes and differentiation states of immune cells. Using single-molecule fluorescent in situ hybridization (smFISH) and its derivatives, amplified smFISH (ampFISH) and iterative smFISH, we developed a platform for imaging mRNAs encoding immune markers in rabbit and macaque tuberculosis granulomas. Multiplexed imaging for several mRNA and protein markers was followed by quantitative measurement of expression of these markers in single cells in situ. A quantitative analysis of combinatorial expressions of these markers allowed us to classify the cells into several subtypes and chart their distributions within granulomas. For one mRNA target, HIF-1α, we were able to image its mRNA and protein in the same cells, demonstrating the specificity of probes. This method paves the way for defining granular differentiation states and cell subtypes from transcriptomic data, identifying key mRNA markers for these cell subtypes, and then locating the cells in the spatial context of granulomas.
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Affiliation(s)
- Ranjeet Kumar
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey
| | - Afsal Kolloli
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey
| | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, New Jersey
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | - Lanbo Shi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, New Jersey
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, New Jersey
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15
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Fingerhut JM, Yamashita YM. Analysis of Gene Expression Patterns and RNA Localization by Fluorescence in Situ Hybridization in Whole Mount Drosophila Testes. Methods Mol Biol 2023; 2666:15-28. [PMID: 37166654 DOI: 10.1007/978-1-0716-3191-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Researchers have used RNA in situ hybridization to detect the presence of RNA in cells and tissues for approximately 50 years. The recent development of a method capable of visualizing a single RNA molecule by utilizing tiled fluorescently labeled oligonucleotide probes that together produce a diffraction-limited spot has greatly increased the resolution of this technique, allowing for the precise determination of subcellular RNA localization and relative abundance. Here, we present our method for single molecule RNA fluorescence in situ hybridization (smFISH) in whole mount Drosophila testes and discuss how we have utilized this method to better understand the expression pattern of the highly unusual Y-linked genes.
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Affiliation(s)
- Jaclyn M Fingerhut
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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16
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Slowest possible replicative life at frigid temperatures for yeast. Nat Commun 2022; 13:7518. [PMID: 36473846 PMCID: PMC9726825 DOI: 10.1038/s41467-022-35151-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Determining whether life can progress arbitrarily slowly may reveal fundamental barriers to staying out of thermal equilibrium for living systems. By monitoring budding yeast's slowed-down life at frigid temperatures and with modeling, we establish that Reactive Oxygen Species (ROS) and a global gene-expression speed quantitatively determine yeast's pace of life and impose temperature-dependent speed limits - shortest and longest possible cell-doubling times. Increasing cells' ROS concentration increases their doubling time by elongating the cell-growth (G1-phase) duration that precedes the cell-replication (S-G2-M) phase. Gene-expression speed constrains cells' ROS-reducing rate and sets the shortest possible doubling-time. To replicate, cells require below-threshold concentrations of ROS. Thus, cells with sufficiently abundant ROS remain in G1, become unsustainably large and, consequently, burst. Therefore, at a given temperature, yeast's replicative life cannot progress arbitrarily slowly and cells with the lowest ROS-levels replicate most rapidly. Fundamental barriers may constrain the thermal slowing of other organisms' lives.
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17
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Winkenbach LP, Parker DM, Williams RTP, Nishimura EO. The ERM-1 membrane-binding domain directs erm-1 mRNA localization to the plasma membrane in the C. elegans embryo. Development 2022; 149:279335. [PMID: 36314842 PMCID: PMC9793419 DOI: 10.1242/dev.200930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
mRNA localization and transport are integral in regulating gene expression. In Caenorhabditis elegans embryos, the maternally inherited mRNA erm-1 (Ezrin/Radixin/Moesin) becomes concentrated in anterior blastomeres. erm-1 mRNA localizes within those blastomeres to the plasma membrane where the essential ERM-1 protein, a membrane-actin linker, is also found. We demonstrate that the localization of erm-1 mRNA to the plasma membrane is translation dependent and requires its encoded N-terminal, membrane-binding (FERM) domain. By perturbing translation through multiple methods, we found that erm-1 mRNA localization at the plasma membrane persisted only if the nascent peptide remained in complex with the translating mRNA. Indeed, re-coding the erm-1 mRNA coding sequence while preserving the encoded amino acid sequence did not disrupt erm-1 mRNA localization, corroborating that the information directing mRNA localization resides within its membrane-binding protein domain. A single-molecule inexpensive fluorescence in situ hybridization screen of 17 genes encoding similar membrane-binding domains identified three plasma membrane-localized mRNAs in the early embryo. Ten additional transcripts showed potential membrane localization later in development. These findings point to a translation-dependent pathway for localization of mRNAs encoding membrane-associated proteins.
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Affiliation(s)
- Lindsay P. Winkenbach
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Dylan M. Parker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA,Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80303, USA
| | - Robert T. P. Williams
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Erin Osborne Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA,Author for correspondence ()
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18
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Beucher A, Miguel-Escalada I, Balboa D, De Vas MG, Maestro MA, Garcia-Hurtado J, Bernal A, Gonzalez-Franco R, Vargiu P, Heyn H, Ravassard P, Ortega S, Ferrer J. The HASTER lncRNA promoter is a cis-acting transcriptional stabilizer of HNF1A. Nat Cell Biol 2022; 24:1528-1540. [PMID: 36202974 PMCID: PMC9586874 DOI: 10.1038/s41556-022-00996-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/16/2022] [Indexed: 11/08/2022]
Abstract
The biological purpose of long non-coding RNAs (lncRNAs) is poorly understood. Haploinsufficient mutations in HNF1A homeobox A (HNF1A), encoding a homeodomain transcription factor, cause diabetes mellitus. Here, we examine HASTER, the promoter of an lncRNA antisense to HNF1A. Using mouse and human models, we show that HASTER maintains cell-specific physiological HNF1A concentrations through positive and negative feedback loops. Pancreatic β cells from Haster mutant mice consequently showed variegated HNF1A silencing or overexpression, resulting in hyperglycaemia. HASTER-dependent negative feedback was essential to prevent HNF1A binding to inappropriate genomic regions. We demonstrate that the HASTER promoter DNA, rather than the lncRNA, modulates HNF1A promoter-enhancer interactions in cis and thereby regulates HNF1A transcription. Our studies expose a cis-regulatory element that is unlike classic enhancers or silencers, it stabilizes the transcription of its target gene and ensures the fidelity of a cell-specific transcription factor program. They also show that disruption of a mammalian lncRNA promoter can cause diabetes mellitus.
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Affiliation(s)
- Anthony Beucher
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Irene Miguel-Escalada
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | - Diego Balboa
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | - Matías G De Vas
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Miguel Angel Maestro
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | - Javier Garcia-Hurtado
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | - Aina Bernal
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | - Roser Gonzalez-Franco
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | | | - Holger Heyn
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Philippe Ravassard
- Biotechnology and Biotherapy Team, Institut du Cerveau et de la Moelle, CNRS UMR7225, INSERM U975, University Pierre et Marie Curie, Paris, France
| | - Sagrario Ortega
- Transgenics Unit, Spanish National Cancer Research Centre, Madrid, Spain
| | - Jorge Ferrer
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain.
