151
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Courchaine EM, Lu A, Neugebauer KM. Droplet organelles? EMBO J 2016; 35:1603-12. [PMID: 27357569 DOI: 10.15252/embj.201593517] [Citation(s) in RCA: 211] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 06/03/2016] [Indexed: 12/12/2022] Open
Abstract
Cells contain numerous, molecularly distinct cellular compartments that are not enclosed by lipid bilayers. These compartments are implicated in a wide range of cellular activities, and they have been variously described as bodies, granules, or organelles. Recent evidence suggests that a liquid-liquid phase separation (LLPS) process may drive their formation, possibly justifying the unifying term "droplet organelle". A veritable deluge of recent publications points to the importance of low-complexity proteins and RNA in determining the physical properties of phase-separated structures. Many of the proteins linked to such structures are implicated in human diseases, such as amyotrophic lateral sclerosis (ALS). We provide an overview of the organizational principles that characterize putative "droplet organelles" in healthy and diseased cells, connecting protein biochemistry with cell physiology.
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Affiliation(s)
- Edward M Courchaine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Alice Lu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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152
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Nam JW, Choi SW, You BH. Incredible RNA: Dual Functions of Coding and Noncoding. Mol Cells 2016; 39:367-74. [PMID: 27137091 PMCID: PMC4870183 DOI: 10.14348/molcells.2016.0039] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/20/2016] [Accepted: 03/29/2016] [Indexed: 11/27/2022] Open
Abstract
Since the RNA world hypothesis was proposed, a large number of regulatory noncoding RNAs (ncRNAs) have been identified in many species, ranging from microorganisms to mammals. During the characterization of these newly discovered RNAs, RNAs having both coding and noncoding functions were discovered, and these were considered bifunctional RNAs. The recent use of computational and high-throughput experimental approaches has revealed increasing evidence of various sources of bifunctional RNAs, such as protein-coding mRNAs with a noncoding isoform and long ncRNAs bearing a small open reading frame. Therefore, the genomic diversity of Janus-faced RNA molecules that have dual characteristics of coding and noncoding indicates that the functional roles of RNAs have to be revisited in cells on a genome-wide scale. Such studies would allow us to further understand the complex gene-regulatory network in cells. In this review, we discuss three major genomic sources of bifunctional RNAs and present a handful of examples of bifunctional RNA along with their functional roles.
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Affiliation(s)
- Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763,
Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763,
Korea
| | - Seo-Won Choi
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763,
Korea
| | - Bo-Hyun You
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763,
Korea
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153
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Galzitskaya OV. Repeats are one of the main characteristics of RNA-binding proteins with prion-like domains. MOLECULAR BIOSYSTEMS 2016; 11:2210-8. [PMID: 26022110 DOI: 10.1039/c5mb00273g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is not surprising that a large number of diseases related to amyloid fibril depositions are formed in various organs. Therefore, it is necessary to understand the transformation of native proteins into amyloid fibrils in order to clarify which key elements of this process determine the pathway of protein misfolding. Significant attention has been directed recently to investigating the mechanism of formation of cross-β structures that have the properties of liquids but can also exist in gel-like forms, thus facilitating the retention of both RNAs and RNA-binding proteins. Proteins that form stress granules are believed to do this rapidly, and they are expected to contain a prion-like domain that can facilitate this process. By analyzing the known yeast prion proteins and 29 RNA-binding proteins with prion-like domains, we demonstrate here that the existence of repeats is one of the general characteristics of prion-like domains. The presence of repeats should help to determine the border of prion domains as in the case of Rnq1: five found repeats shift the border of the prion domain from the 153-rd to at least the 133-th residue. One can suggest that such repeats assist in the rapid initiation of the process of assembly and formation of cross-β structures and such domains most likely should be disordered. These repeats should contain aromatic amino acid residues for the formation of a hydrogel because its amino acid context modulates the strength of interaction. The key factors determined here can be used to control the process of aggregation to prevent the development of pathologies and diseases caused by prion-like domains.
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Affiliation(s)
- Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation.
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154
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Wang Q, Sawyer IA, Sung MH, Sturgill D, Shevtsov SP, Pegoraro G, Hakim O, Baek S, Hager GL, Dundr M. Cajal bodies are linked to genome conformation. Nat Commun 2016; 7:10966. [PMID: 26997247 PMCID: PMC4802181 DOI: 10.1038/ncomms10966] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/07/2016] [Indexed: 12/12/2022] Open
Abstract
The mechanisms underlying nuclear body (NB) formation and their contribution to genome function are unknown. Here we examined the non-random positioning of Cajal bodies (CBs), major NBs involved in spliceosomal snRNP assembly and their role in genome organization. CBs are predominantly located at the periphery of chromosome territories at a multi-chromosome interface. Genome-wide chromosome conformation capture analysis (4C-seq) using CB-interacting loci revealed that CB-associated regions are enriched with highly expressed histone genes and U small nuclear or nucleolar RNA (sn/snoRNA) loci that form intra- and inter-chromosomal clusters. In particular, we observed a number of CB-dependent gene-positioning events on chromosome 1. RNAi-mediated disassembly of CBs disrupts the CB-targeting gene clusters and suppresses the expression of U sn/snoRNA and histone genes. This loss of spliceosomal snRNP production results in increased splicing noise, even in CB-distal regions. Therefore, we conclude that CBs contribute to genome organization with global effects on gene expression and RNA splicing fidelity. Nuclear bodies can nucleate at sites of active transcription and are beneficial for efficient gene expression. Here, the authors show that Cajal bodies, a prominent type of nuclear body, contribute to genome organization with global effects on gene expression and RNA splicing fidelity.
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Affiliation(s)
- Qiuyan Wang
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, 60064 Ilinois, USA.,Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Iain A Sawyer
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, 60064 Ilinois, USA.,Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Sergey P Shevtsov
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, 60064 Ilinois, USA
| | - Gianluca Pegoraro
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA.,High-Throughput Imaging Facility (HiTIF), Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Ofir Hakim
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, 60064 Ilinois, USA
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155
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Falahati H, Pelham-Webb B, Blythe S, Wieschaus E. Nucleation by rRNA Dictates the Precision of Nucleolus Assembly. Curr Biol 2016; 26:277-85. [PMID: 26776729 PMCID: PMC5866055 DOI: 10.1016/j.cub.2015.11.065] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/27/2015] [Accepted: 11/25/2015] [Indexed: 02/05/2023]
Abstract
Membrane-less organelles are intracellular compartments specialized to carry out specific cellular functions. There is growing evidence supporting the possibility that such organelles form as a new phase, separating from cytoplasm or nucleoplasm. However, a main challenge to such phase separation models is that the initial assembly, or nucleation, of the new phase is typically a highly stochastic process and does not allow for the spatiotemporal precision observed in biological systems. Here, we investigate the initial assembly of the nucleolus, a membrane-less organelle involved in different cellular functions including ribosomal biogenesis. We demonstrate that the nucleolus formation is precisely timed in D. melanogaster embryos and follows the transcription of rRNA. We provide evidence that transcription of rRNA is necessary for overcoming the highly stochastic nucleation step in the formation of the nucleolus, through a seeding mechanism. In the absence of rDNA, the nucleolar proteins studied are able to form high-concentration assemblies. However, unlike the nucleolus, these assemblies are highly variable in number, location, and time at which they form. In addition, quantitative study of the changes in the nucleoplasmic concentration and distribution of these nucleolar proteins in the wild-type embryos is consistent with the role of rRNA in seeding the nucleolus formation.
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Affiliation(s)
- Hanieh Falahati
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Bobbie Pelham-Webb
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Shelby Blythe
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
| | - Eric Wieschaus
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.
