51
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Tikhomirova MA, Sheval EV. Formation of Biomolecular Condensates: Regulation of Embryogenesis at the Cellular Level. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421020077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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52
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Pathak RU, Soujanya M, Mishra RK. Deterioration of nuclear morphology and architecture: A hallmark of senescence and aging. Ageing Res Rev 2021; 67:101264. [PMID: 33540043 DOI: 10.1016/j.arr.2021.101264] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/04/2021] [Accepted: 01/26/2021] [Indexed: 12/15/2022]
Abstract
The metazoan nucleus is a highly structured organelle containing several well-defined sub-organelles. It is the largest organelle inside a cell taking up from one tenth to half of entire cell volume. This makes it one of the easiest organelles to identify and study under the microscope. Abnormalities in the nuclear morphology and architecture are commonly observed in an aged and senescent cell. For example, the nuclei enlarge, loose their shape, appear lobulated, harbour nuclear membrane invaginations, carry enlarged/fragmented nucleolus, loose heterochromatin, etc. In this review we discuss about the age-related changes in nuclear features and elaborate upon the molecular reasons driving the change. Many of these changes can be easily imaged under a microscope and analysed in silico. Thus, computational image analysis of nuclear features appears to be a promising tool to evaluate physiological age of a cell and offers to be a legitimate biomarker. It can be used to examine progression of age-related diseases and evaluate therapies.
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Affiliation(s)
| | - Mamilla Soujanya
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, Telangana, India
| | - Rakesh Kumar Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, Telangana, India.
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53
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Long non-coding RNAs and splicing. Essays Biochem 2021; 65:723-729. [PMID: 33835135 DOI: 10.1042/ebc20200087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/05/2021] [Accepted: 03/15/2021] [Indexed: 12/25/2022]
Abstract
In this review I focus on the role of splicing in long non-coding RNA (lncRNA) life. First, I summarize differences between the splicing efficiency of protein-coding genes and lncRNAs and discuss why non-coding RNAs are spliced less efficiently. In the second half of the review, I speculate why splice sites are the most conserved sequences in lncRNAs and what additional roles could splicing play in lncRNA metabolism. I discuss the hypothesis that the splicing machinery can, besides its dominant role in intron removal and exon joining, protect cells from undesired transcripts.
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54
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Hosoya Y, Ohkanda J. Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets. Molecules 2021; 26:2118. [PMID: 33917117 PMCID: PMC8067799 DOI: 10.3390/molecules26082118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/31/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are critical players in the dynamic control of diverse cellular processes, and provide potential new drug targets because their dysregulation is closely related to many diseases. This review focuses on several medicinal studies that have identified low-molecular-weight inhibitors of IDPs. In addition, clinically relevant liquid-liquid phase separations-which critically involve both intermolecular interactions between IDPs and their posttranslational modification-are analyzed to understand the potential of IDPs as new drug targets.
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Affiliation(s)
| | - Junko Ohkanda
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano 399-4598, Japan;
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55
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King JT, Shakya A. Phase separation of DNA: From past to present. Biophys J 2021; 120:1139-1149. [PMID: 33582138 PMCID: PMC8059212 DOI: 10.1016/j.bpj.2021.01.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/11/2021] [Accepted: 01/22/2021] [Indexed: 02/08/2023] Open
Abstract
Phase separation of biological molecules, such as nucleic acids and proteins, has garnered widespread attention across many fields in recent years. For instance, liquid-liquid phase separation has been implicated not only in membraneless intracellular organization but also in many biochemical processes, including transcription, translation, and cellular signaling. Here, we present a historical background of biological phase separation and survey current work on nuclear organization and its connection to DNA phase separation from the perspective of DNA sequence, structure, and genomic context.
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Affiliation(s)
- John T King
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, Republic of Korea.
| | - Anisha Shakya
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, Republic of Korea.
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56
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p53 mediates target gene association with nuclear speckles for amplified RNA expression. Mol Cell 2021; 81:1666-1681.e6. [PMID: 33823140 DOI: 10.1016/j.molcel.2021.03.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/05/2021] [Accepted: 03/03/2021] [Indexed: 01/01/2023]
Abstract
Nuclear speckles are prominent nuclear bodies that contain proteins and RNA involved in gene expression. Although links between nuclear speckles and gene activation are emerging, the mechanisms regulating association of genes with speckles are unclear. We find that speckle association of p53 target genes is driven by the p53 transcription factor. Focusing on p21, a key p53 target, we demonstrate that speckle association boosts expression by elevating nascent RNA amounts. p53-regulated speckle association did not depend on p53 transactivation functions but required an intact proline-rich domain and direct DNA binding, providing mechanisms within p53 for regulating gene-speckle association. Beyond p21, a substantial subset of p53 targets have p53-regulated speckle association. Strikingly, speckle-associating p53 targets are more robustly activated and occupy a distinct niche of p53 biology compared with non-speckle-associating p53 targets. Together, our findings illuminate regulated speckle association as a mechanism used by a transcription factor to boost gene expression.
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57
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Luo J, Qu L, Gao F, Lin J, Liu J, Lin A. LncRNAs: Architectural Scaffolds or More Potential Roles in Phase Separation. Front Genet 2021; 12:626234. [PMID: 33868368 PMCID: PMC8044363 DOI: 10.3389/fgene.2021.626234] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/25/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecules specifically aggregate in the cytoplasm and nucleus, driving liquid-liquid phase separation (LLPS) formation and diverse biological processes. Extensive studies have focused on revealing multiple functional membraneless organelles in both the nucleus and cytoplasm. Condensation compositions of LLPS, such as proteins and RNAs affecting the formation of phase separation, have been gradually unveiled. LncRNAs possessing abundant second structures usually promote phase separation formation by providing architectural scaffolds for diverse RNAs and proteins interaction in both the nucleus and cytoplasm. Beyond scaffolds, lncRNAs may possess more diverse functions, such as functioning as enhancer RNAs or buffers. In this review, we summarized current studies on the function of phase separation and its related lncRNAs, mainly in the nucleus. This review will facilitate our understanding of the formation and function of phase separation and the role of lncRNAs in these processes and related biological activities. A deeper understanding of the formation and maintaining of phase separation will be beneficial for disease diagnosis and treatment.
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Affiliation(s)
- Jie Luo
- Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lei Qu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Feiran Gao
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.,Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Jun Lin
- Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jian Liu
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.,Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Aifu Lin
- College of Life Sciences, Zhejiang University, Hangzhou, China.,Breast Center of The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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58
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Dopie J, Sweredoski MJ, Moradian A, Belmont AS. Tyramide signal amplification mass spectrometry (TSA-MS) ratio identifies nuclear speckle proteins. J Cell Biol 2021; 219:151914. [PMID: 32609799 PMCID: PMC7480118 DOI: 10.1083/jcb.201910207] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 04/03/2020] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
We present a simple ratio method to infer protein composition within cellular structures using proximity labeling approaches but compensating for the diffusion of free radicals. We used tyramide signal amplification (TSA) and label-free mass spectrometry (MS) to compare proteins in nuclear speckles versus centromeres. Our “TSA-MS ratio” approach successfully identified known nuclear speckle proteins. For example, 96% and 67% of proteins in the top 30 and 100 sorted proteins, respectively, are known nuclear speckle proteins, including proteins that we validated here as enriched in nuclear speckles. We show that MFAP1, among the top 20 in our list, forms droplets under certain circumstances and that MFAP1 expression levels modulate the size, stability, and dynamics of nuclear speckles. Localization of MFAP1 and its binding partner, PRPF38A, in droplet-like nuclear bodies precedes formation of nuclear speckles during telophase. Our results update older proteomic studies of nuclear speckles and should provide a useful reference dataset to guide future experimental dissection of nuclear speckle structure and function.
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Affiliation(s)
- Joseph Dopie
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Department of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, CA
| | - Annie Moradian
- Proteome Exploration Laboratory, Department of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, CA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
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59
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Sabari BR. Biomolecular Condensates and Gene Activation in Development and Disease. Dev Cell 2021; 55:84-96. [PMID: 33049213 DOI: 10.1016/j.devcel.2020.09.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/18/2020] [Accepted: 09/04/2020] [Indexed: 01/04/2023]
Abstract
Activating the right gene at the right time and place is essential for development. Emerging evidence suggests that this process is regulated by the mesoscale compartmentalization of the gene-control machinery, RNA polymerase II and its cofactors, within biomolecular condensates. Coupling gene activity to the reversible and dynamic process of condensate formation is proposed to enable the robust and precise changes in gene-regulatory programs during signaling and development. The macromolecular features that enable condensates and the regulatory pathways that control them are dysregulated in disease, highlighting their importance for normal physiology. In this review, we will discuss the role of condensates in gene activation; the multivalent features of protein, RNA, and DNA that enable reversible condensate formation; and how these processes are utilized in normal and disease biology. Understanding the regulation of condensates promises to provide novel insights into how organization of the gene-control machinery regulates development and disease.
