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Hristov P, Flynn RA. Imaging glycosylated RNAs at the subcellular scale. Nat Biotechnol 2024; 42:574-575. [PMID: 37872411 DOI: 10.1038/s41587-023-02021-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Affiliation(s)
- Petar Hristov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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2
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Peltan EL, Riley NM, Flynn RA, Roberts DS, Bertozzi CR. Galectin-3 does not interact with RNA directly. Glycobiology 2024; 34:cwad076. [PMID: 37815932 DOI: 10.1093/glycob/cwad076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/08/2023] [Accepted: 09/09/2023] [Indexed: 10/12/2023] Open
Abstract
Galectin-3, well characterized as a glycan binding protein, has been identified as a putative RNA binding protein, possibly through participation in pre-mRNA maturation through interactions with splicosomes. Given recent developments with cell surface RNA biology, the putative dual-function nature of galectin-3 evokes a possible non-classical connection between glycobiology and RNA biology. However, with limited functional evidence of a direct RNA interaction, many molecular-level observations rely on affinity reagents and lack appropriate genetic controls. Thus, evidence of a direct interaction remains elusive. We demonstrate that antibodies raised to endogenous human galectin-3 can isolate RNA-protein crosslinks, but this activity remains insensitive to LGALS3 knock-out. Proteomic characterization of anti-galectin-3 IPs revealed enrichment of galectin-3, but high abundance of hnRNPA2B1, an abundant, well-characterized RNA-binding protein with weak homology to the N-terminal domain of galectin-3, in the isolate. Genetic ablation of HNRNPA2B1, but not LGALS3, eliminates the ability of the anti-galectin-3 antibodies to isolate RNA-protein crosslinks, implying either an indirect interaction or cross-reactivity. To address this, we introduced an epitope tag to the endogenous C-terminal locus of LGALS3. Isolation of the tagged galectin-3 failed to reveal any RNA-protein crosslinks. This result suggests that the galectin-3 does not directly interact with RNA and may be misidentified as an RNA-binding protein, at least in HeLa where the putative RNA associations were first identified. We encourage further investigation of this phenomenon employ gene deletions and, when possible, endogenous epitope tags to achieve the specificity required to evaluate potential interactions.
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Affiliation(s)
- Egan L Peltan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 269 Campus Drive CCSR 4145 Stanford, CA 94305, United States
- Sarafan ChEM-H, Stanford University, Stanford ChEM-H Building 290 Jane Stanford Way Stanford, CA 94305, United States
| | - Nicholas M Riley
- Sarafan ChEM-H, Stanford University, Stanford ChEM-H Building 290 Jane Stanford Way Stanford, CA 94305, United States
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, CA 94305, United States
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, 1 Blackfan Circle, Boston, MA 02445, United States
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave, Cambridge, MA 02138, United States
| | - David S Roberts
- Sarafan ChEM-H, Stanford University, Stanford ChEM-H Building 290 Jane Stanford Way Stanford, CA 94305, United States
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, CA 94305, United States
| | - Carolyn R Bertozzi
- Sarafan ChEM-H, Stanford University, Stanford ChEM-H Building 290 Jane Stanford Way Stanford, CA 94305, United States
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, CA 94305, United States
- Howard Hughes Medical Institute, Stanford University, 279 Campus Drive Room B202 Stanford, CA 94305-5323, United States
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3
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Xie Y, Liu X, Zhao C, Chen S, Wang S, Lin Z, Robison FM, George BM, Flynn RA, Lebrilla CB, Garcia BA. Development and application of GlycanDIA workflow for glycomic analysis. bioRxiv 2024:2024.03.12.584702. [PMID: 38559279 PMCID: PMC10980037 DOI: 10.1101/2024.03.12.584702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Glycans modify protein, lipid, and even RNA molecules to form the regulatory outer coat on cells called the glycocalyx. The changes in glycosylation have been linked to the initiation and progression of many diseases. Thus, while the significance of glycosylation is well established, a lack of accessible methods to characterize glycans has hindered the ability to understand their biological functions. Mass spectrometry (MS)-based methods have generally been at the core of most glycan profiling efforts; however, modern data-independent acquisition (DIA), which could increase sensitivity and simplify workflows, has not been benchmarked for analyzing glycans. Herein, we developed a DIA-based glycomic workflow, termed GlycanDIA, to identify and quantify glycans with high sensitivity and accuracy. The GlycanDIA workflow combined higher energy collisional dissociation (HCD)-MS/MS and staggered windows for glycomic analysis, which facilitates the sensitivity in identification and the accuracy in quantification compared to conventional data-dependent acquisition (DDA)-based glycomics. To facilitate its use, we also developed a generic search engine, GlycanDIA Finder, incorporating an iterative decoy searching for confident glycan identification and quantification from DIA data. The results showed that GlycanDIA can distinguish glycan composition and isomers from N-glycans, O-glycans, and human milk oligosaccharides (HMOs), while it also reveals information on low-abundant modified glycans. With the improved sensitivity, we performed experiments to profile N-glycans from RNA samples, which have been underrepresented due to their low abundance. Using this integrative workflow to unravel the N-glycan profile in cellular and tissue glycoRNA samples, we found that RNA-glycans have specific forms as compared to protein-glycans and are also tissue-specific differences, suggesting distinct functions in biological processes. Overall, GlycanDIA can provide comprehensive information for glycan identification and quantification, enabling researchers to obtain in-depth and refined details on the biological roles of glycosylation.