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156
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Cheng L, Ming H, Zhu M, Wen B. Long noncoding RNAs as Organizers of Nuclear Architecture. SCIENCE CHINA-LIFE SCIENCES 2016; 59:236-44. [PMID: 26825945 DOI: 10.1007/s11427-016-5012-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/06/2015] [Indexed: 12/25/2022]
Abstract
In the eukaryotic cell nucleus, chromatin and its associated macromolecules must be organized into a higher-ordered conformation to function normally. However, mechanisms underlying the organization and dynamics of the nucleus remain unclear. Long noncoding RNAs (lncRNAs), i.e., transcripts longer than 200 nucleotides with little or no protein-coding capacity, are increasingly recognized as important regulators in diverse biological processes. Recent studies have shown that some lncRNAs are involved in various aspects of genome organization, including the facilitation of chromosomal interactions and establishment of nuclear bodies, suggesting that lncRNAs act as general organizers of the nuclear architecture. Here, we discuss recent advances in this emerging and intriguing field.
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Affiliation(s)
- Lu Cheng
- Department of Biochemistry and Molecular Biology and Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hui Ming
- Department of Biochemistry and Molecular Biology and Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Minzhe Zhu
- Department of Biochemistry and Molecular Biology and Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Bo Wen
- Department of Biochemistry and Molecular Biology and Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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157
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Zhou H, Zhang J, Gu Y, Gan X, Gan Y, Zheng W, Kim BW, Xu X, Lu X, Dong Q, Zheng S, Huang W, Xu R. Identification of a novel RNA giant nuclear body in cancer cells. Oncotarget 2016; 7:4724-34. [PMID: 26678034 PMCID: PMC4826238 DOI: 10.18632/oncotarget.6619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/25/2015] [Indexed: 12/18/2022] Open
Abstract
Constitutive synthesis of oncogenic mRNAs is essential for maintaining the uncontrolled growth of cancer cells. However, little is known about how these mRNAs are exported from the nucleus to the cytoplasm. Here, we report the identification of a RNA giant nuclear body (RNA-GNB) that is abundant in cancer cells but rare in normal cells. The RNA-GNB contains a RNA core surrounded by a protein shell. We identify 782 proteins from cancer-associated RNA-GNBs, 40% of which are involved in the nuclear mRNA trafficking. RNA-GNB is required for cell proliferation, and its abundance is positively associated with tumor burden and outcome of therapies. Our findings suggest that the RNA-GNB is a novel nuclear RNA trafficking organelle that may contribute to the nuclear mRNA exporting and proliferation of cancer cells.
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Affiliation(s)
- Hong Zhou
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.,Cancer Institute of Zhejiang University, Hangzhou 310009, China.,Hangzhou First People's Hospital, Hangzhou 310006, China
| | - Jiawei Zhang
- Cancer Institute of Zhejiang University, Hangzhou 310009, China.,Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Ying Gu
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.,Cancer Institute of Zhejiang University, Hangzhou 310009, China.,Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Xiaoxian Gan
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA.,Zhejiang Academy of Medical Sciences, Hangzhou 310012, China
| | - Yichao Gan
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.,Cancer Institute of Zhejiang University, Hangzhou 310009, China
| | - Weiwei Zheng
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.,Cancer Institute of Zhejiang University, Hangzhou 310009, China
| | - Byung-Wook Kim
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Xiaohua Xu
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Xiaoya Lu
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.,Cancer Institute of Zhejiang University, Hangzhou 310009, China
| | - Qi Dong
- Cancer Institute of Zhejiang University, Hangzhou 310009, China
| | - Shu Zheng
- Cancer Institute of Zhejiang University, Hangzhou 310009, China
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Rongzhen Xu
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.,Cancer Institute of Zhejiang University, Hangzhou 310009, China
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158
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Zhang H, Elbaum-Garfinkle S, Langdon EM, Taylor N, Occhipinti P, Bridges AA, Brangwynne CP, Gladfelter AS. RNA Controls PolyQ Protein Phase Transitions. Mol Cell 2016; 60:220-30. [PMID: 26474065 DOI: 10.1016/j.molcel.2015.09.017] [Citation(s) in RCA: 492] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/09/2015] [Accepted: 09/17/2015] [Indexed: 12/28/2022]
Abstract
Compartmentalization in cells is central to the spatial and temporal control of biochemistry. In addition to membrane-bound organelles, membrane-less compartments form partitions in cells. Increasing evidence suggests that these compartments assemble through liquid-liquid phase separation. However, the spatiotemporal control of their assembly, and how they maintain distinct functional and physical identities, is poorly understood. We have previously shown an RNA-binding protein with a polyQ-expansion called Whi3 is essential for the spatial patterning of cyclin and formin transcripts in cytosol. Here, we show that specific mRNAs that are known physiological targets of Whi3 drive phase separation. mRNA can alter the viscosity of droplets, their propensity to fuse, and the exchange rates of components with bulk solution. Different mRNAs impart distinct biophysical properties of droplets, indicating mRNA can bring individuality to assemblies. Our findings suggest that mRNAs can encode not only genetic information but also the biophysical properties of phase-separated compartments.
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Affiliation(s)
- Huaiying Zhang
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Shana Elbaum-Garfinkle
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Erin M Langdon
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Nicole Taylor
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Patricia Occhipinti
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Andrew A Bridges
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
| | - Amy S Gladfelter
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
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159
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Ciechonska M, Grob A, Isalan M. From noise to synthetic nucleoli: can synthetic biology achieve new insights? Integr Biol (Camb) 2016; 8:383-93. [PMID: 26751735 DOI: 10.1039/c5ib00271k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Synthetic biology aims to re-organise and control biological components to make functional devices. Along the way, the iterative process of designing and testing gene circuits has the potential to yield many insights into the functioning of the underlying chassis of cells. Thus, synthetic biology is converging with disciplines such as systems biology and even classical cell biology, to give a new level of predictability to gene expression, cell metabolism and cellular signalling networks. This review gives an overview of the contributions that synthetic biology has made in understanding gene expression, in terms of cell heterogeneity (noise), the coupling of growth and energy usage to expression, and spatiotemporal considerations. We mainly compare progress in bacterial and mammalian systems, which have some of the most-developed engineering frameworks. Overall, one view of synthetic biology can be neatly summarised as "creating in order to understand."
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Affiliation(s)
- Marta Ciechonska
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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160
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Wilusz JE. Long noncoding RNAs: Re-writing dogmas of RNA processing and stability. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:128-38. [PMID: 26073320 PMCID: PMC4676738 DOI: 10.1016/j.bbagrm.2015.06.003] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/16/2015] [Accepted: 06/04/2015] [Indexed: 12/14/2022]
Abstract
Most of the human genome is transcribed, yielding a complex network of transcripts that includes tens of thousands of long noncoding RNAs. Many of these transcripts have a 5' cap and a poly(A) tail, yet some of the most abundant long noncoding RNAs are processed in unexpected ways and lack these canonical structures. Here, I highlight the mechanisms by which several of these well-characterized noncoding RNAs are generated, stabilized, and function. The MALAT1 and MEN β (NEAT1_2) long noncoding RNAs each accumulate to high levels in the nucleus, where they play critical roles in cancer progression and the formation of nuclear paraspeckles, respectively. Nevertheless, MALAT1 and MEN β are not polyadenylated as the tRNA biogenesis machinery generates their mature 3' ends. In place of a poly(A) tail, these transcripts are stabilized by highly conserved triple helical structures. Sno-lncRNAs likewise lack poly(A) tails and instead have snoRNA structures at their 5' and 3' ends. Recent work has additionally identified a number of abundant circular RNAs generated by the pre-mRNA splicing machinery that are resistant to degradation by exonucleases. As these various transcripts use non-canonical strategies to ensure their stability, it is becoming increasingly clear that long noncoding RNAs may often be regulated by unique post-transcriptional control mechanisms. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States.