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Affiliation(s)
- Benjamin R Sabari
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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60
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Etibor TA, Yamauchi Y, Amorim MJ. Liquid Biomolecular Condensates and Viral Lifecycles: Review and Perspectives. Viruses 2021; 13:366. [PMID: 33669141 PMCID: PMC7996568 DOI: 10.3390/v13030366] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/16/2021] [Accepted: 02/20/2021] [Indexed: 02/06/2023] Open
Abstract
Viruses are highly dependent on the host they infect. Their dependence triggers processes of virus-host co-adaptation, enabling viruses to explore host resources whilst escaping immunity. Scientists have tackled viral-host interplay at differing levels of complexity-in individual hosts, organs, tissues and cells-and seminal studies advanced our understanding about viral lifecycles, intra- or inter-species transmission, and means to control infections. Recently, it emerged as important to address the physical properties of the materials in biological systems; membrane-bound organelles are only one of many ways to separate molecules from the cellular milieu. By achieving a type of compartmentalization lacking membranes known as biomolecular condensates, biological systems developed alternative mechanisms of controlling reactions. The identification that many biological condensates display liquid properties led to the proposal that liquid-liquid phase separation (LLPS) drives their formation. The concept of LLPS is a paradigm shift in cellular structure and organization. There is an unprecedented momentum to revisit long-standing questions in virology and to explore novel antiviral strategies. In the first part of this review, we focus on the state-of-the-art about biomolecular condensates. In the second part, we capture what is known about RNA virus-phase biology and discuss future perspectives of this emerging field in virology.
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Affiliation(s)
- Temitope Akhigbe Etibor
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal;
| | - Yohei Yamauchi
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TL, UK;
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal;
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61
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Imada T, Shimi T, Kaiho A, Saeki Y, Kimura H. RNA polymerase II condensate formation and association with Cajal and histone locus bodies in living human cells. Genes Cells 2021; 26:298-312. [PMID: 33608942 PMCID: PMC8252594 DOI: 10.1111/gtc.12840] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/24/2022]
Abstract
In eukaryotic nuclei, a number of phase‐separated nuclear bodies (NBs) are present. RNA polymerase II (Pol II) is the main player in transcription and forms large condensates in addition to localizing at numerous transcription foci. Cajal bodies (CBs) and histone locus bodies (HLBs) are NBs that are involved in transcriptional and post‐transcriptional regulation of small nuclear RNA and histone genes. By live‐cell imaging using human HCT116 cells, we here show that Pol II condensates (PCs) nucleated near CBs and HLBs, and the number of PCs increased during S phase concomitantly with the activation period of histone genes. Ternary PC–CB–HLB associates were formed via three pathways: nucleation of PCs and HLBs near CBs, interaction between preformed PC–HLBs with CBs and nucleation of PCs near preformed CB–HLBs. Coilin knockout increased the co‐localization rate between PCs and HLBs, whereas the number, nucleation timing and phosphorylation status of PCs remained unchanged. Depletion of PCs did not affect CBs and HLBs. Treatment with 1,6‐hexanediol revealed that PCs were more liquid‐like than CBs and HLBs. Thus, PCs are dynamic structures often nucleated following the activation of gene clusters associated with other NBs.
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Affiliation(s)
- Takashi Imada
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Takeshi Shimi
- World Research Hub InitiativeInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
- Cell Biology CenterInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
| | - Ai Kaiho
- Protein Metabolism ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
- Institute for Advanced Life SciencesHoshi UniversityTokyoJapan
| | - Yasushi Saeki
- Protein Metabolism ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Hiroshi Kimura
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
- World Research Hub InitiativeInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
- Cell Biology CenterInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
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62
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N 6-methyladenosine modification of MALAT1 promotes metastasis via reshaping nuclear speckles. Dev Cell 2021; 56:702-715.e8. [PMID: 33609462 DOI: 10.1016/j.devcel.2021.01.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/25/2020] [Accepted: 01/24/2021] [Indexed: 01/05/2023]
Abstract
N6-methyladenosine (m6A), one of the most prevalent RNA post-transcriptional modifications, is involved in numerous biological processes. In previous studies, the functions of m6A were typically identified by perturbing the activity of the methyltransferase complex. Here, we dissect the contribution of m6A to an individual-long noncoding RNA-metastasis-associated lung adenocarcinoma transcript 1 (MALAT1). The mutant MALAT1 lacking m6A-motifs significantly suppressed the metastatic potential of cancer cells both in vitro and in vivo in mouse. Super-resolution imaging showed that the concatenated m6A residues on MALAT1 acted as a scaffold for recruiting YTH-domain-containing protein 1 (YTHDC1) to nuclear speckles. We further reveal that the recognition of MALAT1-m6A by YTHDC1 played a critical role in maintaining the composition and genomic binding sites of nuclear speckles, which regulate the expression of several key oncogenes. Furthermore, artificially tethering YTHDC1 onto m6A-deficient MALAT1 largely rescues the metastatic potential of cancer cells.
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63
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Alriquet M, Calloni G, Martínez-Limón A, Delli Ponti R, Hanspach G, Hengesbach M, Tartaglia GG, Vabulas RM. The protective role of m1A during stress-induced granulation. J Mol Cell Biol 2021; 12:870-880. [PMID: 32462207 PMCID: PMC7883823 DOI: 10.1093/jmcb/mjaa023] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional methylation of N6-adenine and N1-adenine can affect transcriptome turnover and translation. Furthermore, the regulatory function of N6-methyladenine (m6A) during heat shock has been uncovered, including the enhancement of the phase separation potential of RNAs. In response to acute stress, e.g. heat shock, the orderly sequestration of mRNAs in stress granules (SGs) is considered important to protect transcripts from the irreversible aggregation. Until recently, the role of N1-methyladenine (m1A) on mRNAs during acute stress response remains largely unknown. Here we show that the methyltransferase complex TRMT6/61A, which generates the m1A tag, is involved in transcriptome protection during heat shock. Our bioinformatics analysis indicates that occurrence of the m1A motif is increased in mRNAs known to be enriched in SGs. Accordingly, the m1A-generating methyltransferase TRMT6/61A accumulated in SGs and mass spectrometry confirmed enrichment of m1A in the SG RNAs. The insertion of a single methylation motif in the untranslated region of a reporter RNA leads to more efficient recovery of protein synthesis from that transcript after the return to normal temperature. Our results demonstrate far-reaching functional consequences of a minimal RNA modification on N1-adenine during acute proteostasis stress.
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Affiliation(s)
- Marion Alriquet
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Giulia Calloni
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Adrían Martínez-Limón
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Riccardo Delli Ponti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Gerd Hanspach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Gian G. Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Department of Biology ‘Charles Darwin’, Sapienza University of Rome, 00185 Rome, Italy
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - R. Martin Vabulas
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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Abstract
Cancers and developmental disorders are associated with alterations in the 3D genome architecture in space and time (the fourth dimension). Mammalian 3D genome organization is complex and dynamic and plays an essential role in regulating gene expression and cellular function. To study the causal relationship between genome function and its spatio-temporal organization in the nucleus, new technologies for engineering and manipulating the 3D organization of the genome have been developed. In particular, CRISPR-Cas technologies allow programmable manipulation at specific genomic loci, enabling unparalleled opportunities in this emerging field of 3D genome engineering. We review advances in mammalian 3D genome engineering with a focus on recent manipulative technologies using CRISPR-Cas and related technologies.
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65
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Edginton-White B, Bonifer C. The transcriptional regulation of normal and malignant blood cell development. FEBS J 2021; 289:1240-1255. [PMID: 33511785 DOI: 10.1111/febs.15735] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/11/2021] [Accepted: 01/26/2021] [Indexed: 11/27/2022]
Abstract
Development of multicellular organisms requires the differential usage of our genetic information to change one cell fate into another. This process drives the appearance of different cell types that come together to form specialized tissues sustaining a healthy organism. In the last decade, by moving away from studying single genes toward a global view of gene expression control, a revolution has taken place in our understanding of how genes work together and how cells communicate to translate the information encoded in the genome into a body plan. The development of hematopoietic cells has long served as a paradigm of development in general. In this review, we highlight how transcription factors and chromatin components work together to shape the gene regulatory networks controlling gene expression in the hematopoietic system and to drive blood cell differentiation. In addition, we outline how this process goes astray in blood cancers. We also touch upon emerging concepts that place these processes firmly into their associated subnuclear structures adding another layer of the control of differential gene expression.
