1
|
Bellec M, Chen R, Dhayni J, Trullo A, Avinens D, Karaki H, Mazzarda F, Lenden-Hasse H, Favard C, Lehmann R, Bertrand E, Lagha M, Dufourt J. Boosting the toolbox for live imaging of translation. RNA (NEW YORK, N.Y.) 2024; 30:1374-1394. [PMID: 39060168 PMCID: PMC11404453 DOI: 10.1261/rna.080140.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 06/30/2024] [Indexed: 07/28/2024]
Abstract
Live imaging of translation based on tag recognition by a single-chain antibody is a powerful technique to assess translation regulation in living cells. However, this approach is challenging and requires optimization in terms of expression level and detection sensitivity of the system, especially in a multicellular organism. Here, we improved existing fluorescent tools and developed new ones to image and quantify nascent translation in the living Drosophila embryo and in mammalian cells. We tested and characterized five different green fluorescent protein variants fused to the single-chain fragment variable (scFv) and uncovered photobleaching, aggregation, and intensity disparities. Using different strengths of germline and somatic drivers, we determined that the availability of the scFv is critical in order to detect translation throughout development. We introduced a new translation imaging method based on a nanobody/tag system named ALFA-array, allowing the sensitive and simultaneous detection of the translation of several distinct mRNA species. Finally, we developed a largely improved RNA imaging system based on an MCP-tdStaygold fusion.
Collapse
Affiliation(s)
- Maëlle Bellec
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, 34293 Montpellier, France
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Ruoyu Chen
- Vilcek Institute of Graduate Studies, NYU School of Medicine, New York 10016, USA
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Jana Dhayni
- Institut de Génétique Humaine, University of Montpellier, CNRS, 34396 Montpellier, France
| | - Antonello Trullo
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, 34293 Montpellier, France
| | - Damien Avinens
- Institut de Recherche en Infectiologie de Montpellier, CNRS UMR 9004, University of Montpellier, Montpellier, 34293 Cedex 5, France
| | - Hussein Karaki
- Institut de Génétique Humaine, University of Montpellier, CNRS, 34396 Montpellier, France
| | - Flavia Mazzarda
- Institut de Génétique Humaine, University of Montpellier, CNRS, 34396 Montpellier, France
| | - Helene Lenden-Hasse
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, 34293 Montpellier, France
| | - Cyril Favard
- Institut de Recherche en Infectiologie de Montpellier, CNRS UMR 9004, University of Montpellier, Montpellier, 34293 Cedex 5, France
| | - Ruth Lehmann
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Edouard Bertrand
- Institut de Génétique Humaine, University of Montpellier, CNRS, 34396 Montpellier, France
| | - Mounia Lagha
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, 34293 Montpellier, France
| | - Jeremy Dufourt
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, 34293 Montpellier, France
- Institut de Recherche en Infectiologie de Montpellier, CNRS UMR 9004, University of Montpellier, Montpellier, 34293 Cedex 5, France
| |
Collapse
|
2
|
Hussain A, Wang M, Yu D, Zhang J, Naseer QA, Ullah A, Milon Essola J, Zhang X. Medical and molecular biophysical techniques as substantial tools in the era of mRNA-based vaccine technology. Biomater Sci 2024; 12:4117-4135. [PMID: 39016519 DOI: 10.1039/d4bm00561a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The COVID-19 pandemic prompted the advancement of vaccine technology using mRNA delivery into the host cells. Consequently, mRNA-based vaccines have emerged as a practical approach against SARS-CoV-2 owing to their inherent properties, such as cost-effectiveness, rapid manufacturing, and preservation. These features are vital, especially in resource-constrained regions. Nevertheless, the design of mRNA-based vaccines is intricately intertwined with the refinement of biophysical technologies, thereby establishing their high potential. The preparation of mRNA-based vaccines involves a sequence of phases combining medical and molecular biophysical technologies. Furthermore, their efficiency depends on the capability to optimize their positive attributes, thus paving the way for their subsequent preclinical and clinical evaluations. Using biophysical techniques, the characterization of nucleic acids extends from their initial formulation to their cellular internalization abilities and encapsulation in biomolecule complexes, such as lipid nanoparticles (LNPs), for designing mRNA-based LNPs. Furthermore, nanoparticles are subjected to a series of careful screening steps to assess their physical and chemical characteristics before achieving an optimum formulation suitable for preclinical and clinical studies. This review provides a comprehensive understanding of the fundamental role of biophysical techniques in the complex development of mRNA-based vaccines and their role in the recent success during the COVID-19 pandemic.
Collapse
Affiliation(s)
- Abid Hussain
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
| | - Maoye Wang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
| | - Dan Yu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
| | - Jiahui Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
| | - Qais Ahmad Naseer
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Aftab Ullah
- School of Medicine, Huaqiao University, No. 269 Chenghua North Rd., Quanzhou, Fujian 362021, China.
| | - Julien Milon Essola
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Centre for Nanoscience and Technology of China, No. 11, First North Road, Zhongguancun, Beijing, 100190, P.R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xu Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
| |
Collapse
|
3
|
Liu Z, Bai T, Liu B, Yu L. MulStack: An ensemble learning prediction model of multilabel mRNA subcellular localization. Comput Biol Med 2024; 175:108289. [PMID: 38688123 DOI: 10.1016/j.compbiomed.2024.108289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 05/02/2024]
Abstract
Subcellular localization of mRNA is related to protein synthesis, cell polarity, cell movement and other biological regulation mechanisms. The distribution of mRNAs in subcellulars is similar to that of proteins, and most mRNAs are distributed in multiple subcellulars. Recently, some computational methods have been designed to predict the subcellular localization of mRNA. However, these methods only employed a sin-gle level of mRNA features and did not employ the position encoding of nucleotides in mRNA. In this paper, an ensemble learning prediction model is proposed, named MulStack, which is based on random forest and deep learning for multilabel mRNA subcellular localization. The proposed method employs two levels of mRNA features, including sequence-level and residue-level features, and position encoding is employed for the first time in the field of subcellular localization of mRNA. Random forest is employed to learn mRNA sequence-level feature, deep learning is employed to learn mRNA sequence-level feature and mRNA residue-level combined with position encoding. And the outputs of random forest and deep learning model will be weighted sum as the prediction probability. Compared with existing methods, the results show that MulStack is the best in the localization of the nucleus, cytosol and exosome. In addition, position weight matrices (PWMs) are extracted by convolutional neural networks (CNNs) that can be matched with known RNA binding protein motifs. Gene ontology (GO) enrichment analysis shows biological processes, molecular functions and cellular components of mRNA genes. The prediction web server of MulStack is freely accessible at http://bliulab.net/MulStack.
Collapse
Affiliation(s)
- Ziqi Liu
- School of Computer Science and Technology, Xidian University, Xian, 710075, China.
| | - Tao Bai
- School of Mathematics & Computer Science, Yan'an University, Shaanxi, 716000, China; School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Liang Yu
- School of Computer Science and Technology, Xidian University, Xian, 710075, China.
| |
Collapse
|
4
|
Zhou F, Tan P, Liu S, Chang L, Yang J, Sun M, Guo Y, Si Y, Wang D, Yu J, Ma Y. Subcellular RNA distribution and its change during human embryonic stem cell differentiation. Stem Cell Reports 2024; 19:126-140. [PMID: 38134924 PMCID: PMC10828685 DOI: 10.1016/j.stemcr.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/24/2023] Open
Abstract
The spatial localization of RNA within cells is closely related to its function and also involved in cell fate determination. However, the atlas of RNA distribution within cells and dynamic changes during the developmental process are largely unknown. In this study, five subcellular components, including cytoplasmic extract, membrane extract, soluble nuclear extract, chromatin-bound nuclear extract, and cytoskeletal extract, were isolated and the rules of subcellular RNA distribution in human embryonic stem cells (hESCs) and its change during hESC differentiation are summarized for the first time. The overall distribution patterns of coding and non-coding RNAs are revealed. Interestingly, some developmental genes are found to be transcribed but confined to the chromatin in undifferentiated hESC. Unexpectedly, alternative splicing and polyadenylation endow spatial heterogeneity among different isoforms of the same gene. Finally, the dynamic pattern of RNA distribution during hESC differentiation is characterized, which provides new clues for a comprehensive understanding hESC pluripotency and differentiation.
Collapse
Affiliation(s)
- Fanqi Zhou
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Puwen Tan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Siqi Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Le Chang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Jiabin Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Mengyao Sun
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yuehong Guo
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yanmin Si
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Dong Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China; Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, Sichuan, China; State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
| | - Yanni Ma
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China; Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, Sichuan, China.
| |
Collapse
|
5
|
Shilo A, Pegoraro G, Misteli T. High-Throughput RNA-HCR-FISH Detection of Endogenous Pre-mRNA Splice Variants. Methods Mol Biol 2024; 2784:133-146. [PMID: 38502483 DOI: 10.1007/978-1-0716-3766-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
RNA-fluorescence in situ hybridization (RNA-FISH) is an essential and widely used tool for visualizing RNA molecules in intact cells. Recent advances have increased RNA-FISH sensitivity, signal detection efficiency, and throughput. However, detection of endogenous mRNA splice variants has been challenging due to the limits of visualization of RNA-FISH fluorescence signals and due to the limited number of RNA-FISH probes per target. HiFENS (high-throughput FISH detection of endogenous pre-mRNA splicing isoforms) is a method that enables visualization and relative quantification of mRNA splice variants at single-cell resolution in an automated high-throughput manner. HiFENS incorporates HCR (hybridization chain reaction) signal amplification strategies to enhance the fluorescence signal generated by low abundance transcripts or a small number of FISH probes targeting short stretches of RNA, such as single exons. The technique offers a significant advance in high-throughput FISH-based RNA detection and provides a powerful tool that can be used as a readout in functional genomics screens to discover and dissect cellular pathways regulating gene expression and alternative pre-mRNA splicing events.