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19
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Yang LZ, Gao BQ, Huang Y, Wang Y, Yang L, Chen LL. Multi-color RNA imaging with CRISPR-Cas13b systems in living cells. CELL INSIGHT 2022; 1:100044. [PMID: 37192858 PMCID: PMC10120316 DOI: 10.1016/j.cellin.2022.100044] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 05/18/2023]
Abstract
Visualizing RNA dynamics is important for understanding RNA function. Catalytically dead (d) CRISPR-Cas13 systems have been established to image and track RNAs in living cells, but efficient dCas13 for RNA imaging is still limited. Here, we analyzed metagenomic and bacterial genomic databases to comprehensively screen Cas13 homologies for their RNA labeling capabilities in living mammalian cells. Among eight previously unreported dCas13 proteins that can be used for RNA labeling, dHgm4Cas13b and dMisCas13b displayed comparable, if not higher, efficiencies to the best-known ones when targeting endogenous MUC4 and NEAT1_2 by single guide (g) RNAs. Further examination of the labeling robustness of different dCas13 systems using the GCN4 repeats revealed that a minimum of 12 GCN4 repeats was required for dHgm4Cas13b and dMisCas13b imaging at the single RNA molecule level, while >24 GCN4 repeats were required for reported dLwaCas13a, dRfxCas13d and dPguCas13b. Importantly, by silencing pre-crRNA processing activity of dMisCas13b (ddMisCas13b) and further incorporating RNA aptamers including PP7, MS2, Pepper or BoxB to individual gRNAs, a CRISPRpalette system was developed to successfully achieve multi-color RNA visualization in living cells.
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Affiliation(s)
- Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bao-Qing Gao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Youkui Huang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ying Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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20
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Antel M, Raj R, Masoud MYG, Pan Z, Li S, Mellone BG, Inaba M. Interchromosomal interaction of homologous Stat92E alleles regulates transcriptional switch during stem-cell differentiation. Nat Commun 2022; 13:3981. [PMID: 35810185 PMCID: PMC9271046 DOI: 10.1038/s41467-022-31737-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 06/30/2022] [Indexed: 01/24/2023] Open
Abstract
Pairing of homologous chromosomes in somatic cells provides the opportunity of interchromosomal interaction between homologous gene regions. In the Drosophila male germline, the Stat92E gene is highly expressed in a germline stem cell (GSC) and gradually downregulated during the differentiation. Here we show that the pairing of Stat92E is always tight in GSCs and immediately loosened in differentiating daughter cells, gonialblasts (GBs). Disturbance of Stat92E pairing by relocation of one locus to another chromosome or by knockdown of global pairing/anti-pairing factors both result in a failure of Stat92E downregulation, suggesting that the pairing is required for the decline in transcription. Furthermore, the Stat92E enhancer, but not its transcription, is required for the change in pairing state, indicating that pairing is not a consequence of transcriptional changes. Finally, we show that the change in Stat92E pairing is dependent on asymmetric histone inheritance during the asymmetric division of GSCs. Taken together, we propose that the changes in Stat92E pairing status is an intrinsically programmed mechanism for enabling prompt cell fate switch during the differentiation of stem cells. Asymmetric inheritance of organelles, proteins and RNAs occurs during stem cell division. Here the authors show the strength of pairing of homologous Stat92E loci, a stem cell-specific gene, changes immediately after the asymmetric division due to asymmetric inheritance of new histones to one of the daughter cells and is important for turning off gene expression in this cell as it differentiates.
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Affiliation(s)
- Matthew Antel
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Romir Raj
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Madona Y G Masoud
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Ziwei Pan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Department of Genetics and Genomic Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Department of Genetics and Genomic Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Barbara G Mellone
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Mayu Inaba
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA.
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21
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Guo Y, Lee RE. Long-term imaging of individual mRNA molecules in living cells. CELL REPORTS METHODS 2022; 2:100226. [PMID: 35784652 PMCID: PMC9243547 DOI: 10.1016/j.crmeth.2022.100226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/10/2022] [Accepted: 05/04/2022] [Indexed: 12/04/2022]
Abstract
Single-cell imaging of individual mRNAs has revealed core mechanisms of the central dogma. However, most approaches require cell fixation or have limited sensitivity for live-cell applications. Here, we describe SunRISER (SunTag-based reporter for imaging signal-enriched mRNA), a computationally and experimentally optimized approach for unambiguous detection of single mRNA molecules in living cells. When viewed by epifluorescence microscopy, SunRISER-labeled mRNAs show strong signal to background and resistance to photobleaching, which together enable long-term mRNA imaging studies. SunRISER variants, using 8× and 10× stem-loop arrays, demonstrate effective mRNA detection while significantly reducing alterations to target mRNA sequences. We characterize SunRISER to observe mRNA inheritance during mitosis and find that stressors enhance diversity among post-mitotic sister cells. Taken together, SunRISER enables a glimpse into living cells to observe aspects of the central dogma and the role of mRNAs in rare and dynamical trafficking events.
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Affiliation(s)
- Yue Guo
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Robin E.C. Lee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Systems Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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22
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Li R, Zou Z, Wang W, Zou P. Metabolic incorporation of electron-rich ribonucleosides enhances APEX-seq for profiling spatially restricted nascent transcriptome. Cell Chem Biol 2022; 29:1218-1231.e8. [PMID: 35245437 DOI: 10.1016/j.chembiol.2022.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 07/30/2021] [Accepted: 02/10/2022] [Indexed: 12/13/2022]
Abstract
The spatial arrangement of newly synthesized transcriptome in eukaryotic cells underlies various biological processes including cell proliferation and differentiation. In this study, we combine metabolic incorporation of electron-rich ribonucleosides (e.g., 6-thioguanosine and 4-thiouridine) with a peroxidase-mediated proximity-dependent RNA labeling technique (APEX-seq) to develop a sensitive method, termed MERR APEX-seq, for selectively profiling newly transcribed RNAs at specific subcellular locations in live cells. We demonstrate that MERR APEX-seq is 20-fold more efficient than APEX-seq and offers both high spatial specificity and high coverage in mitochondrial matrix. At the ER membrane, 91% of the transcripts captured by MERR APEX-seq encode for secretory pathway proteins, thus demonstrating the high spatial specificity of MERR APEX-seq in open subcellular compartments. Application of MERR APEX-seq to the nuclear lamina of human cells reveals a local transcriptome of 1,012 RNAs, many of which encode for nuclear proteins involved in histone modification, chromosomal structure maintenance, and RNA processing.
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Affiliation(s)
- Ran Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Zhongyu Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Wentao Wang
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Peng Zou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China; Chinese Institute for Brain Research (CIBR), Beijing 102206, China.
