1
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Wu C, Wang X, Li Y, Zhen W, Wang C, Wang X, Xie Z, Xu X, Guo S, Botella JR, Zheng B, Wang W, Song CP, Hu Z. Sequestration of DBR1 to stress granules promotes lariat intronic RNAs accumulation for heat-stress tolerance. Nat Commun 2024; 15:7696. [PMID: 39227617 PMCID: PMC11371829 DOI: 10.1038/s41467-024-52034-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 08/22/2024] [Indexed: 09/05/2024] Open
Abstract
Heat stress (HS) poses a significant challenge to plant survival, necessitating sophisticated molecular mechanisms to maintain cellular homeostasis. Here, we identify SICKLE (SIC) as a key modulator of HS responses in Arabidopsis (Arabidopsis thaliana). SIC is required for the sequestration of RNA DEBRANCHING ENZYME 1 (DBR1), a rate-limiting enzyme of lariat intronic RNA (lariRNA) decay, into stress granules (SGs). The sequestration of DBR1 by SIC enhances the accumulation of lariRNAs, branched circular RNAs derived from excised introns during pre-mRNA splicing, which in turn promote the transcription of their parental genes. Our findings further demonstrate that SIC-mediated DBR1 sequestration in SGs is crucial for plant HS tolerance, as deletion of the N-terminus of SIC (SIC1-244) impairs DBR1 sequestration and compromises plant response to HS. Overall, our study unveils a mechanism of transcriptional regulation in the HS response, where lariRNAs are enriched through DBR1 sequestration, ultimately promoting the transcription of heat stress tolerance genes.
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Affiliation(s)
- Chengyun Wu
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Sanya Institute, Henan University, Sanya, 572025, China
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Xingsong Wang
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Yan Li
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Weibo Zhen
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Chunfei Wang
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiaoqing Wang
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Zhouli Xie
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xiumei Xu
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Sanya Institute, Henan University, Sanya, 572025, China
| | - Siyi Guo
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Sanya Institute, Henan University, Sanya, 572025, China
| | - José Ramón Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Wei Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Center for Life Sciences, Beijing, 100871, China
| | - Chun-Peng Song
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
- Sanya Institute, Henan University, Sanya, 572025, China.
| | - Zhubing Hu
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
- Sanya Institute, Henan University, Sanya, 572025, China.
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2
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Yao J, Xu H, Ferrick-Kiddie EA, Nottingham RM, Wu DC, Ares M, Lambowitz AM. Human cells contain myriad excised linear intron RNAs with links to gene regulation and potential utility as biomarkers. PLoS Genet 2024; 20:e1011416. [PMID: 39325823 PMCID: PMC11460701 DOI: 10.1371/journal.pgen.1011416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 10/08/2024] [Accepted: 09/03/2024] [Indexed: 09/28/2024] Open
Abstract
A previous study using Thermostable Group II Intron Reverse Transcriptase sequencing (TGIRT-seq) found human plasma contains short (≤300 nt) structured full-length excised linear intron (FLEXI) RNAs with potential to serve as blood-based biomarkers. Here, TGIRT-seq identified >9,000 different FLEXI RNAs in human cell lines, including relatively abundant FLEXIs with cell-type-specific expression patterns. Analysis of public CLIP-seq datasets identified 126 RNA-binding proteins (RBPs) that have binding sites within the region corresponding to the FLEXI or overlapping FLEXI splice sites in pre-mRNAs, including 53 RBPs with binding sites for ≥30 different FLEXIs. These included splicing factors, transcription factors, a chromatin remodeling protein, cellular growth regulators, and proteins with cytoplasmic functions. Analysis of ENCODE datasets identified subsets of these RBPs whose knockdown impacted FLEXI host gene mRNA levels or proximate alternative splicing, indicating functional interactions. Hierarchical clustering identified six subsets of RBPs whose FLEXI binding sites were co-enriched in six subsets of functionally related host genes: AGO1-4 and DICER, including but not limited to agotrons or mirtron pre-miRNAs; DKC1, NOLC1, SMNDC1, and AATF (Apoptosis Antagonizing Transcription Factor), including but not limited to snoRNA-encoding FLEXIs; two subsets of alternative splicing factors; and two subsets that included RBPs with cytoplasmic functions (e.g., LARP4, PABPC4, METAP2, and ZNF622) together with regulatory proteins. Cell fractionation experiments showed cytoplasmic enrichment of FLEXI RNAs with binding sites for RBPs with cytoplasmic functions. The subsets of host genes encoding FLEXIs with binding sites for different subsets of RBPs were co-enriched with non-FLEXI other short and long introns with binding sites for the same RBPs, suggesting overarching mechanisms for coordinately regulating expression of functionally related genes. Our findings identify FLEXIs as a previously unrecognized large class of cellular RNAs and provide a comprehensive roadmap for further analyzing their biological functions and the relationship of their RBPs to cellular regulatory mechanisms.