Collapse
Affiliation(s)
- Asaf Shilo
- Cell Biology of Genomes, Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility (HiTIF), Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD, USA
| | - Tom Misteli
- Cell Biology of Genomes, Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD, USA.
| |
Collapse
|
6
|
Cochard A, Safieddine A, Combe P, Benassy M, Weil D, Gueroui Z. Condensate functionalization with microtubule motors directs their nucleation in space and allows manipulating RNA localization. EMBO J 2023; 42:e114106. [PMID: 37724036 PMCID: PMC10577640 DOI: 10.15252/embj.2023114106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/20/2023] Open
Abstract
The localization of RNAs in cells is critical for many cellular processes. Whereas motor-driven transport of ribonucleoprotein (RNP) condensates plays a prominent role in RNA localization in cells, their study remains limited by the scarcity of available tools allowing to manipulate condensates in a spatial manner. To fill this gap, we reconstitute in cellula a minimal RNP transport system based on bioengineered condensates, which were functionalized with kinesins and dynein-like motors, allowing for their positioning at either the cell periphery or centrosomes. This targeting mostly occurs through the active transport of the condensate scaffolds, which leads to localized nucleation of phase-separated condensates. Then, programming the condensates to recruit specific mRNAs is able to shift the localization of these mRNAs toward the cell periphery or the centrosomes. Our method opens novel perspectives for examining the role of RNA localization as a driver of cellular functions.
Collapse
Affiliation(s)
- Audrey Cochard
- Department of Chemistry, École Normale SupérieurePSL University, Sorbonne Université, CNRSParisFrance
- Sorbonne Université, CNRS, Institut de Biologie Paris‐Seine (IBPS), Laboratoire de Biologie du DéveloppementParisFrance
| | - Adham Safieddine
- Sorbonne Université, CNRS, Institut de Biologie Paris‐Seine (IBPS), Laboratoire de Biologie du DéveloppementParisFrance
| | - Pauline Combe
- Department of Chemistry, École Normale SupérieurePSL University, Sorbonne Université, CNRSParisFrance
| | - Marie‐Noëlle Benassy
- Sorbonne Université, CNRS, Institut de Biologie Paris‐Seine (IBPS), Laboratoire de Biologie du DéveloppementParisFrance
| | - Dominique Weil
- Sorbonne Université, CNRS, Institut de Biologie Paris‐Seine (IBPS), Laboratoire de Biologie du DéveloppementParisFrance
| | - Zoher Gueroui
- Department of Chemistry, École Normale SupérieurePSL University, Sorbonne Université, CNRSParisFrance
| |
Collapse
|
7
|
Gala DS, Titlow JS, Teodoro RO, Davis I. Far from home: the role of glial mRNA localization in synaptic plasticity. RNA (NEW YORK, N.Y.) 2023; 29:153-169. [PMID: 36442969 PMCID: PMC9891262 DOI: 10.1261/rna.079422.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Neurons and glia are highly polarized cells, whose distal cytoplasmic functional subdomains require specific proteins. Neurons have axonal and dendritic cytoplasmic extensions containing synapses whose plasticity is regulated efficiently by mRNA transport and localized translation. The principles behind these mechanisms are equally attractive for explaining rapid local regulation of distal glial cytoplasmic projections, independent of their cell nucleus. However, in contrast to neurons, mRNA localization has received little experimental attention in glia. Nevertheless, there are many functionally diverse glial subtypes containing extensive networks of long cytoplasmic projections with likely localized regulation that influence neurons and their synapses. Moreover, glia have many other neuron-like properties, including electrical activity, secretion of gliotransmitters and calcium signaling, influencing, for example, synaptic transmission, plasticity and axon pruning. Here, we review previous studies concerning glial transcripts with important roles in influencing synaptic plasticity, focusing on a few cases involving localized translation. We discuss a variety of important questions about mRNA transport and localized translation in glia that remain to be addressed, using cutting-edge tools already available for neurons.
Collapse
Affiliation(s)
- Dalia S Gala
- Department of Biochemistry, The University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Joshua S Titlow
- Department of Biochemistry, The University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Rita O Teodoro
- iNOVA4Health, NOVA Medical School-Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa 1169-056, Portugal
| | - Ilan Davis
- Department of Biochemistry, The University of Oxford, Oxford OX1 3QU, United Kingdom
| |
Collapse
|
8
|
Cai J, Wang T, Deng X, Tang L, Liu L. GM-lncLoc: LncRNAs subcellular localization prediction based on graph neural network with meta-learning. BMC Genomics 2023; 24:52. [PMID: 36709266 PMCID: PMC9883864 DOI: 10.1186/s12864-022-09034-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/21/2022] [Indexed: 01/29/2023] Open
Abstract
In recent years, a large number of studies have shown that the subcellular localization of long non-coding RNAs (lncRNAs) can bring crucial information to the recognition of lncRNAs function. Therefore, it is of great significance to establish a computational method to accurately predict the subcellular localization of lncRNA. Previous prediction models are based on low-level sequences information and are troubled by the few samples problem. In this study, we propose a new prediction model, GM-lncLoc, which is based on the initial information extracted from the lncRNA sequence, and also combines the graph structure information to extract high level features of lncRNA. In addition, the training mode of meta-learning is introduced to obtain meta-parameters by training a series of tasks. With the meta-parameters, the final parameters of other similar tasks can be learned quickly, so as to solve the problem of few samples in lncRNA subcellular localization. Compared with the previous methods, GM-lncLoc achieved the best results with an accuracy of 93.4 and 94.2% in the benchmark datasets of 5 and 4 subcellular compartments, respectively. Furthermore, the prediction performance of GM-lncLoc was also better on the independent dataset. It shows the effectiveness and great potential of our proposed method for lncRNA subcellular localization prediction. The datasets and source code are freely available at https://github.com/JunzheCai/GM-lncLoc .
Collapse
Affiliation(s)
- Junzhe Cai
- grid.410739.80000 0001 0723 6903School of Information, Yunnan Normal University, Kunming, Yunnan China
| | - Ting Wang
- grid.410739.80000 0001 0723 6903School of Information, Yunnan Normal University, Kunming, Yunnan China
| | - Xi Deng
- grid.410739.80000 0001 0723 6903School of Information, Yunnan Normal University, Kunming, Yunnan China
| | - Lin Tang
- grid.410739.80000 0001 0723 6903Key Laboratory of Educational Information for Nationalities Ministry of Education, Yunnan Normal University, Kunming, Yunnan China
| | - Lin Liu
- grid.410739.80000 0001 0723 6903School of Information, Yunnan Normal University, Kunming, Yunnan China
| |
Collapse
|
9
|
Zhang J, Lin X, Chen Y, Li T, Lee AC, Chow EY, Cho WC, Chan T. LAFITE Reveals the Complexity of Transcript Isoforms in Subcellular Fractions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203480. [PMID: 36461702 PMCID: PMC9875686 DOI: 10.1002/advs.202203480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Characterization of the subcellular distribution of RNA is essential for understanding the molecular basis of biological processes. Here, the subcellular nanopore direct RNA-sequencing (DRS) of four lung cancer cell lines (A549, H1975, H358, and HCC4006) is performed, coupled with a computational pipeline, Low-abundance Aware Full-length Isoform clusTEr (LAFITE), to comprehensively analyze the full-length cytoplasmic and nuclear transcriptome. Using additional DRS and orthogonal data sets, it is shown that LAFITE outperforms current methods for detecting full-length transcripts, particularly for low-abundance isoforms that are usually overlooked due to poor read coverage. Experimental validation of six novel isoforms exclusively identified by LAFITE further confirms the reliability of this pipeline. By applying LAFITE to subcellular DRS data, the complexity of the nuclear transcriptome is revealed in terms of isoform diversity, 3'-UTR usage, m6A modification patterns, and intron retention. Overall, LAFITE provides enhanced full-length isoform identification and enables a high-resolution view of the RNA landscape at the isoform level.