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Affiliation(s)
- Benjamin Edginton-White
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, UK
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66
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Enukashvily NI, Dobrynin MA, Chubar AV. RNA-seeded membraneless bodies: Role of tandemly repeated RNA. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 126:151-193. [PMID: 34090614 DOI: 10.1016/bs.apcsb.2020.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
Abstract
Membraneless organelles (bodies, granules, etc.) are spatially distinct sub-nuclear and cytoplasmic foci involved in all the processes in a living cell, such as development, cell death, carcinogenesis, proliferation, and differentiation. Today the list of the membraneless organelles includes a wide spectrum of intranuclear and cytoplasmic bodies. Proteins with intrinsically disordered regions are the key players in the membraneless body assembly. However, recent data assume an important role of RNA molecules in the process of the liquid-liquid phase separation. High-level expression of RNA above a critical concentration threshold is mandatory to nucleate interactions with specific proteins and for seeding membraneless organelles. RNA components are considered by many authors as the principal determinants of organelle identity. Tandemly repeated (TR) DNA of big satellites (a TR family that includes centromeric and pericentromeric DNA sequences) was believed to be transcriptionally silent for a long period. Now we know about the TR transcription upregulation during gameto- and embryogenesis, carcinogenesis, stress response. In the review, we summarize the recent data about the involvement of TR RNA in the formation of nuclear membraneless granules, bodies, etc., with different functions being in some cases an initiator of the structures assembly. These RNP structures sequestrate and inactivate different proteins and transcripts. The TR induced sequestration is one of the key principles of nuclear architecture and genome functioning. Studying the role of the TR-based membraneless organelles in stress and disease will bring some new ideas for translational medicine.
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Affiliation(s)
- Natella I Enukashvily
- Institute of Cytology RAS, St. Petersburg, Russia; North-Western Medical State University named after I.I. Mechnikov, St. Petersburg, Russia.
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67
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Puente-Bedia A, Berciano MT, Tapia O, Martínez-Cué C, Lafarga M, Rueda N. Nuclear Reorganization in Hippocampal Granule Cell Neurons from a Mouse Model of Down Syndrome: Changes in Chromatin Configuration, Nucleoli and Cajal Bodies. Int J Mol Sci 2021; 22:ijms22031259. [PMID: 33514010 PMCID: PMC7865916 DOI: 10.3390/ijms22031259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 01/05/2023] Open
Abstract
Down syndrome (DS) or trisomy of chromosome 21 (Hsa21) is characterized by impaired hippocampal-dependent learning and memory. These alterations are due to defective neurogenesis and to neuromorphological and functional anomalies of numerous neuronal populations, including hippocampal granular cells (GCs). It has been proposed that the additional gene dose in trisomic cells induces modifications in nuclear compartments and on the chromatin landscape, which could contribute to some DS phenotypes. The Ts65Dn (TS) mouse model of DS carries a triplication of 92 genes orthologous to those found in Hsa21, and shares many phenotypes with DS individuals, including cognitive and neuromorphological alterations. Considering its essential role in hippocampal memory formation, we investigated whether the triplication of this set of Hsa21 orthologous genes in TS mice modifies the nuclear architecture of their GCs. Our results show that the TS mouse presents alterations in the nuclear architecture of its GCs, affecting nuclear compartments involved in transcription and pre-rRNA and pre-mRNA processing. In particular, the GCs of the TS mouse show alterations in the nucleolar fusion pattern and the molecular assembly of Cajal bodies (CBs). Furthermore, hippocampal GCs of TS mice present an epigenetic dysregulation of chromatin that results in an increased heterochromatinization and reduced global transcriptional activity. These nuclear alterations could play an important role in the neuromorphological and/or functional alterations of the hippocampal GCs implicated in the cognitive dysfunction characteristic of TS mice.
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Affiliation(s)
- Alba Puente-Bedia
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, 39011 Santander, Spain; (A.P.-B.); (C.M.-C.)
| | - María T. Berciano
- Department of Molecular Biology, “Red sobre Enfermedades Neurodegenerativas (CIBERNED)” and University of Cantabria-IDIVAL, 39011 Santander, Spain;
| | - Olga Tapia
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), “Red sobre Enfermedades Neurodegenerativas (CIBERNED)” and Universidad Europea del Atlántico, 39011 Santander, Spain;
| | - Carmen Martínez-Cué
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, 39011 Santander, Spain; (A.P.-B.); (C.M.-C.)
| | - Miguel Lafarga
- Department of Anatomy and Cell Biology, “Red sobre Enfermedades Neurodegenerativas (CIBERNED)” and University of Cantabria-IDIVAL, 39011 Santander, Spain
- Correspondence: (M.L.); (N.R.); Tel.: +34-942201966 (N.R.); Fax: +34-942201903 (N.R.)
| | - Noemí Rueda
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, 39011 Santander, Spain; (A.P.-B.); (C.M.-C.)
- Correspondence: (M.L.); (N.R.); Tel.: +34-942201966 (N.R.); Fax: +34-942201903 (N.R.)
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Huang Y, Wang J, Zhao Y, Wang H, Liu T, Li Y, Cui T, Li W, Feng Y, Luo J, Gong J, Ning L, Zhang Y, Wang D, Zhang Y. cncRNAdb: a manually curated resource of experimentally supported RNAs with both protein-coding and noncoding function. Nucleic Acids Res 2021; 49:D65-D70. [PMID: 33010163 PMCID: PMC7778915 DOI: 10.1093/nar/gkaa791] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/30/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
RNA endowed with both protein-coding and noncoding functions is referred to as 'dual-function RNA', 'binary functional RNA (bifunctional RNA)' or 'cncRNA (coding and noncoding RNA)'. Recently, an increasing number of cncRNAs have been identified, including both translated ncRNAs (ncRNAs with coding functions) and untranslated mRNAs (mRNAs with noncoding functions). However, an appropriate database for storing and organizing cncRNAs is still lacking. Here, we developed cncRNAdb, a manually curated database of experimentally supported cncRNAs, which aims to provide a resource for efficient manipulation, browsing and analysis of cncRNAs. The current version of cncRNAdb documents about 2600 manually curated entries of cncRNA functions with experimental evidence, involving more than 2,000 RNAs (including over 1300 translated ncRNAs and over 600 untranslated mRNAs) across over 20 species. In summary, we believe that cncRNAdb will help elucidate the functions and mechanisms of cncRNAs and develop new prediction methods. The database is available at http://www.rna-society.org/cncrnadb/.
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MESH Headings
- 3' Untranslated Regions
- 5' Untranslated Regions
- Animals
- Databases, Nucleic Acid/organization & administration
- Drosophila melanogaster/genetics
- Humans
- Mice
- MicroRNAs/classification
- MicroRNAs/genetics
- Pan troglodytes/genetics
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Messenger/classification
- RNA, Messenger/genetics
- RNA, Ribosomal/classification
- RNA, Ribosomal/genetics
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Transfer/classification
- RNA, Transfer/genetics
- Software
- Zebrafish/genetics
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Affiliation(s)
- Yan Huang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
| | - Jing Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yue Zhao
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou 310053, China
| | - Huafeng Wang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
| | - Tianyuan Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yuhe Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Weiyi Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yige Feng
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaxin Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaqi Gong
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lin Ning
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yong Zhang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
| | - Dong Wang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yang Zhang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
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Rhine K, Makurath MA, Liu J, Skanchy S, Lopez C, Catalan KF, Ma Y, Fare CM, Shorter J, Ha T, Chemla YR, Myong S. ALS/FTLD-Linked Mutations in FUS Glycine Residues Cause Accelerated Gelation and Reduced Interactions with Wild-Type FUS. Mol Cell 2020; 80:666-681.e8. [PMID: 33159856 PMCID: PMC7688085 DOI: 10.1016/j.molcel.2020.10.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/06/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022]
Abstract
The RNA-binding protein fused in sarcoma (FUS) can form pathogenic inclusions in neurodegenerative diseases like amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD). Over 70 mutations in Fus are linked to ALS/FTLD. In patients, all Fus mutations are heterozygous, indicating that the mutant drives disease progression despite the presence of wild-type (WT) FUS. Here, we demonstrate that ALS/FTLD-linked FUS mutations in glycine (G) strikingly drive formation of droplets that do not readily interact with WT FUS, whereas arginine (R) mutants form mixed condensates with WT FUS. Remarkably, interactions between WT and G mutants are disfavored at the earliest stages of FUS nucleation. In contrast, R mutants physically interact with the WT FUS such that WT FUS recovers the mutant defects by reducing droplet size and increasing dynamic interactions with RNA. This result suggests disparate molecular mechanisms underlying ALS/FTLD pathogenesis and differing recovery potential depending on the type of mutation.
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Affiliation(s)
- Kevin Rhine
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Monika A Makurath
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - James Liu
- Department of Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sophie Skanchy
- Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Christian Lopez
- Department of Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Kevin F Catalan
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Ye Ma
- Department of Biomedical Engineering, Johns Hopkins Medical Institute, 615 N Wolfe St, Baltimore, MD 21231, USA
| | - Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Taekjip Ha
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins Medical Institute, 615 N Wolfe St, Baltimore, MD 21231, USA; Howard Hughes Medical Institute, Baltimore, MD 21218, USA
| | - Yann R Chemla
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sua Myong
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA.