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Affiliation(s)
- Jun Yao
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Hengyi Xu
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Elizabeth A. Ferrick-Kiddie
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Ryan M. Nottingham
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Douglas C. Wu
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Manuel Ares
- Department of Molecular, Cell, and Developmental Biology University of California, Santa Cruz, California, United States of America
| | - Alan M. Lambowitz
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
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3
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Xiao W, Halabi R, Lin CH, Nazim M, Yeom KH, Black DL. The lncRNA Malat1 is trafficked to the cytoplasm as a localized mRNA encoding a small peptide in neurons. Genes Dev 2024; 38:294-307. [PMID: 38688681 PMCID: PMC11146593 DOI: 10.1101/gad.351557.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Synaptic function in neurons is modulated by local translation of mRNAs that are transported to distal portions of axons and dendrites. The metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is broadly expressed across cell types, almost exclusively as a nuclear long noncoding RNA. We found that in differentiating neurons, a portion of Malat1 RNA redistributes to the cytoplasm. Depletion of Malat1 using antisense oligonucleotides (ASOs) stimulates the expression of particular pre- and postsynaptic proteins, implicating Malat1 in their regulation. Neuronal Malat1 is localized in puncta of both axons and dendrites that costain with Staufen1 protein, similar to neuronal RNA granules formed by locally translated mRNAs. Ribosome profiling of cultured mouse cortical neurons identified ribosome footprints within a 5' region of Malat1 containing short open reading frames. The upstream-most reading frame (M1) of the Malat1 locus was linked to the GFP-coding sequence in mouse embryonic stem cells. When these gene-edited cells were differentiated into glutamatergic neurons, the M1-GFP fusion protein was expressed. Antibody staining for the M1 peptide confirmed its presence in wild-type neurons and showed that M1 expression was enhanced by synaptic stimulation with KCl. Our results indicate that Malat1 serves as a cytoplasmic coding RNA in the brain that is both modulated by and modulates synaptic function.
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Affiliation(s)
- Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Reem Halabi
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Mohammad Nazim
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Kyu-Hyeon Yeom
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA;
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
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4
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Xiao W, Halabi R, Lin CH, Nazim M, Yeom KH, Black DL. The lncRNA Malat1 is trafficked to the cytoplasm as a localized mRNA encoding a small peptide in neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578240. [PMID: 38352368 PMCID: PMC10862813 DOI: 10.1101/2024.02.01.578240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Synaptic function is modulated by local translation of mRNAs that are transported to distal portions of axons and dendrites. The Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is broadly expressed across cell types, almost exclusively as a nuclear non-coding RNA. We found that in differentiating neurons, a portion of Malat1 RNA redistributes to the cytoplasm. Depletion of Malat1 from neurons stimulated expression of particular pre- and post- synaptic proteins, implicating Malat1 in their regulation. Neuronal Malat1 is localized to both axons and dendrites in puncta that co-stain with Staufen1 protein, similar to neuronal granules formed by locally translated mRNAs. Ribosome profiling of mouse cortical neurons identified ribosome footprints within a region of Malat1 containing short open reading frames. The upstream-most reading frame (M1) of the Malat1 locus was linked to the GFP coding sequence in mouse ES cells. When these gene-edited cells were differentiated into glutamatergic neurons, the M1-GFP fusion protein was expressed. Antibody staining for the M1 peptide confirmed its presence in wildtype neurons, and showed enhancement of M1 expression after synaptic stimulation with KCL. Our results indicate that Malat1 serves as a cytoplasmic coding RNA in the brain that is both modulated by and modulates synaptic function.