Collapse
Affiliation(s)
- Jizhou Zhang
- School of Life SciencesThe Chinese University of Hong KongShatinHong Kong SARChina
- State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Xiao Lin
- School of Life SciencesThe Chinese University of Hong KongShatinHong Kong SARChina
- State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Yuelong Chen
- School of Life SciencesThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Tsz‐Ho Li
- School of Life SciencesThe Chinese University of Hong KongShatinHong Kong SARChina
- State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Alan Chun‐Kit Lee
- School of Life SciencesThe Chinese University of Hong KongShatinHong Kong SARChina
| | | | | | - Ting‐Fung Chan
- School of Life SciencesThe Chinese University of Hong KongShatinHong Kong SARChina
- State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SARChina
| |
Collapse
|
10
|
Tingey M, Schnell SJ, Yu W, Saredy J, Junod S, Patel D, Alkurdi AA, Yang W. Technologies Enabling Single-Molecule Super-Resolution Imaging of mRNA. Cells 2022; 11:3079. [PMID: 36231040 PMCID: PMC9564294 DOI: 10.3390/cells11193079] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
The transient nature of RNA has rendered it one of the more difficult biological targets for imaging. This difficulty stems both from the physical properties of RNA as well as the temporal constraints associated therewith. These concerns are further complicated by the difficulty in imaging endogenous RNA within a cell that has been transfected with a target sequence. These concerns, combined with traditional concerns associated with super-resolution light microscopy has made the imaging of this critical target difficult. Recent advances have provided researchers the tools to image endogenous RNA in live cells at both the cellular and single-molecule level. Here, we review techniques used for labeling and imaging RNA with special emphases on various labeling methods and a virtual 3D super-resolution imaging technique.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| |
Collapse
|
11
|
Wang Q, Xiao F, Su H, Liu H, Xu J, Tang H, Qin S, Fang Z, Lu Z, Wu J, Weng X, Zhou X. Inert Pepper aptamer-mediated endogenous mRNA recognition and imaging in living cells. Nucleic Acids Res 2022; 50:e84. [PMID: 35580055 PMCID: PMC9371900 DOI: 10.1093/nar/gkac368] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/01/2022] [Accepted: 05/12/2022] [Indexed: 02/06/2023] Open
Abstract
The development of RNA aptamers/fluorophores system is highly desirable for understanding the dynamic molecular biology of RNAs in vivo. Peppers-based imaging systems have been reported and applied for mRNA imaging in living cells. However, the need to insert corresponding RNA aptamer sequences into target RNAs and relatively low fluorescence signal limit its application in endogenous mRNA imaging. Herein, we remolded the original Pepper aptamer and developed a tandem array of inert Pepper (iPepper) fluorescence turn-on system. iPepper allows for efficient and selective imaging of diverse endogenous mRNA species in live cells with minimal agitation of the target mRNAs. We believe iPepper would significantly expand the applications of the aptamer/fluorophore system in endogenous mRNA imaging, and it has the potential to become a powerful tool for real-time studies in living cells and biological processing.
Collapse
Affiliation(s)
- Qi Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Feng Xiao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Haomiao Su
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China.,Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
| | - Hui Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Jinglei Xu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Heng Tang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Shanshan Qin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Zhentian Fang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Ziang Lu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Jian Wu
- School of Medicine, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China.,The Institute of Advanced Studies, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| |
Collapse
|
12
|
Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS. Subcellular Transcriptomics and Proteomics: A Comparative Methods Review. Mol Cell Proteomics 2022; 21:100186. [PMID: 34922010 PMCID: PMC8864473 DOI: 10.1016/j.mcpro.2021.100186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
The internal environment of cells is molecularly crowded, which requires spatial organization via subcellular compartmentalization. These compartments harbor specific conditions for molecules to perform their biological functions, such as coordination of the cell cycle, cell survival, and growth. This compartmentalization is also not static, with molecules trafficking between these subcellular neighborhoods to carry out their functions. For example, some biomolecules are multifunctional, requiring an environment with differing conditions or interacting partners, and others traffic to export such molecules. Aberrant localization of proteins or RNA species has been linked to many pathological conditions, such as neurological, cancer, and pulmonary diseases. Differential expression studies in transcriptomics and proteomics are relatively common, but the majority have overlooked the importance of subcellular information. In addition, subcellular transcriptomics and proteomics data do not always colocate because of the biochemical processes that occur during and after translation, highlighting the complementary nature of these fields. In this review, we discuss and directly compare the current methods in spatial proteomics and transcriptomics, which include sequencing- and imaging-based strategies, to give the reader an overview of the current tools available. We also discuss current limitations of these strategies as well as future developments in the field of spatial -omics.
Collapse
Affiliation(s)
- Josie A Christopher
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Aikaterini Geladaki
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Department of Genetics, University of Cambridge, Cambridge, UK
| | - Charlotte S Dawson
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Owen L Vennard
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
| |
Collapse
|
13
|
Abstract
The imaging of chromatin, genomic loci, RNAs, and proteins is very important to study their localization, interaction, and coordinated regulation. Recently, several clustered regularly interspaced short palindromic repeats (CRISPR) based imaging methods have been established. The refurbished tool kits utilizing deactivated Cas9 (dCas9) and dCas13 have been established to develop applications of CRISPR-Cas technology beyond genome editing. Here, we review recent advancements in CRISPR-based methods that enable efficient imaging and visualization of chromatin, genomic loci, RNAs, and proteins. RNA aptamers, Pumilio, SuperNova tagging system, molecular beacons, halotag, bimolecular fluorescence complementation, RNA-guided endonuclease in situ labeling, and oligonucleotide-based imaging methods utilizing fluorescent proteins, organic dyes, or quantum dots have been developed to achieve improved fluorescence and signal-to-noise ratio for the imaging of chromatin or genomic loci. RNA-guided RNA targeting CRISPR systems (CRISPR/dCas13) and gene knock-in strategies based on CRISPR/Cas9 mediated site-specific cleavage and DNA repair mechanisms have been employed for efficient RNA and protein imaging, respectively. A few CRISPR-Cas-based methods to investigate the coordinated regulation of DNA-protein, DNA-RNA, or RNA-protein interactions for understanding chromatin dynamics, transcription, and protein function are also available. Overall, the CRISPR-based methods offer a significant improvement in elucidating chromatin organization and dynamics, RNA visualization, and protein imaging. The current and future advancements in CRISPR-based imaging techniques can revolutionize genome biology research for various applications.
Collapse
Affiliation(s)
- Vikram Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
14
|
Meher PK, Rai A, Rao AR. mLoc-mRNA: predicting multiple sub-cellular localization of mRNAs using random forest algorithm coupled with feature selection via elastic net. BMC Bioinformatics 2021; 22:342. [PMID: 34167457 PMCID: PMC8223360 DOI: 10.1186/s12859-021-04264-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 06/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Localization of messenger RNAs (mRNAs) plays a crucial role in the growth and development of cells. Particularly, it plays a major role in regulating spatio-temporal gene expression. The in situ hybridization is a promising experimental technique used to determine the localization of mRNAs but it is costly and laborious. It is also a known fact that a single mRNA can be present in more than one location, whereas the existing computational tools are capable of predicting only a single location for such mRNAs. Thus, the development of high-end computational tool is required for reliable and timely prediction of multiple subcellular locations of mRNAs. Hence, we develop the present computational model to predict the multiple localizations of mRNAs. RESULTS The mRNA sequences from 9 different localizations were considered. Each sequence was first transformed to a numeric feature vector of size 5460, based on the k-mer features of sizes 1-6. Out of 5460 k-mer features, 1812 important features were selected by the Elastic Net statistical model. The Random Forest supervised learning algorithm was then employed for predicting the localizations with the selected features. Five-fold cross-validation accuracies of 70.87, 68.32, 68.36, 68.79, 96.46, 73.44, 70.94, 97.42 and 71.77% were obtained for the cytoplasm, cytosol, endoplasmic reticulum, exosome, mitochondrion, nucleus, pseudopodium, posterior and ribosome respectively. With an independent test set, accuracies of 65.33, 73.37, 75.86, 72.99, 94.26, 70.91, 65.53, 93.60 and 73.45% were obtained for the respective localizations. The developed approach also achieved higher accuracies than the existing localization prediction tools. CONCLUSIONS This study presents a novel computational tool for predicting the multiple localization of mRNAs. Based on the proposed approach, an online prediction server "mLoc-mRNA" is accessible at http://cabgrid.res.in:8080/mlocmrna/ . The developed approach is believed to supplement the existing tools and techniques for the localization prediction of mRNAs.
Collapse
Affiliation(s)
- Prabina Kumar Meher
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
| | | |
Collapse
|
15
|
Mangan H, McStay B. Human nucleoli comprise multiple constrained territories, tethered to individual chromosomes. Genes Dev 2021; 35:483-488. [PMID: 33664058 PMCID: PMC8015717 DOI: 10.1101/gad.348234.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/01/2021] [Indexed: 11/24/2022]
Abstract
It is unknown how ribosomal gene (rDNA) arrays from multiple chromosomal nucleolar organizers (NORs) partition within human nucleoli. Exploration of this paradigm for chromosomal organization is complicated by the shared DNA sequence composition of five NOR-bearing acrocentric chromosome p-arms. Here, we devise a methodology for genetic manipulation of individual NORs. Efficient "scarless" genome editing of rDNA repeats is achieved on "poised" human NORs held within monochromosomal cell hybrids. Subsequent transfer to human cells introduces "active" NORs yielding readily discernible functional customized ribosomes. We reveal that ribosome biogenesis occurs entirely within constrained territories, tethered to individual NORs inside a larger nucleolus.