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70
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Abstract
RNA, the transcriptional output of genomes, not only templates protein synthesis or directly engages in catalytic functions, but can feed back to the genome and serve as regulatory input for gene expression. Transcripts affecting the RNA abundance of other genes act by mechanisms similar to and in concert with protein factors that control transcription. Through recruitment or blocking of activating and silencing complexes to specific genomic loci, RNA and protein factors can favor transcription or lower the local gene expression potential. Most regulatory proteins enter nuclei from all directions to start the search for increased affinity to specific DNA sequences or to other proteins nearby genuine gene targets. In contrast, RNAs emerge from spatial point sources within nuclei, their encoding genes. A transcriptional burst can result in the local appearance of multiple nascent RNA copies at once, in turn increasing local nucleic acid density and RNA motif abundance before diffusion into the nuclear neighborhood. The confined initial localization of regulatory RNAs causing accumulation of protein co-factors raises the intriguing possibility that target specificity of non-coding, and probably coding, RNAs is achieved through gene/RNA positioning and spatial proximity to regulated genomic regions. Here we review examples of positional cis conservation of regulatory RNAs with respect to target genes, spatial proximity of enhancer RNAs to promoters through DNA looping and RNA-mediated formation of membrane-less structures to control chromatin structure and expression. We speculate that linear and spatial proximity between regulatory RNA-encoding genes and gene targets could possibly ease the evolutionary pressure on maintaining regulatory RNA sequence conservation.
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Affiliation(s)
- Jörg Morf
- Jeffrey Cheah Biomedical Centre, Wellcome - Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Srinjan Basu
- Jeffrey Cheah Biomedical Centre, Wellcome - Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Paulo P Amaral
- Jeffrey Cheah Biomedical Centre, The Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
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71
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Sabari BR, Dall'Agnese A, Young RA. Biomolecular Condensates in the Nucleus. Trends Biochem Sci 2020; 45:961-977. [PMID: 32684431 PMCID: PMC7572565 DOI: 10.1016/j.tibs.2020.06.007] [Citation(s) in RCA: 217] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 12/28/2022]
Abstract
Nuclear processes such as DNA replication, transcription, and RNA processing each depend on the concerted action of many different protein and RNA molecules. How biomolecules with shared functions find their way to specific locations has been assumed to occur largely by diffusion-mediated collisions. Recent studies have shown that many nuclear processes occur within condensates that compartmentalize and concentrate the protein and RNA molecules required for each process, typically at specific genomic loci. These condensates have common features and emergent properties that provide the cell with regulatory capabilities beyond canonical molecular regulatory mechanisms. We describe here the shared features of nuclear condensates, the components that produce locus-specific condensates, elements of specificity, and the emerging understanding of mechanisms regulating these compartments.
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Affiliation(s)
- Benjamin R Sabari
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA; Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390 USA; Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142 USA.
| | | | - Richard A Young
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142 USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139 USA.
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72
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Thakur J, Henikoff S. Architectural RNA in chromatin organization. Biochem Soc Trans 2020; 48:1967-1978. [PMID: 32897323 PMCID: PMC7609026 DOI: 10.1042/bst20191226] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/20/2022]
Abstract
RNA plays a well-established architectural role in the formation of membraneless interchromatin nuclear bodies. However, a less well-known role of RNA is in organizing chromatin, whereby specific RNAs have been found to recruit chromatin modifier proteins. Whether or not RNA can act as an architectural molecule for chromatin remains unclear, partly because dissecting the architectural role of RNA from its regulatory role remains challenging. Studies that have addressed RNA's architectural role in chromatin organization rely on in situ RNA depletion using Ribonuclease A (RNase A) and suggest that RNA plays a major direct architectural role in chromatin organization. In this review, we will discuss these findings, candidate chromatin architectural long non-coding RNAs and possible mechanisms by which RNA, along with RNA binding proteins might be mediating chromatin organization.
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Affiliation(s)
- Jitendra Thakur
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, U.S.A
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, U.S.A
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, U.S.A
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73
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Pessina F, Gioia U, Brandi O, Farina S, Ceccon M, Francia S, d'Adda di Fagagna F. DNA Damage Triggers a New Phase in Neurodegeneration. Trends Genet 2020; 37:337-354. [PMID: 33020022 DOI: 10.1016/j.tig.2020.09.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/28/2020] [Accepted: 09/03/2020] [Indexed: 12/21/2022]
Abstract
Subcellular compartmentalization contributes to the organization of a plethora of molecular events occurring within cells. This can be achieved in membraneless organelles generated through liquid-liquid phase separation (LLPS), a demixing process that separates and concentrates cellular reactions. RNA is often a critical factor in mediating LLPS. Recent evidence indicates that DNA damage response foci are membraneless structures formed via LLPS and modulated by noncoding transcripts synthesized at DNA damage sites. Neurodegeneration is often associated with DNA damage, and dysfunctional LLPS events can lead to the formation of toxic aggregates. In this review, we discuss those gene products involved in neurodegeneration that undergo LLPS and their involvement in the DNA damage response.
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Affiliation(s)
- Fabio Pessina
- IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy
| | - Ubaldo Gioia
- IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy
| | - Ornella Brandi
- Istituto di Genetica Molecolare 'Luigi Luca Cavalli-Sforza' CNR - Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
| | - Stefania Farina
- Istituto di Genetica Molecolare 'Luigi Luca Cavalli-Sforza' CNR - Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy; University School for Advanced Studies IUSS, 27100 Pavia, Italy
| | - Marta Ceccon
- IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy
| | - Sofia Francia
- IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy; Istituto di Genetica Molecolare 'Luigi Luca Cavalli-Sforza' CNR - Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy.
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy; Istituto di Genetica Molecolare 'Luigi Luca Cavalli-Sforza' CNR - Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy.
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74
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Gotor NL, Armaos A, Calloni G, Torrent Burgas M, Vabulas R, De Groot NS, Tartaglia GG. RNA-binding and prion domains: the Yin and Yang of phase separation. Nucleic Acids Res 2020; 48:9491-9504. [PMID: 32857852 PMCID: PMC7515694 DOI: 10.1093/nar/gkaa681] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/08/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022] Open
Abstract
Proteins and RNAs assemble in membrane-less organelles that organize intracellular spaces and regulate biochemical reactions. The ability of proteins and RNAs to form condensates is encoded in their sequences, yet it is unknown which domains drive the phase separation (PS) process and what are their specific roles. Here, we systematically investigated the human and yeast proteomes to find regions promoting condensation. Using advanced computational methods to predict the PS propensity of proteins, we designed a set of experiments to investigate the contributions of Prion-Like Domains (PrLDs) and RNA-binding domains (RBDs). We found that one PrLD is sufficient to drive PS, whereas multiple RBDs are needed to modulate the dynamics of the assemblies. In the case of stress granule protein Pub1 we show that the PrLD promotes sequestration of protein partners and the RBD confers liquid-like behaviour to the condensate. Our work sheds light on the fine interplay between RBDs and PrLD to regulate formation of membrane-less organelles, opening up the avenue for their manipulation.
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Affiliation(s)
- Nieves Lorenzo Gotor
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Alexandros Armaos
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, RNA System Biology Lab, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Giulia Calloni
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main,60438, Germany
| | - Marc Torrent Burgas
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - R Martin Vabulas
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main,60438, Germany
- Charité – Universitätsmedizin Berlin, Institute of Biochemistry, 10117 Berlin, Germany
| | - Natalia Sanchez De Groot
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, RNA System Biology Lab, Via Enrico Melen 83, 16152 Genoa, Italy
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluis Companys, 08010 Barcelona, Spain
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
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75
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Hasenson SE, Shav‐Tal Y. Speculating on the Roles of Nuclear Speckles: How RNA‐Protein Nuclear Assemblies Affect Gene Expression. Bioessays 2020; 42:e2000104. [DOI: 10.1002/bies.202000104] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/17/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Sarah E. Hasenson
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials Bar‐Ilan University Ramat Gan 4481400 Israel
| | - Yaron Shav‐Tal
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials Bar‐Ilan University Ramat Gan 4481400 Israel
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76
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Simko EAJ, Liu H, Zhang T, Velasquez A, Teli S, Haeusler AR, Wang J. G-quadruplexes offer a conserved structural motif for NONO recruitment to NEAT1 architectural lncRNA. Nucleic Acids Res 2020; 48:7421-7438. [PMID: 32496517 PMCID: PMC7367201 DOI: 10.1093/nar/gkaa475] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/02/2020] [Indexed: 12/11/2022] Open
Abstract
The long non-coding RNA NEAT1 serves as a scaffold for the assembly of paraspeckles, membraneless nuclear organelles involved in gene regulation. Paraspeckle assembly requires NEAT1 recruitment of the RNA-binding protein NONO, however the NEAT1 elements responsible for recruitment are unknown. Herein we present evidence that previously unrecognized structural features of NEAT1 serve an important role in these interactions. Led by the initial observation that NONO preferentially binds the G-quadruplex conformation of G-rich C9orf72 repeat RNA, we find that G-quadruplex motifs are abundant and conserved features of NEAT1. Furthermore, we determine that NONO binds NEAT1 G-quadruplexes with structural specificity and provide evidence that G-quadruplex motifs mediate NONO-NEAT1 association, with NONO binding sites on NEAT1 corresponding largely to G-quadruplex motifs, and treatment with a G-quadruplex-disrupting small molecule causing dissociation of native NONO-NEAT1 complexes. Together, these findings position G-quadruplexes as a primary candidate for the NONO-recruiting elements of NEAT1 and provide a framework for further investigation into the role of G-quadruplexes in paraspeckle formation and function.