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161
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Fan AC, Leung AKL. RNA Granules and Diseases: A Case Study of Stress Granules in ALS and FTLD. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:263-96. [PMID: 27256390 DOI: 10.1007/978-3-319-29073-7_11] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA granules are microscopically visible cellular structures that aggregate by protein-protein and protein-RNA interactions. Using stress granules as an example, we discuss the principles of RNA granule formation, which rely on the multivalency of RNA and multi-domain proteins as well as low-affinity interactions between proteins with prion-like/low-complexity domains (e.g. FUS and TDP-43). We then explore how dysregulation of RNA granule formation is linked to neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), and discuss possible strategies for therapeutic intervention.
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Affiliation(s)
- Alexander C Fan
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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162
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Kulikova T, Chervyakova D, Zlotina A, Krasikova A, Gaginskaya E. Giant poly(A)-rich RNP aggregates form at terminal regions of avian lampbrush chromosomes. Chromosoma 2015; 125:709-24. [DOI: 10.1007/s00412-015-0563-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 11/12/2015] [Accepted: 11/24/2015] [Indexed: 01/30/2023]
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163
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Abstract
Our current view of the nucleolus has been shaped by the concept that the organization of this prominent compartment within the nucleus is primarily dictated by its function, the making of ribosome subunits. Whether ribosome biogenesis is framed by a dedicated nucleolar scaffold has remained unclear. In this issue of The EMBO Journal, Caudron‐Herger and colleagues present evidence for a nucleolar skeleton composed of non‐coding RNA enriched in Alu repeat elements.
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Affiliation(s)
- Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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164
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Brielle S, Gura R, Kaganovich D. Imaging stress. Cell Stress Chaperones 2015; 20:867-74. [PMID: 26139131 PMCID: PMC4595435 DOI: 10.1007/s12192-015-0615-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022] Open
Abstract
Recent innovations in cell biology and imaging approaches are changing the way we study cellular stress, protein misfolding, and aggregation. Studies have begun to show that stress responses are even more variegated and dynamic than previously thought, encompassing nano-scale reorganization of cytosolic machinery that occurs almost instantaneously, much faster than transcriptional responses. Moreover, protein and mRNA quality control is often organized into highly dynamic macromolecular assemblies, or dynamic droplets, which could easily be mistaken for dysfunctional "aggregates," but which are, in fact, regulated functional compartments. The nano-scale architecture of stress-response ranges from diffraction-limited structures like stress granules, P-bodies, and stress foci to slightly larger quality control inclusions like juxta nuclear quality control compartment (JUNQ) and insoluble protein deposit compartment (IPOD), as well as others. Examining the biochemical and physical properties of these dynamic structures necessitates live cell imaging at high spatial and temporal resolution, and techniques to make quantitative measurements with respect to movement, localization, and mobility. Hence, it is important to note some of the most recent observations, while casting an eye towards new imaging approaches that offer the possibility of collecting entirely new kinds of data from living cells.
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Affiliation(s)
- Shlomi Brielle
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Alexander Grass Center for Bioengineering, Hebrew University of Jerusalem, Jerusalem, Israel, 91904
| | - Rotem Gura
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Daniel Kaganovich
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
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165
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Abstract
Initially identified as a marker of coiled bodies (now Cajal bodies or CBs), the protein coilin was discovered a quarter of century ago. Coilin is now known to scaffold the CB, but its structure and function are poorly understood. Nearly devoid of predicted structural motifs, coilin has numerous reported molecular interactions that must underlie its role in the formation and function of CBs. In this review, we summarize what we have learned in the past 25 years about coilin's structure, post-transcriptional modifications, and interactions with RNA and proteins. We show that genes with homology to human coilin are found in primitive metazoans and comment on differences among model organisms. Coilin's function in Cajal body formation and RNP metabolism will be discussed in the light of these developments.
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Affiliation(s)
- Martin Machyna
- a Department of Molecular Biophysics & Biochemistry ; Yale University ; New Haven , CT USA
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166
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Caudron-Herger M, Pankert T, Seiler J, Németh A, Voit R, Grummt I, Rippe K. Alu element-containing RNAs maintain nucleolar structure and function. EMBO J 2015; 34:2758-74. [PMID: 26464461 DOI: 10.15252/embj.201591458] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/31/2015] [Indexed: 01/05/2023] Open
Abstract
Non-coding RNAs play a key role in organizing the nucleus into functional subcompartments. By combining fluorescence microscopy and RNA deep-sequencing-based analysis, we found that RNA polymerase II transcripts originating from intronic Alu elements (aluRNAs) were enriched in the nucleolus. Antisense-oligo-mediated depletion of aluRNAs or drug-induced inhibition of RNA polymerase II activity disrupted nucleolar structure and impaired RNA polymerase I-dependent transcription of rRNA genes. In contrast, overexpression of a prototypic aluRNA sequence increased both nucleolus size and levels of pre-rRNA, suggesting a functional link between aluRNA, nucleolus integrity and pre-rRNA synthesis. Furthermore, we show that aluRNAs interact with nucleolin and target ectopic genomic loci to the nucleolus. Our study suggests an aluRNA-based mechanism that links RNA polymerase I and II activities and modulates nucleolar structure and rRNA production.
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Affiliation(s)
- Maïwen Caudron-Herger
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Teresa Pankert
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Jeanette Seiler
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Attila Németh
- Department of Biochemistry III, Biochemistry Center Regensburg University of Regensburg, Regensburg, Germany
| | - Renate Voit
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Karsten Rippe
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
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167
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Merelo V, Durand D, Lescallette AR, Vrana KE, Hong LE, Faghihi MA, Bellon A. Associating schizophrenia, long non-coding RNAs and neurostructural dynamics. Front Mol Neurosci 2015; 8:57. [PMID: 26483630 PMCID: PMC4588008 DOI: 10.3389/fnmol.2015.00057] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/10/2015] [Indexed: 01/10/2023] Open
Abstract
Several lines of evidence indicate that schizophrenia has a strong genetic component. But the exact nature and functional role of this genetic component in the pathophysiology of this mental illness remains a mystery. Long non-coding RNAs (lncRNAs) are a recently discovered family of molecules that regulate gene transcription through a variety of means. Consequently, lncRNAs could help us bring together apparent unrelated findings in schizophrenia; namely, genomic deficiencies on one side and neuroimaging, as well as postmortem results on the other. In fact, the most consistent finding in schizophrenia is decreased brain size together with enlarged ventricles. This anomaly appears to originate from shorter and less ramified dendrites and axons. But a decrease in neuronal arborizations cannot explain the complex pathophysiology of this psychotic disorder; however, dynamic changes in neuronal structure present throughout life could. It is well recognized that the structure of developing neurons is extremely plastic. This structural plasticity was thought to stop with brain development. However, breakthrough discoveries have shown that neuronal structure retains some degree of plasticity throughout life. What the neuroscientific field is still trying to understand is how these dynamic changes are regulated and lncRNAs represent promising candidates to fill this knowledge gap. Here, we present evidence that associates specific lncRNAs with schizophrenia. We then discuss the potential role of lncRNAs in neurostructural dynamics. Finally, we explain how dynamic neurostructural modifications present throughout life could, in theory, reconcile apparent unrelated findings in schizophrenia.