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Affiliation(s)
- Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
- Department of Chemistry, University of California, Davis, Davis, California, United States
| | - Xingyu Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Chenfeng Zhao
- Department of Computer Science & Engineering, Washington University, St. Louis, Missouri, United States
| | - Siyu Chen
- Department of Chemistry, University of California, Davis, Davis, California, United States
| | - Shunyang Wang
- Department of Chemistry, University of California, Davis, Davis, California, United States
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Faith M Robison
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Benson M George
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, California, United States
- Department of Biochemistry, University of California, Davis, Davis, California, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
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4
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Aryan F, Detrés D, Luo CC, Kim SX, Shah AN, Bartusel M, Flynn RA, Calo E. Nucleolus activity-dependent recruitment and biomolecular condensation by pH sensing. Mol Cell 2023; 83:4413-4423.e10. [PMID: 37979585 PMCID: PMC10803072 DOI: 10.1016/j.molcel.2023.10.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 06/20/2023] [Accepted: 10/23/2023] [Indexed: 11/20/2023]
Abstract
DEAD-box ATPases are major regulators of biomolecular condensates and orchestrate diverse biochemical processes that are critical for the functioning of cells. How DEAD-box proteins are selectively recruited to their respective biomolecular condensates is unknown. We explored this in the context of the nucleolus and DEAD-box protein DDX21. We find that the pH of the nucleolus is intricately linked to the transcriptional activity of the organelle and facilitates the recruitment and condensation of DDX21. We identify an evolutionarily conserved feature of the C terminus of DDX21 responsible for nucleolar localization. This domain is essential for zebrafish development, and its intrinsically disordered and isoelectric properties are necessary and sufficient for the ability of DDX21 to respond to changes in pH and form condensates. Molecularly, the enzymatic activities of poly(ADP-ribose) polymerases contribute to maintaining the nucleolar pH and, consequently, DDX21 recruitment and nucleolar partitioning. These observations reveal an activity-dependent physicochemical mechanism for the selective recruitment of biochemical activities to biomolecular condensates.
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Affiliation(s)
- Fardin Aryan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Diego Detrés
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Claire C Luo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Skylar X Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arish N Shah
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michaela Bartusel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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5
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Chai P, Lebedenko CG, Flynn RA. RNA Crossing Membranes: Systems and Mechanisms Contextualizing Extracellular RNA and Cell Surface GlycoRNAs. Annu Rev Genomics Hum Genet 2023; 24:85-107. [PMID: 37068783 DOI: 10.1146/annurev-genom-101722-101224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
The subcellular localization of a biopolymer often informs its function. RNA is traditionally confined to the cytosolic and nuclear spaces, where it plays critical and conserved roles across nearly all biochemical processes. Our recent observation of cell surface glycoRNAs may further explain the extracellular role of RNA. While cellular membranes are efficient gatekeepers of charged polymers such as RNAs, a large body of research has demonstrated the accumulation of specific RNA species outside of the cell, termed extracellular RNAs (exRNAs). Across various species and forms of life, protein pores have evolved to transport RNA across membranes, thus providing a mechanistic path for exRNAs to achieve their extracellular topology. Here, we review types of exRNAs and the pores capable of RNA transport to provide a logical and testable path toward understanding the biogenesis and regulation of cell surface glycoRNAs.
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Affiliation(s)
- Peiyuan Chai
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Charlotta G Lebedenko
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
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6
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Spencley AL, Bar S, Swigut T, Flynn RA, Lee CH, Chen LF, Bassik MC, Wysocka J. Co-transcriptional genome surveillance by HUSH is coupled to termination machinery. Mol Cell 2023; 83:1623-1639.e8. [PMID: 37164018 PMCID: PMC10915761 DOI: 10.1016/j.molcel.2023.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/12/2023] [Accepted: 04/12/2023] [Indexed: 05/12/2023]
Abstract
The HUSH complex recognizes and silences foreign DNA such as viruses, transposons, and transgenes without prior exposure to its targets. Here, we show that endogenous targets of the HUSH complex fall into two distinct classes based on the presence or absence of H3K9me3. These classes are further distinguished by their transposon content and differential response to the loss of HUSH. A de novo genomic rearrangement at the Sox2 locus induces a switch from H3K9me3-independent to H3K9me3-associated HUSH targeting, resulting in silencing. We further demonstrate that HUSH interacts with the termination factor WDR82 and-via its component MPP8-with nascent RNA. HUSH accumulates at sites of high RNAPII occupancy including long exons and transcription termination sites in a manner dependent on WDR82 and CPSF. Together, our results uncover the functional diversity of HUSH targets and show that this vertebrate-specific complex exploits evolutionarily ancient transcription termination machinery for co-transcriptional chromatin targeting and genome surveillance.
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Affiliation(s)
- Andrew L Spencley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Shiran Bar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Cameron H Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Liang-Fu Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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7
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Zheng R, Dunlap M, Lyu J, Gonzalez-Figueroa C, Bobkov G, Harvey SE, Chan TW, Quinones-Valdez G, Choudhury M, Vuong A, Flynn RA, Chang HY, Xiao X, Cheng C. LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity. bioRxiv 2023:2023.02.23.529804. [PMID: 36865202 PMCID: PMC9980139 DOI: 10.1101/2023.02.23.529804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
RNA splicing plays a critical role in post-transcriptional gene regulation. Exponential expansion of intron length poses a challenge for accurate splicing. Little is known about how cells prevent inadvertent and often deleterious expression of intronic elements due to cryptic splicing. In this study, we identify hnRNPM as an essential RNA binding protein that suppresses cryptic splicing through binding to deep introns, preserving transcriptome integrity. Long interspersed nuclear elements (LINEs) harbor large amounts of pseudo splice sites in introns. hnRNPM preferentially binds at intronic LINEs and represses LINE-containing pseudo splice site usage for cryptic splicing. Remarkably, a subgroup of the cryptic exons can form long dsRNAs through base-pairing of inverted Alu transposable elements scattered in between LINEs and trigger interferon immune response, a well-known antiviral defense mechanism. Notably, these interferon-associated pathways are found to be upregulated in hnRNPM-deficient tumors, which also exhibit elevated immune cell infiltration. These findings unveil hnRNPM as a guardian of transcriptome integrity. Targeting hnRNPM in tumors may be used to trigger an inflammatory immune response thereby boosting cancer surveillance.