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Affiliation(s)
- Eric A J Simko
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Honghe Liu
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tao Zhang
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Adan Velasquez
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shraddha Teli
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Aaron R Haeusler
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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77
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Nozawa RS, Yamamoto T, Takahashi M, Tachiwana H, Maruyama R, Hirota T, Saitoh N. Nuclear microenvironment in cancer: Control through liquid-liquid phase separation. Cancer Sci 2020; 111:3155-3163. [PMID: 32594560 PMCID: PMC7469853 DOI: 10.1111/cas.14551] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
The eukaryotic nucleus is not a homogenous single‐spaced but a highly compartmentalized organelle, partitioned by various types of membraneless structures, including nucleoli, PML bodies, paraspeckles, DNA damage foci and RNA clouds. Over the past few decades, these nuclear structures have been implicated in biological reactions such as gene regulation and DNA damage response and repair, and are thought to provide “microenvironments,” facilitating these reactions in the nucleus. Notably, an altered morphology of these nuclear structures is found in many cancers, which may relate to so‐called “nuclear atypia” in histological examinations. While the diagnostic significance of nuclear atypia has been established, its nature has remained largely enigmatic and awaits characterization. Here, we review the emerging biophysical principles that govern biomolecular condensate assembly in the nucleus, namely, liquid‐liquid phase separation (LLPS), to investigate the nature of the nuclear microenvironment. In the nucleus, LLPS is typically driven by multivalent interactions between proteins with intrinsically disordered regions, and is also facilitated by protein interaction with nucleic acids, including nuclear non–coding RNAs. Importantly, an altered LLPS leads to dysregulation of nuclear events and epigenetics, and often to tumorigenesis and tumor progression. We further note the possibility that LLPS could represent a new therapeutic target for cancer intervention.
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Affiliation(s)
- Ryu-Suke Nozawa
- Division of Experimental Pathology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Tatsuro Yamamoto
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Motoko Takahashi
- Division of Experimental Pathology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Hiroaki Tachiwana
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Reo Maruyama
- Project for Cancer Epigenomics, The Cancer Institute of JFCR, Tokyo, Japan
| | - Toru Hirota
- Division of Experimental Pathology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, Japan
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78
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Zeng C, Hamada M. RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines. Genes (Basel) 2020; 11:E820. [PMID: 32708427 PMCID: PMC7397181 DOI: 10.3390/genes11070820] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing, a ubiquitous phenomenon in eukaryotes, is a regulatory mechanism for the biological diversity of individual genes. Most studies have focused on the effects of alternative splicing for protein synthesis. However, the transcriptome-wide influence of alternative splicing on RNA subcellular localization has rarely been studied. By analyzing RNA-seq data obtained from subcellular fractions across 13 human cell lines, we identified 8720 switching genes between the cytoplasm and the nucleus. Consistent with previous reports, intron retention was observed to be enriched in the nuclear transcript variants. Interestingly, we found that short and structurally stable introns were positively correlated with nuclear localization. Motif analysis reveals that fourteen RNA-binding protein (RBPs) are prone to be preferentially bound with such introns. To our knowledge, this is the first transcriptome-wide study to analyze and evaluate the effect of alternative splicing on RNA subcellular localization. Our findings reveal that alternative splicing plays a promising role in regulating RNA subcellular localization.
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Affiliation(s)
- Chao Zeng
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo 169-8555, Japan
- Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Michiaki Hamada
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo 169-8555, Japan
- Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan
- Institute for Medical-oriented Structural Biology, Waseda University, Tokyo 162-8480, Japan
- Graduate School of Medicine, Nippon Medical School, Tokyo 113-8602, Japan
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79
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Wang C, Duan Y, Duan G, Wang Q, Zhang K, Deng X, Qian B, Gu J, Ma Z, Zhang S, Guo L, Liu C, Fang Y. Stress Induces Dynamic, Cytotoxicity-Antagonizing TDP-43 Nuclear Bodies via Paraspeckle LncRNA NEAT1-Mediated Liquid-Liquid Phase Separation. Mol Cell 2020; 79:443-458.e7. [PMID: 32649883 DOI: 10.1016/j.molcel.2020.06.019] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 05/01/2020] [Accepted: 06/09/2020] [Indexed: 12/13/2022]
Abstract
Despite the prominent role of TDP-43 in neurodegeneration, its physiological and pathological functions are not fully understood. Here, we report an unexpected role of TDP-43 in the formation of dynamic, reversible, liquid droplet-like nuclear bodies (NBs) in response to stress. Formation of NBs alleviates TDP-43-mediated cytotoxicity in mammalian cells and fly neurons. Super-resolution microscopy reveals distinct functions of the two RRMs in TDP-43 NB formation. TDP-43 NBs are partially colocalized with nuclear paraspeckles, whose scaffolding lncRNA NEAT1 is dramatically upregulated in stressed neurons. Moreover, increase of NEAT1 promotes TDP-43 liquid-liquid phase separation (LLPS) in vitro. Finally, we discover that the ALS-associated mutation D169G impairs the NEAT1-mediated TDP-43 LLPS and NB assembly, causing excessive cytoplasmic translocation of TDP-43 to form stress granules, which become phosphorylated TDP-43 cytoplasmic foci upon prolonged stress. Together, our findings suggest a stress-mitigating role and mechanism of TDP-43 NBs, whose dysfunction may be involved in ALS pathogenesis.
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Affiliation(s)
- Chen Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongjia Duan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Duan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiangqiang Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Kai Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Deng
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Beituo Qian
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinge Gu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiwei Ma
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Shuang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Lin Guo
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yanshan Fang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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80
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Frank L, Rippe K. Repetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation. J Mol Biol 2020; 432:4270-4286. [DOI: 10.1016/j.jmb.2020.04.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/21/2022]
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81
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Hur W, Kemp JP, Tarzia M, Deneke VE, Marzluff WF, Duronio RJ, Di Talia S. CDK-Regulated Phase Separation Seeded by Histone Genes Ensures Precise Growth and Function of Histone Locus Bodies. Dev Cell 2020; 54:379-394.e6. [PMID: 32579968 DOI: 10.1016/j.devcel.2020.06.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 02/17/2020] [Accepted: 05/30/2020] [Indexed: 10/24/2022]
Abstract
Many membraneless organelles form through liquid-liquid phase separation, but how their size is controlled and whether size is linked to function remain poorly understood. The histone locus body (HLB) is an evolutionarily conserved nuclear body that regulates the transcription and processing of histone mRNAs. Here, we show that Drosophila HLBs form through phase separation. During embryogenesis, the size of HLBs is controlled in a precise and dynamic manner that is dependent on the cell cycle and zygotic histone gene activation. Control of HLB growth is achieved by a mechanism integrating nascent mRNAs at the histone locus, which facilitates phase separation, and the nuclear concentration of the scaffold protein multi-sex combs (Mxc), which is controlled by the activity of cyclin-dependent kinases. Reduced Cdk2 activity results in smaller HLBs and the appearance of nascent, misprocessed histone mRNAs. Thus, our experiments identify a mechanism linking nuclear body growth and size with gene expression.
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Affiliation(s)
- Woonyung Hur
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - James P Kemp
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marco Tarzia
- LPTMC, CNRS-UMR 7600, Sorbonne Université, 4 Pl. Jussieu, 75005 Paris, France
| | - Victoria E Deneke
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - William F Marzluff
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert J Duronio
- Department of Biology, Department of Genetics, Integrative Program for Biological and Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA.
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82
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Zaytseva O, Mitchell NC, Guo L, Marshall OJ, Parsons LM, Hannan RD, Levens DL, Quinn LM. Transcriptional repression of Myc underlies the tumour suppressor function of AGO1 in Drosophila. Development 2020; 147:147/11/dev190231. [PMID: 32527935 PMCID: PMC7295588 DOI: 10.1242/dev.190231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/27/2020] [Indexed: 12/29/2022]
Abstract
Here, we report novel tumour suppressor activity for the Drosophila Argonaute family RNA-binding protein AGO1, a component of the miRNA-dependent RNA-induced silencing complex (RISC). The mechanism for growth inhibition does not, however, involve canonical roles as part of the RISC; rather, AGO1 controls cell and tissue growth by functioning as a direct transcriptional repressor of the master regulator of growth, Myc. AGO1 depletion in wing imaginal discs drives a significant increase in ribosome biogenesis, nucleolar expansion and cell growth in a manner dependent on Myc abundance. Moreover, increased Myc promoter activity and elevated Myc mRNA in AGO1-depleted animals requires RNA polymerase II transcription. Further support for transcriptional AGO1 functions is provided by physical interaction with the RNA polymerase II transcriptional machinery (chromatin remodelling factors and Mediator Complex), punctate nuclear localisation in euchromatic regions and overlap with Polycomb Group transcriptional silencing loci. Moreover, significant AGO1 enrichment is observed on the Myc promoter and AGO1 interacts with the Myc transcriptional activator Psi. Together, our data show that Drosophila AGO1 functions outside of the RISC to repress Myc transcription and inhibit developmental cell and tissue growth. This article has an associated ‘The people behind the papers’ interview. Highlighted Article: In the Drosophila wing, the Argonaute family protein AGO1 acts independently of the miRNA-silencing pathway to restrict tissue growth by directly repressing transcription of the master growth regulator Myc.