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23
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van Sluijs L, Bosman KJ, Pankok F, Blokhina T, Wilten JIHA, te Molder DM, Riksen JAG, Snoek BL, Pijlman GP, Kammenga JE, Sterken MG. Balancing Selection of the Intracellular Pathogen Response in Natural Caenorhabditis elegans Populations. Front Cell Infect Microbiol 2022; 11:758331. [PMID: 35174100 PMCID: PMC8841876 DOI: 10.3389/fcimb.2021.758331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/21/2021] [Indexed: 12/17/2022] Open
Abstract
Genetic variation in host populations may lead to differential viral susceptibilities. Here, we investigate the role of natural genetic variation in the Intracellular Pathogen Response (IPR), an important antiviral pathway in the model organism Caenorhabditis elegans against Orsay virus (OrV). The IPR involves transcriptional activity of 80 genes including the pals-genes. We examine the genetic variation in the pals-family for traces of selection and explore the molecular and phenotypic effects of having distinct pals-gene alleles. Genetic analysis of 330 global C. elegans strains reveals that genetic diversity within the IPR-related pals-genes can be categorized in a few haplotypes worldwide. Importantly, two key IPR regulators, pals-22 and pals-25, are in a genomic region carrying signatures of balancing selection, suggesting that different evolutionary strategies exist in IPR regulation. We infected eleven C. elegans strains that represent three distinct pals-22 pals-25 haplotypes with Orsay virus to determine their susceptibility. For two of these strains, N2 and CB4856, the transcriptional response to infection was also measured. The results indicate that pals-22 pals-25 haplotype shapes the defense against OrV and host genetic variation can result in constitutive activation of IPR genes. Our work presents evidence for balancing genetic selection of immunity genes in C. elegans and provides a novel perspective on the functional diversity that can develop within a main antiviral response in natural host populations.
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Affiliation(s)
- Lisa van Sluijs
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
| | - Kobus J. Bosman
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Frederik Pankok
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Tatiana Blokhina
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Jop I. H. A. Wilten
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Dennie M. te Molder
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Joost A. G. Riksen
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Basten L. Snoek
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Gorben P. Pijlman
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
| | - Jan E. Kammenga
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Mark G. Sterken
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
- *Correspondence: Mark G. Sterken,
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24
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Transcriptional Regulation and Implications for Controlling Hox Gene Expression. J Dev Biol 2022; 10:jdb10010004. [PMID: 35076545 PMCID: PMC8788451 DOI: 10.3390/jdb10010004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
Hox genes play key roles in axial patterning and regulating the regional identity of cells and tissues in a wide variety of animals from invertebrates to vertebrates. Nested domains of Hox expression generate a combinatorial code that provides a molecular framework for specifying the properties of tissues along the A–P axis. Hence, it is important to understand the regulatory mechanisms that coordinately control the precise patterns of the transcription of clustered Hox genes required for their roles in development. New insights are emerging about the dynamics and molecular mechanisms governing transcriptional regulation, and there is interest in understanding how these may play a role in contributing to the regulation of the expression of the clustered Hox genes. In this review, we summarize some of the recent findings, ideas and emerging mechanisms underlying the regulation of transcription in general and consider how they may be relevant to understanding the transcriptional regulation of Hox genes.
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25
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Jaquet V, Wallerich S, Voegeli S, Túrós D, Viloria EC, Becskei A. Determinants of the temperature adaptation of mRNA degradation. Nucleic Acids Res 2022; 50:1092-1110. [PMID: 35018460 PMCID: PMC8789057 DOI: 10.1093/nar/gkab1261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 12/26/2022] Open
Abstract
The rate of chemical reactions increases proportionally with temperature, but the interplay of biochemical reactions permits deviations from this relation and adaptation. The degradation of individual mRNAs in yeast increased to varying degrees with temperature. We examined how these variations are influenced by the translation and codon composition of mRNAs. We developed a method that revealed the existence of a neutral half-life above which mRNAs are stabilized by translation but below which they are destabilized. The proportion of these two mRNA subpopulations remained relatively constant under different conditions, even with slow cell growth due to nutrient limitation, but heat shock reduced the proportion of translationally stabilized mRNAs. At the same time, the degradation of these mRNAs was partially temperature-compensated through Upf1, the mediator of nonsense-mediated decay. Compensation was also promoted by some asparagine and serine codons, whereas tyrosine codons promote temperature sensitization. These codons play an important role in the degradation of mRNAs encoding key cell membrane and cell wall proteins, which promote cell integrity.
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Affiliation(s)
- Vincent Jaquet
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Sandrine Wallerich
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Sylvia Voegeli
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Demeter Túrós
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Eduardo C Viloria
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Attila Becskei
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
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26
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Swaffer MP, Kim J, Chandler-Brown D, Langhinrichs M, Marinov GK, Greenleaf WJ, Kundaje A, Schmoller KM, Skotheim JM. Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size. Mol Cell 2021; 81:4861-4875.e7. [PMID: 34731644 PMCID: PMC8642314 DOI: 10.1016/j.molcel.2021.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/01/2021] [Accepted: 10/11/2021] [Indexed: 10/19/2022]
Abstract
Biosynthesis scales with cell size such that protein concentrations generally remain constant as cells grow. As an exception, synthesis of the cell-cycle inhibitor Whi5 "sub-scales" with cell size so that its concentration is lower in larger cells to promote cell-cycle entry. Here, we find that transcriptional control uncouples Whi5 synthesis from cell size, and we identify histones as the major class of sub-scaling transcripts besides WHI5 by screening for similar genes. Histone synthesis is thereby matched to genome content rather than cell size. Such sub-scaling proteins are challenged by asymmetric cell division because proteins are typically partitioned in proportion to newborn cell volume. To avoid this fate, Whi5 uses chromatin-binding to partition similar protein amounts to each newborn cell regardless of cell size. Disrupting both Whi5 synthesis and chromatin-based partitioning weakens G1 size control. Thus, specific transcriptional and partitioning mechanisms determine protein sub-scaling to control cell size.
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Affiliation(s)
| | - Jacob Kim
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kurt M Schmoller
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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27
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Wu M, Xu G, Han C, Luan PF, Xing YH, Nan F, Yang LZ, Huang Y, Yang ZH, Shan L, Yang L, Liu J, Chen LL. lncRNA SLERT controls phase separation of FC/DFCs to facilitate Pol I transcription. Science 2021; 373:547-555. [PMID: 34326237 DOI: 10.1126/science.abf6582] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/15/2021] [Accepted: 05/13/2021] [Indexed: 12/24/2022]
Abstract
RNA polymerase I (Pol I) transcription takes place at the border of the fibrillar center (FC) and the dense fibrillar component (DFC) in the nucleolus. Here, we report that individual spherical FC/DFC units are coated by the DEAD-box RNA helicase DDX21 in human cells. The long noncoding RNA (lncRNA) SLERT binds to DDX21 RecA domains to promote DDX21 to adopt a closed conformation at a substoichiometric ratio through a molecular chaperone-like mechanism resulting in the formation of hypomultimerized and loose DDX21 clusters that coat DFCs, which is required for proper FC/DFC liquidity and Pol I processivity. Our results suggest that SLERT is an RNA regulator that controls the biophysical properties of FC/DFCs and thus ribosomal RNA production.
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Affiliation(s)
- Man Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Guang Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Chong Han
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Peng-Fei Luan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Yu-Hang Xing
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Fang Nan
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Youkui Huang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Zheng-Hu Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lin Shan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Li Yang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jiaquan Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China.