Collapse
Affiliation(s)
- Hazel Mangan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway H91 W2TY, Ireland
| | - Brian McStay
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway H91 W2TY, Ireland
| |
Collapse
|
16
|
Ahmad A, Lin H, Shatabda S. Locate-R: Subcellular localization of long non-coding RNAs using nucleotide compositions. Genomics 2020; 112:2583-2589. [PMID: 32068122 DOI: 10.1016/j.ygeno.2020.02.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/11/2019] [Accepted: 02/12/2020] [Indexed: 12/12/2022]
Abstract
Knowledge of the sub-cellular localization of the most diverse class of transcribed RNA, long non-coding RNAs (lncRNAs) will lead us to identify different types of cancers and other diseases as lncRNAs play key role in related cellular functions. In recent days with the exponential growth of known records, it becomes essential to establish new machine learning based techniques to identify the new one due to faster and cheaper solutions provided compared to laboratory methods. In this paper, we propose Locate-R, a novel method for predicting the sub-cellular location of lncRNAs. We have used only n-gapped l-mer composition and l-mer composition as features and select best 655 features to build the model. This model is based locally deep support vector machines which significantly enhance the prediction accuracy with respect to exiting state-of-the-art methods. Our predictor is readily available for use as a stand-alone web application from: http://locate-r.azurewebsites.net/.
Collapse
Affiliation(s)
- Ahsan Ahmad
- Department of Computer Science and Engineering, United International University, Plot 2, United City, Madani Avenue, Satarkul, Badda, Dhaka 1212, Bangladesh
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, China
| | - Swakkhar Shatabda
- Department of Computer Science and Engineering, United International University, Plot 2, United City, Madani Avenue, Satarkul, Badda, Dhaka 1212, Bangladesh.
| |
Collapse
|
17
|
Pichon X, Robert MC, Bertrand E, Singer RH, Tutucci E. New Generations of MS2 Variants and MCP Fusions to Detect Single mRNAs in Living Eukaryotic Cells. Methods Mol Biol 2020; 2166:121-144. [PMID: 32710406 DOI: 10.1007/978-1-0716-0712-1_7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Live imaging of single RNA from birth to death brought important advances in our understanding of the spatiotemporal regulation of gene expression. These studies have provided a comprehensive understanding of RNA metabolism by describing the process step by step. Most of these studies used for live imaging a genetically encoded RNA-tagging system fused to fluorescent proteins. One of the best characterized RNA-tagging systems is derived from the bacteriophage MS2 and it allows single RNA imaging in real-time and live cells. This system has been successfully used to track the different steps of mRNA processing in many living organisms. The recent development of optimized MS2 and MCP variants now allows the labeling of endogenous RNAs and their imaging without modifying their behavior. In this chapter, we discuss the improvements in detecting single mRNAs with different variants of MCP and fluorescent proteins that we tested in yeast and mammalian cells. Moreover, we describe protocols using MS2-MCP systems improved for real-time imaging of single mRNAs and transcription dynamics in S. cerevisiae and mammalian cells, respectively.
Collapse
Affiliation(s)
- Xavier Pichon
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.,Equipe labélisée Ligue Nationale Contre le Cancer, Montpellier, France
| | - Marie-Cécile Robert
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.,Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.,Janelia Research Campus of the HHMI, Ashburn, VA, USA
| | - Evelina Tutucci
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
18
|
Su ZD, Huang Y, Zhang ZY, Zhao YW, Wang D, Chen W, Chou KC, Lin H. iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC. Bioinformatics 2019; 34:4196-4204. [PMID: 29931187 DOI: 10.1093/bioinformatics/bty508] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/19/2018] [Indexed: 12/20/2022] Open
Abstract
Motivation Long non-coding RNAs (lncRNAs) are a class of RNA molecules with more than 200 nucleotides. They have important functions in cell development and metabolism, such as genetic markers, genome rearrangements, chromatin modifications, cell cycle regulation, transcription and translation. Their functions are generally closely related to their localization in the cell. Therefore, knowledge about their subcellular locations can provide very useful clues or preliminary insight into their biological functions. Although biochemical experiments could determine the localization of lncRNAs in a cell, they are both time-consuming and expensive. Therefore, it is highly desirable to develop bioinformatics tools for fast and effective identification of their subcellular locations. Results We developed a sequence-based bioinformatics tool called 'iLoc-lncRNA' to predict the subcellular locations of LncRNAs by incorporating the 8-tuple nucleotide features into the general PseKNC (Pseudo K-tuple Nucleotide Composition) via the binomial distribution approach. Rigorous jackknife tests have shown that the overall accuracy achieved by the new predictor on a stringent benchmark dataset is 86.72%, which is over 20% higher than that by the existing state-of-the-art predictor evaluated on the same tests. Availability and implementation A user-friendly webserver has been established at http://lin-group.cn/server/iLoc-LncRNA, by which users can easily obtain their desired results. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Zhen-Dong Su
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan Huang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhao-Yue Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Ya-Wei Zhao
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dong Wang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wei Chen
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China.,Gordon Life Science Institute, Boston, MA, USA
| | - Kuo-Chen Chou
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Gordon Life Science Institute, Boston, MA, USA
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Gordon Life Science Institute, Boston, MA, USA
| |
Collapse
|
19
|
Fazal FM, Han S, Parker KR, Kaewsapsak P, Xu J, Boettiger AN, Chang HY, Ting AY. Atlas of Subcellular RNA Localization Revealed by APEX-Seq. Cell 2019; 178:473-490.e26. [PMID: 31230715 PMCID: PMC6786773 DOI: 10.1016/j.cell.2019.05.027] [Citation(s) in RCA: 354] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/31/2018] [Accepted: 05/14/2019] [Indexed: 01/25/2023]
Abstract
We introduce APEX-seq, a method for RNA sequencing based on direct proximity labeling of RNA using the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome as a resource, revealing extensive patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.
Collapse
Affiliation(s)
- Furqan M Fazal
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shuo Han
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Kevin R Parker
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pornchai Kaewsapsak
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jin Xu
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alistair N Boettiger
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Alice Y Ting
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| |
Collapse
|
20
|
mRNA Detection with Fluorescence-base Imaging Techniques for Arthritis Diagnosis. JOURNAL OF RHEUMATOLOGY RESEARCH 2019; 1:39-46. [PMID: 33709083 PMCID: PMC7946156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
21
|
Bayer LV, Omar OS, Bratu DP, Catrina IE. PinMol: Python application for designing molecular beacons for live cell imaging of endogenous mRNAs. RNA (NEW YORK, N.Y.) 2019; 25:305-318. [PMID: 30573696 PMCID: PMC6380279 DOI: 10.1261/rna.069542.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Molecular beacons are nucleic acid oligomers labeled with a fluorophore and a quencher that fold in a hairpin-shaped structure, which fluoresce only when bound to their target RNA. They are used for the visualization of endogenous mRNAs in live cells. Here, we report a Python program (PinMol) that designs molecular beacons best suited for live cell imaging by using structural information from secondary structures of the target RNA, predicted via energy minimization approaches. PinMol takes into account the accessibility of the targeted regions, as well as the inter- and intramolecular interactions of each selected probe. To demonstrate its applicability, we synthesized an oskar mRNA-specific molecular beacon (osk1236), which is selected by PinMol to target a more accessible region than a manually designed oskar-specific molecular beacon (osk2216). We previously demonstrated osk2216 to be efficient in detecting oskar mRNA in in vivo experiments. Here, we show that osk1236 outperformed osk2216 in live cell imaging experiments.
Collapse
Affiliation(s)
- Livia V Bayer
- Biological Sciences Department, Hunter College, City University of New York, New York, New York 10065, USA
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Omar S Omar
- Biological Sciences Department, Hunter College, City University of New York, New York, New York 10065, USA
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Diana P Bratu
- Biological Sciences Department, Hunter College, City University of New York, New York, New York 10065, USA
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Irina E Catrina
- Biological Sciences Department, Hunter College, City University of New York, New York, New York 10065, USA
| |
Collapse
|
22
|
Wan Y, Zhu N, Lu Y, Wong PK. DNA Transformer for Visualizing Endogenous RNA Dynamics in Live Cells. Anal Chem 2019; 91:2626-2633. [DOI: 10.1021/acs.analchem.8b02826] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ying Wan
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, P. R. China
| | - Ninghao Zhu
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yi Lu
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Pak Kin Wong
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Mechanical Engineering and Department of Surgery, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
23
|
Abstract
With its rapid development, ease of collection, and the presence of a unique layer of nuclei located close to the surface, the Drosophila syncytial embryo is ideally suited to study the establishment of gene expression patterns during development. Recent improvements in RNA labeling technologies and confocal microscopy allow for visualizing gene activation and quantifying transcriptional dynamics in living Drosophila embryos. Here we review the available tools for mRNA fluorescent labeling and detection in live embryos and precisely describe the overall procedure, from design to mounting and confocal imaging.