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Affiliation(s)
- Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Reem Halabi
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Mohammad Nazim
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Kyu-Hyeon Yeom
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
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5
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Xie J, Wang L, Lin RJ. Variations of intronic branchpoint motif: identification and functional implications in splicing and disease. Commun Biol 2023; 6:1142. [PMID: 37949953 PMCID: PMC10638238 DOI: 10.1038/s42003-023-05513-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
The branchpoint (BP) motif is an essential intronic element for spliceosomal pre-mRNA splicing. In mammals, its sequence composition, distance to the downstream exon, and number of BPs per 3´ splice site are highly variable, unlike the GT/AG dinucleotides at the intron ends. These variations appear to provide evolutionary advantages for fostering alternative splicing, satisfying more diverse cellular contexts, and promoting resilience to genetic changes, thus contributing to an extra layer of complexity for gene regulation. Importantly, variants in the BP motif itself or in genes encoding BP-interacting factors cause human genetic diseases or cancers, highlighting the critical function of BP motif and the need to precisely identify functional BPs for faithful interpretation of their roles in splicing. In this perspective, we will succinctly summarize the major findings related to BP motif variations, discuss the relevant issues/challenges, and provide our insights.
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Affiliation(s)
- Jiuyong Xie
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
| | - Ren-Jang Lin
- Center for RNA Biology & Therapeutics, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
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6
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Rasmussen A, Okholm T, Knudsen M, Vang S, Dyrskjøt L, Hansen T, Pedersen J. Circular stable intronic RNAs possess distinct biological features and are deregulated in bladder cancer. NAR Cancer 2023; 5:zcad041. [PMID: 37554968 PMCID: PMC10405568 DOI: 10.1093/narcan/zcad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Until recently, intronic lariats were regarded as short-lasting splicing byproducts with no apparent function; however, increasing evidence of stable derivatives suggests regulatory roles. Yet little is known about their characteristics, functions, distribution, and expression in healthy and tumor tissue. Here, we profiled and characterized circular stable intronic sequence RNAs (sisRNAs) using total RNA-Seq data from bladder cancer (BC; n = 457, UROMOL cohort), healthy tissue (n = 46), and fractionated cell lines (n = 5). We found that the recently-discovered full-length intronic circles and the stable lariats formed distinct subclasses, with a surprisingly high intronic circle fraction in BC (∼45%) compared to healthy tissues (0-20%). The stable lariats and their host introns were characterized by small transcript sizes, highly conserved BP regions, enriched BP motifs, and localization in multiple cell fractions. Additionally, circular sisRNAs showed tissue-specific expression patterns. We found nine circular sisRNAs as differentially expressed across early-stage BC patients with different prognoses, and sisHNRNPK expression correlated with progression-free survival. In conclusion, we identify distinguishing biological features of circular sisRNAs and point to specific candidates (incl. sisHNRNPK, sisWDR13 and sisMBNL1) that were highly expressed, had evolutionary conserved sequences, or had clinical correlations, which may facilitate future studies and further insights into their functional roles.
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Affiliation(s)
- Asta M Rasmussen
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus 8000, Denmark
| | - Trine Line H Okholm
- Departments of Otolaryngology-Head and Neck Surgery and Microbiology & Immunology, University of California, San Francisco, CA, USA
| | - Michael Knudsen
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
| | - Søren Vang
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
| | - Thomas B Hansen
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus 8000, Denmark
| | - Jakob S Pedersen
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus 8000, Denmark
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7
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Duan L, Zaepfel BL, Aksenova V, Dasso M, Rothstein JD, Kalab P, Hayes LR. Nuclear RNA binding regulates TDP-43 nuclear localization and passive nuclear export. Cell Rep 2022; 40:111106. [PMID: 35858577 PMCID: PMC9345261 DOI: 10.1016/j.celrep.2022.111106] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/26/2022] [Accepted: 06/27/2022] [Indexed: 11/27/2022] Open
Abstract
Nuclear clearance of the RNA-binding protein TDP-43 is a hallmark of neurodegeneration and an important therapeutic target. Our current understanding of TDP-43 nucleocytoplasmic transport does not fully explain its predominantly nuclear localization or mislocalization in disease. Here, we show that TDP-43 exits nuclei by passive diffusion, independent of facilitated mRNA export. RNA polymerase II blockade and RNase treatment induce TDP-43 nuclear efflux, suggesting that nuclear RNAs sequester TDP-43 in nuclei and limit its availability for passive export. Induction of TDP-43 nuclear efflux by short, GU-rich oligomers (presumably by outcompeting TDP-43 binding to endogenous nuclear RNAs), and nuclear retention conferred by splicing inhibition, demonstrate that nuclear TDP-43 localization depends on binding to GU-rich nuclear RNAs. Indeed, RNA-binding domain mutations markedly reduce TDP-43 nuclear localization and abolish transcription blockade-induced nuclear efflux. Thus, the nuclear abundance of GU-RNAs, dictated by the balance of transcription, pre-mRNA processing, and RNA export, regulates TDP-43 nuclear localization.