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Affiliation(s)
- Veronica Merelo
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miller School of Medicine Miami, FL, USA
| | - Dante Durand
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miller School of Medicine Miami, FL, USA
| | - Adam R Lescallette
- Penn State Hershey Medical Center, Department of Pharmacology Hershey, PA, USA ; Penn State Hershey Medical Center, Department of Psychiatry Hershey, PA, USA
| | - Kent E Vrana
- Penn State Hershey Medical Center, Department of Pharmacology Hershey, PA, USA
| | - L Elliot Hong
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine Baltimore, MD, USA
| | - Mohammad Ali Faghihi
- Center for Therapeutic Innovation, Department of Psychiatry and Behavioral Sciences University of Miami, Miller School of Medicine Miami, FL, USA
| | - Alfredo Bellon
- Penn State Hershey Medical Center, Department of Pharmacology Hershey, PA, USA ; Penn State Hershey Medical Center, Department of Psychiatry Hershey, PA, USA
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168
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Dovidchenko NV, Leonova EI, Galzitskaya OV. Mechanisms of amyloid fibril formation. BIOCHEMISTRY (MOSCOW) 2015; 79:1515-27. [PMID: 25749162 DOI: 10.1134/s0006297914130057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Amyloid and amyloid-like aggregates are elongated unbranched fibrils consisting of β-structures of separate monomers positioned perpendicular to the fibril axis and stacked strictly above each other. In their physicochemical properties, amyloid fibrils are reminiscent of synthetic polymers rather than usual proteins because they are stable to the action of denaturing agents and proteases. Their mechanical stability can be compared to a spider's web, that in spite of its ability to stretch, is stronger than steel. It is not surprising that a large number of diseases are accompanied with amyloid fibril depositing in different organs. Pathologies provoked by depositing of incorrectly folded proteins include Alzheimer's, Parkinson's, and Huntington's diseases. In addition, this group of diseases involves mucoviscidosis, some types of diabetes, and hereditary cataracts. Each type of amyloidosis is characterized by aggregation of a certain type of protein that is soluble in general, and thus leads to specific distortions of functions of the corresponding organs. Therefore, it is important to understand the process of transformation of "native" proteins to amyloid fibrils to clarify how these molecules acquire such strength and what key elements of this process determine the pathway of erroneous protein folding. This review presents our analysis of complied information on the mechanisms of formation and biochemical properties of amyloid fibrils.
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Affiliation(s)
- N V Dovidchenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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169
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Abstract
Multiple biological processes are regulated by complicated interaction networks formed by protein-protein or protein-RNA interactions. Nuclear bodies (NBs) are a class of membrane-less subnuclear structures, acting as reaction sites, storage and modification sites, or transcription regulating sites involved in signaling transduction. Biochemical and fluorescence-based methods are widely used to study protein-protein interactions, but false-positive results are a major issue, especially for some fluorescence-based methods. Moreover, these methods fail to be applied to study the formation of NBs, which were characterized by a popular bacterial Lac operator and/or repressor (LacO/LacI) system in mammalian cells. Methods investigating assembly of plant NBs are not available. We have recently developed a nucleolar marker protein nucleolin2 (Nuc2)-based method named Nucleolus-tethering System (NoTS) and showed its application in interaction assay among nucleoplasmic proteins and initiation of plant specific NBs, photobodies. In this extraview, we will compare NoTS with the traditional methods and discuss the assembly mechanisms of NBs, in addition to advantages, limitations, and perspectives about the application of NoTS.
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Affiliation(s)
- Yin Liu
- a National Key Laboratory of Plant Molecular Genetics; Shanghai Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai, China
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170
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Blythe AJ, Fox AH, Bond CS. The ins and outs of lncRNA structure: How, why and what comes next? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:46-58. [PMID: 26325022 DOI: 10.1016/j.bbagrm.2015.08.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/07/2015] [Accepted: 08/27/2015] [Indexed: 12/20/2022]
Abstract
The field of structural biology has the unique advantage of being able to provide a comprehensive picture of biological mechanisms at the molecular and atomic level. Long noncoding RNAs (lncRNAs) represent the new frontier in the molecular biology of complex organisms yet remain the least characterised of all the classes of RNA. Thousands of new lncRNAs are being reported each year yet very little structural data exists for this rapidly expanding field. The length of lncRNAs ranges from 200 nt to over 100 kb in length and they generally exhibit low cellular abundance. Therefore, obtaining sufficient quantities of lncRNA to use for structural analysis is challenging. However, as technologies develop structures of lncRNAs are starting to emerge providing important information regarding their mechanism of action. Here we review the current methods used to determine the structure of lncRNA and lncRNA:protein complexes and describe the significant contribution structural biology has and will make to the field of lncRNA research. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Amanda J Blythe
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| | - Archa H Fox
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia.
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171
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Oh I, Choi S, Jung Y, Kim JS. Phase separation of a Lennard-Jones fluid interacting with a long, condensed polymer chain: implications for the nuclear body formation near chromosomes. SOFT MATTER 2015; 11:6450-6459. [PMID: 26179211 DOI: 10.1039/c5sm01096a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Phase separation in a biological cell nucleus occurs in a heterogeneous environment filled with a high density of chromatins and thus it is inevitably influenced by interactions with chromatins. As a model system of nuclear body formation in a cell nucleus filled with chromatins, we simulate the phase separation of a low-density Lennard-Jones (LJ) fluid interacting with a long, condensed polymer chain. The influence of the density variation of LJ particles above and below the phase boundary and the role of attractive interactions between LJ particles and polymer segments are investigated at a fixed value of strong self-interaction between LJ particles. For a density of LJ particles above the phase boundary, phase separation occurs and a dense domain of LJ particles forms irrespective of interactions with the condensed polymer chain whereas its localization relative to the polymer chain is determined by the LJ-polymer attraction strength. Especially, in the case of moderately weak attractions, the domain forms separately from the polymer chain and subsequently associates with the polymer chain. When the density is below the phase boundary, however, the formation of a dense domain is possible only when the LJ-polymer attraction is strong enough, for which the domain grows in direct contact with the interacting polymer chain. In this work, different growth behaviors of LJ particles result from the differences in the density of LJ particles and in the LJ-polymer interaction, and this work suggests that the distinct formation of activity-dependent and activity-independent nuclear bodies (NBs) in a cell nucleus may originate from the differences in the concentrations of body-specific NB components and in their interaction with chromatins.
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Affiliation(s)
- Inrok Oh
- Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea.
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172
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Hennig S, Kong G, Mannen T, Sadowska A, Kobelke S, Blythe A, Knott GJ, Iyer KS, Ho D, Newcombe EA, Hosoki K, Goshima N, Kawaguchi T, Hatters D, Trinkle-Mulcahy L, Hirose T, Bond CS, Fox AH. Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles. J Cell Biol 2015; 210:529-39. [PMID: 26283796 PMCID: PMC4539981 DOI: 10.1083/jcb.201504117] [Citation(s) in RCA: 222] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 07/02/2015] [Indexed: 12/21/2022] Open
Abstract
Prion-like domains (PLDs) are low complexity sequences found in RNA binding proteins associated with the neurodegenerative disorder amyotrophic lateral sclerosis. Recently, PLDs have been implicated in mediating gene regulation via liquid-phase transitions that drive ribonucleoprotein granule assembly. In this paper, we report many PLDs in proteins associated with paraspeckles, subnuclear bodies that form around long noncoding RNA. We mapped the interactome network of paraspeckle proteins, finding enrichment of PLDs. We show that one protein, RBM14, connects key paraspeckle subcomplexes via interactions mediated by its PLD. We further show that the RBM14 PLD, as well as the PLD of another essential paraspeckle protein, FUS, is required to rescue paraspeckle formation in cells in which their endogenous counterpart has been knocked down. Similar to FUS, the RBM14 PLD also forms hydrogels with amyloid-like properties. These results suggest a role for PLD-mediated liquid-phase transitions in paraspeckle formation, highlighting this nuclear body as an excellent model system for understanding the perturbation of such processes in neurodegeneration.