Collapse
Affiliation(s)
- Carola Fernandez
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, Cedex 5, France
| | - Mounia Lagha
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, Cedex 5, France.
| |
Collapse
|
24
|
Li Y, Ke K, Spitale RC. Biochemical Methods To Image and Analyze RNA Localization: From One to Many. Biochemistry 2018; 58:379-386. [DOI: 10.1021/acs.biochem.8b01087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
25
|
Uddin MI, Kilburn TC, Yang R, McCollum GW, Wright DW, Penn JS. Targeted Imaging of VCAM-1 mRNA in a Mouse Model of Laser-Induced Choroidal Neovascularization Using Antisense Hairpin-DNA-Functionalized Gold-Nanoparticles. Mol Pharm 2018; 15:5514-5520. [PMID: 30350640 DOI: 10.1021/acs.molpharmaceut.8b00661] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mouse laser-induced choroidal neovascularization (mouse LCNV) recapitulates the "wet" form of human age-related macular degeneration (AMD). Vascular cell adhesion molecule-1 (VCAM-1) is a known inflammatory biomarker, and it increases in the choroidal neovascular tissues characteristic of this experimental model. We have designed and constructed gold nanoparticles (AuNPs) functionalized with hairpin-DNA that incorporates an antisense sequence complementary to VCAM-1 mRNA (AS-VCAM-1 hAuNPs) and tested them as optical imaging probes. The 3' end of the hairpin is coupled to a near-infrared fluorophore that is quenched by the AuNP surface via Förster resonance energy transfer (FRET). Hybridization of the antisense sequence to VCAM-1 mRNA displaces the fluorophore away from the AuNP surface, inducing fluorescent activity. In vitro testing showed that hAuNPs hybridize to an exogenous complementary oligonucleotide within a pH range of 4.5-7.4, and that they are stable at reduced pH. LCNV mice received tail-vein injections of AS-VCAM-1 hAuNPs. Hyperspectral imaging revealed the delivery of AS-VCAM-1 hAuNPs to excised choroidal tissues. Fluorescent images of CNV lesions were obtained, presumably in response to the hybridization of AS-hAuNPs to LCNV-induced VCAM-1 mRNA. This is the first demonstration of systemic delivery of hAuNPs to ocular tissues to facilitate mRNA imaging of any target.
Collapse
Affiliation(s)
- Md Imam Uddin
- Department of Ophthalmology and Visual Sciences , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States
| | - Tyler C Kilburn
- Department of Ophthalmology and Visual Sciences , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States
| | - Rong Yang
- Department of Ophthalmology and Visual Sciences , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States
| | - Gary W McCollum
- Department of Ophthalmology and Visual Sciences , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States
| | - David W Wright
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - John S Penn
- Department of Ophthalmology and Visual Sciences , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States.,Department of Molecular Physiology and Biophysics , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States
| |
Collapse
|
26
|
Suter B. RNA localization and transport. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:938-951. [PMID: 30496039 DOI: 10.1016/j.bbagrm.2018.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 12/30/2022]
Abstract
RNA localization serves numerous purposes from controlling development and differentiation to supporting the physiological activities of cells and organisms. After a brief introduction into the history of the study of mRNA localization I will focus on animal systems, describing in which cellular compartments and in which cell types mRNA localization was observed and studied. In recent years numerous novel localization patterns have been described, and countless mRNAs have been documented to accumulate in specific subcellular compartments. These fascinating revelations prompted speculations about the purpose of localizing all these mRNAs. In recent years experimental evidence for an unexpected variety of different functions has started to emerge. Aside from focusing on the functional aspects, I will discuss various ways of localizing mRNAs with a focus on the mechanism of active and directed transport on cytoskeletal tracks. Structural studies combined with imaging of transport and biochemical studies have contributed to the enormous recent progress, particularly in understanding how dynein/dynactin/BicD (DDB) dependent transport on microtubules works. This transport process actively localizes diverse cargo in similar ways to the minus end of microtubules and, at least in flies, also individual mRNA molecules. A sophisticated mechanism ensures that cargo loading licenses processive transport.
Collapse
Affiliation(s)
- Beat Suter
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland.
| |
Collapse
|
27
|
Kim HJ, Kang DH, Yang SH, Lee E, Ha T, Lee BC, Kim Y, Hwang KS, Shin HJ, Kim J. A Simple Separation Method of the Protein and Polystyrene Bead-Labeled Protein for Enhancing the Performance of Fluorescent Sensor. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2018; 2018:8461380. [PMID: 30116650 PMCID: PMC6079413 DOI: 10.1155/2018/8461380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/31/2018] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
Dielectrophoresis- (DEP-) based separation method between a protein, amyloid beta 42, and polystyrene (PS) beads in different microholes was demonstrated for enhancement of performance for bead-based fluorescent sensor. An intensity of ∇|E|2 was relative to a diameter of a microhole, and the diameters of two microholes for separation between the protein and PS beads were simulated to 3 μm and 15 μm, respectively. The microholes were fabricated by microelectromechanical systems (MEMS). The separation between the protein and the PS beads was demonstrated by comparing the average intensity of fluorescence (AIF) by each molecule. Relative AIF was measured in various applying voltage and time conditions, and the conditions for allocating the PS beads into 15 μm hole were optimized at 80 mV and 15 min, respectively. In the optimized condition, the relative AIF was observed approximately 4.908 ± 0.299. Finally, in 3 μm and 15 μm hole, the AIFs were approximately 3.143 and -1.346 by 2 nm of protein and about -2.515 and 4.211 by 30 nm of the PS beads, respectively. The results showed that 2 nm of the protein and 30 nm of PS beads were separated by DEP force in each microhole effectively, and that our method is applicable as a new method to verify an efficiency of the labeling for bead-based fluorescent sensor ∇|E|2.
Collapse
Affiliation(s)
- Hye Jin Kim
- Department of Clinical Pharmacology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Dong-Hoon Kang
- Center for Bionics, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Seung-Hoon Yang
- Systems Biotechnology Research Center, Korea Institute of Science and Technology, Gangneung 25451, Republic of Korea
| | - Eunji Lee
- Department of Medical Biotechnology, Dongguk University, Seoul 04620, Republic of Korea
| | - Taewon Ha
- Center for Nano-Photonics Convergence Technology, Korea Institute of Industrial Technology (KITECH), Gwangju 61012, Republic of Korea
| | - Byung Chul Lee
- Center for BioMicrosystems, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Youngbaek Kim
- Center for Nano-Photonics Convergence Technology, Korea Institute of Industrial Technology (KITECH), Gwangju 61012, Republic of Korea
| | - Kyo Seon Hwang
- Department of Clinical Pharmacology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hyun-Joon Shin
- Center for Bionics, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Jinsik Kim
- Department of Medical Biotechnology, Dongguk University, Seoul 04620, Republic of Korea
| |
Collapse
|
28
|
Bakthavachalu B, Huelsmeier J, Sudhakaran IP, Hillebrand J, Singh A, Petrauskas A, Thiagarajan D, Sankaranarayanan M, Mizoue L, Anderson EN, Pandey UB, Ross E, VijayRaghavan K, Parker R, Ramaswami M. RNP-Granule Assembly via Ataxin-2 Disordered Domains Is Required for Long-Term Memory and Neurodegeneration. Neuron 2018; 98:754-766.e4. [PMID: 29772202 DOI: 10.1016/j.neuron.2018.04.032] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/07/2018] [Accepted: 04/23/2018] [Indexed: 02/07/2023]
Abstract
Human Ataxin-2 is implicated in the cause and progression of amyotrophic lateral sclerosis (ALS) and type 2 spinocerebellar ataxia (SCA-2). In Drosophila, a conserved atx2 gene is essential for animal survival as well as for normal RNP-granule assembly, translational control, and long-term habituation. Like its human homolog, Drosophila Ataxin-2 (Atx2) contains polyQ repeats and additional intrinsically disordered regions (IDRs). We demonstrate that Atx2 IDRs, which are capable of mediating liquid-liquid phase transitions in vitro, are essential for efficient formation of neuronal mRNP assemblies in vivo. Remarkably, ΔIDR mutants that lack neuronal RNP granules show normal animal development, survival, and fertility. However, they show defects in long-term memory formation/consolidation as well as in C9ORF72 dipeptide repeat or FUS-induced neurodegeneration. Together, our findings demonstrate (1) that higher-order mRNP assemblies contribute to long-term neuronal plasticity and memory, and (2) that a targeted reduction in RNP-granule formation efficiency can alleviate specific forms of neurodegeneration.