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Affiliation(s)
- Lauren Duan
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Benjamin L Zaepfel
- Biochemistry, Cellular and Molecular Biology Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vasilisa Aksenova
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Petr Kalab
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Lindsey R Hayes
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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8
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Tyzack GE, Neeves J, Crerar H, Klein P, Ziff O, Taha DM, Luisier R, Luscombe NM, Patani R. Aberrant cytoplasmic intron retention is a blueprint for RNA binding protein mislocalization in VCP-related amyotrophic lateral sclerosis. Brain 2021; 144:1985-1993. [PMID: 33693641 PMCID: PMC8370440 DOI: 10.1093/brain/awab078] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/22/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022] Open
Abstract
We recently described aberrantly increased cytoplasmic SFPQ intron-retaining transcripts (IRTs) and concurrent SFPQ protein mislocalization as new hallmarks of amyotrophic lateral sclerosis (ALS). However, the generalizability and potential roles of cytoplasmic IRTs in health and disease remain unclear. Here, using time-resolved deep sequencing of nuclear and cytoplasmic fractions of human induced pluripotent stem cells undergoing motor neurogenesis, we reveal that ALS-causing VCP gene mutations lead to compartment-specific aberrant accumulation of IRTs. Specifically, we identify >100 IRTs with increased cytoplasmic abundance in ALS samples. Furthermore, these aberrant cytoplasmic IRTs possess sequence-specific attributes and differential predicted binding affinity to RNA binding proteins. Remarkably, TDP-43, SFPQ and FUS—RNA binding proteins known for nuclear-to-cytoplasmic mislocalization in ALS—abundantly and specifically bind to this aberrant cytoplasmic pool of IRTs. Our data are therefore consistent with a novel role for cytoplasmic IRTs in regulating compartment-specific protein abundance. This study provides new molecular insight into potential pathomechanisms underlying ALS and highlights aberrant cytoplasmic IRTs as potential therapeutic targets.
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Affiliation(s)
- Giulia E Tyzack
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jacob Neeves
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Hamish Crerar
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Pierre Klein
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Oliver Ziff
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Doaa M Taha
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,Zoology Department, Faculty of Science, Alexandria University, Alexandria 21511, Egypt
| | - Raphaëlle Luisier
- Genomics and Health Informatics Group, Idiap Research Institute, CH - 1920 Martigny, Switzerland
| | - Nicholas M Luscombe
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Rickie Patani
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
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9
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Alon S, Goodwin DR, Sinha A, Wassie AT, Chen F, Daugharthy ER, Bando Y, Kajita A, Xue AG, Marrett K, Prior R, Cui Y, Payne AC, Yao CC, Suk HJ, Wang R, Yu CCJ, Tillberg P, Reginato P, Pak N, Liu S, Punthambaker S, Iyer EPR, Kohman RE, Miller JA, Lein ES, Lako A, Cullen N, Rodig S, Helvie K, Abravanel DL, Wagle N, Johnson BE, Klughammer J, Slyper M, Waldman J, Jané-Valbuena J, Rozenblatt-Rosen O, Regev A, Church GM, Marblestone AH, Boyden ES. Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. Science 2021; 371:eaax2656. [PMID: 33509999 PMCID: PMC7900882 DOI: 10.1126/science.aax2656] [Citation(s) in RCA: 193] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/13/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022]
Abstract
Methods for highly multiplexed RNA imaging are limited in spatial resolution and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to the mouse brain, which yielded the readout of thousands of genes, including splice variants. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in the neurons of the mouse hippocampus, revealing patterns across multiple cell types, layer-specific cell types across the mouse visual cortex, and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus, ExSeq enables highly multiplexed mapping of RNAs from nanoscale to system scale.
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Affiliation(s)
- Shahar Alon
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Faculty of Engineering, Gonda Brain Research Center and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Daniel R Goodwin
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Anubhav Sinha
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Asmamaw T Wassie
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Fei Chen
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Evan R Daugharthy
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Yosuke Bando
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Kioxia Corporation, Minato-ku, Tokyo, Japan
| | | | - Andrew G Xue
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
| | | | | | - Yi Cui
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Andrew C Payne
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chun-Chen Yao
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ho-Jun Suk
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Ru Wang
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
| | - Chih-Chieh Jay Yu
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Paul Tillberg
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
| | - Paul Reginato
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Nikita Pak
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Mechanical Engineering, MIT, Cambridge, MA, USA
| | - Songlei Liu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Sukanya Punthambaker
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Eswar P R Iyer
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Richie E Kohman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ana Lako
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicole Cullen
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott Rodig
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Karla Helvie
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Daniel L Abravanel
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Nikhil Wagle
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bruce E Johnson
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Michal Slyper
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Waldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | | | - Edward S Boyden
- Department of Media Arts and Sciences, MIT, Cambridge, MA, USA.