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8
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Miao W, Porter DF, Lopez-Pajares V, Siprashvili Z, Meyers RM, Bai Y, Nguyen DT, Ko LA, Zarnegar BJ, Ferguson ID, Mills MM, Jilly-Rehak CE, Wu CG, Yang YY, Meyers JM, Hong AW, Reynolds DL, Ramanathan M, Tao S, Jiang S, Flynn RA, Wang Y, Nolan GP, Khavari PA. Glucose dissociates DDX21 dimers to regulate mRNA splicing and tissue differentiation. Cell 2023; 186:80-97.e26. [PMID: 36608661 PMCID: PMC10171372 DOI: 10.1016/j.cell.2022.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/17/2022] [Accepted: 12/02/2022] [Indexed: 01/07/2023]
Abstract
Glucose is a universal bioenergy source; however, its role in controlling protein interactions is unappreciated, as are its actions during differentiation-associated intracellular glucose elevation. Azido-glucose click chemistry identified glucose binding to a variety of RNA binding proteins (RBPs), including the DDX21 RNA helicase, which was found to be essential for epidermal differentiation. Glucose bound the ATP-binding domain of DDX21, altering protein conformation, inhibiting helicase activity, and dissociating DDX21 dimers. Glucose elevation during differentiation was associated with DDX21 re-localization from the nucleolus to the nucleoplasm where DDX21 assembled into larger protein complexes containing RNA splicing factors. DDX21 localized to specific SCUGSDGC motif in mRNA introns in a glucose-dependent manner and promoted the splicing of key pro-differentiation genes, including GRHL3, KLF4, OVOL1, and RBPJ. These findings uncover a biochemical mechanism of action for glucose in modulating the dimerization and function of an RNA helicase essential for tissue differentiation.
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Affiliation(s)
- Weili Miao
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Douglas F Porter
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Vanessa Lopez-Pajares
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Zurab Siprashvili
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robin M Meyers
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yunhao Bai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Duy T Nguyen
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa A Ko
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian J Zarnegar
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ian D Ferguson
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA; Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Matthew M Mills
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | | | - Cheng-Guo Wu
- Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yen-Yu Yang
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Jordan M Meyers
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Audrey W Hong
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - David L Reynolds
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Shiying Tao
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sizun Jiang
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Ryan A Flynn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA; Program in Cancer Biology, Stanford University, Stanford, CA, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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9
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Leon KE, Khalid MM, Flynn RA, Fontaine KA, Nguyen TT, Kumar GR, Simoneau CR, Tomar S, Jimenez-Morales D, Dunlap M, Kaye J, Shah PS, Finkbeiner S, Krogan NJ, Bertozzi C, Carette JE, Ott M. Nuclear accumulation of host transcripts during Zika Virus Infection. PLoS Pathog 2023; 19:e1011070. [PMID: 36603024 PMCID: PMC9847913 DOI: 10.1371/journal.ppat.1011070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 01/18/2023] [Accepted: 12/17/2022] [Indexed: 01/06/2023] Open
Abstract
Zika virus (ZIKV) infects fetal neural progenitor cells (NPCs) causing severe neurodevelopmental disorders in utero. Multiple pathways involved in normal brain development are dysfunctional in infected NPCs but how ZIKV centrally reprograms these pathways remains unknown. Here we show that ZIKV infection disrupts subcellular partitioning of host transcripts critical for neurodevelopment in NPCs and functionally link this process to the up-frameshift protein 1 (UPF1). UPF1 is an RNA-binding protein known to regulate decay of cellular and viral RNAs and is less expressed in ZIKV-infected cells. Using infrared crosslinking immunoprecipitation and RNA sequencing (irCLIP-Seq), we show that a subset of mRNAs loses UPF1 binding in ZIKV-infected NPCs, consistent with UPF1's diminished expression. UPF1 target transcripts, however, are not altered in abundance but in subcellular localization, with mRNAs accumulating in the nucleus of infected or UPF1 knockdown cells. This leads to diminished protein expression of FREM2, a protein required for maintenance of NPC identity. Our results newly link UPF1 to the regulation of mRNA transport in NPCs, a process perturbed during ZIKV infection.
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Affiliation(s)
- Kristoffer E. Leon
- J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, California, United States of America
- Medical Scientist Training Program, University of California, San Francisco, California, United States of America
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, United States of America
| | - Mir M. Khalid
- J. David Gladstone Institutes, San Francisco, California, United States of America
| | - Ryan A. Flynn
- Stem Cell Program, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Krystal A. Fontaine
- J. David Gladstone Institutes, San Francisco, California, United States of America
| | - Thong T. Nguyen
- J. David Gladstone Institutes, San Francisco, California, United States of America
| | - G. Renuka Kumar
- J. David Gladstone Institutes, San Francisco, California, United States of America
| | - Camille R. Simoneau
- J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, California, United States of America
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, United States of America
| | - Sakshi Tomar
- J. David Gladstone Institutes, San Francisco, California, United States of America
| | - David Jimenez-Morales
- J. David Gladstone Institutes, San Francisco, California, United States of America
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Mariah Dunlap
- J. David Gladstone Institutes, San Francisco, California, United States of America
| | - Julia Kaye
- J. David Gladstone Institutes, San Francisco, California, United States of America
| | - Priya S. Shah
- Departments of Chemical Engineering and Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
| | - Steven Finkbeiner
- J. David Gladstone Institutes, San Francisco, California, United States of America
- Center for Systems and Therapeutics and Taube/Koret Center for Neurodegenerative Disease Research, San Francisco, California, United States of America
- Departments of Neurology and Physiology, University of California, San Francisco, California, United States of America
| | - Nevan J. Krogan
- J. David Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
| | - Carolyn Bertozzi
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jan E. Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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10
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Caldwell RM, Flynn RA. Discovering glycoRNA: Traditional and Non‐Canonical Approaches to Studying RNA Modifications. Isr J Chem 2022. [DOI: 10.1002/ijch.202200059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Reese M. Caldwell
- Stem Cell Program, Boston Children's Hospital Boston 02115 Massachusetts United States
- Stem Cell and Regenerative Biology Department, Harvard University Cambridage 02138 Massachusetts United States
| | - Ryan A. Flynn
- Stem Cell Program, Boston Children's Hospital Boston 02115 Massachusetts United States
- Stem Cell and Regenerative Biology Department, Harvard University Cambridage 02138 Massachusetts United States
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11
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Richards CM, Jabs S, Qiao W, Varanese LD, Schweizer M, Mosen PR, Riley NM, Klüssendorf M, Zengel JR, Flynn RA, Rustagi A, Widen JC, Peters CE, Ooi YS, Xie X, Shi PY, Bartenschlager R, Puschnik AS, Bogyo M, Bertozzi CR, Blish CA, Winter D, Nagamine CM, Braulke T, Carette JE. The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection. Science 2022; 378:eabn5648. [PMID: 36074821 PMCID: PMC9547973 DOI: 10.1126/science.abn5648] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Lysosomes are key degradative compartments of the cell. Transport to lysosomes relies on GlcNAc-1-phosphotransferase-mediated tagging of soluble enzymes with mannose 6-phosphate (M6P). GlcNAc-1-phosphotransferase deficiency leads to the severe lysosomal storage disorder mucolipidosis II (MLII). Several viruses require lysosomal cathepsins to cleave structural proteins and thus depend on functional GlcNAc-1-phosphotransferase. Here, we used genome-scale CRISPR screens to identify Lysosomal Enzyme Trafficking factor (LYSET) as essential for infection by cathepsin-dependent viruses including SARS-CoV-2. LYSET deficiency resulted in global loss of M6P tagging and mislocalization of GlcNAc-1-phosphotransferase from the Golgi complex to lysosomes. Lyset knockout mice exhibited MLII-like phenotypes and human pathogenic LYSET alleles failed to restore lysosomal sorting defects. Thus, LYSET is required for correct functioning of the M6P trafficking machinery, and mutations in LYSET can explain the phenotype of the associated disorder.