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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28
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Yao RW, Luan PF, Chen LL. An optimized fixation method containing glyoxal and paraformaldehyde for imaging nuclear bodies. RNA (NEW YORK, N.Y.) 2021; 27:725-733. [PMID: 33846273 PMCID: PMC8127994 DOI: 10.1261/rna.078671.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/08/2021] [Indexed: 05/26/2023]
Abstract
The mammalian cell nucleus contains different types of membrane-less nuclear bodies (NBs) consisting of proteins and RNAs. Microscopic imaging has been widely applied to study the organization and structure of NBs. However, current fixation methods are not optimized for such imaging: When a fixation method is chosen to maximize the quality of the RNA fluorescence in situ hybridization (FISH), it often limits the labeling efficiency of proteins or affects the ultrastructure of NBs. Here, we report that addition of glyoxal (GO) into the classical paraformaldehyde (PFA) fixation step not only improves FISH signals for RNAs in NBs via augmented permeability of the fixed nucleus and enhanced accessibility of probes, but also largely preserves protein fluorescent signals during fixation and immunostaining. We also show that GO/PFA fixation enables the covisualization of different types of nuclear bodies with minimal impact on their ultrastructures under super-resolution microscopy.
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Affiliation(s)
- Run-Wen Yao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Peng-Fei Luan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 330106, China
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29
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A Highly Conserved Circular RNA Is Required to Keep Neural Cells in a Progenitor State in the Mammalian Brain. Cell Rep 2021; 30:2170-2179.e5. [PMID: 32075758 DOI: 10.1016/j.celrep.2020.01.083] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 11/19/2019] [Accepted: 01/23/2020] [Indexed: 11/22/2022] Open
Abstract
circSLC45A4 is the main RNA splice isoform produced from its genetic locus and one of the highest expressed circRNAs in the developing human frontal cortex. Knockdown of this highly conserved circRNA in a human neuroblastoma cell line is sufficient to induce spontaneous neuronal differentiation, measurable by increased expression of neuronal marker genes. Depletion of circSlc45a4 in the developing mouse cortex causes a significant reduction of the basal progenitor pool and increases the expression of neurogenic regulators. Furthermore, knockdown of circSlc45a4a induces a significant depletion of cells in the cortical plate. In addition, deconvolution of the bulk RNA-seq data with the help of single-cell RNA-seq data validates the depletion of basal progenitors and reveals an increase in Cajal-Retzius cells. In summary, we present a detailed study of a highly conserved circular RNA that is necessary to maintain the pool of neural progenitors in vitro and in vivo.
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30
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Carpenter BS, Lee TW, Plott CF, Rodriguez JD, Brockett JS, Myrick DA, Katz DJ. Caenorhabditis elegans establishes germline versus soma by balancing inherited histone methylation. Development 2021; 148:dev.196600. [PMID: 33462111 DOI: 10.1242/dev.196600] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022]
Abstract
Formation of a zygote is coupled with extensive epigenetic reprogramming to enable appropriate inheritance of histone methylation and prevent developmental delays. In Caenorhabditis elegans, this reprogramming is mediated by the H3K4me2 demethylase SPR-5 and the H3K9 methyltransferase, MET-2. In contrast, the H3K36 methyltransferase MES-4 maintains H3K36me2/3 at germline genes between generations to facilitate re-establishment of the germline. To determine whether the MES-4 germline inheritance pathway antagonizes spr-5; met-2 reprogramming, we examined the interaction between these two pathways. We found that the developmental delay of spr-5; met-2 mutant progeny is associated with ectopic H3K36me3 and the ectopic expression of MES-4-targeted germline genes in somatic tissues. Furthermore, the developmental delay is dependent upon MES-4 and the H3K4 methyltransferase, SET-2. We propose that MES-4 prevents crucial germline genes from being repressed by antagonizing maternal spr-5; met-2 reprogramming. Thus, the balance of inherited histone modifications is necessary to distinguish germline versus soma and prevent developmental delay.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Brandon S Carpenter
- Department of Cell Biology, Emory University School of Medicine, Atlanta GA 30322, USA
| | - Teresa W Lee
- Department of Cell Biology, Emory University School of Medicine, Atlanta GA 30322, USA
| | - Caroline F Plott
- Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
| | - Juan D Rodriguez
- Department of Cell Biology, Emory University School of Medicine, Atlanta GA 30322, USA
| | - Jovan S Brockett
- Department of Biology, Oglethorpe University, Atlanta GA 30319, USA
| | - Dexter A Myrick
- Department of Cell Biology, Emory University School of Medicine, Atlanta GA 30322, USA
| | - David J Katz
- Department of Cell Biology, Emory University School of Medicine, Atlanta GA 30322, USA
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Ladyzhets S, Antel M, Simao T, Gasek N, Cowan AE, Inaba M. Self-limiting stem-cell niche signaling through degradation of a stem-cell receptor. PLoS Biol 2020; 18:e3001003. [PMID: 33315855 PMCID: PMC7769618 DOI: 10.1371/journal.pbio.3001003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 12/28/2020] [Accepted: 11/30/2020] [Indexed: 11/29/2022] Open
Abstract
Stem-cell niche signaling is short-range in nature, such that only stem cells but not their differentiating progeny receive self-renewing signals. At the apical tip of the Drosophila testis, 8 to 10 germline stem cells (GSCs) surround the hub, a cluster of somatic cells that organize the stem-cell niche. We have previously shown that GSCs form microtubule-based nanotubes (MT-nanotubes) that project into the hub cells, serving as the platform for niche signal reception; this spatial arrangement ensures the reception of the niche signal specifically by stem cells but not by differentiating cells. The receptor Thickveins (Tkv) is expressed by GSCs and localizes to the surface of MT-nanotubes, where it receives the hub-derived ligand Decapentaplegic (Dpp). The fate of Tkv receptor after engaging in signaling on the MT-nanotubes has been unclear. Here we demonstrate that the Tkv receptor is internalized into hub cells from the MT-nanotube surface and subsequently degraded in the hub cell lysosomes. Perturbation of MT-nanotube formation and Tkv internalization from MT-nanotubes into hub cells both resulted in an overabundance of Tkv protein in GSCs and hyperactivation of a downstream signal, suggesting that the MT-nanotubes also serve a second purpose to dampen the niche signaling. Together, our results demonstrate that MT-nanotubes play dual roles to ensure the short-range nature of niche signaling by (1) providing an exclusive interface for the niche ligand-receptor interaction; and (2) limiting the amount of stem cell receptors available for niche signal reception. A stem cell niche is the specialized micro-environment that provides the signal to the resident stem cells to support their undifferentiated, self-renewing state. This study shows that the cells that compose the niche do not only provide the signal, but also take up the receptor of stem cells for subsequent lysosomal degradation; this mechanism is essential for restriction of niche signal range.