Collapse
Affiliation(s)
| | - Joern Huelsmeier
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2, Ireland
| | | | - Jens Hillebrand
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2, Ireland
| | - Amanjot Singh
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | - Arnas Petrauskas
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2, Ireland
| | | | | | - Laura Mizoue
- Department of Chemistry, University of Colorado, Boulder, CO 80309, USA; HHMI, University of Colorado, Boulder, CO 80309, USA
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Eric Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - K VijayRaghavan
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | - Roy Parker
- Department of Chemistry, University of Colorado, Boulder, CO 80309, USA; HHMI, University of Colorado, Boulder, CO 80309, USA
| | - Mani Ramaswami
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India; Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2, Ireland.
| |
Collapse
|
29
|
Noh JH, Kim KM, McClusky WG, Abdelmohsen K, Gorospe M. Cytoplasmic functions of long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018. [PMID: 29516680 DOI: 10.1002/wrna.1471] [Citation(s) in RCA: 279] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides found throughout the cell that lack protein-coding function. Their functions are closely linked to their interaction with RNA-binding proteins (RBPs) and nucleic acids. Nuclear lncRNAs have been studied extensively, revealing complexes with structural and regulatory roles that enable gene organization and control transcription. Cytoplasmic lncRNAs are less well understood, but accumulating evidence indicates that they also form complexes with diverse structural and regulatory functions. Here, we review our current knowledge of cytoplasmic lncRNAs and the different levels of gene regulation controlled by cytoplasmic lncRNA complexes, including mRNA turnover, translation, protein stability, sponging of cytosolic factors, and modulation of signaling pathways. We conclude by discussing areas of future study needed to elucidate comprehensively the biology of lncRNAs, to further understand the impact of lncRNAs on physiology and design lncRNA-centered therapeutic strategies. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Ji Heon Noh
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Kyoung Mi Kim
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Waverly G McClusky
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| |
Collapse
|
30
|
Lefebvre FA, Lécuyer É. Flying the RNA Nest: Drosophila Reveals Novel Insights into the Transcriptome Dynamics of Early Development. J Dev Biol 2018; 6:jdb6010005. [PMID: 29615554 PMCID: PMC5875563 DOI: 10.3390/jdb6010005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/01/2018] [Accepted: 03/05/2018] [Indexed: 01/02/2023] Open
Abstract
Early development is punctuated by a series of pervasive and fast paced transitions. These events reshape a differentiated oocyte into a totipotent embryo and allow it to gradually mount a genetic program of its own, thereby framing a new organism. Specifically, developmental transitions that ensure the maternal to embryonic control of developmental events entail a deep remodeling of transcriptional and transcriptomic landscapes. Drosophila provides an elegant and genetically tractable system to investigate these conserved changes at a dazzling developmental pace. Here, we review recent studies applying emerging technologies such as ribosome profiling, in situ Hi-C chromatin probing and live embryo RNA imaging to investigate the transcriptional dynamics at play during Drosophila embryogenesis. In light of this new literature, we revisit the main models of zygotic genome activation (ZGA). We also review the contributions played by zygotic transcription in shaping embryogenesis and explore emerging concepts of processes such as transcriptional bursting and transcriptional memory.
Collapse
Affiliation(s)
- Fabio Alexis Lefebvre
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada.
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada.
| | - Éric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada.
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada.
- Division of Experimental Medicine, McGill University, Montréal, QC H3A 0G4, Canada.
- IRCM, RNA Biology Laboratory, 110 Avenue des Pins, Ouest, Montréal, QC H2W 1R7, Canada.
| |
Collapse
|
31
|
Rajesh Kumar M, Joice Sophia P. Nanoparticles as Precious Stones in the Crown of Modern Molecular Biology. TRENDS IN INSECT MOLECULAR BIOLOGY AND BIOTECHNOLOGY 2018. [PMCID: PMC7123693 DOI: 10.1007/978-3-319-61343-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
32
|
He D, Wong KW, Dong Z, Li HW. Recent progress in live cell mRNA/microRNA imaging probes based on smart and versatile nanomaterials. J Mater Chem B 2018; 6:7773-7793. [DOI: 10.1039/c8tb02285b] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We summarize the recent progress in live cell mRNA/miRNA imaging probes based on various versatile nanomaterials, describing their structures and their working principles of bio-imaging applications.
Collapse
Affiliation(s)
- Dinggeng He
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
- State Key Laboratory of Developmental Biology of Freshwater Fish
| | - Ka-Wang Wong
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Zhenzhen Dong
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Hung-Wing Li
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| |
Collapse
|
33
|
Yoshimura H. Live Cell Imaging of Endogenous RNAs Using Pumilio Homology Domain Mutants: Principles and Applications. Biochemistry 2017; 57:200-208. [PMID: 29164876 DOI: 10.1021/acs.biochem.7b00983] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recently, dynamic changes in the location of RNA in space and time in living cells have become a target of interest in biology because of their essential roles in controlling physiological phenomena. To visualize RNA, methods for the fluorescent labeling of RNA in living cells have been developed. For RNA labeling, oligonucleotide-based RNA probes have mainly been used because of their high selectivity for target RNAs. By contrast, protein-based RNA probes have not been used widely because of their lack of design flexibility, although they have various potential advantages compared with nucleotide-based probes, such as controllability of intracellular localization, high detectability, and ease of introduction into cells and transgenic organisms in a cell type and tissue specific manner by genetic engineering techniques. This Perspective focuses on a possible approach to the development of protein-based RNA probes using Pumilio homology domain (PUM-HD) mutants. The PUM-HD is a domain of an RNA binding protein that allows custom-made modifications to recognize a given eight-base RNA sequence. PUM-HD-based RNA probes have been applied to visualize various RNAs in living cells. Here, the techniques and RNA imaging results obtained using the PUM-HD are introduced.
Collapse
Affiliation(s)
- Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| |
Collapse
|
34
|
Gaspar I, Wippich F, Ephrussi A. Enzymatic production of single-molecule FISH and RNA capture probes. RNA (NEW YORK, N.Y.) 2017; 23:1582-1591. [PMID: 28698239 PMCID: PMC5602115 DOI: 10.1261/rna.061184.117] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 06/22/2017] [Indexed: 05/20/2023]
Abstract
Arrays of singly labeled short oligonucleotides that hybridize to a specific target revolutionized RNA biology, enabling quantitative, single-molecule microscopy analysis and high-efficiency RNA/RNP capture. Here, we describe a simple and efficient method that allows flexible functionalization of inexpensive DNA oligonucleotides by different fluorescent dyes or biotin using terminal deoxynucleotidyl transferase and custom-made functional group conjugated dideoxy-UTP. We show that (i) all steps of the oligonucleotide labeling-including conjugation, enzymatic synthesis, and product purification-can be performed in a standard biology laboratory, (ii) the process yields >90%, often >95% labeled product with minimal carryover of impurities, and (iii) the oligonucleotides can be labeled with different dyes or biotin, allowing single-molecule FISH, RNA affinity purification, and Northern blot analysis to be performed.
Collapse
Affiliation(s)
- Imre Gaspar
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Frank Wippich
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| |
Collapse
|
35
|
Zhou CY, Alexander SC, Devaraj NK. Fluorescent turn-on probes for wash-free mRNA imaging via covalent site-specific enzymatic labeling. Chem Sci 2017; 8:7169-7173. [PMID: 29081948 PMCID: PMC5635419 DOI: 10.1039/c7sc03150e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/28/2017] [Indexed: 11/21/2022] Open
Abstract
Investigating the many roles RNA plays in cellular regulation and function has increased demand for tools to explore RNA tracking and localization within cells.
Investigating the many roles RNA plays in cellular regulation and function has increased demand for tools to explore RNA tracking and localization within cells. Our recently reported RNA-TAG (transglycosylation at guanine) approach uses an RNA-modifying enzyme, tRNA-guanine transglycosylase (TGT), to accomplish covalent labeling of an RNA of interest with fluorescent tracking agents in a highly selective and efficient manner. Unfortunately, labeling by this method currently suffers from a high nonspecific fluorescent background and is currently unsuitable for imaging RNA within complex cellular environments. Herein we report the design and synthesis of novel fluorogenic thiazole orange probes that significantly lower nonspecific binding and background fluorescence and, as a result, provide up to a 100-fold fluorescence intensity increase after labeling. Using these fluorogenic labeling agents, we were able to image mRNA expressed in Chinese Hamster Ovary cells in a wash-free manner.
Collapse
Affiliation(s)
- Cun Yu Zhou
- Department of Chemistry and Biochemistry , University of California , 9500 Gilman Dr La Jolla , San Diego , CA 92093 , USA .
| | - Seth C Alexander
- Department of Chemistry and Biochemistry , University of California , 9500 Gilman Dr La Jolla , San Diego , CA 92093 , USA .
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry , University of California , 9500 Gilman Dr La Jolla , San Diego , CA 92093 , USA .
| |
Collapse
|
36
|
Kirschman JL, Bhosle S, Vanover D, Blanchard EL, Loomis KH, Zurla C, Murray K, Lam BC, Santangelo PJ. Characterizing exogenous mRNA delivery, trafficking, cytoplasmic release and RNA-protein correlations at the level of single cells. Nucleic Acids Res 2017; 45:e113. [PMID: 28449134 PMCID: PMC5499550 DOI: 10.1093/nar/gkx290] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/06/2017] [Accepted: 04/11/2017] [Indexed: 12/25/2022] Open
Abstract
The use of synthetic messenger ribonucleic acid (mRNA) to express specific proteins is a highly promising therapeutic and vaccine approach that avoids many safety issues associated with viral or DNA-based systems. However, in order to optimize mRNA designs and delivery, technology advancements are required to study fundamental mechanisms of mRNA uptake and localization at the single-cell and tissue level. Here, we present a single RNA sensitive fluorescent labeling method which allows us to label and visualize synthetic mRNA without significantly affecting function. This approach enabled single cell characterization of mRNA uptake and release kinetics from endocytic compartments, the measurement of mRNA/protein correlations, and motivated the investigation of mRNA induced cellular stress, all important mechanisms influencing protein production. In addition, we demonstrated this approach can facilitate near-infrared imaging of mRNA localization in vivo and in ex-vivo tissue sections, which will facilitate mRNA trafficking studies in pre-clinical models. Overall, we demonstrate the ability to study fundamental mechanisms necessary to optimize delivery and therapeutic strategies, in order to design the next generation of novel mRNA therapeutics and vaccines.
