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Schulte SJ, Fornace ME, Hall JK, Shin GJ, Pierce NA. HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples. Development 2024; 151:dev202307. [PMID: 38415752 PMCID: PMC10941662 DOI: 10.1242/dev.202307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/21/2023] [Indexed: 02/29/2024]
Abstract
Signal amplification based on the mechanism of hybridization chain reaction (HCR) provides a unified framework for multiplex, quantitative, high-resolution imaging of RNA and protein targets in highly autofluorescent samples. With conventional bandpass imaging, multiplexing is typically limited to four or five targets owing to the difficulty in separating signals generated by fluorophores with overlapping spectra. Spectral imaging has offered the conceptual promise of higher levels of multiplexing, but it has been challenging to realize this potential in highly autofluorescent samples, including whole-mount vertebrate embryos. Here, we demonstrate robust HCR spectral imaging with linear unmixing, enabling simultaneous imaging of ten RNA and/or protein targets in whole-mount zebrafish embryos and mouse brain sections. Further, we demonstrate that the amplified and unmixed signal in each of the ten channels is quantitative, enabling accurate and precise relative quantitation of RNA and/or protein targets with subcellular resolution, and RNA absolute quantitation with single-molecule resolution, in the anatomical context of highly autofluorescent samples.
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Affiliation(s)
- Samuel J. Schulte
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mark E. Fornace
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John K. Hall
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grace J. Shin
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Niles A. Pierce
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Division of Engineering & Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
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Saga Y, Shimoyama Y, Yamada Y, Morikawa N, Kawata T. The cytosolic lncRNA dutA affects STATa signaling and developmental commitment in Dictyostelium. Genes Cells 2023; 28:111-128. [PMID: 36504347 DOI: 10.1111/gtc.12997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/27/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
STATa is a pivotal transcription factor for Dictyostelium development. dutA is the most abundant RNA transcribed by RNA polymerase II in Dictyostelium, and its functional interplay with STATa has been suggested. This study demonstrates that dutA RNA molecules are distributed as spot-like structures in the cytoplasm, and that its cell type-specific expression changes dramatically during development. dutA RNA was exclusively detectable in the prespore region of slugs and then predominantly localized in prestalk cells, including the organizer region, at the Mexican hat stage before most dutA transcripts, excluding those in prestalk O cells, disappeared as culmination proceeded. dutA RNA was not translated into small peptides from any potential open reading frame, which confirmed that it is a cytoplasmic lncRNA. Ectopic expression of dutA RNA in the organizer region of slugs caused a prolonged slug migration period. In addition, buffered suspension-cultured cells of the strain displayed reduced STATa nuclear translocation and phosphorylation on Tyr702. Analysis of gene expression in various dutA mutants revealed changes in the levels of several STATa-regulated genes, such as the transcription factors mybC and gtaG, which might affect the phenotype. dutA RNA may regulate several mRNA species, thereby playing an indirect role in STATa activation.
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Affiliation(s)
- Yukika Saga
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan.,Department of Pharmacology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Yudai Shimoyama
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Yoko Yamada
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan.,Department of Materials and Life Sciences, Sophia University, Tokyo, Japan
| | - Naoki Morikawa
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Takefumi Kawata
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ly S, Didiot MC, Ferguson CM, Coles AH, Miller R, Chase K, Echeverria D, Wang F, Sadri-Vakili G, Aronin N, Khvorova A. Mutant huntingtin messenger RNA forms neuronal nuclear clusters in rodent and human brains. Brain Commun 2022; 4:fcac248. [PMID: 36458209 PMCID: PMC9707646 DOI: 10.1093/braincomms/fcac248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/14/2022] [Accepted: 10/12/2022] [Indexed: 01/25/2023] Open
Abstract
Mutant messenger RNA (mRNA) and protein contribute to the clinical manifestation of many repeat-associated neurological disorders, with the presence of nuclear RNA clusters being a common pathological feature. Yet, investigations into Huntington's disease-caused by a CAG repeat expansion in exon 1 of the huntingtin (HTT) gene-have primarily focused on toxic protein gain-of-function as the primary disease-causing feature. To date, mutant HTT mRNA has not been identified as an in vivo hallmark of Huntington's disease. Here, we report that, in two Huntington's disease mouse models (YAC128 and BACHD-97Q-ΔN17), mutant HTT mRNA is retained in the nucleus. Widespread formation of large mRNA clusters (∼0.6-5 µm3) occurred in 50-75% of striatal and cortical neurons. Cluster formation was independent of age and driven by expanded repeats. Clusters associate with chromosomal transcriptional sites and quantitatively co-localize with the aberrantly processed N-terminal exon 1-intron 1 mRNA isoform, HTT1a. HTT1a mRNA clusters are observed in a subset of neurons from human Huntington's disease post-mortem brain and are likely caused by somatic expansion of repeats. In YAC128 mice, clusters, but not individual HTT mRNA, are resistant to antisense oligonucleotide treatment. Our findings identify mutant HTT/HTT1a mRNA clustering as an early, robust molecular signature of Huntington's disease, providing in vivo evidence that Huntington's disease is a repeat expansion disease with mRNA involvement.