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Affiliation(s)
- Christopher M Richards
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sabrina Jabs
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Wenjie Qiao
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lauren D Varanese
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michaela Schweizer
- Department of Electron Microscopy, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter R Mosen
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | | | - Malte Klüssendorf
- Department of Osteology and Biomechanics, Cell Biology of Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - James R Zengel
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.,Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
| | - Arjun Rustagi
- Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - John C Widen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christine E Peters
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yaw Shin Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany.,Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Matthew Bogyo
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford, CA, USA
| | - Catherine A Blish
- Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Claude M Nagamine
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas Braulke
- Department of Osteology and Biomechanics, Cell Biology of Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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12
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Teng J, De Jeronimo Diaz C, Flynn RA, Lin M, Rogers CJ, Korzick DH. Evans Blue Dye Interferes with Gating for Certain Fluorochrome‐Conjugated Antibodies Using Flow Cytometry in the Ischemic Rat Heart. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r5171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jiajing Teng
- Integrative and Biomedical Physiology Graduate ProgramPenn State UniversityState CollegePA
| | - Cesar De Jeronimo Diaz
- Integrative and Biomedical Physiology Graduate ProgramPenn State UniversityState CollegePA
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13
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De Jeronimo Diaz C, Teng J, Flynn RA, Lin M, Yuan J, Rogers CJ, Korzick DH. Phenotypic Characterization of Macrophage and Monocyte Populations in the NLRP3 KO DAHL/SS‐
Nlrp3
em2Mcwi
Rat Model. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r5071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Matthew Lin
- Pennsylvania State UniversityUniversity ParkPA
| | - Junyao Yuan
- Pennsylvania State UniversityUniversity ParkPA
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14
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England WE, Wang J, Chen S, Baldi P, Flynn RA, Spitale RC. An atlas of posttranslational modifications on RNA binding proteins. Nucleic Acids Res 2022; 50:4329-4339. [PMID: 35438783 PMCID: PMC9071496 DOI: 10.1093/nar/gkac243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/24/2022] [Accepted: 04/15/2022] [Indexed: 12/13/2022] Open
Abstract
RNA structure and function are intimately tied to RNA binding protein recognition and regulation. Posttranslational modifications are chemical modifications which can control protein biology. The role of PTMs in the regulation RBPs is not well understood, in part due to a lacking analysis of PTM deposition on RBPs. Herein, we present an analysis of posttranslational modifications (PTMs) on RNA binding proteins (RBPs; a PTM RBP Atlas). We curate published datasets and primary literature to understand the landscape of PTMs and use protein-protein interaction data to understand and potentially provide a framework for understanding which enzymes are controlling PTM deposition and removal on the RBP landscape. Intersection of our data with The Cancer Genome Atlas also provides researchers understanding of mutations that would alter PTM deposition. Additional characterization of the RNA-protein interface provided from in-cell UV crosslinking experiments provides a framework for hypotheses about which PTMs could be regulating RNA binding and thus RBP function. Finally, we provide an online database for our data that is easy to use for the community. It is our hope our efforts will provide researchers will an invaluable tool to test the function of PTMs controlling RBP function and thus RNA biology.