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Affiliation(s)
- Sophia Ladyzhets
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Matthew Antel
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Taylor Simao
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Nathan Gasek
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Ann E. Cowan
- Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, Connecticut, United States of America
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Mayu Inaba
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut, United States of America
- * E-mail:
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Pascual R, Segura-Morales C, Omerzu M, Bellora N, Belloc E, Castellazzi CL, Reina O, Eyras E, Maurice MM, Millanes-Romero A, Méndez R. mRNA spindle localization and mitotic translational regulation by CPEB1 and CPEB4. RNA (NEW YORK, N.Y.) 2020; 27:rna.077552.120. [PMID: 33323527 PMCID: PMC7901846 DOI: 10.1261/rna.077552.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/02/2020] [Indexed: 05/04/2023]
Abstract
Transition through cell cycle phases requires temporal and spatial regulation of gene expression to ensure accurate chromosome duplication and segregation. This regulation involves dynamic reprogramming of gene expression at multiple transcriptional and posttranscriptional levels. In transcriptionally silent oocytes, the CPEB-family of RNAbinding proteins coordinates temporal and spatial translation regulation of stored maternal mRNAs to drive meiotic progression. CPEB1 mediates mRNA localization to the meiotic spindle, which is required to ensure proper chromosome segregation. Temporal translational regulation also takes place in mitosis, where a large repertoire of transcripts are activated or repressed in specific cell cycle phases. However, whether control of localized translation at the spindle is required for mitosis is unclear, as mitotic and acentriolar-meiotic spindles are functionally and structurally different. Furthermore, the large differences in scale-ratio between cell volume and spindle size in oocytes compared to somatic mitotic cells may generate distinct requirements for gene expression compartmentalization in meiosis and mitosis. Here we show that mitotic spindles contain CPE-localized mRNAs and translating ribosomes. Moreover, CPEB1 and CPEB4 localize in the spindles and they may function sequentially in promoting mitotic stage transitions and correct chromosome segregation. Thus, CPEB1 and CPEB4 bind to specific spindle-associated transcripts controlling the expression and/or localization of their encoded factors that, respectively, drive metaphase and anaphase/cytokinesis.
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Affiliation(s)
- Rosa Pascual
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology
| | - Carolina Segura-Morales
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology
| | - Manja Omerzu
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht
| | - Nicolás Bellora
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue - CONICET
| | - Eulàlia Belloc
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology
| | - Chiara Lara Castellazzi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology
| | - Oscar Reina
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology
| | - Eduardo Eyras
- Department of Experimental and Health Sciences, Universidad Pompeu Fabra
| | - Madelon M Maurice
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht
| | - Alba Millanes-Romero
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology
| | - Raúl Méndez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology;
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Li K, Varden L, Henderson A, Lufkin T, Kraus P. Simultaneous detection of multiple mRNAs and proteins in bovine IVD cells and tissue with single cell resolution. Biotechnol Lett 2020; 43:13-24. [PMID: 32902710 DOI: 10.1007/s10529-020-02997-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 09/01/2020] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Interactions of cells with their neighbors and influences by the surrounding extracellular matrix (ECM) is reflected in a cells transcriptome and proteome. In tissues comprised of heterogeneous cell populations or cells depending on ECM signalling cues such as those of the intervertebral disc (IVD), this information is obscured or lost when cells are pooled for the commonly used transcript analysis by quantitative PCR or RNA sequencing. Instead, these cells require means to analyse RNA transcript and protein distribution at a single cell or subcellular level to identify different cell types and functions, without removing them from their surrounding signalling cues. RESULTS We developed a simple, sequential protocol combining RNA is situ hybridisation (RISH) and immunohistochemistry (IHC) for the simultaneous analysis of multiple transcripts alongside proteins. This allows one to characterize heterogeneous cell populations at the single cell level in the natural cell environment and signalling context, both in vivo and in vitro. This protocol is demonstrated on cells of the bovine IVD, for transcripts and proteins involved in mechanotransduction, stemness and cell proliferation. CONCLUSIONS A simple, sequential protocol combining RISH and IHC is presented that allows for simultaneous information on RNA transcripts and proteins to characterize cells within a heterogeneous cell population and complex signalling environments such as those of the IVD.
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Affiliation(s)
- Kangning Li
- Department of Biology, Clarkson University, Potsdam, NY, USA
| | - Lara Varden
- Department of Biology, Clarkson University, Potsdam, NY, USA
| | | | - Thomas Lufkin
- Department of Biology, Clarkson University, Potsdam, NY, USA
| | - Petra Kraus
- Department of Biology, Clarkson University, Potsdam, NY, USA.
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Raddaoui N, Croce S, Geiger F, Borodavka A, Möckl L, Stazzoni S, Viverge B, Bräuchle C, Frischmuth T, Engelke H, Carell T. Supersensitive Multifluorophore RNA-FISH for Early Virus Detection and Flow-FISH by Using Click Chemistry. Chembiochem 2020; 21:2214-2218. [PMID: 32187837 PMCID: PMC7496099 DOI: 10.1002/cbic.202000081] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/11/2020] [Indexed: 01/25/2023]
Abstract
The reliable detection of transcription events through the quantification of the corresponding mRNA is of paramount importance for the diagnostics of infections and diseases. The quantification and localization analysis of the transcripts of a particular gene allows disease states to be characterized more directly compared to an analysis on the transcriptome wide level. This is particularly needed for the early detection of virus infections as now required for emergent viral diseases, e. g. Covid-19. In situ mRNA analysis, however, is a formidable challenge and currently performed with sets of single-fluorophore-containing oligonucleotide probes that hybridize to the mRNA in question. Often a large number of probe strands (>30) are required to get a reliable signal. The more oligonucleotide probes are used, however, the higher the potential off-target binding effects that create background noise. Here, we used click chemistry and alkyne-modified DNA oligonucleotides to prepare multiple-fluorophore-containing probes. We found that these multiple-dye probes allow reliable detection and direct visualization of mRNA with only a very small number (5-10) of probe strands. The new method enabled the in situ detection of viral transcripts as early as 4 hours after infection.
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Affiliation(s)
- Nada Raddaoui
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | - Stefano Croce
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
- Baseclick GmbHFloriansbogen 2–482061Neuried (MünchenGermany
| | - Florian Geiger
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | - Alexander Borodavka
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular Biology, University of LeedsLeedsLS2 9JTUK
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QWUK
| | - Leonhard Möckl
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | - Samuele Stazzoni
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | - Bastien Viverge
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | - Christoph Bräuchle
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | | | - Hanna Engelke
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | - Thomas Carell
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
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Parker DM, Winkenbach LP, Boyson S, Saxton MN, Daidone C, Al-Mazaydeh ZA, Nishimura MT, Mueller F, Osborne Nishimura E. mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage. Development 2020; 147:dev186817. [PMID: 32541012 PMCID: PMC7358130 DOI: 10.1242/dev.186817] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/30/2020] [Indexed: 01/01/2023]
Abstract
Caenorhabditis elegans early embryos generate cell-specific transcriptomes despite lacking active transcription, thereby presenting an opportunity to study mechanisms of post-transcriptional regulatory control. We observed that some cell-specific mRNAs accumulate non-homogenously within cells, localizing to membranes, P granules (associated with progenitor germ cells in the P lineage) and P-bodies (associated with RNA processing). The subcellular distribution of transcripts differed in their dependence on 3'UTRs and RNA binding proteins, suggesting diverse regulatory mechanisms. Notably, we found strong but imperfect correlations between low translational status and P granule localization within the progenitor germ lineage. By uncoupling translation from mRNA localization, we untangled a long-standing question: Are mRNAs directed to P granules to be translationally repressed, or do they accumulate there as a consequence of this repression? We found that translational repression preceded P granule localization and could occur independently of it. Further, disruption of translation was sufficient to send homogenously distributed mRNAs to P granules. These results implicate transcriptional repression as a means to deliver essential maternal transcripts to the progenitor germ lineage for later translation.