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Affiliation(s)
- Sven Hennig
- The Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Nedlands, WA 6009, Australia The Centre for Medical Research, The University of Western Australia, Crawley, WA 6009, Australia
| | - Geraldine Kong
- The Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Nedlands, WA 6009, Australia The Centre for Medical Research, The University of Western Australia, Crawley, WA 6009, Australia
| | - Taro Mannen
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Agata Sadowska
- The Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Nedlands, WA 6009, Australia The Centre for Medical Research, The University of Western Australia, Crawley, WA 6009, Australia
| | - Simon Kobelke
- The Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Nedlands, WA 6009, Australia The Centre for Medical Research, The University of Western Australia, Crawley, WA 6009, Australia
| | - Amanda Blythe
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | - Gavin J Knott
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | - K Swaminathan Iyer
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | - Diwei Ho
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | - Estella A Newcombe
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kana Hosoki
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute for Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Tetsuya Kawaguchi
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Danny Hatters
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5 Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | - Archa H Fox
- The Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Nedlands, WA 6009, Australia The Centre for Medical Research, The University of Western Australia, Crawley, WA 6009, Australia
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173
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Smith CS, Preibisch S, Joseph A, Abrahamsson S, Rieger B, Myers E, Singer RH, Grunwald D. Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking. ACTA ACUST UNITED AC 2015; 209:609-19. [PMID: 26008747 PMCID: PMC4442804 DOI: 10.1083/jcb.201411032] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Imaging single proteins or RNAs allows direct visualization of the inner workings of the cell. Typically, three-dimensional (3D) images are acquired by sequentially capturing a series of 2D sections. The time required to step through the sample often impedes imaging of large numbers of rapidly moving molecules. Here we applied multifocus microscopy (MFM) to instantaneously capture 3D single-molecule real-time images in live cells, visualizing cell nuclei at 10 volumes per second. We developed image analysis techniques to analyze messenger RNA (mRNA) diffusion in the entire volume of the nucleus. Combining MFM with precise registration between fluorescently labeled mRNA, nuclear pore complexes, and chromatin, we obtained globally optimal image alignment within 80-nm precision using transformation models. We show that β-actin mRNAs freely access the entire nucleus and fewer than 60% of mRNAs are more than 0.5 µm away from a nuclear pore, and we do so for the first time accounting for spatial inhomogeneity of nuclear organization.
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Affiliation(s)
- Carlas S Smith
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Stephan Preibisch
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461 Howard Hughes Medical Institute Janelia Farm, Ashburn, VA 20147 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Aviva Joseph
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Sara Abrahamsson
- Howard Hughes Medical Institute Janelia Farm, Ashburn, VA 20147 The Rockefeller University, New York, NY 10065
| | - Bernd Rieger
- Department of Imaging Sciences, Technical University Delft, Delft 2628CJ, Netherlands
| | - Eugene Myers
- Howard Hughes Medical Institute Janelia Farm, Ashburn, VA 20147 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461 Howard Hughes Medical Institute Janelia Farm, Ashburn, VA 20147
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
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174
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Abstract
The nucleus is physically distinct from the cytoplasm in ways that suggest new ideas and approaches for interrogating the operation of this organelle. Chemical bond formation and breakage underlie the lives of cells, but as this special issue of Molecular Biology of the Cell attests, the nonchemical aspects of cell nuclei present a new frontier to biologists and biophysicists.
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Affiliation(s)
- Thoru Pederson
- Program in Cell and Developmental Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - John F Marko
- Department of Molecular Biosciences and Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208
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175
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Chujo T, Yamazaki T, Hirose T. Architectural RNAs (arcRNAs): A class of long noncoding RNAs that function as the scaffold of nuclear bodies. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:139-46. [PMID: 26021608 DOI: 10.1016/j.bbagrm.2015.05.007] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/16/2015] [Accepted: 05/19/2015] [Indexed: 01/15/2023]
Abstract
Mammalian transcriptome analyses elucidated the presence of thousands of unannotated long noncoding RNAs (lncRNAs) with distinct transcriptional units. Molecular characterization and functional classification of these lncRNAs are important challenges in the next decade. A subset of these lncRNAs is the core of nuclear bodies, which are the sites of the biogenesis, maturation, storage, and sequestration of specific RNAs, proteins, and ribonucleoprotein complexes. Here, we define a class of lncRNAs termed architectural RNAs (arcRNAs) that function as the essential scaffold or platform of nuclear bodies. Presently, five lncRNAs from mammals, insects, and yeast are classified as arcRNAs. These arcRNAs are temporarily upregulated upon specific cellular stresses, in developmental stages, or in various disease conditions, and sequestrate specific regulatory proteins, thereby changing gene expression patterns. In this review, we introduce common aspects of these arcRNAs and discuss why RNA is used as the architectural component of nuclear bodies. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Takeshi Chujo
- Institute for Genetic Medicine, Hokkaido University, Nishi-7-chome, Kita 15-jo, Kita-ku, Sapporo, Hokkaido 060-0815, Japan
| | - Tomohiro Yamazaki
- Institute for Genetic Medicine, Hokkaido University, Nishi-7-chome, Kita 15-jo, Kita-ku, Sapporo, Hokkaido 060-0815, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Nishi-7-chome, Kita 15-jo, Kita-ku, Sapporo, Hokkaido 060-0815, Japan.
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176
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Zhu L, Brangwynne CP. Nuclear bodies: the emerging biophysics of nucleoplasmic phases. Curr Opin Cell Biol 2015; 34:23-30. [PMID: 25942753 DOI: 10.1016/j.ceb.2015.04.003] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/16/2015] [Accepted: 04/14/2015] [Indexed: 01/02/2023]
Abstract
The cell nucleus contains a large number of membrane-less bodies that play important roles in the spatiotemporal regulation of gene expression. Recent work suggests that low complexity/disordered protein motifs and repetitive binding domains drive assembly of droplets of nuclear RNA/protein by promoting nucleoplasmic phase separation. Nucleation and maturation of these structures is regulated by, and may in turn affect, factors including post-translational modifications, protein concentration, transcriptional activity, and chromatin state. Here we present a concise review of these exciting recent advances, and discuss current and future challenges in understanding the assembly, regulation, and function of nuclear RNA/protein bodies.
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Affiliation(s)
- Lian Zhu
- Princeton University, Department of Chemical and Biological Engineering, Princeton, NJ 08544, USA
| | - Clifford P Brangwynne
- Princeton University, Department of Chemical and Biological Engineering, Princeton, NJ 08544, USA.
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177
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Henriksson S, Farnebo M. On the road with WRAP53β: guardian of Cajal bodies and genome integrity. Front Genet 2015; 6:91. [PMID: 25852739 PMCID: PMC4371746 DOI: 10.3389/fgene.2015.00091] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/19/2015] [Indexed: 12/16/2022] Open
Abstract
The WRAP53 gene encodes both an antisense transcript (WRAP53α) that stabilizes the tumor suppressor p53 and a protein (WRAP53β) involved in maintenance of Cajal bodies, telomere elongation and DNA repair. WRAP53β is one of many proteins containing WD40 domains, known to mediate a variety of cellular processes. These proteins lack enzymatic activity, acting instead as platforms for the assembly of large complexes of proteins and RNAs thus facilitating their interactions. WRAP53β mediates site-specific interactions between Cajal body factors and DNA repair proteins. Moreover, dysfunction of this protein has been linked to premature aging, cancer and neurodegeneration. Here we summarize the current state of knowledge concerning the multifaceted roles of WRAP53β in intracellular trafficking, formation of the Cajal body, DNA repair and maintenance of genomic integrity and discuss potential crosstalk between these processes.