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Affiliation(s)
| | | | | | - Andrew H Coles
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kathryn Chase
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Feng Wang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Ghazaleh Sadri-Vakili
- Mass General Institute for Neurodegenerative Disease, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Neil Aronin
- Correspondence may also be addressed to: Neil Aronin 368 Plantation Street, Albert Sherman Center Worcester, MA 01655, USA. E-mail:
| | - Anastasia Khvorova
- Correspondence to: Anastasia Khvorova 368 Plantation Street, Albert Sherman Center Worcester, MA 01655, USA E-mail:
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Chen X, Chen B, Shang X, Fang S. RNA in situ hybridization and expression of related genes regulating the accumulation of triterpenoids in Cyclocarya paliurus. Tree Physiol 2021; 41:2189-2197. [PMID: 33960380 DOI: 10.1093/treephys/tpab067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Cyclocarya paliurus (Batal.) Iljinskaja, a woody medicinal species in the Juglandaceae, grows extensively in subtropical areas of China. Triterpenoids in the leaves have health-promoting effects, including hypoglycemic and hypolipidemic activities. To understand triterpenoid biosynthesis, transport and accumulation in C. paliurus during the growing season, gene cloning, gene expression and RNA in situ hybridization of related genes were used, and accumulation was examined in various organs. The complete coding sequences (CDSs) of three genes, CpHMGR, CpDXR and CpSQS, were obtained from GenBank and RACE. RNA in situ hybridization signals of the three genes mainly occurred in the epidermis, palisade tissue, phloem and xylem of leaf, shoot and root, with the signals generally consistent with the accumulation of metabolites in tissues, except in the xylem. Both gene expression and triterpenoid accumulations showed seasonal variations in all organs. However, total triterpenoid content in the leaves was significantly higher than that in the shoots, with the maximum in shoots in August and in leaves in October. According to Pearson correlation analysis, triterpenoid accumulation in the leaves was significantly positively related with the relative expression of CpSQS. However, the relation between gene expression and accumulation was dependent on the role of the gene in the pathway as well as on the plant organ. The results suggested that most of the intermediates catalyzed by CpHMGR and CpDXR in young shoots and roots were used in growth and flowering in the spring, whereas subsequent triterpenoid biosynthesis in the downstream catalyzed by CpSQS mainly occurred in the leaves by using transferred and in situ intermediates as substrates. Thus, this study provides a reference to improve triterpenoid accumulation in future C. paliurus plantations.
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Affiliation(s)
- Xiaoling Chen
- College of Forestry, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
| | - Biqin Chen
- College of Forestry, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
| | - Xulan Shang
- College of Forestry, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
| | - Shengzuo Fang
- College of Forestry, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
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Yao RW, Luan PF, Chen LL. An optimized fixation method containing glyoxal and paraformaldehyde for imaging nuclear bodies. RNA 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Didiot MC, Ferguson CM, Ly S, Coles AH, Smith AO, Bicknell AA, Hall LM, Sapp E, Echeverria D, Pai AA, DiFiglia M, Moore MJ, Hayward LJ, Aronin N, Khvorova A. Nuclear Localization of Huntingtin mRNA Is Specific to Cells of Neuronal Origin. Cell Rep 2018; 24:2553-2560.e5. [PMID: 30184490 DOI: 10.1016/j.celrep.2018.07.106] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 06/30/2018] [Accepted: 07/30/2018] [Indexed: 12/21/2022] Open
Abstract
Huntington's disease (HD) is a monogenic neurodegenerative disorder representing an ideal candidate for gene silencing with oligonucleotide therapeutics (i.e., antisense oligonucleotides [ASOs] and small interfering RNAs [siRNAs]). Using an ultra-sensitive branched fluorescence in situ hybridization (FISH) method, we show that ∼50% of wild-type HTT mRNA localizes to the nucleus and that its nuclear localization is observed only in neuronal cells. In mouse brain sections, we detect Htt mRNA predominantly in neurons, with a wide range of Htt foci observed per cell. We further show that siRNAs and ASOs efficiently eliminate cytoplasmic HTT mRNA and HTT protein, but only ASOs induce a partial but significant reduction of nuclear HTT mRNA. We speculate that, like other mRNAs, HTT mRNA subcellular localization might play a role in important neuronal regulatory mechanisms.
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