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Affiliation(s)
- Dylan M Parker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Lindsay P Winkenbach
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Sam Boyson
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Matthew N Saxton
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Camryn Daidone
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Zainab A Al-Mazaydeh
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- Department of Biology and Biotechnology, Hashemite University, Zarqa, 13115, Jordan
| | - Marc T Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Florian Mueller
- Département Biologie Cellulaire et Infections, Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, 28 rue du Docteur Roux, 75015 Paris, France
| | - Erin Osborne Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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Markey FB, Parashar V, Batish M. Methods for spatial and temporal imaging of the different steps involved in RNA processing at single-molecule resolution. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1608. [PMID: 32543077 DOI: 10.1002/wrna.1608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/26/2022]
Abstract
RNA plays a quintessential role as a messenger of information from genotype (DNA) to phenotype (proteins), as well as acts as a regulatory molecule (noncoding RNAs). All steps in the journey of RNA from synthesis (transcription), splicing, transport, localization, translation, to its eventual degradation, comprise important steps in gene expression, thereby controlling the fate of the cell. This lifecycle refers to the majority of RNAs (primarily mRNAs), but not other RNAs such as tRNAs. Imaging these processes in fixed cells and in live cells has been an important tool in developing an understanding of the regulatory steps in RNAs journey. Single-cell and single-molecule imaging techniques enable a much deeper understanding of cellular biology, which is not possible with bulk studies involving RNA isolated from a large pool of cells. Classic techniques, such as fluorescence in situ hybridization (FISH), as well as more recent aptamer-based approaches, have provided detailed insights into RNA localization, and have helped to predict the functions carried out by many RNA species. However, there are still certain processing steps that await high-resolution imaging, which is an exciting and upcoming area of research. In this review, we will discuss the methods that have revolutionized single-molecule resolution imaging in general, the steps of RNA processing in which these methods have been used, and new emerging technologies. This article is categorized under: RNA Export and Localization > RNA Localization RNA Methods > RNA Analyses in Cells RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions.
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Affiliation(s)
- Fatu Badiane Markey
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Vijay Parashar
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Mona Batish
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA.,Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
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Abstract
The premise of this book is the importance of the tumor microenvironment (TME). Until recently, most research on and clinical attention to cancer biology, diagnosis, and prognosis were focused on the malignant (or premalignant) cellular compartment that could be readily appreciated using standard morphology-based imaging.
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38
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Li CC, Li Y, Zhang Y, Zhang CY. Single-molecule fluorescence resonance energy transfer and its biomedical applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115753] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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39
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Yang LZ, Wang Y, Li SQ, Yao RW, Luan PF, Wu H, Carmichael GG, Chen LL. Dynamic Imaging of RNA in Living Cells by CRISPR-Cas13 Systems. Mol Cell 2019; 76:981-997.e7. [PMID: 31757757 DOI: 10.1016/j.molcel.2019.10.024] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/25/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022]
Abstract
Visualizing the location and dynamics of RNAs in live cells is key to understanding their function. Here, we identify two endonuclease-deficient, single-component programmable RNA-guided and RNA-targeting Cas13 RNases (dCas13s) that allow robust real-time imaging and tracking of RNAs in live cells, even when using single 20- to 27-nt-long guide RNAs. Compared to the aptamer-based MS2-MCP strategy, an optimized dCas13 system is user friendly, does not require genetic manipulation, and achieves comparable RNA-labeling efficiency. We demonstrate that the dCas13 system is capable of labeling NEAT1, SatIII, MUC4, and GCN4 RNAs and allows the study of paraspeckle-associated NEAT1 dynamics. Applying orthogonal dCas13 proteins or combining dCas13 and MS2-MCP allows dual-color imaging of RNAs in single cells. Further combination of dCas13 and dCas9 systems allows simultaneous visualization of genomic DNA and RNA transcripts in living cells.
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Affiliation(s)
- Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yang Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Si-Qi Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Run-Wen Yao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Peng-Fei Luan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Huang Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Gordon G Carmichael
- Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, University of Connecticut Health Center, Farmington, CT 06030-3301, USA
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
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Yao RW, Xu G, Wang Y, Shan L, Luan PF, Wang Y, Wu M, Yang LZ, Xing YH, Yang L, Chen LL. Nascent Pre-rRNA Sorting via Phase Separation Drives the Assembly of Dense Fibrillar Components in the Human Nucleolus. Mol Cell 2019; 76:767-783.e11. [PMID: 31540874 DOI: 10.1016/j.molcel.2019.08.014] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 02/04/2019] [Accepted: 08/13/2019] [Indexed: 12/21/2022]
Abstract
Fibrillar centers (FCs) and dense fibrillar components (DFCs) are essential morphologically distinct sub-regions of mammalian cell nucleoli for rDNA transcription and pre-rRNA processing. Here, we report that a human nucleolus consists of several dozen FC/DFC units, each containing 2-3 transcriptionally active rDNAs at the FC/DFC border. Pre-rRNA processing factors, such as fibrillarin (FBL), form 18-24 clusters that further assemble into the DFC surrounding the FC. Mechanistically, the 5' end of nascent 47S pre-rRNA binds co-transcriptionally to the RNA-binding domain of FBL. FBL diffuses to the DFC, where local self-association via its glycine- and arginine-rich (GAR) domain forms phase-separated clusters to immobilize FBL-interacting pre-rRNA, thus promoting directional traffic of nascent pre-rRNA while facilitating pre-rRNA processing and DFC formation. These results unveil FC/DFC ultrastructures in nucleoli and suggest a conceptual framework for considering nascent RNA sorting using multivalent interactions of their binding proteins.
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Affiliation(s)
- Run-Wen Yao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Guang Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Ying Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Lin Shan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Peng-Fei Luan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yang Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Man Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yu-Hang Xing
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Li Yang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
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Grimaldi A, Pediconi N, Oieni F, Pizzarelli R, Rosito M, Giubettini M, Santini T, Limatola C, Ruocco G, Ragozzino D, Di Angelantonio S. Neuroinflammatory Processes, A1 Astrocyte Activation and Protein Aggregation in the Retina of Alzheimer's Disease Patients, Possible Biomarkers for Early Diagnosis. Front Neurosci 2019; 13:925. [PMID: 31551688 PMCID: PMC6737046 DOI: 10.3389/fnins.2019.00925] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/19/2019] [Indexed: 12/28/2022] Open
Abstract
Alzheimer’s disease (AD), a primary cause of dementia in the aging population, is characterized by extracellular amyloid-beta peptides aggregation, intracellular deposits of hyperphosphorylated tau, neurodegeneration and glial activation in the brain. It is commonly thought that the lack of early diagnostic criteria is among the main causes of pharmacological therapy and clinical trials failure; therefore, the actual challenge is to define new biomarkers and non-invasive technologies to measure neuropathological changes in vivo at pre-symptomatic stages. Recent evidences obtained from human samples and mouse models indicate the possibility to detect protein aggregates and other pathological features in the retina, paving the road for non-invasive rapid detection of AD biomarkers. Here, we report the presence of amyloid beta plaques, tau tangles, neurodegeneration and detrimental astrocyte and microglia activation according to a disease associated microglia phenotype (DAM). Thus, we propose the human retina as a useful site for the detection of cellular and molecular changes associated with Alzheimer’s disease.