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
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10
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Beyond Back Splicing, a Still Poorly Explored World: Non-Canonical Circular RNAs. Genes (Basel) 2020; 11:genes11091111. [PMID: 32972011 PMCID: PMC7565381 DOI: 10.3390/genes11091111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 12/20/2022] Open
Abstract
Most of the circRNAs reported to date originate from back splicing of a pre-mRNA, and these exonic circRNAs are termed canonical circRNAs. Our objective was to provide an overview of all other (non-canonical) circRNAs that do not originate from the junction of two exons and to characterize their common properties. Those generated through a failure of intron lariat debranching are the best known, even though studies on them are rare. These circRNAs retain the 2′–5′ bond derived from the intron lariat, and this feature probably explains the difficulties in obtaining efficient reverse transcription through the circular junction. Here, we provide an unprecedented overview of non-canonical circRNAs (lariat-derived intronic circRNAs, sub-exonic circRNAs, intron circles, tricRNAs), which all derive from non-coding sequences. As there are few data suggesting their involvement in cellular regulatory processes, we believe that it is early to propose a general function for circRNAs, even for lariat-derived circRNAs. We suggest that their small size and probably strong secondary structures could be major obstacles to their reliable detection. Nevertheless, we believe there are still several possible ways to advance our knowledge of this class of non-coding RNA.
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11
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Fazal FM, Chang HY. Subcellular Spatial Transcriptomes: Emerging Frontier for Understanding Gene Regulation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:31-45. [PMID: 32482897 PMCID: PMC7426137 DOI: 10.1101/sqb.2019.84.040352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNAs are trafficked and localized with exquisite precision inside the cell. Studies of candidate messenger RNAs have shown the vital importance of RNA subcellular location in development and cellular function. New sequencing- and imaging-based methods are providing complementary insights into subcellular localization of RNAs transcriptome-wide. APEX-seq and ribosome profiling as well as proximity-labeling approaches have revealed thousands of transcript isoforms are localized to distinct cytotopic locations, including locations that defy biochemical fractionation and hence were missed by prior studies. Sequences in the 3' and 5' untranslated regions (UTRs) serve as "zip codes" to direct transcripts to particular locales, and it is clear that intronic and retrotransposable sequences within transcripts have been co-opted by cells to control localization. Molecular motors, nuclear-to-cytosol RNA export, liquid-liquid phase separation, RNA modifications, and RNA structure dynamically shape the subcellular transcriptome. Location-based RNA regulation continues to pose new mysteries for the field, yet promises to reveal insights into fundamental cell biology and disease mechanisms.
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Affiliation(s)
- Furqan M Fazal
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA
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12
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Saini H, Bicknell AA, Eddy SR, Moore MJ. Free circular introns with an unusual branchpoint in neuronal projections. eLife 2019; 8:e47809. [PMID: 31697236 PMCID: PMC6879206 DOI: 10.7554/elife.47809] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
The polarized structure of axons and dendrites in neuronal cells depends in part on RNA localization. Previous studies have looked at which polyadenylated RNAs are enriched in neuronal projections or at synapses, but less is known about the distribution of non-adenylated RNAs. By physically dissecting projections from cell bodies of primary rat hippocampal neurons and sequencing total RNA, we found an unexpected set of free circular introns with a non-canonical branchpoint enriched in neuronal projections. These introns appear to be tailless lariats that escape debranching. They lack ribosome occupancy, sequence conservation, and known localization signals, and their function, if any, is not known. Nonetheless, their enrichment in projections has important implications for our understanding of the mechanisms by which RNAs reach distal compartments of asymmetric cells.
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Affiliation(s)
- Harleen Saini
- RNA Therapeutics InstituteUniversity of Massachusetts Medical SchoolWorcesterUnited States
- Department of Molecular and Cellular BiologyHoward Hughes Medical Institute, Harvard UniversityCambridgeUnited States
| | - Alicia A Bicknell
- RNA Therapeutics InstituteUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Sean R Eddy
- Department of Molecular and Cellular BiologyHoward Hughes Medical Institute, Harvard UniversityCambridgeUnited States
- John A Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeUnited States
| | - Melissa J Moore
- RNA Therapeutics InstituteUniversity of Massachusetts Medical SchoolWorcesterUnited States
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