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Affiliation(s)
- Whitney E England
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA, USA
| | - Jingtian Wang
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA, USA
| | - Siwei Chen
- School of Information and Computer Sciences, University of California, Irvine. Irvine, CA, USA
| | - Pierre Baldi
- School of Information and Computer Sciences, University of California, Irvine. Irvine, CA, USA
| | - Ryan A Flynn
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA, USA.,Department of Developmental and Cellular Biology, University of California, Irvine. Irvine, CA, USA.,Department of Chemistry, University of California, Irvine. Irvine, CA, USA
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15
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Pluvinage JV, Sun J, Claes C, Flynn RA, Haney MS, Iram T, Meng X, Lindemann R, Riley NM, Danhash E, Chadarevian JP, Tapp E, Gate D, Kondapavulur S, Cobos I, Chetty S, Pașca AM, Pașca SP, Berry-Kravis E, Bertozzi CR, Blurton-Jones M, Wyss-Coray T. The CD22-IGF2R interaction is a therapeutic target for microglial lysosome dysfunction in Niemann-Pick type C. Sci Transl Med 2021; 13:eabg2919. [PMID: 34851695 PMCID: PMC9067636 DOI: 10.1126/scitranslmed.abg2919] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Lysosome dysfunction is a shared feature of rare lysosomal storage diseases and common age-related neurodegenerative diseases. Microglia, the brain-resident macrophages, are particularly vulnerable to lysosome dysfunction because of the phagocytic stress of clearing dying neurons, myelin, and debris. CD22 is a negative regulator of microglial homeostasis in the aging mouse brain, and soluble CD22 (sCD22) is increased in the cerebrospinal fluid of patients with Niemann-Pick type C disease (NPC). However, the role of CD22 in the human brain remains unknown. In contrast to previous findings in mice, here, we show that CD22 is expressed by oligodendrocytes in the human brain and binds to sialic acid–dependent ligands on microglia. Using unbiased genetic and proteomic screens, we identify insulin-like growth factor 2 receptor (IGF2R) as the binding partner of sCD22 on human myeloid cells. Targeted truncation of IGF2R revealed that sCD22 docks near critical mannose 6-phosphate–binding domains, where it disrupts lysosomal protein trafficking. Interfering with the sCD22-IGF2R interaction using CD22 blocking antibodies ameliorated lysosome dysfunction in human NPC1 mutant induced pluripotent stem cell–derived microglia-like cells without harming oligodendrocytes in vitro. These findings reinforce the differences between mouse and human microglia and provide a candidate microglia-directed immunotherapeutic to treat NPC.
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Affiliation(s)
- John V. Pluvinage
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Jerry Sun
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Christel Claes
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
| | - Ryan A. Flynn
- Stem Cell Program, Children’s Hospital Boston, Boston, MA 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael S. Haney
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Tal Iram
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Xiangling Meng
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Rachel Lindemann
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Nicholas M. Riley
- Department of Chemistry and ChEM-H, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94304, USA
| | - Emma Danhash
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Jean Paul Chadarevian
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - Emma Tapp
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - David Gate
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sravani Kondapavulur
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Inma Cobos
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sundari Chetty
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anca M. Pașca
- Division of Neonatology, Department of Pediatrics, Stanford University, Stanford, CA 94304, USA
| | - Sergiu P. Pașca
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | | | - Carolyn R. Bertozzi
- Department of Chemistry and ChEM-H, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94304, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94304, USA
- Wu Tsai Neurosciences Institute, Stanford, CA, 94305, USA
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16
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Corley M, Flynn RA, Blue SM, Yee BA, Chang HY, Yeo GW. fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins. STAR Protoc 2021; 2:100762. [PMID: 34485935 PMCID: PMC8406031 DOI: 10.1016/j.xpro.2021.100762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) structure probing techniques characterize the secondary structure of RNA molecules, which influence their functions and interactions. A variation of SHAPE, footprinting SHAPE (fSHAPE), probes RNA in the presence and absence of protein to identify RNA bases that hydrogen-bond with protein. SHAPE or fSHAPE coupled with enhanced crosslinking and immunoprecipitation (SHAPE-eCLIP or fSHAPE-eCLIP) pulls down RNAs bound by any protein of interest and returns their structure or protein interaction information, respectively. Here, we describe detailed protocols for SHAPE-eCLIP and fSHAPE-eCLIP and an analysis protocol for fSHAPE. For complete details on the use and execution of these protocols, please refer to Corley et al. (2020).
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Affiliation(s)
- Meredith Corley
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Ryan A. Flynn
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Steven M. Blue
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA
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17
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Flynn RA, Pedram K, Malaker SA, Batista PJ, Smith BAH, Johnson AG, George BM, Majzoub K, Villalta PW, Carette JE, Bertozzi CR. Small RNAs are modified with N-glycans and displayed on the surface of living cells. Cell 2021; 184:3109-3124.e22. [PMID: 34004145 DOI: 10.1016/j.cell.2021.04.023] [Citation(s) in RCA: 204] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/18/2020] [Accepted: 04/14/2021] [Indexed: 12/20/2022]
Abstract
Glycans modify lipids and proteins to mediate inter- and intramolecular interactions across all domains of life. RNA is not thought to be a major target of glycosylation. Here, we challenge this view with evidence that mammals use RNA as a third scaffold for glycosylation. Using a battery of chemical and biochemical approaches, we found that conserved small noncoding RNAs bear sialylated glycans. These "glycoRNAs" were present in multiple cell types and mammalian species, in cultured cells, and in vivo. GlycoRNA assembly depends on canonical N-glycan biosynthetic machinery and results in structures enriched in sialic acid and fucose. Analysis of living cells revealed that the majority of glycoRNAs were present on the cell surface and can interact with anti-dsRNA antibodies and members of the Siglec receptor family. Collectively, these findings suggest the existence of a direct interface between RNA biology and glycobiology, and an expanded role for RNA in extracellular biology.
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Affiliation(s)
- Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Kayvon Pedram
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin A H Smith
- Department of Chemical and Systems Biology and ChEM-H, Stanford University, Stanford, CA, USA
| | - Alex G Johnson
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Benson M George
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
| | - Karim Majzoub
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; IGMM, CNRS, University of Montpellier, Montpellier, France
| | - Peter W Villalta
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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18
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Flynn RA, Belk JA, Qi Y, Yasumoto Y, Wei J, Alfajaro MM, Shi Q, Mumbach MR, Limaye A, DeWeirdt PC, Schmitz CO, Parker KR, Woo E, Chang HY, Horvath TL, Carette JE, Bertozzi CR, Wilen CB, Satpathy AT. Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions. Cell 2021; 184:2394-2411.e16. [PMID: 33743211 PMCID: PMC7951565 DOI: 10.1016/j.cell.2021.03.012] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/03/2021] [Accepted: 03/04/2021] [Indexed: 12/22/2022]
Abstract
SARS-CoV-2 is the cause of a pandemic with growing global mortality. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host proteins that bind the SARS-CoV-2 RNA during active infection. Integration of this data with ChIRP-MS data from three other RNA viruses defined viral specificity of RNA-host protein interactions. Targeted CRISPR screens revealed that the majority of functional RNA-binding proteins protect the host from virus-induced cell death, and comparative CRISPR screens across seven RNA viruses revealed shared and SARS-specific antiviral factors. Finally, by combining the RNA-centric approach and functional CRISPR screens, we demonstrated a physical and functional connection between SARS-CoV-2 and mitochondria, highlighting this organelle as a general platform for antiviral activity. Altogether, these data provide a comprehensive catalog of functional SARS-CoV-2 RNA-host protein interactions, which may inform studies to understand the host-virus interface and nominate host pathways that could be targeted for therapeutic benefit.