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Affiliation(s)
- Alfonso Grimaldi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
| | - Natalia Pediconi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
| | - Francesca Oieni
- Department of Physiology and Pharmacology, Sapienza University, Rome, Italy
| | - Rocco Pizzarelli
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
| | - Maria Rosito
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
| | | | - Tiziana Santini
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
| | - Cristina Limatola
- Department of Physiology and Pharmacology, Sapienza University, Rome, Italy.,IRCCS Neuromed, Pozzilli, Italy
| | - Giancarlo Ruocco
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy.,Department of Physics, Sapienza University, Rome, Italy
| | - Davide Ragozzino
- Department of Physiology and Pharmacology, Sapienza University, Rome, Italy.,IRCCS Neuromed, Pozzilli, Italy
| | - Silvia Di Angelantonio
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy.,Department of Physiology and Pharmacology, Sapienza University, Rome, Italy
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42
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Issa AR, Picao-Osorio J, Rito N, Chiappe ME, Alonso CR. A Single MicroRNA-Hox Gene Module Controls Equivalent Movements in Biomechanically Distinct Forms of Drosophila. Curr Biol 2019; 29:2665-2675.e4. [PMID: 31327720 PMCID: PMC6710004 DOI: 10.1016/j.cub.2019.06.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/18/2019] [Accepted: 06/27/2019] [Indexed: 12/19/2022]
Abstract
Movement is the main output of the nervous system. It emerges during development to become a highly coordinated physiological process essential to survival and adaptation of the organism to the environment. Similar movements can be observed in morphologically distinct developmental stages of an organism, but it is currently unclear whether or not these movements have a common molecular cellular basis. Here we explore this problem in Drosophila, focusing on the roles played by the microRNA (miRNA) locus miR-iab4/8, which we previously showed to be essential for the normal corrective response displayed by the fruit fly larva when turned upside down (self-righting). Our study shows that miR-iab4 is required for normal self-righting across all three Drosophila larval stages. Unexpectedly, we also discover that this miRNA is essential for normal self-righting behavior in the adult fly, an organism with different morphology, neural constitution, and biomechanics. Through the combination of gene expression, optical imaging, and quantitative behavioral approaches, we provide evidence that miR-iab4 exerts its effects on adult self-righting behavior in part through repression of the Hox gene Ultrabithorax (Ubx) in a specific set of adult motor neurons, the NB2-3/lin15 neurons. Our results show that miRNA controls the function, rather than the morphology, of these neurons and demonstrate that post-developmental changes in Hox gene expression can modulate behavior in the adult. Our work reveals that a common miRNA-Hox genetic module can be re-deployed in different neurons to control functionally equivalent movements in biomechanically distinct organisms and describes a novel post-developmental role of the Hox genes in adult neural function. The fruit fly miRNA gene miR-iab4 controls the same behavior in the larva and adult miR-iab4 exerts its behavioral roles via repression of the Hox gene Ultrabithorax miRNA/Hox inputs affect the physiology and not the anatomy of specific motor neurons Conditional expression shows a novel role of the Hox genes in adult neural function
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Affiliation(s)
- A Raouf Issa
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Biology Road, Brighton BN1 9QG, UK
| | - João Picao-Osorio
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Biology Road, Brighton BN1 9QG, UK
| | - Nuno Rito
- Champalimaud Neuroscience Programme, Champalimaud Center for the Unknown, Brasília Avenue, Doca de Pedrouços, 1400-038 Lisbon, Portugal
| | - M Eugenia Chiappe
- Champalimaud Neuroscience Programme, Champalimaud Center for the Unknown, Brasília Avenue, Doca de Pedrouços, 1400-038 Lisbon, Portugal
| | - Claudio R Alonso
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Biology Road, Brighton BN1 9QG, UK.
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43
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Omerzu M, Fenderico N, de Barbanson B, Sprangers J, de Ridder J, Maurice MM. Three-dimensional analysis of single molecule FISH in human colon organoids. Biol Open 2019; 8:bio.042812. [PMID: 31362950 PMCID: PMC6737975 DOI: 10.1242/bio.042812] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The culturing of mini-organs (organoids) in three-dimensions (3D) presents a simple and powerful tool to investigate the principles underlying human organ development and tissue self-organization in both healthy and diseased states. Applications of single molecule analysis are highly informative for a comprehensive understanding of the complexity underlying tissue and organ physiology. To fully exploit the potential of single molecule technologies, the adjustment of protocols and tools to 3D tissue culture is required. Single molecule RNA fluorescence in situ hybridization (smFISH) is a robust technique for visualizing and quantifying individual transcripts. In addition, smFISH can be employed to study splice variants, fusion transcripts as well as transcripts of multiple genes at the same time. Here, we develop a 3-day protocol and validation method to perform smFISH in 3D in whole human organoids. We provide a number of applications to exemplify the diverse possibilities for the simultaneous detection of distinct mRNA transcripts, evaluation of their spatial distribution and the identification of divergent cell lineages in 3D in organoids.
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Affiliation(s)
- Manja Omerzu
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands
| | - Nicola Fenderico
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands
| | - Buys de Barbanson
- Oncode Institute and Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands.,Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Joep Sprangers
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands
| | - Jeroen de Ridder
- Oncode Institute and Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Madelon M Maurice
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands
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44
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Cui Y, Hu D, Markillie LM, Chrisler WB, Gaffrey MJ, Ansong C, Sussel L, Orr G. Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells. Nucleic Acids Res 2019; 46:e7. [PMID: 29040675 PMCID: PMC5778465 DOI: 10.1093/nar/gkx874] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/02/2017] [Indexed: 12/17/2022] Open
Abstract
Quantitative gene expression analysis in intact single cells can be achieved using single molecule-based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple oligonucleotide probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific probe binding and tissue autofluorescence, especially when only a small number of probes can be fitted to the target transcript. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on on-off duty cycles of photoswitchable dyes. This fluctuation localization imaging-based FISH (fliFISH) uses on-time fractions (measured over a series of exposures) collected from transcripts bound to as low as 8 probes, which are distinct from on-time fractions collected from nonspecifically bound probes or autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2 and their ratio (Nkx2-2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct on-time fractions, laying the foundation for reliable single-cell transcriptomics.