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Affiliation(s)
- Olga Zaytseva
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Naomi C Mitchell
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Linna Guo
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | | | | | - Ross D Hannan
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - David L Levens
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Leonie M Quinn
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
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83
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Corbet GA, Parker R. RNP Granule Formation: Lessons from P-Bodies and Stress Granules. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:203-215. [PMID: 32482896 DOI: 10.1101/sqb.2019.84.040329] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
It is now clear that cells form a wide collection of large RNA-protein assemblies, referred to as RNP granules. RNP granules exist in bacterial cells and can be found in both the cytosol and nucleus of eukaryotic cells. Recent approaches have begun to define the RNA and protein composition of a number of RNP granules. Herein, we review the composition and assembly of RNP granules, as well as how RNPs are targeted to RNP granules using stress granules and P-bodies as model systems. Taken together, these reveal that RNP granules form through the summative effects of a combination of protein-protein, protein-RNA, and RNA-RNA interactions. Similarly, the partitioning of individual RNPs into stress granules is determined by the combinatorial effects of multiple elements. Thus, RNP granules are assemblies generally dominated by combinatorial effects, thereby providing rich opportunities for biological regulation.
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Affiliation(s)
- Giulia Ada Corbet
- Department of Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
- Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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84
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Koreski KP, Rieder LE, McLain LM, Chaubal A, Marzluff WF, Duronio RJ. Drosophila histone locus body assembly and function involves multiple interactions. Mol Biol Cell 2020; 31:1525-1537. [PMID: 32401666 PMCID: PMC7359574 DOI: 10.1091/mbc.e20-03-0176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The histone locus body (HLB) assembles at replication-dependent (RD) histone loci and concentrates factors required for RD histone mRNA biosynthesis. The Drosophila melanogaster genome has a single locus comprised of ∼100 copies of a tandemly arrayed 5-kB repeat unit containing one copy of each of the 5 RD histone genes. To determine sequence elements required for D. melanogaster HLB formation and histone gene expression, we used transgenic gene arrays containing 12 copies of the histone repeat unit that functionally complement loss of the ∼200 endogenous RD histone genes. A 12x histone gene array in which all H3-H4 promoters were replaced with H2a-H2b promoters (12xPR) does not form an HLB or express high levels of RD histone mRNA in the presence of the endogenous histone genes. In contrast, this same transgenic array is active in HLB assembly and RD histone gene expression in the absence of the endogenous RD histone genes and rescues the lethality caused by homozygous deletion of the RD histone locus. The HLB formed in the absence of endogenous RD histone genes on the mutant 12x array contains all known factors present in the wild-type HLB including CLAMP, which normally binds to GAGA repeats in the H3-H4 promoter. These data suggest that multiple protein–protein and/or protein–DNA interactions contribute to HLB formation, and that the large number of endogenous RD histone gene copies sequester available factor(s) from attenuated transgenic arrays, thereby preventing HLB formation and gene expression on these arrays.
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Affiliation(s)
- Kaitlin P Koreski
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Leila E Rieder
- Department of Biology, Emory University, Atlanta, GA 30322
| | - Lyndsey M McLain
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Ashlesha Chaubal
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - William F Marzluff
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599.,Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
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85
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Kuo TC, Kung HJ, Shih JW. Signaling in and out: long-noncoding RNAs in tumor hypoxia. J Biomed Sci 2020; 27:59. [PMID: 32370770 PMCID: PMC7201962 DOI: 10.1186/s12929-020-00654-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023] Open
Abstract
Over the past few years, long non-coding RNAs (lncRNAs) are recognized as key regulators of gene expression at chromatin, transcriptional and posttranscriptional level with pivotal roles in various biological and pathological processes, including cancer. Hypoxia, a common feature of the tumor microenvironment, profoundly affects gene expression and is tightly associated with cancer progression. Upon tumor hypoxia, the central regulator HIF (hypoxia-inducible factor) is upregulated and orchestrates transcription reprogramming, contributing to aggressive phenotypes in numerous cancers. Not surprisingly, lncRNAs are also transcriptional targets of HIF and serve as effectors of hypoxia response. Indeed, the number of hypoxia-associated lncRNAs (HALs) identified has risen sharply, illustrating the expanding roles of lncRNAs in hypoxia signaling cascade and responses. Moreover, through extra-cellular vesicles, lncRNAs could transmit hypoxia responses between cancer cells and the associated microenvironment. Notably, the aberrantly expressed cellular or exosomal HALs can serve as potential prognostic markers and therapeutic targets. In this review, we provide an update of the current knowledge about the expression, involvement and potential clinical impact of lncRNAs in tumor hypoxia, with special focus on their unique molecular regulation of HIF cascade and hypoxia-induced malignant progression.
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Affiliation(s)
- Tse-Chun Kuo
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County, 35053, Taiwan, ROC
| | - Hsing-Jien Kung
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County, 35053, Taiwan, ROC.,Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan, ROC.,Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan, ROC.,Department of Biochemistry and Molecular Medicine, Comprehensive Cancer Center, University of California at Davis, Sacramento, CA, 95817, USA.,TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, 110, Taiwan, ROC
| | - Jing-Wen Shih
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan, ROC. .,Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan, ROC. .,TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, 110, Taiwan, ROC. .,Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan, ROC.
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86
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Hiraoka Y. Phase separation drives pairing of homologous chromosomes. Curr Genet 2020; 66:881-887. [PMID: 32285141 DOI: 10.1007/s00294-020-01077-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 01/06/2023]
Abstract
Pairing of homologous chromosomes is crucial for ensuring accurate segregation of chromosomes during meiosis. Molecular mechanisms of homologous chromosome pairing in meiosis have been extensively studied in the fission yeast Schizosaccharomyces pombe. In this organism, meiosis-specific noncoding RNA transcribed from specific genes accumulates at the respective gene loci, and chromosome-associated RNA-protein complexes mediate meiotic pairing of homologous loci through phase separation. Pairing of homologous chromosomes also occurs in somatic diploid cells in certain situations. For example, somatic pairing of homologous chromosomes occurs during the early embryogenesis in diptera, and relies on the transcription-associated chromatin architecture. Earlier models also suggest that transcription factories along the chromosome mediate pairing of homologous chromosomes in plants. These studies suggest that RNA bodies formed on chromosomes mediate the pairing of homologous chromosomes. This review summarizes lessons from S. pombe to provide general insights into mechanisms of homologous chromosome pairing mediated by phase separation of chromosome-associated RNA-protein complexes.
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Affiliation(s)
- Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, 565-0871, Japan.
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87
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Greig JA, Nguyen TA, Lee M, Holehouse AS, Posey AE, Pappu RV, Jedd G. Arginine-Enriched Mixed-Charge Domains Provide Cohesion for Nuclear Speckle Condensation. Mol Cell 2020; 77:1237-1250.e4. [PMID: 32048997 PMCID: PMC10715173 DOI: 10.1016/j.molcel.2020.01.025] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/04/2019] [Accepted: 01/23/2020] [Indexed: 12/29/2022]
Abstract
Low-complexity protein domains promote the formation of various biomolecular condensates. However, in many cases, the precise sequence features governing condensate formation and identity remain unclear. Here, we investigate the role of intrinsically disordered mixed-charge domains (MCDs) in nuclear speckle condensation. Proteins composed exclusively of arginine-aspartic acid dipeptide repeats undergo length-dependent condensation and speckle incorporation. Substituting arginine with lysine in synthetic and natural speckle-associated MCDs abolishes these activities, identifying a key role for multivalent contacts through arginine's guanidinium ion. MCDs can synergize with a speckle-associated RNA recognition motif to promote speckle specificity and residence. MCD behavior is tunable through net-charge: increasing negative charge abolishes condensation and speckle incorporation. Contrastingly, increasing positive charge through arginine leads to enhanced condensation, speckle enlargement, decreased splicing factor mobility, and defective mRNA export. Together, these results identify key sequence determinants of MCD-promoted speckle condensation and link the dynamic material properties of speckles with function in mRNA processing.