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Affiliation(s)
- Sofia Henriksson
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet Stockholm, Sweden
| | - Marianne Farnebo
- Department of Oncology-Pathology, Cancer Centrum Karolinska, Karolinska Institutet Stockholm, Sweden
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178
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Ishizuka A, Hasegawa Y, Ishida K, Yanaka K, Nakagawa S. Formation of nuclear bodies by the lncRNA Gomafu-associating proteins Celf3 and SF1. Genes Cells 2015; 19:704-21. [PMID: 25145264 PMCID: PMC4255692 DOI: 10.1111/gtc.12169] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 06/28/2014] [Indexed: 12/19/2022]
Abstract
Gomafu/MIAT/Rncr2 is a long noncoding RNA that has been proposed to control retinal cell specification, stem cell differentiation and alternative splicing of schizophrenia-related genes. However, how Gomafu controls these biological processes at the molecular level has remained largely unknown. In this study, we identified the RNA-binding protein Celf3 as a novel Gomafu-associating protein. Knockdown of Celf3 led to the down-regulation of Gomafu, and cross-link RNA precipitation analysis confirmed specific binding between Celf3 and Gomafu. In the neuroblastoma cell line Neuro2A, Celf3 formed novel nuclear bodies (named CS bodies) that colocalized with SF1, another Gomafu-binding protein. Gomafu, however, was not enriched in the CS bodies; instead, it formed distinct nuclear bodies in separate regions in the nucleus. These observations suggest that Gomafu indirectly modulates the function of the splicing factors SF1 and Celf3 by sequestering these proteins into separate nuclear bodies.
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Affiliation(s)
- Akira Ishizuka
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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179
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Gavrilov AA, Razin SV. Compartmentalization of the cell nucleus and spatial organization of the genome. Mol Biol 2015. [DOI: 10.1134/s0026893315010033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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180
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Abstract
Long noncoding RNAs are becoming increasingly appreciated as major players in gene regulation. They have been reported to play diverse roles in many biological processes. Here, we discuss their discovery, features, and known functions in cells. While not comprehensive, this chapter should serve to illustrate the power and promise of studying long noncoding RNAs.
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181
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Ulianov SV, Gavrilov AA, Razin SV. Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:183-244. [DOI: 10.1016/bs.ircmb.2014.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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182
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Khodyuchenko TA, Krasikova AV. Cajal bodies and histone locus bodies: Molecular composition and function. Russ J Dev Biol 2014. [DOI: 10.1134/s106236041406006x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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183
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Machyna M, Kehr S, Straube K, Kappei D, Buchholz F, Butter F, Ule J, Hertel J, Stadler PF, Neugebauer KM. The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies. Mol Cell 2014; 56:389-399. [PMID: 25514182 DOI: 10.1016/j.molcel.2014.10.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/25/2014] [Accepted: 10/02/2014] [Indexed: 12/21/2022]
Abstract
Coilin protein scaffolds Cajal bodies (CBs)-subnuclear compartments enriched in small nuclear RNAs (snRNAs)-and promotes efficient spliceosomal snRNP assembly. The molecular function of coilin, which is intrinsically disordered with no defined motifs, is poorly understood. We use UV crosslinking and immunoprecipitation (iCLIP) to determine whether mammalian coilin binds RNA in vivo and to identify targets. Robust detection of snRNA transcripts correlated with coilin ChIP-seq peaks on snRNA genes, indicating that coilin binding to nascent snRNAs is a site-specific CB nucleator. Surprisingly, several hundred small nucleolar RNAs (snoRNAs) were identified as coilin interactors, including numerous unannotated mouse and human snoRNAs. We show that all classes of snoRNAs concentrate in CBs. Moreover, snoRNAs lacking specific CB retention signals traffic through CBs en route to nucleoli, consistent with the role of CBs in small RNP assembly. Thus, coilin couples snRNA and snoRNA biogenesis, making CBs the cellular hub of small ncRNA metabolism.
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Affiliation(s)
- Martin Machyna
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Department of Molecular Biophysics & Biochemistry, Yale University, 333 Cedar Street, New Haven, CT 06520, USA
| | - Stephanie Kehr
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany
| | - Korinna Straube
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Department of Molecular Biophysics & Biochemistry, Yale University, 333 Cedar Street, New Haven, CT 06520, USA
| | - Dennis Kappei
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Frank Buchholz
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Jana Hertel
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany
| | - Karla M Neugebauer
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Department of Molecular Biophysics & Biochemistry, Yale University, 333 Cedar Street, New Haven, CT 06520, USA.
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184
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Schoborg T, Labrador M. Expanding the roles of chromatin insulators in nuclear architecture, chromatin organization and genome function. Cell Mol Life Sci 2014; 71:4089-113. [PMID: 25012699 PMCID: PMC11113341 DOI: 10.1007/s00018-014-1672-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/31/2014] [Accepted: 06/23/2014] [Indexed: 01/08/2023]
Abstract
Of the numerous classes of elements involved in modulating eukaryotic chromosome structure and function, chromatin insulators arguably remain the most poorly understood in their contribution to these processes in vivo. Indeed, our view of chromatin insulators has evolved dramatically since their chromatin boundary and enhancer blocking properties were elucidated roughly a quarter of a century ago as a result of recent genome-wide, high-throughput methods better suited to probing the role of these elements in their native genomic contexts. The overall theme that has emerged from these studies is that chromatin insulators function as general facilitators of higher-order chromatin loop structures that exert both physical and functional constraints on the genome. In this review, we summarize the result of recent work that supports this idea as well as a number of other studies linking these elements to a diverse array of nuclear processes, suggesting that chromatin insulators exert master control over genome organization and behavior.
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Affiliation(s)
- Todd Schoborg
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996 USA
- Present Address: Laboratory of Molecular Machines and Tissue Architecture, Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, 50 South Dr Rm 2122, Bethesda, MD 20892 USA
| | - Mariano Labrador
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996 USA
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185
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Long noncoding RNAs: an emerging link between gene regulation and nuclear organization. Trends Cell Biol 2014; 24:651-63. [PMID: 25441720 DOI: 10.1016/j.tcb.2014.08.009] [Citation(s) in RCA: 242] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/18/2014] [Accepted: 08/28/2014] [Indexed: 02/07/2023]
Abstract
Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs) that play important roles in diverse biological processes. As a class, lncRNAs are generally enriched in the nucleus and, specifically, within the chromatin-associated fraction. Consistent with their localization, many lncRNAs have been implicated in the regulation of gene expression and in shaping 3D nuclear organization. In this review, we discuss the evidence that many nuclear-retained lncRNAs can interact with various chromatin regulatory proteins and recruit them to specific sites on DNA to regulate gene expression. Furthermore, we discuss the role of specific lncRNAs in shaping nuclear organization and their emerging mechanisms. Based on these examples, we propose a model that explains how lncRNAs may shape aspects of nuclear organization to regulate gene expression.
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186
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Yang XC, Sabath I, Kunduru L, van Wijnen AJ, Marzluff WF, Dominski Z. A conserved interaction that is essential for the biogenesis of histone locus bodies. J Biol Chem 2014; 289:33767-82. [PMID: 25339177 DOI: 10.1074/jbc.m114.616466] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Nuclear protein, ataxia-telangiectasia locus (NPAT) and FLICE-associated huge protein (FLASH) are two major components of discrete nuclear structures called histone locus bodies (HLBs). NPAT is a key co-activator of histone gene transcription, whereas FLASH through its N-terminal region functions in 3' end processing of histone primary transcripts. The C-terminal region of FLASH contains a highly conserved domain that is also present at the end of Yin Yang 1-associated protein-related protein (YARP) and its Drosophila homologue, Mute, previously shown to localize to HLBs in Drosophila cells. Here, we show that the C-terminal domain of human FLASH and YARP interacts with the C-terminal region of NPAT and that this interaction is essential and sufficient to drive FLASH and YARP to HLBs in HeLa cells. Strikingly, only the last 16 amino acids of NPAT are sufficient for the interaction. We also show that the C-terminal domain of Mute interacts with a short region at the end of the Drosophila NPAT orthologue, multi sex combs (Mxc). Altogether, our data indicate that the conserved C-terminal domain shared by FLASH, YARP, and Mute recognizes the C-terminal sequence of NPAT orthologues, thus acting as a signal targeting proteins to HLBs. Finally, we demonstrate that the C-terminal domain of human FLASH can be directly joined with its N-terminal region through alternative splicing. The resulting 190-amino acid MiniFLASH, despite lacking 90% of full-length FLASH, contains all regions necessary for 3' end processing of histone pre-mRNA in vitro and accumulates in HLBs.