Collapse
Affiliation(s)
- Jonathan L. Kirschman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Sushma Bhosle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Daryll Vanover
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Emmeline L. Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Kristin H. Loomis
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Chiara Zurla
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Kathryn Murray
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Blaine C. Lam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Philip J. Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| |
Collapse
|
37
|
Warminski M, Sikorski PJ, Warminska Z, Lukaszewicz M, Kropiwnicka A, Zuberek J, Darzynkiewicz E, Kowalska J, Jemielity J. Amino-Functionalized 5' Cap Analogs as Tools for Site-Specific Sequence-Independent Labeling of mRNA. Bioconjug Chem 2017; 28:1978-1992. [PMID: 28613834 DOI: 10.1021/acs.bioconjchem.7b00291] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
mRNA is a template for protein biosynthesis, and consequently mRNA transport, translation, and turnover are key elements in the overall regulation of gene expression. Along with growing interest in the mechanisms regulating mRNA decay and localization, there is an increasing need for tools enabling convenient fluorescent labeling or affinity tagging of mRNA. We report new mRNA 5' cap analog-based tools that enable site-specific labeling of RNA within the cap using N-hydroxysuccinimide (NHS) chemistry. We explored two complementary methods: a co-transcriptional labeling method, in which the label is first attached to a cap analog and then incorporated into RNA by in vitro transcription, and a post-transcriptional labeling method, in which an amino-functionalized cap analog is incorporated into RNA followed by chemical labeling of the resulting transcript. After testing the biochemical properties of RNAs carrying the novel modified cap structures, we demonstrated the utility of fluorescently labeled RNAs in decapping assays, RNA decay assays, and RNA visualization in cells. Finally, we also demonstrated that mRNAs labeled by the reported method are translationally active. We envisage that the novel analogs will provide an alternative to radiolabeling of mRNA caps for in vitro studies and open possibilities for new applications related to the study of mRNA fates in vivo.
Collapse
Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw , 02-097, Warsaw, Poland
| | - Zofia Warminska
- Centre of New Technologies, University of Warsaw , 02-097, Warsaw, Poland.,College of Interfaculty Individual Studies of Mathematics and Natural Sciences, University of Warsaw , 02-093, Warsaw, Poland
| | - Maciej Lukaszewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Anna Kropiwnicka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland.,Centre of New Technologies, University of Warsaw , 02-097, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw , 02-097, Warsaw, Poland
| |
Collapse
|
38
|
Xia Y, Zhang R, Wang Z, Tian J, Chen X. Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes. Chem Soc Rev 2017; 46:2824-2843. [PMID: 28345687 PMCID: PMC5472208 DOI: 10.1039/c6cs00675b] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.
Collapse
Affiliation(s)
- Yuqiong Xia
- Engineering Research Center of Molecular-imaging and Neuro-imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China.
| | | | | | | | | |
Collapse
|
39
|
Brown CW, Buckhout-White S, Díaz SA, Melinger JS, Ancona MG, Goldman ER, Medintz IL. Evaluating Dye-Labeled DNA Dendrimers for Potential Applications in Molecular Biosensing. ACS Sens 2017; 2:401-410. [PMID: 28723206 DOI: 10.1021/acssensors.6b00778] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA nanostructures provide a reliable and predictable scaffold for precisely positioning fluorescent dyes to form energy transfer cascades. Furthermore, these structures and their attendant dye networks can be dynamically manipulated by biochemical inputs, with the changes reflected in the spectral response. However, the complexity of DNA structures that have undergone such types of manipulation for direct biosensing applications is quite limited. Here, we investigate four different modification strategies to effect such dynamic manipulations using a DNA dendrimer scaffold as a testbed, and with applications to biosensing in mind. The dendrimer has a 2:1 branching ratio that organizes the dyes into a FRET-based antenna in which excitonic energy generated on multiple initial Cy3 dyes displayed at the periphery is then transferred inward through Cy3.5 and/or Cy5 relay dyes to a Cy5.5 final acceptor at the focus. Advantages of this design included good transfer efficiency, large spectral separation between the initial donor and final acceptor emissions for signal transduction, and an inherent tolerance to defects. Of the approaches to structural rearrangement, the first two mechanisms we consider employed either toehold-mediated strand displacement or strand replacement and their impact was mainly via direct transfer efficiency, while the other two were more global in their effect using either a belting mechanism or an 8-arm star nanostructure to compress the nanostructure and thereby modulate its spectral response through an enhancement in parallelism. The performance of these mechanisms, their ability to reset, and how they might be utilized in biosensing applications are discussed.
Collapse
Affiliation(s)
- Carl W. Brown
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | | | - Sebastián A. Díaz
- American Society for Engineering Education, Washington, DC 20036, United States
| | | | | | | | | |
Collapse
|
40
|
Ong WQ, Citron YR, Sekine S, Huang B. Live Cell Imaging of Endogenous mRNA Using RNA-Based Fluorescence "Turn-On" Probe. ACS Chem Biol 2017; 12:200-205. [PMID: 28103687 DOI: 10.1021/acschembio.6b00586] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Messenger RNA (mRNA) plays a critical role in cellular growth and development. However, there have been limited methods available to visualize endogenous mRNA in living cells with ease. We have designed RNA-based fluorescence "turn-on" probes that target mRNA by fusing an unstable form of Spinach with target-complementary sequences. These probes have been demonstrated to be selective, stable, and capable of targeting various mRNAs for live E. coli imaging.
Collapse
Affiliation(s)
- Wei Qiang Ong
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, San
Francisco, California 94143, United States
| | - Y. Rose Citron
- Graduate
Program of Biophysics, University of California, San Francisco, San Francisco, California 94143, United States
| | - Sayaka Sekine
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, San
Francisco, California 94143, United States
| | - Bo Huang
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, San
Francisco, California 94143, United States
| |
Collapse
|
41
|
Cui Y, Liu J, Irudayaraj J. Beyond quantification: in situ analysis of transcriptome and pre-mRNA alternative splicing at the nanoscale. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [PMID: 27813271 DOI: 10.1002/wnan.1443] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/02/2016] [Accepted: 10/02/2016] [Indexed: 11/08/2022]
Abstract
In situ analysis offers a venue for dissecting the complex transcriptome in its natural context to tap into cellular processes that could explain the phenotypic physiology and pathology yet to be understood. Over the past decades, enormous progress has been made to improve the resolution, sensitivity, and specificity of single-cell technologies. The continued efforts in RNA research not only facilitates mechanistic studies of molecular biology but also provides state-of-the-art strategies for diagnostic purposes. The implementation of novel bio-imaging platforms has yielded valuable information for inspecting gene expression, mapping regulatory networks, and classifying cell types. In this article, we discuss the merits and technical challenges in single-molecule in situ RNA profiling. Advanced in situ hybridization methodologies developed for a variety of detection modalities are reviewed. Considering the fact that in mammalian cells the number of protein products immensely exceeds that of the actual coding genes due to pre-mRNA alternative splicing, tools capable of elucidating this process in intact cells are highlighted. To conclude, we point out future directions for in situ transcriptome analysis and expect a plethora of opportunities and discoveries in this field. WIREs Nanomed Nanobiotechnol 2017, 9:e1443. doi: 10.1002/wnan.1443 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Yi Cui
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA.,Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jing Liu
- Department of Nanoscience and Nanoengineering, South Dakota School of Mines & Technology, Rapid City, SD, USA
| | - Joseph Irudayaraj
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
42
|
Sawyer IA, Sturgill D, Sung MH, Hager GL, Dundr M. Cajal body function in genome organization and transcriptome diversity. Bioessays 2016; 38:1197-1208. [PMID: 27767214 DOI: 10.1002/bies.201600144] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nuclear bodies contribute to non-random organization of the human genome and nuclear function. Using a major prototypical nuclear body, the Cajal body, as an example, we suggest that these structures assemble at specific gene loci located across the genome as a result of high transcriptional activity. Subsequently, target genes are physically clustered in close proximity in Cajal body-containing cells. However, Cajal bodies are observed in only a limited number of human cell types, including neuronal and cancer cells. Ultimately, Cajal body depletion perturbs splicing kinetics by reducing target small nuclear RNA (snRNA) transcription and limiting the levels of spliceosomal snRNPs, including their modification and turnover following each round of RNA splicing. As such, Cajal bodies are capable of shaping the chromatin interaction landscape and the transcriptome by influencing spliceosome kinetics. Future studies should concentrate on characterizing the direct influence of Cajal bodies upon snRNA gene transcriptional dynamics. Also see the video abstract here.