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Affiliation(s)
- Jamie A Greig
- Temasek Life Sciences Laboratory and Department of Biological Sciences, The National University of Singapore, Singapore 117604, Singapore
| | - Tu Anh Nguyen
- Temasek Life Sciences Laboratory and Department of Biological Sciences, The National University of Singapore, Singapore 117604, Singapore
| | - Michelle Lee
- Temasek Life Sciences Laboratory and Department of Biological Sciences, The National University of Singapore, Singapore 117604, Singapore
| | - Alex S Holehouse
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ammon E Posey
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Gregory Jedd
- Temasek Life Sciences Laboratory and Department of Biological Sciences, The National University of Singapore, Singapore 117604, Singapore.
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88
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Yamazaki T, Nakagawa S, Hirose T. Architectural RNAs for Membraneless Nuclear Body Formation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:227-237. [PMID: 32019862 DOI: 10.1101/sqb.2019.84.039404] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Long noncoding RNAs (lncRNAs) are fundamental regulators of various cellular processes. A subset of lncRNAs, termed architectural RNAs (arcRNAs), function in the formation and maintenance of phase-separated membraneless organelles in multiple eukaryotic species. These membraneless organelles represent an important type of compartmentalization in the crowded cellular environment and have several distinct features. The NEAT1_2 lncRNA is a well-characterized arcRNA that functions as an essential scaffold of paraspeckle nuclear bodies. Here, we describe the biogenesis of paraspeckles on arcRNAs through phase separation, focusing on the specific functions of multiple NEAT1_2 RNA domains and their partner RNA-binding proteins. Finally, we present an updated model of paraspeckle formation and discuss future perspectives of research into arcRNA-instructed architectures of phase-separated nuclear bodies.
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Affiliation(s)
- Tomohiro Yamazaki
- Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815 Japan
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812 Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815 Japan
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89
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Wingett SW, Andrews S, Fraser P, Morf J. RNA proximity sequencing data and analysis pipeline from a human neuroblastoma nuclear transcriptome. Sci Data 2020; 7:35. [PMID: 31992717 PMCID: PMC6987088 DOI: 10.1038/s41597-020-0372-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/09/2020] [Indexed: 11/09/2022] Open
Abstract
We have previously developed and described a method for measuring RNA co-locations within cells, called Proximity RNA-seq, which promises insights into RNA expression, processing, storage and translation. Here, we describe transcriptome-wide proximity RNA-seq datasets obtained from human neuroblastoma SH-SY5Y cell nuclei. To aid future users of this method, we also describe and release our analysis pipeline, CloseCall, which maps cDNA to a custom transcript annotation and allocates cDNA-linked barcodes to barcode groups. CloseCall then performs Monte Carlo simulations on the data to identify pairs of transcripts, which are co-barcoded more frequently than expected by chance. Furthermore, derived co-barcoding frequencies for individual transcripts, dubbed valency, serve as proxies for RNA density or connectivity for that given transcript. We outline how this pipeline was applied to these sequencing datasets and openly share the processed data outputs and access to a virtual machine that runs CloseCall. The resulting data specify the spatial organization of RNAs and builds hypotheses for potential regulatory relationships between RNAs. Measurement(s) | RNA • Proximity | Technology Type(s) | RNA sequencing | Factor Type(s) | biological replicate | Sample Characteristic - Organism | Homo sapiens |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11627397
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Affiliation(s)
- Steven W Wingett
- Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK. .,Bioinformatics, Babraham Institute, Cambridge, UK.
| | | | - Peter Fraser
- Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK.,Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Jörg Morf
- Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK.
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90
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Krasikova A, Kulikova T. Identification of Genomic Loci Responsible for the Formation of Nuclear Domains Using Lampbrush Chromosomes. Noncoding RNA 2019; 6:ncrna6010001. [PMID: 31881720 PMCID: PMC7151628 DOI: 10.3390/ncrna6010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/19/2019] [Accepted: 12/22/2019] [Indexed: 12/12/2022] Open
Abstract
In the cell nuclei, various types of nuclear domains assemble as a result of transcriptional activity at specific chromosomal loci. Giant transcriptionally active lampbrush chromosomes, which form in oocyte nuclei of amphibians and birds enable the mapping of genomic sequences with high resolution and the visualization of individual transcription units. This makes avian and amphibian oocyte nuclei an advantageous model for studying locus-specific nuclear domains. We developed two strategies for identification and comprehensive analysis of the genomic loci involved in nuclear domain formation on lampbrush chromosomes. The first approach was based on the sequential FISH-mapping of BAC clones containing genomic DNA fragments with a known chromosomal position close to the locus of a nuclear domain. The second approach involved mechanical microdissection of the chromosomal region adjacent to the nuclear domain followed by the generation of FISH-probes and DNA sequencing. Furthermore, deciphering the DNA sequences from the dissected material by high throughput sequencing technologies and their mapping to the reference genome helps to identify the genomic region responsible for the formation of the nuclear domain. For those nuclear domains structured by nascent transcripts, identification of genomic loci of their formation is a crucial step in the identification of scaffold RNAs.
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91
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Khosraviani N, Ostrowski LA, Mekhail K. Roles for Non-coding RNAs in Spatial Genome Organization. Front Cell Dev Biol 2019; 7:336. [PMID: 31921848 PMCID: PMC6930868 DOI: 10.3389/fcell.2019.00336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 11/29/2019] [Indexed: 12/15/2022] Open
Abstract
Genetic loci are non-randomly arranged in the nucleus of the cell. This order, which is important to overall genome expression and stability, is maintained by a growing number of factors including the nuclear envelope, various genetic elements and dedicated protein complexes. Here, we review evidence supporting roles for non-coding RNAs (ncRNAs) in the regulation of spatial genome organization and its impact on gene expression and cell survival. Specifically, we discuss how ncRNAs from single-copy and repetitive DNA loci contribute to spatial genome organization by impacting perinuclear chromosome tethering, major nuclear compartments, chromatin looping, and various chromosomal structures. Overall, our analysis of the literature highlights central functions for ncRNAs and their transcription in the modulation of spatial genome organization with connections to human health and disease.
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Affiliation(s)
- Negin Khosraviani
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Lauren A. Ostrowski
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Canada Research Chairs Program, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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92
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McDonel P, Guttman M. Approaches for Understanding the Mechanisms of Long Noncoding RNA Regulation of Gene Expression. Cold Spring Harb Perspect Biol 2019; 11:11/12/a032151. [PMID: 31791999 DOI: 10.1101/cshperspect.a032151] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mammalian genomes encode tens of thousands of long noncoding RNAs (lncRNAs) that have been implicated in a diverse array of biological processes and human diseases. In recent years, the development of new tools for studying lncRNAs has enabled important progress in defining the mechanisms by which Xist and other lncRNAs function. This collective work provides a framework for how to define the mechanisms by which lncRNAs act. This includes defining lncRNA function, identifying and characterizing lncRNA-protein interactions, and lncRNA localization in the cell. In this review, we discuss various experimental approaches for deciphering lncRNA mechanisms and discuss issues and limitations in interpreting these results. We explore what these data can reveal about lncRNA function and mechanism as well as emerging insights into lncRNA biology that have been derived from these studies.
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Affiliation(s)
- Patrick McDonel
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
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93
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Spannl S, Tereshchenko M, Mastromarco GJ, Ihn SJ, Lee HO. Biomolecular condensates in neurodegeneration and cancer. Traffic 2019; 20:890-911. [PMID: 31606941 DOI: 10.1111/tra.12704] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 10/03/2019] [Accepted: 10/06/2019] [Indexed: 12/14/2022]
Abstract
The intracellular environment is partitioned into functionally distinct compartments containing specific sets of molecules and reactions. Biomolecular condensates, also referred to as membrane-less organelles, are diverse and abundant cellular compartments that lack membranous enclosures. Molecules assemble into condensates by phase separation; multivalent weak interactions drive molecules to separate from their surroundings and concentrate in discrete locations. Biomolecular condensates exist in all eukaryotes and in some prokaryotes, and participate in various essential house-keeping, stress-response and cell type-specific processes. An increasing number of recent studies link abnormal condensate formation, composition and material properties to a number of disease states. In this review, we discuss current knowledge and models describing the regulation of condensates and how they become dysregulated in neurodegeneration and cancer. Further research on the regulation of biomolecular phase separation will help us to better understand their role in cell physiology and disease.
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Affiliation(s)
- Stephanie Spannl
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Maria Tereshchenko
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Sean J Ihn
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Canada Research Chairs Program, University of Toronto, Toronto, Ontario, Canada
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94
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McSwiggen DT, Mir M, Darzacq X, Tjian R. Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences. Genes Dev 2019; 33:1619-1634. [PMID: 31594803 PMCID: PMC6942051 DOI: 10.1101/gad.331520.119] [Citation(s) in RCA: 370] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The idea that liquid-liquid phase separation (LLPS) may be a general mechanism by which molecules in the complex cellular milieu may self-organize has generated much excitement and fervor in the cell biology community. While this concept is not new, its rise to preeminence has resulted in renewed interest in the mechanisms that shape and drive diverse cellular self-assembly processes from gene expression to cell division to stress responses. In vitro biochemical data have been instrumental in deriving some of the fundamental principles and molecular grammar by which biological molecules may phase separate, and the molecular basis of these interactions. Definitive evidence is lacking as to whether the same principles apply in the physiological environment inside living cells. In this Perspective, we analyze the evidence supporting phase separation in vivo across multiple cellular processes. We find that the evidence for in vivo LLPS is often phenomenological and inadequate to discriminate between phase separation and other possible mechanisms. Moreover, the causal relationship and functional consequences of LLPS in vivo are even more elusive. We underscore the importance of performing quantitative measurements on proteins in their endogenous state and physiological abundance, as well as make recommendations for experiments that may yield more conclusive results.