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Affiliation(s)
- Ryan A Flynn
- Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Julia A Belk
- Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yuki Yasumoto
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT, USA
| | - Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Aditi Limaye
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Peter C DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cameron O Schmitz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Elizabeth Woo
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Tamas L Horvath
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Carolyn R Bertozzi
- Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
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19
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Corley M, Flynn RA, Lee B, Blue SM, Chang HY, Yeo GW. Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces. Mol Cell 2020; 80:903-914.e8. [PMID: 33242392 PMCID: PMC8074864 DOI: 10.1016/j.molcel.2020.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 12/20/2022]
Abstract
Discovering the interaction mechanism and location of RNA-binding proteins (RBPs) on RNA is critical for understanding gene expression regulation. Here, we apply selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) on in vivo transcripts compared to protein-absent transcripts in four human cell lines to identify transcriptome-wide footprints (fSHAPE) on RNA. Structural analyses indicate that fSHAPE precisely detects nucleobases that hydrogen bond with protein. We demonstrate that fSHAPE patterns predict binding sites of known RBPs, such as iron response elements in both known loci and previously unknown loci in CDC34, SLC2A4RG, COASY, and H19. Furthermore, by integrating SHAPE and fSHAPE with crosslinking and immunoprecipitation (eCLIP) of desired RBPs, we interrogate specific RNA-protein complexes, such as histone stem-loop elements and their nucleotides that hydrogen bond with stem-loop-binding proteins. Together, these technologies greatly expand our ability to study and understand specific cellular RNA interactions in RNA-protein complexes.
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Affiliation(s)
- Meredith Corley
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Byron Lee
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA.
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20
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Salahudeen AA, Choi SS, Rustagi A, Zhu J, van Unen V, de la O SM, Flynn RA, Margalef-Català M, Santos AJM, Ju J, Batish A, Usui T, Zheng GXY, Edwards CE, Wagar LE, Luca V, Anchang B, Nagendran M, Nguyen K, Hart DJ, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Harbury PB, Glenn JS, Garcia KC, Davis MM, Baric RS, Sabatti C, Amieva MR, Blish CA, Desai TJ, Kuo CJ. Progenitor identification and SARS-CoV-2 infection in human distal lung organoids. Nature 2020; 588:670-675. [PMID: 33238290 PMCID: PMC8003326 DOI: 10.1038/s41586-020-3014-1] [Citation(s) in RCA: 209] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 11/18/2020] [Indexed: 12/17/2022]
Abstract
The distal lung contains terminal bronchioles and alveoli that facilitate gas exchange. Three-dimensional in vitro human distal lung culture systems would strongly facilitate the investigation of pathologies such as interstitial lung disease, cancer and coronavirus disease 2019 (COVID-19) pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here we describe the development of a long-term feeder-free, chemically defined culture system for distal lung progenitors as organoids derived from single adult human alveolar epithelial type II (AT2) or KRT5+ basal cells. AT2 organoids were able to differentiate into AT1 cells, and basal cell organoids developed lumens lined with differentiated club and ciliated cells. Single-cell analysis of KRT5+ cells in basal organoids revealed a distinct population of ITGA6+ITGB4+ mitotic cells, whose offspring further segregated into a TNFRSF12Ahi subfraction that comprised about ten per cent of KRT5+ basal cells. This subpopulation formed clusters within terminal bronchioles and exhibited enriched clonogenic organoid growth activity. We created distal lung organoids with apical-out polarity to present ACE2 on the exposed external surface, facilitating infection of AT2 and basal cultures with SARS-CoV-2 and identifying club cells as a target population. This long-term, feeder-free culture of human distal lung organoids, coupled with single-cell analysis, identifies functional heterogeneity among basal cells and establishes a facile in vitro organoid model of human distal lung infections, including COVID-19-associated pneumonia.
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Affiliation(s)
- Ameen A Salahudeen
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - Shannon S Choi
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Arjun Rustagi
- Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Junjie Zhu
- Stanford University School of Engineering, Department of Electrical Engineering, Stanford, CA, USA
| | - Vincent van Unen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean M de la O
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Mar Margalef-Català
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - António J M Santos
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jihang Ju
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Arpit Batish
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Tatsuya Usui
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Caitlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lisa E Wagar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Vincent Luca
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benedict Anchang
- Division of Biomedical Data Science, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Monica Nagendran
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Khanh Nguyen
- Division of Gastroenterology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel J Hart
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | | | - Pehr B Harbury
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey S Glenn
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Gastroenterology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chiara Sabatti
- Division of Biomedical Data Science, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Manuel R Amieva
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Blish
- Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Tushar J Desai
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Calvin J Kuo
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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21
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Zaro BW, Noh JJ, Mascetti VL, Demeter J, George B, Zukowska M, Gulati GS, Sinha R, Flynn RA, Banuelos A, Zhang A, Wilkinson AC, Jackson P, Weissman IL. Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells. eLife 2020; 9:e62210. [PMID: 33236985 PMCID: PMC7688314 DOI: 10.7554/elife.62210] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
The balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for a healthy blood supply; imbalances underlie hematological diseases. The importance of HSCs and their progenitors have led to their extensive characterization at genomic and transcriptomic levels. However, the proteomics of hematopoiesis remains incompletely understood. Here we report a proteomics resource from mass spectrometry of mouse young adult and old adult mouse HSCs, multipotent progenitors and oligopotent progenitors; 12 cell types in total. We validated differential protein levels, including confirmation that Dnmt3a protein levels are undetected in young adult mouse HSCs until forced into cycle. Additionally, through integrating proteomics and RNA-sequencing datasets, we identified a subset of genes with apparent post-transcriptional repression in young adult mouse HSCs. In summary, we report proteomic coverage of young and old mouse HSCs and progenitors, with broader implications for understanding mechanisms for stem cell maintenance, niche interactions and fate determination.