Collapse
Affiliation(s)
- Iain A Sawyer
- Department of Cell Biology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA.,Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Miroslav Dundr
- Department of Cell Biology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| |
Collapse
|
43
|
Kikuchi N, Kolpashchikov DM. Split Spinach Aptamer for Highly Selective Recognition of DNA and RNA at Ambient Temperatures. Chembiochem 2016; 17:1589-92. [PMID: 27305425 DOI: 10.1002/cbic.201600323] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Indexed: 12/25/2022]
Abstract
Split spinach aptamer (SSA) probes for fluorescent analysis of nucleic acids were designed and tested. In SSA design, two RNA or RNA/DNA strands hybridized to a specific nucleic acid analyte and formed a binding site for low-fluorescent 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) dye, which resulted in up to a 270-fold increase in fluorescence. The major advantage of the SSA over state-of-the art fluorescent probes is high selectivity: it produces only background fluorescence in the presence of a single-base-mismatched analyte, even at room temperature. SSA is therefore a promising tool for label-free analysis of nucleic acids at ambient temperatures.
Collapse
Affiliation(s)
- Nanami Kikuchi
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA.
| |
Collapse
|
44
|
Abstract
Labeling RNA is of utmost interest, particularly in living cells, and thus RNA imaging is an emerging field. There are numerous methods relying on different concepts ranging from hybridization-based probes, over RNA-binding proteins to chemo-enzymatic modification of RNA. These methods have different benefits and limitations. This review aims to outline the current state-of-the-art techniques and point out their benefits and limitations.
Collapse
Affiliation(s)
- Lilith V.J.C. Mannack
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
- Cells in Motion, Cluster of Excellence, Münster, Germany
| | - Sebastian Eising
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
- Cells in Motion, Cluster of Excellence, Münster, Germany
| |
Collapse
|
45
|
Kellermann SJ, Rentmeister A. A Genetically Encodable System for Sequence-Specific Detection of RNAs in Two Colors. Chembiochem 2016; 17:895-9. [PMID: 26919688 DOI: 10.1002/cbic.201500705] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Indexed: 12/28/2022]
Abstract
Multicolor readout is an important feature of RNA detection techniques aiming at the investigation of RNA localization. Several detection methods have been developed, however they require either transfection of cells with the probe or prior tagging of the target RNA. We report a fully genetically encodable system for simultaneous detection of two RNAs by using green and yellow fluorescence based on tetramolecular fluorescence complementation (TetFC). To obtain yellow fluorescent protein (YFP), substitution T203Y was introduced into one of the three non-fluorescent GFP fragments; this was fused to different variants of the Homo sapiens Pumilio homology domain. Using different sets of fusion proteins we were able to discriminate between two closely related target RNAs based on the fluorescence signals at the respective wavelengths.
Collapse
Affiliation(s)
- Stefanie J Kellermann
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Andrea Rentmeister
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany. .,Cells-in-Motion Cluster of Excellence (EXC 1003-CiM), University of Münster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.
| |
Collapse
|
46
|
McFadden EJ, Hargrove AE. Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin. Biochemistry 2016; 55:1615-30. [PMID: 26859437 DOI: 10.1021/acs.biochem.5b01141] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs), defined as nontranslated transcripts greater than 200 nucleotides in length, are often differentially expressed throughout developmental stages, tissue types, and disease states. The identification, visualization, and suppression/overexpression of these sequences have revealed impacts on a wide range of biological processes, including epigenetic regulation. Biochemical investigations on select systems have revealed striking insight into the biological roles of lncRNAs and lncRNA:protein complexes, which in turn prompt even more unanswered questions. To begin, multiple protein- and RNA-centric technologies have been employed to isolate lncRNA:protein and lncRNA:chromatin complexes. LncRNA interactions with the multi-subunit protein complex PRC2, which acts as a transcriptional silencer, represent some of the few cases where the binding affinity, selectivity, and activity of a lncRNA:protein complex have been investigated. At the same time, recent reports of full-length lncRNA secondary structures suggest the formation of complex structures with multiple independent folding domains and pave the way for more detailed structural investigations and predictions of lncRNA three-dimensional structure. This review will provide an overview of the methods and progress made to date as well as highlight new methods that promise to further inform the molecular recognition, specificity, and function of lncRNAs.
Collapse
Affiliation(s)
- Emily J McFadden
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Amanda E Hargrove
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States.,Department of Chemistry, Duke University , 124 Science Drive, Durham, North Carolina 27708, United States
| |
Collapse
|
47
|
Fontenete S, Leite M, Cappoen D, Santos R, Ginneken CV, Figueiredo C, Wengel J, Cos P, Azevedo NF. Fluorescence In Vivo Hybridization (FIVH) for Detection of Helicobacter pylori Infection in a C57BL/6 Mouse Model. PLoS One 2016; 11:e0148353. [PMID: 26848853 PMCID: PMC4743915 DOI: 10.1371/journal.pone.0148353] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/18/2016] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION In this study, we applied fluorescence in vivo hybridization (FIVH) using locked nucleic acid (LNA) probes targeting the bacterial rRNA gene for in vivo detection of H. pylori infecting the C57BL/6 mouse model. A previously designed Cy3_HP_LNA/2OMe_PS probe, complementary to a sequence of the H. pylori 16S rRNA gene, was used. First, the potential cytotoxicity and genotoxicity of the probe was assessed by commercial assays. Further, the performance of the probe for detecting H. pylori at different pH conditions was tested in vitro, using fluorescence in situ hybridization (FISH). Finally, the efficiency of FIVH to detect H. pylori SS1 strain in C57BL/6 infected mice was evaluated ex vivo in mucus samples, in cryosections and paraffin-embedded sections by epifluorescence and confocal microscopy. RESULTS H. pylori SS1 strain infecting C57BL/6 mice was successfully detected by the Cy3_HP_LNA/2OMe_PS probe in the mucus, attached to gastric epithelial cells and colonizing the gastric pits. The specificity of the probe for H. pylori was confirmed by microscopy. CONCLUSIONS In the future this methodology can be used in combination with a confocal laser endomicroscope for in vivo diagnosis of H. pylori infection using fluorescent LNA probes, which would be helpful to obtain an immediate diagnosis. Our results proved for the first time that FIVH method is applicable inside the body of a higher-order animal.
Collapse
Affiliation(s)
- Sílvia Fontenete
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
- ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Marina Leite
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Davie Cappoen
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Rita Santos
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Gent, Belgium
| | - Chris Van Ginneken
- Laboratory of Applied Veterinary Morphology, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Céu Figueiredo
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FMUP, Faculty of Medicine of the University of Porto, University, Porto, Portugal
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Nuno Filipe Azevedo
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
| |
Collapse
|
48
|
Yoshimura H, Ozawa T. Monitoring of RNA Dynamics in Living Cells Using PUM-HD and Fluorescent Protein Reconstitution Technique. Methods Enzymol 2016; 572:65-85. [DOI: 10.1016/bs.mie.2016.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
49
|
Warford A. In situ hybridisation: Technologies and their application to understanding disease. ACTA ACUST UNITED AC 2015; 50:37-48. [PMID: 26797255 DOI: 10.1016/j.proghi.2015.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 12/23/2022]
Abstract
In situ hybridisation (ISH) is unique amongst molecular analysis methods in providing for the precise microscopic localisation of genes, mRNA and microRNA in metaphase spreads, cell and tissue preparations. The method is well established as a tool to guide appropriate therapeutic intervention in breast, gastric and lung cancer. With the description of ultrasensitive ISH technologies for low copy mRNA demonstration and the relative ease by which microRNA can be visualised, the applications for research and diagnostic purposes is set to increase dramatically. In this review ISH is considered with emphasis on recent technological developments and surveyed for present and future applications in the context of the demonstration of genes, mRNA and microRNA in health and disease.
Collapse
Affiliation(s)
- Anthony Warford
- University of Westminster, 115 New Cavendish Street, London W1W 6UW, United Kingdom.
| |
Collapse
|
50
|
Abstract
mRNA localisation coupled to translational regulation provides an important means of dictating when and where proteins function in a variety of model systems. This mechanism is particularly relevant in polarised or migrating cells. Although many of the models for how this is achieved were first proposed over 20 years ago, some of the molecular details are still poorly understood. Nevertheless, advanced imaging, biochemical and computational approaches have started to shed light on the cis-acting localisation signals and trans-acting factors that dictate the final destination of localised transcripts. In this Cell Science at a Glance article and accompanying poster, we provide an overview of mRNA localisation, from transcription to degradation, focusing on the microtubule-dependent active transport and anchoring mechanism, which we will use to explain the general paradigm. However, it is clear that there are diverse ways in which mRNAs become localised and target protein expression, and we highlight some of the similarities and differences between these mechanisms.
Collapse
Affiliation(s)
- Richard M Parton
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Alexander Davidson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Timothy T Weil
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| |
Collapse
|