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Affiliation(s)
- Xiao-cui Yang
- From the Department of Biochemistry and Biophysics, Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and
| | - Ivan Sabath
- From the Department of Biochemistry and Biophysics, Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and
| | - Lalitha Kunduru
- From the Department of Biochemistry and Biophysics, Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and
| | - Andre J van Wijnen
- the Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
| | - William F Marzluff
- From the Department of Biochemistry and Biophysics, Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and
| | - Zbigniew Dominski
- From the Department of Biochemistry and Biophysics, Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and
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187
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Gao Y, Meng H, Liu S, Hu J, Zhang Y, Jiao T, Liu Y, Ou J, Wang D, Yao L, Liu S, Hui N. LncRNA-HOST2 regulates cell biological behaviors in epithelial ovarian cancer through a mechanism involving microRNA let-7b. Hum Mol Genet 2014; 24:841-52. [PMID: 25292198 DOI: 10.1093/hmg/ddu502] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Recently, a large number of long non-coding RNAs (lncRNAs) have been reported in mammalian genomes and are evolutionarily conserved and presumably function in many biological events, especially in the pathogenesis of diverse human cancers. A lncRNA, named HOST2 (human ovarian cancer-specific transcript 2), was once reported to specifically be expressed at high level in human ovarian cancer. However, how HOST2 acts to regulate gene functions in ovarian carcinogenesis has remained enigmatic. Here we report, for the first time, that HOST2 promotes tumor cell migration, invasion and proliferation in epithelial ovarian cancer by working in key aspects of biological behaviors. In the present study, bioinformatics analysis indicated that HOST2 binds with microRNA let-7b, a potent tumor suppressor, which was then verified to target HOST2. Our results showed that HOST2 harbors a let-7b binding site and modulates let-7b availability by acting as a molecular sponge. HOST2 inhibits let-7b functions, which post-transcriptionally suppress the expression of targets, including some oncogenes that regulate cell growth and motility. Additionally, understanding HOST2/let-7b-dependent regulation may lead to alternative approaches for the diagnosis and cure of this deadly disease.
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Affiliation(s)
- Yuan Gao
- Chinese PLA General Hospital, Beijing 100853, China Changhai Hospital of Second Military Medical University, Shanghai 200433, China
| | - Hao Meng
- Air Force General Hospital, Beijing 100142, China and Beijing Military Region General Hospital, Beijing 100700, China
| | - Shupeng Liu
- Changhai Hospital of Second Military Medical University, Shanghai 200433, China
| | - Jingjing Hu
- Changhai Hospital of Second Military Medical University, Shanghai 200433, China
| | - Yemin Zhang
- Changhai Hospital of Second Military Medical University, Shanghai 200433, China
| | - Tingting Jiao
- Changhai Hospital of Second Military Medical University, Shanghai 200433, China
| | - Yujie Liu
- Changhai Hospital of Second Military Medical University, Shanghai 200433, China
| | - Jun Ou
- Changhai Hospital of Second Military Medical University, Shanghai 200433, China
| | - Dan Wang
- Changhai Hospital of Second Military Medical University, Shanghai 200433, China
| | - Lin Yao
- Changhai Hospital of Second Military Medical University, Shanghai 200433, China
| | - Shanrong Liu
- Changhai Hospital of Second Military Medical University, Shanghai 200433, China
| | - Ning Hui
- Changhai Hospital of Second Military Medical University, Shanghai 200433, China
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188
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Generation of cell-based systems to visualize chromosome damage and translocations in living cells. Nat Protoc 2014; 9:2476-92. [PMID: 25255091 DOI: 10.1038/nprot.2014.167] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Traditional methods for the generation of DNA damage are not well suited for the observation of spatiotemporal aspects of damaged chromosomal loci. We describe a protocol for the derivation of a cellular system to induce and to visualize chromosome damage at specific sites of the mammalian genome in living cells. The system is based on the stable integration of endonuclease I-SceI recognition sites flanked by bacterial LacO/TetO operator arrays, coupled with retroviral-mediated integration of their fluorescent repressors (LacR/TetR) to visualize the LacO/TetO sites. Expression of the I-SceI endonuclease induces double-strand breaks (DSBs) specifically at the sites of integration, and it permits the dynamics of damaged chromatin to be followed by time-lapse microscopy. Sequential LacO-I-SceI/TetO-I-SceI integrations in multiple chromosomes permit the generation of a system to visualize the formation of chromosome translocations in living cells. This protocol requires intermediate cell culture and molecular biology skills, and it is adaptable to the efficient derivation of any integrated clonal reporter system of interest in ≈ 3-5 months.
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189
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Engelke R, Riede J, Hegermann J, Wuerch A, Eimer S, Dengjel J, Mittler G. The Quantitative Nuclear Matrix Proteome as a Biochemical Snapshot of Nuclear Organization. J Proteome Res 2014; 13:3940-56. [DOI: 10.1021/pr500218f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rudolf Engelke
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Julia Riede
- Freiburg
Institute for Advanced Studies, School of Life Sciences − LifeNet, University of Freiburg, Albertstrasse 19, 79104 Freiburg, Germany
- Center
for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse
49, 79104 Freiburg, Germany
| | - Jan Hegermann
- European Neuroscience Institute and Center for Molecular Physiology of the Brain (CMPB), 37077 Göttingen, Germany
| | - Andreas Wuerch
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Stefan Eimer
- European Neuroscience Institute and Center for Molecular Physiology of the Brain (CMPB), 37077 Göttingen, Germany
| | - Joern Dengjel
- Freiburg
Institute for Advanced Studies, School of Life Sciences − LifeNet, University of Freiburg, Albertstrasse 19, 79104 Freiburg, Germany
- Center
for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse
49, 79104 Freiburg, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
- BIOSS,
Center for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
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190
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Abstract
Distinct properties of poly(ADP-ribose)—including its structural diversity, nucleation potential, and low complexity, polyvalent, highly charged nature—could contribute to organizing cellular architectures. Emergent data indicate that poly(ADP-ribose) aids in the formation of nonmembranous structures, such as DNA repair foci, spindle poles, and RNA granules. Informatics analyses reported here show that RNA granule proteins enriched for low complexity regions, which aid self-assembly, are preferentially modified by poly(ADP-ribose), indicating how poly(ADP-ribose) could direct cellular organization.