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Affiliation(s)
- Balyn W Zaro
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Joseph J Noh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Victoria L Mascetti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of MedicineStanfordUnited States
| | - Benson George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Monika Zukowska
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Ryan A Flynn
- Department of Chemistry, Stanford UniversityStanfordUnited States
| | - Allison Banuelos
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Allison Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
| | - Peter Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of MedicineStanfordUnited States
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
- Department of Developmental Biology and the Stanford UC-Berkeley Stem Cell InstituteStanfordUnited States
- Department of Pathology, Stanford University School of MedicineStanfordUnited States
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22
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Flynn RA, Belk JA, Qi Y, Yasumoto Y, Schmitz CO, Mumbach MR, Limaye A, Wei J, Alfajaro MM, Parker KR, Chang HY, Horvath TL, Carette JE, Bertozzi C, Wilen CB, Satpathy AT. Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection. bioRxiv 2020:2020.10.06.327445. [PMID: 33052334 PMCID: PMC7553159 DOI: 10.1101/2020.10.06.327445] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a pandemic with growing global mortality. There is an urgent need to understand the molecular pathways required for host infection and anti-viral immunity. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host proteins that bind the SARS-CoV-2 RNA during active infection. Integration of this data with viral ChIRP-MS data from three other positive-sense RNA viruses defined pan-viral and SARS-CoV-2-specific host interactions. Functional interrogation of these factors with a genome-wide CRISPR screen revealed that the vast majority of viral RNA-binding proteins protect the host from virus-induced cell death, and we identified known and novel anti-viral proteins that regulate SARS-CoV-2 pathogenicity. Finally, our RNA-centric approach demonstrated a physical connection between SARS-CoV-2 RNA and host mitochondria, which we validated with functional and electron microscopy data, providing new insights into a more general virus-specific protein logic for mitochondrial interactions. Altogether, these data provide a comprehensive catalogue of SARS-CoV-2 RNA-host protein interactions, which may inform future studies to understand the mechanisms of viral pathogenesis, as well as nominate host pathways that could be targeted for therapeutic benefit. HIGHLIGHTS · ChIRP-MS of SARS-CoV-2 RNA identifies a comprehensive viral RNA-host protein interaction network during infection across two species· Comparison to RNA-protein interaction networks with Zika virus, dengue virus, and rhinovirus identify SARS-CoV-2-specific and pan-viral RNA protein complexes and highlights distinct intracellular trafficking pathways· Intersection of ChIRP-MS and genome-wide CRISPR screens identify novel SARS-CoV-2-binding proteins with pro- and anti-viral function· Viral RNA-RNA and RNA-protein interactions reveal specific SARS-CoV-2-mediated mitochondrial dysfunction during infection.
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Affiliation(s)
- Ryan A. Flynn
- Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA
- These authors contributed equally
| | - Julia A. Belk
- Department of Computer Science, Stanford University, Stanford, CA
- Department of Pathology, Stanford University, Stanford, CA
- These authors contributed equally
| | - Yanyan Qi
- Department of Pathology, Stanford University, Stanford, CA
| | - Yuki Yasumoto
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT
| | - Cameron O. Schmitz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Maxwell R. Mumbach
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA
| | - Aditi Limaye
- Department of Pathology, Stanford University, Stanford, CA
| | - Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Kevin R. Parker
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Tamas L. Horvath
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT
| | - Jan E. Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA
| | - Carolyn Bertozzi
- Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
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23
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Johnson AG, Flynn RA, Lapointe CP, Ooi YS, Zhao ML, Richards CM, Qiao W, Yamada SB, Couthouis J, Gitler AD, Carette JE, Puglisi JD. A memory of eS25 loss drives resistance phenotypes. Nucleic Acids Res 2020; 48:7279-7297. [PMID: 32463448 PMCID: PMC7367175 DOI: 10.1093/nar/gkaa444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/11/2020] [Accepted: 05/24/2020] [Indexed: 12/26/2022] Open
Abstract
In order to maintain cellular protein homeostasis, ribosomes are safeguarded against dysregulation by myriad processes. Remarkably, many cell types can withstand genetic lesions of certain ribosomal protein genes, some of which are linked to diverse cellular phenotypes and human disease. Yet the direct and indirect consequences from these lesions are poorly understood. To address this knowledge gap, we studied in vitro and cellular consequences that follow genetic knockout of the ribosomal proteins RPS25 or RACK1 in a human cell line, as both proteins are implicated in direct translational control. Prompted by the unexpected detection of an off-target ribosome alteration in the RPS25 knockout, we closely interrogated cellular phenotypes. We found that multiple RPS25 knockout clones display viral- and toxin-resistance phenotypes that cannot be rescued by functional cDNA expression, suggesting that RPS25 loss elicits a cell state transition. We characterized this state and found that it underlies pleiotropic phenotypes and has a common rewiring of gene expression. Rescuing RPS25 expression by genomic locus repair failed to correct for the phenotypic and expression hysteresis. Our findings illustrate how the elasticity of cells to a ribosome perturbation can drive specific phenotypic outcomes that are indirectly linked to translation and suggests caution in the interpretation of ribosomal protein gene mutation data.