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Affiliation(s)
- David T McSwiggen
- Department of Molecular and Cell Biology, University of California Berkeley, California 94720, USA
- California Institute of Regenerative Medicine Center of Excellence, University of California Berkeley, California 94720, USA
| | - Mustafa Mir
- Department of Molecular and Cell Biology, University of California Berkeley, California 94720, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California Berkeley, California 94720, USA
- California Institute of Regenerative Medicine Center of Excellence, University of California Berkeley, California 94720, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California Berkeley, California 94720, USA
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95
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Strom AR, Brangwynne CP. The liquid nucleome - phase transitions in the nucleus at a glance. J Cell Sci 2019; 132:132/22/jcs235093. [PMID: 31754043 DOI: 10.1242/jcs.235093] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cells organize membrane-less internal compartments through a process called liquid-liquid phase separation (LLPS) to create chemically distinct compartments, referred to as condensates, which emerge from interactions among biological macromolecules. These condensates include various cytoplasmic structures such as P-granules and stress granules. However, an even wider array of condensates subcompartmentalize the cell nucleus, forming liquid-like structures that range from nucleoli and Cajal bodies to nuclear speckles and gems. Phase separation provides a biophysical assembly mechanism underlying this non-covalent form of fluid compartmentalization and functionalization. In this Cell Science at a Glance article and the accompanying poster, we term these phase-separated liquids that organize the nucleus the liquid nucleome; we discuss examples of biological phase transitions in the nucleus, how the cell utilizes biophysical aspects of phase separation to form and regulate condensates, and suggest interpretations for the role of phase separation in nuclear organization and function.
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Affiliation(s)
- Amy R Strom
- Department of Chemical and Biological Engineering, Howard Hughes Medical Institute, Princeton University, Princeton NJ 08544, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Howard Hughes Medical Institute, Princeton University, Princeton NJ 08544, USA
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96
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A P, Weber SC. Evidence for and against Liquid-Liquid Phase Separation in the Nucleus. Noncoding RNA 2019; 5:E50. [PMID: 31683819 PMCID: PMC6958436 DOI: 10.3390/ncrna5040050] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/23/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022] Open
Abstract
Enclosed by two membranes, the nucleus itself is comprised of various membraneless compartments, including nuclear bodies and chromatin domains. These compartments play an important though still poorly understood role in gene regulation. Significant progress has been made in characterizing the dynamic behavior of nuclear compartments and liquid-liquid phase separation (LLPS) has emerged as a prominent mechanism governing their assembly. However, recent work reveals that certain nuclear structures violate key predictions of LLPS, suggesting that alternative mechanisms likely contribute to nuclear organization. Here, we review the evidence for and against LLPS for several nuclear compartments and discuss experimental strategies to identify the mechanism(s) underlying their assembly. We propose that LLPS, together with multiple modes of protein-nucleic acid binding, drive spatiotemporal organization of the nucleus and facilitate functional diversity among nuclear compartments.
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Affiliation(s)
- Peng A
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada.
| | - Stephanie C Weber
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada.
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada.
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97
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The Control Centers of Biomolecular Phase Separation: How Membrane Surfaces, PTMs, and Active Processes Regulate Condensation. Mol Cell 2019; 76:295-305. [PMID: 31604601 DOI: 10.1016/j.molcel.2019.09.016] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/30/2022]
Abstract
Biomolecular condensation is emerging as an essential process for cellular compartmentalization. The formation of biomolecular condensates can be driven by liquid-liquid phase separation, which arises from weak, multivalent interactions among proteins and nucleic acids. A substantial body of recent work has revealed that diverse cellular processes rely on biomolecular condensation and that aberrant phase separation may cause disease. Many proteins display an intrinsic propensity to undergo phase separation. However, the mechanisms by which cells regulate phase separation to build functional condensates at the appropriate time and location are only beginning to be understood. Here, we review three key cellular mechanisms that enable the control of biomolecular phase separation: membrane surfaces, post-translational modifications, and active processes. We discuss how these mechanisms may function in concert to provide robust control over biomolecular condensates and suggest new research avenues that will elucidate how cells build and maintain these key centers of cellular compartmentalization.
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98
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Abstract
Mammalian genomes are extensively transcribed, which produces a large number of both coding and non-coding transcripts. Various RNAs are physically associated with chromatin, through being either retained in cis at their site of transcription or recruited in trans to other genomic regions. Driven by recent technological innovations for detecting chromatin-associated RNAs, diverse roles are being revealed for these RNAs and associated RNA-binding proteins (RBPs) in gene regulation and genome function. Such functions include locus-specific roles in gene activation and silencing, as well as emerging roles in higher-order genome organization, such as involvement in long-range enhancer-promoter interactions, transcription hubs, heterochromatin, nuclear bodies and phase transitions.
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Affiliation(s)
- Xiao Li
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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99
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Correll CC, Bartek J, Dundr M. The Nucleolus: A Multiphase Condensate Balancing Ribosome Synthesis and Translational Capacity in Health, Aging and Ribosomopathies. Cells 2019; 8:cells8080869. [PMID: 31405125 PMCID: PMC6721831 DOI: 10.3390/cells8080869] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022] Open
Abstract
The nucleolus is the largest membrane-less structure in the eukaryotic nucleus. It is involved in the biogenesis of ribosomes, essential macromolecular machines responsible for synthesizing all proteins required by the cell. The assembly of ribosomes is evolutionarily conserved and is the most energy-consuming cellular process needed for cell growth, proliferation, and homeostasis. Despite the significance of this process, the intricate pathophysiological relationship between the nucleolus and protein synthesis has only recently begun to emerge. Here, we provide perspective on new principles governing nucleolar formation and the resulting multiphase organization driven by liquid-liquid phase separation. With recent advances in the structural analysis of ribosome formation, we highlight the current understanding of the step-wise assembly of pre-ribosomal subunits and the quality control required for proper function. Finally, we address how aging affects ribosome genesis and how genetic defects in ribosome formation cause ribosomopathies, complex diseases with a predisposition to cancer.
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Affiliation(s)
- Carl C Correll
- Center for Proteomics and Molecular Therapeutics, Rosalind Franklin University of Medicine & Science, North Chicago, IL 60064, USA.
| | - Jiri Bartek
- Danish Cancer Society Research Center, Genome Integrity Unit, DK-2100 Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Miroslav Dundr
- Center for Cancer Cell Biology Immunology and Infection, Rosalind Franklin University of Medicine & Science, North Chicago, IL 60064, USA.
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100
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Albrecht TR, Shevtsov SP, Wu Y, Mascibroda LG, Peart NJ, Huang KL, Sawyer IA, Tong L, Dundr M, Wagner EJ. Integrator subunit 4 is a 'Symplekin-like' scaffold that associates with INTS9/11 to form the Integrator cleavage module. Nucleic Acids Res 2019; 46:4241-4255. [PMID: 29471365 PMCID: PMC5934644 DOI: 10.1093/nar/gky100] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 02/17/2018] [Indexed: 12/14/2022] Open
Abstract
Integrator (INT) is a transcriptional regulatory complex associated with RNA polymerase II that is required for the 3′-end processing of both UsnRNAs and enhancer RNAs. Integrator subunits 9 (INTS9) and INTS11 constitute the catalytic core of INT and are paralogues of the cleavage and polyadenylation specificity factors CPSF100 and CPSF73. While CPSF73/100 are known to associate with a third protein called Symplekin, there is no paralog of Symplekin within INT raising the question of how INTS9/11 associate with the other INT subunits. Here, we have identified that INTS4 is a specific and conserved interaction partner of INTS9/11 that does not interact with either subunit individually. Although INTS4 has no significant homology with Symplekin, it possesses N-terminal HEAT repeats similar to Symplekin but also contains a β-sheet rich C-terminal region, both of which are important to bind INTS9/11. We assess three functions of INT including UsnRNA 3′-end processing, maintenance of Cajal body structural integrity, and formation of histone locus bodies to conclude that INTS4/9/11 are the most critical of the INT subunits for UsnRNA biogenesis. Altogether, these results indicate that INTS4/9/11 compose a heterotrimeric complex that likely represents the Integrator ‘cleavage module’ responsible for its endonucleolytic activity.
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Affiliation(s)
- Todd R Albrecht
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Sergey P Shevtsov
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, IL 60064, USA
| | - Yixuan Wu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Lauren G Mascibroda
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Natoya J Peart
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Iain A Sawyer
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, IL 60064, USA.,Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, IL 60064, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
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