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Affiliation(s)
- Yi Cui
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
| | - Dehong Hu
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
| | - Lye Meng Markillie
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
| | - William B Chrisler
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
| | - Matthew J Gaffrey
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
| | - Charles Ansong
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
| | - Lori Sussel
- The Barbara Davis Center for Childhood Diabetes, School of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Galya Orr
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
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45
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Taliaferro JM. Classical and emerging techniques to identify and quantify localized RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1542. [PMID: 31044542 DOI: 10.1002/wrna.1542] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022]
Abstract
In essentially every cell, proteins are asymmetrically distributed according to their function. For many genes, this protein sorting problem is solved by transporting RNA molecules encoding the protein, rather than the protein itself, to the desired subcellular location. The protein is then translated on-site to immediately produce a correctly localized protein. This strategy is widely used as thousands of RNAs localize to distinct locations across diverse cell types and species. One of the fundamental challenges to study this process is the determination of the subcellular spatial distribution of any given RNA. The number of tools available for the study of RNA localization, from classical and state-of-the-art methods for the visualization of individual RNA molecules within cells to the profiling of localized transcriptomes, is rapidly growing. These include imaging-based approaches, a variety of biochemical and mechanical fractionation techniques, and proximity-labeling methods. These procedures allow for both the detailed study of the molecular requirements for the localization of individual RNA molecules and computational studies of RNA transport on a genomic scale. Together, they have the ability to allow insight into the regulatory principles that govern the localization of diverse RNAs. These new techniques provide the framework for integrating our knowledge of the regulation of RNA localization with that of other posttranscriptional processes. This article is categorized under: RNA Export and Localization > RNA Localization RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado
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46
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Melby ES, Cui Y, Borgatta J, Mensch AC, Hang MN, Chrisler WB, Dohnalkova A, Van Gilder JM, Alvarez CM, Smith JN, Hamers RJ, Orr G. Impact of lithiated cobalt oxide and phosphate nanoparticles on rainbow trout gill epithelial cells. Nanotoxicology 2018; 12:1166-1181. [DOI: 10.1080/17435390.2018.1508785] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Eric S. Melby
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, (WA), USA
| | - Yi Cui
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, (WA), USA
| | - Jaya Borgatta
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, (WI), USA
| | - Arielle C. Mensch
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, (WA), USA
| | - Mimi N. Hang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, (WI), USA
| | - William B. Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Alice Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, (WA), USA
| | - John M. Van Gilder
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, (WI), USA
| | - Catherine M. Alvarez
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, (WI), USA
| | - Jordan N. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert J. Hamers
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, (WI), USA
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, (WA), USA
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47
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Mehta GD, Ball DA, Eriksson PR, Chereji RV, Clark DJ, McNally JG, Karpova TS. Single-Molecule Analysis Reveals Linked Cycles of RSC Chromatin Remodeling and Ace1p Transcription Factor Binding in Yeast. Mol Cell 2018; 72:875-887.e9. [PMID: 30318444 DOI: 10.1016/j.molcel.2018.09.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/08/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022]
Abstract
It is unknown how the dynamic binding of transcription factors (TFs) is molecularly linked to chromatin remodeling and transcription. Using single-molecule tracking (SMT), we show that the chromatin remodeler RSC speeds up the search process of the TF Ace1p for its response elements (REs) at the CUP1 promoter. We quantified smFISH mRNA data using a gene bursting model and demonstrated that RSC regulates transcription bursts of CUP1 only by modulating TF occupancy but does not affect initiation and elongation rates. We show by SMT that RSC binds to activated promoters transiently, and based on MNase-seq data, that RSC does not affect the nucleosomal occupancy at CUP1. Therefore, transient binding of Ace1p and rapid bursts of transcription at CUP1 may be dependent on short repetitive cycles of nucleosome mobilization. This type of regulation reduces the transcriptional noise and ensures a homogeneous response of the cell population to heavy metal stress.
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Affiliation(s)
- Gunjan D Mehta
- CCR/LRBGE Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A Ball
- CCR/LRBGE Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter R Eriksson
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Razvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - James G McNally
- Institute for Soft Matter and Functional Materials, Helmholtz Center Berlin, Berlin 12489, Germany
| | - Tatiana S Karpova
- CCR/LRBGE Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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48
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Green CD, Ma Q, Manske GL, Shami AN, Zheng X, Marini S, Moritz L, Sultan C, Gurczynski SJ, Moore BB, Tallquist MD, Li JZ, Hammoud SS. A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq. Dev Cell 2018; 46:651-667.e10. [PMID: 30146481 DOI: 10.1016/j.devcel.2018.07.025] [Citation(s) in RCA: 266] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 07/03/2018] [Accepted: 07/30/2018] [Indexed: 02/07/2023]
Abstract
Spermatogenesis requires intricate interactions between the germline and somatic cells. Within a given cross section of a seminiferous tubule, multiple germ and somatic cell types co-occur. This cellular heterogeneity has made it difficult to profile distinct cell types at different stages of development. To address this challenge, we collected single-cell RNA sequencing data from ∼35,000 cells from the adult mouse testis and identified all known germ and somatic cells, as well as two unexpected somatic cell types. Our analysis revealed a continuous developmental trajectory of germ cells from spermatogonia to spermatids and identified candidate transcriptional regulators at several transition points during differentiation. Focused analyses delineated four subtypes of spermatogonia and nine subtypes of Sertoli cells; the latter linked to histologically defined developmental stages over the seminiferous epithelial cycle. Overall, this high-resolution cellular atlas represents a community resource and foundation of knowledge to study germ cell development and in vivo gametogenesis.
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Affiliation(s)
| | - Qianyi Ma
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel L Manske
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | | | - Xianing Zheng
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Simone Marini
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Lindsay Moritz
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Caleb Sultan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Bethany B Moore
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA; Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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49
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Asano SM, Gao R, Wassie AT, Tillberg PW, Chen F, Boyden ES. Expansion Microscopy: Protocols for Imaging Proteins and RNA in Cells and Tissues. ACTA ACUST UNITED AC 2018; 80:e56. [PMID: 30070431 DOI: 10.1002/cpcb.56] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Expansion microscopy (ExM) is a recently developed technique that enables nanoscale-resolution imaging of preserved cells and tissues on conventional diffraction-limited microscopes via isotropic physical expansion of the specimens before imaging. In ExM, biomolecules and/or fluorescent labels in the specimen are linked to a dense, expandable polymer matrix synthesized evenly throughout the specimen, which undergoes 3-dimensional expansion by ∼4.5 fold linearly when immersed in water. Since our first report, versions of ExM optimized for visualization of proteins, RNA, and other biomolecules have emerged. Here we describe best-practice, step-by-step ExM protocols for performing analysis of proteins (protein retention ExM, or proExM) as well as RNAs (expansion fluorescence in situ hybridization, or ExFISH), using chemicals and hardware found in a typical biology lab. Furthermore, a detailed protocol for handling and mounting expanded samples and for imaging them with confocal and light-sheet microscopes is provided. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Shoh M Asano
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Internal Medicine Research Unit, Pfizer Inc., Cambridge, Massachusetts
| | - Ruixuan Gao
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts
| | - Asmamaw T Wassie
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Department of Biological Engineering, MIT, Cambridge, Massachusetts
| | | | - Fei Chen
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Department of Biological Engineering, MIT, Cambridge, Massachusetts.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts.,Koch Institute, MIT, Cambridge, Massachusetts
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50
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Wadsworth GM, Parikh RY, Kim HD. Dual-probe RNA FRET-FISH in Yeast. Bio Protoc 2018; 8:e2867. [PMID: 34285981 PMCID: PMC8275227 DOI: 10.21769/bioprotoc.2867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/09/2018] [Accepted: 05/12/2018] [Indexed: 11/02/2022] Open
Abstract
mRNA Fluorescence In Situ Hybridization (FISH) is a technique commonly used to profile the distribution of transcripts in cells. When combined with the common single molecule technique Fluorescence Resonance Energy Transfer (FRET), FISH can also be used to profile the co-expression of nearby sequences in the transcript to measure processes such as alternate initiation or splicing variation of the transcript. Unlike in a conventional FISH method using multiple probes to target a single transcript, FRET is limited to the use of two probes labeled with matched dyes and requires the use of sensitized emission. Any widefield microscope capable of sensitive single molecule detection of Cy3 and Cy5 should be able to measure FRET in yeast cells. Alternatively, a FRET-FISH method can be used to unambiguously ascertain identity of the transcript without the use of a guide probe set used in other FISH techniques.
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Affiliation(s)
| | - Rasesh Y. Parikh
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Harold D. Kim
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
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