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Affiliation(s)
- Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
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191
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Mahboubi H, Stochaj U. Nucleoli and Stress Granules: Connecting Distant Relatives. Traffic 2014; 15:1179-93. [DOI: 10.1111/tra.12191] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 06/30/2014] [Accepted: 06/30/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Hicham Mahboubi
- Department of Physiology; McGill University; 3655 Promenade Sir William Osler Montreal Quebec H3G 1Y6 Canada
| | - Ursula Stochaj
- Department of Physiology; McGill University; 3655 Promenade Sir William Osler Montreal Quebec H3G 1Y6 Canada
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192
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Shen W, Liang XH, Crooke ST. Phosphorothioate oligonucleotides can displace NEAT1 RNA and form nuclear paraspeckle-like structures. Nucleic Acids Res 2014; 42:8648-62. [PMID: 25013176 PMCID: PMC4117792 DOI: 10.1093/nar/gku579] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Nuclear paraspeckles are built co-transcriptionally around a long non-coding RNA, NEAT1. Here we report that transfected 20-mer phosphorothioate-modified (PS) antisense oligonucleotides (ASOs) can recruit paraspeckle proteins to form morphologically normal and apparently functional paraspeckle-like structures containing no NEAT1 RNA. PS-ASOs can associate with paraspeckle proteins, including P54nrb, PSF, PSPC1 and hnRNPK. NEAT1 RNA can be displaced by transfected PS-ASO from paraspeckles and rapidly degraded. Co-localization of PS-ASOs with P54nrb was observed in canonical NEAT1-containing paraspeckles, in perinucleolar caps upon transcriptional inhibition, and importantly, in paraspeckle-like or filament structures lacking NEAT1 RNA. The induced formation of paraspeckle-like and filament structures occurred in mouse embryonic stem cells expressing little or no NEAT1 RNA, suggesting that PS-ASOs can serve as seeding molecules to assemble paraspeckle-like foci in the absence of NEAT1 RNA. Moreover, CTN, an RNA reported to be functionally retained in paraspeckles, was also observed to localize to paraspeckle-like structures, implying that paraspeckle-like structures assembled on PS-ASOs are functional. Together, our results indicate that functional paraspeckles can form with short nucleic acids other than NEAT1 RNA.
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Affiliation(s)
- Wen Shen
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Xue-hai Liang
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
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193
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Abstract
Meiosis is a process of fundamental importance for sexually reproducing eukaryotes. During meiosis, homologous chromosomes pair with each other and undergo homologous recombination, ultimately producing haploid sets of recombined chromosomes that will be inherited by the offspring. Compared with the extensive progress that has been made in understanding the molecular mechanisms underlying recombination, how homologous sequences pair with each other is still poorly understood. The diversity of the underlying mechanisms of pairing present in different organisms further increases the complexity of this problem. Involvement of meiosis-specific noncoding RNA in the pairing of homologous chromosomes has been found in the fission yeast Schizosaccharomyces pombe. Although different organisms may have developed other or additional systems that are involved in chromosome pairing, the findings in S. pombe will provide new insights into understanding the roles of noncoding RNA in meiosis.
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194
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Nuclear bodies: new insights into assembly/dynamics and disease relevance. Curr Opin Cell Biol 2014; 28:76-83. [DOI: 10.1016/j.ceb.2014.03.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 01/15/2023]
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195
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Abstract
Enhancer elements regulate the tissue- and developmental-stage-specific expression of genes. Recent estimates suggest that there are more than 50,000 enhancers in mammalian cells. At least a subset of enhancers has been shown to recruit RNA polymerase II transcription complexes and to generate enhancer transcripts. Here, we provide an overview of enhancer function and discuss how transcription of enhancers or enhancer-generated transcripts could contribute to the regulation of gene expression during development and differentiation.
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196
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Abstract
This review summarizes the current understanding of the role of nuclear bodies in regulating gene expression. The compartmentalization of cellular processes, such as ribosome biogenesis, RNA processing, cellular response to stress, transcription, modification and assembly of spliceosomal snRNPs, histone gene synthesis and nuclear RNA retention, has significant implications for gene regulation. These functional nuclear domains include the nucleolus, nuclear speckle, nuclear stress body, transcription factory, Cajal body, Gemini of Cajal body, histone locus body and paraspeckle. We herein review the roles of nuclear bodies in regulating gene expression and their relation to human health and disease.
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Affiliation(s)
| | - Cornelius F. Boerkoel
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-604-875-2157; Fax: +1-604-875-2376
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197
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Abstract
The ability to sequence genomes and characterize their products has begun to reveal the central role for regulatory RNAs in biology, especially in complex organisms. It is now evident that the human genome contains not only protein-coding genes, but also tens of thousands of non-protein coding genes that express small and long ncRNAs (non-coding RNAs). Rapid progress in characterizing these ncRNAs has identified a diverse range of subclasses, which vary widely in size, sequence and mechanism-of-action, but share a common functional theme of regulating gene expression. ncRNAs play a crucial role in many cellular pathways, including the differentiation and development of cells and organs and, when mis-regulated, in a number of diseases. Increasing evidence suggests that these RNAs are a major area of evolutionary innovation and play an important role in determining phenotypic diversity in animals.
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198
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Abstract
The coordinated growth of cells and their organelles is a fundamental and poorly understood problem, with implications for processes ranging from embryonic development to oncogenesis. Recent experiments have shed light on the cell size-dependent assembly of membrane-less cytoplasmic and nucleoplasmic structures, including ribonucleoprotein (RNP) granules and other intracellular bodies. Many of these structures behave as condensed liquid-like phases of the cytoplasm/nucleoplasm. The phase transitions that appear to govern their assembly exhibit an intrinsic dependence on cell size, and may explain the size scaling reported for a number of structures. This size scaling could, in turn, play a role in cell growth and size control.
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Affiliation(s)
- Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
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199
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Liu Y, Liu Q, Yan Q, Shi L, Fang Y. Nucleolus-tethering system (NoTS) reveals that assembly of photobodies follows a self-organization model. Mol Biol Cell 2014; 25:1366-73. [PMID: 24554768 PMCID: PMC3983000 DOI: 10.1091/mbc.e13-09-0527] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 01/27/2014] [Accepted: 02/13/2014] [Indexed: 01/08/2023] Open
Abstract
Protein-protein interactions play essential roles in regulating many biological processes. At the cellular level, many proteins form nuclear foci known as nuclear bodies in which many components interact with each other. Photobodies are nuclear bodies containing proteins for light-signaling pathways in plants. What initiates the formation of photobodies is poorly understood. Here we develop a nucleolar marker protein nucleolin2 (Nuc2)-based method called the nucleolus-tethering system (NoTS) by artificially tethering a protein of interest to the nucleolus to analyze the initiation of photobodies. A candidate initiator is evaluated by visualizing whether a protein fused with Nuc2 forms body-like structures at the periphery of the nucleolus, and other components are recruited to the de novo-formed bodies. The interaction between two proteins can also be revealed through relocation and recruitment of interacting proteins to the nucleolus. Using the NoTS, we test the interactions among components in photobodies. In addition, we demonstrate that components of photobodies such as CONSTITUTIVELY PHOTOMORPHOGENIC 1, photoreceptors, and transcription factors tethered to the nucleolus have the capacity to form body-like structures at the periphery of the nucleolus, which contain other components of photobodies, suggesting a self-organization model for the biogenesis of photobodies.
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Affiliation(s)
- Yin Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qi Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qingqing Yan
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Leilei Shi
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuda Fang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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200
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Newhart A, Janicki SM. Seeing is believing: visualizing transcriptional dynamics in single cells. J Cell Physiol 2014; 229:259-65. [PMID: 23929405 DOI: 10.1002/jcp.24445] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 12/29/2022]
Abstract
For a gene to be expressed, the functions of multiple molecular machines must be coordinated at the site of transcription. To understand the role of nuclear organization in transcription, it is necessary to visualize the dynamic interactions of regulatory factors with chromatin and RNA. It is currently possible to localize individual transcription sites in single living mammalian cells by engineering reporter gene constructs to include sequence elements which permit the visualization of nucleic acids in vivo. Upon stable integration, these transgenes form chromatinized arrays, which can be imaged during activation to obtain high-resolution quantitative information about transcriptional dynamics. Modeling can suggest new hypotheses about gene regulation, which can be tested both in the single-cell imaging system and at endogenous genes. This gene-specific imaging strategy has the potential to reveal regulatory mechanisms, which would be difficult to imagine outside of single living cells.
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Affiliation(s)
- Alyshia Newhart
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania
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