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Affiliation(s)
- Alex G Johnson
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.,Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Yaw Shin Ooi
- Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Michael L Zhao
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Wenjie Qiao
- Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Shizuka B Yamada
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julien Couthouis
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jan E Carette
- Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
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24
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Salahudeen AA, Choi SS, Rustagi A, Zhu J, de la O SM, Flynn RA, Margalef-Català M, Santos AJM, Ju J, Batish A, van Unen V, Usui T, Zheng GXY, Edwards CE, Wagar LE, Luca V, Anchang B, Nagendran M, Nguyen K, Hart DJ, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Harbury PB, Glenn JS, Garcia KC, Davis MM, Baric RS, Sabatti C, Amieva MR, Blish CA, Desai TJ, Kuo CJ. Progenitor identification and SARS-CoV-2 infection in long-term human distal lung organoid cultures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.27.212076. [PMID: 32743583 PMCID: PMC7386503 DOI: 10.1101/2020.07.27.212076] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The distal lung contains terminal bronchioles and alveoli that facilitate gas exchange and is affected by disorders including interstitial lung disease, cancer, and SARS-CoV-2-associated COVID-19 pneumonia. Investigations of these localized pathologies have been hindered by a lack of 3D in vitro human distal lung culture systems. Further, human distal lung stem cell identification has been impaired by quiescence, anatomic divergence from mouse and lack of lineage tracing and clonogenic culture. Here, we developed robust feeder-free, chemically-defined culture of distal human lung progenitors as organoids derived clonally from single adult human alveolar epithelial type II (AT2) or KRT5 + basal cells. AT2 organoids exhibited AT1 transdifferentiation potential, while basal cell organoids progressively developed lumens lined by differentiated club and ciliated cells. Organoids consisting solely of club cells were not observed. Upon single cell RNA-sequencing (scRNA-seq), alveolar organoids were composed of proliferative AT2 cells; however, basal organoid KRT5 + cells contained a distinct ITGA6 + ITGB4 + mitotic population whose proliferation segregated to a TNFRSF12A hi subfraction. Clonogenic organoid growth was markedly enriched within the TNFRSF12A hi subset of FACS-purified ITGA6 + ITGB4 + basal cells from human lung or derivative organoids. In vivo, TNFRSF12A + cells comprised ~10% of KRT5 + basal cells and resided in clusters within terminal bronchioles. To model COVID-19 distal lung disease, we everted the polarity of basal and alveolar organoids to rapidly relocate differentiated club and ciliated cells from the organoid lumen to the exterior surface, thus displaying the SARS-CoV-2 receptor ACE2 on the outwardly-facing apical aspect. Accordingly, basal and AT2 apical-out organoids were infected by SARS-CoV-2, identifying club cells as a novel target population. This long-term, feeder-free organoid culture of human distal lung alveolar and basal stem cells, coupled with single cell analysis, identifies unsuspected basal cell functional heterogeneity and exemplifies progenitor identification within a slowly proliferating human tissue. Further, our studies establish a facile in vitro organoid model for human distal lung infectious diseases including COVID-19-associated pneumonia.
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25
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Flynn RA, Ruiz-Ramie JJ, Johannsen NM, Church TS, Sarzynski MA. Effects Of Exercise Training On Circulating Branched-chain Amino Acid And Ketone Levels In Diabetics. Med Sci Sports Exerc 2020. [DOI: 10.1249/01.mss.0000671160.23642.d2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Santoriello C, Sporrij A, Yang S, Flynn RA, Henriques T, Dorjsuren B, Custo Greig E, McCall W, Stanhope ME, Fazio M, Superdock M, Lichtig A, Adatto I, Abraham BJ, Kalocsay M, Jurynec M, Zhou Y, Adelman K, Calo E, Zon LI. RNA helicase DDX21 mediates nucleotide stress responses in neural crest and melanoma cells. Nat Cell Biol 2020; 22:372-379. [PMID: 32231306 PMCID: PMC7185069 DOI: 10.1038/s41556-020-0493-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 02/24/2020] [Indexed: 12/25/2022]
Abstract
The availability of nucleotides has a direct impact on transcription. The inhibition of dihydroorotate dehydrogenase (DHODH) with leflunomide impacts nucleotide pools by reducing pyrimidine levels. Leflunomide abrogates the effective transcription elongation of genes required for neural crest development and melanoma growth in vivo1. To define the mechanism of action, we undertook an in vivo chemical suppressor screen for restoration of neural crest after leflunomide treatment. Surprisingly, we found that alterations in progesterone and progesterone receptor (Pgr) signalling strongly suppressed leflunomide-mediated neural crest effects in zebrafish. In addition, progesterone bypasses the transcriptional elongation block resulting from Paf complex deficiency, rescuing neural crest defects in ctr9 morphant and paf1(alnz24) mutant embryos. Using proteomics, we found that Pgr binds the RNA helicase protein Ddx21. ddx21-deficient zebrafish show resistance to leflunomide-induced stress. At a molecular level, nucleotide depletion reduced the chromatin occupancy of DDX21 in human A375 melanoma cells. Nucleotide supplementation reversed the gene expression signature and DDX21 occupancy changes prompted by leflunomide. Together, our results show that DDX21 acts as a sensor and mediator of transcription during nucleotide stress.
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Affiliation(s)
- Cristina Santoriello
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Audrey Sporrij
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Song Yang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Telmo Henriques
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bilguujin Dorjsuren
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Eugenia Custo Greig
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Wyatt McCall
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Meredith E Stanhope
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Maurizio Fazio
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Michael Superdock
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Asher Lichtig
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Isaac Adatto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marian Kalocsay
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Michael Jurynec
- Department of Orthopedics, University of Utah, Salt Lake City, UT, USA
| | - Yi Zhou
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eliezer Calo
- Department of Biology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leonard I Zon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. .,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA.
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27
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Shao Z, Flynn RA, Crowe JL, Zhu Y, Liang J, Jiang W, Aryan F, Aoude P, Bertozzi CR, Estes VM, Lee BJ, Bhagat G, Zha S, Calo E. DNA-PKcs has KU-dependent function in rRNA processing and haematopoiesis. Nature 2020; 579:291-296. [PMID: 32103174 PMCID: PMC10919329 DOI: 10.1038/s41586-020-2041-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 01/28/2020] [Indexed: 11/09/2022]
Abstract
The DNA-dependent protein kinase (DNA-PK), which comprises the KU heterodimer and a catalytic subunit (DNA-PKcs), is a classical non-homologous end-joining (cNHEJ) factor1. KU binds to DNA ends, initiates cNHEJ, and recruits and activates DNA-PKcs. KU also binds to RNA, but the relevance of this interaction in mammals is unclear. Here we use mouse models to show that DNA-PK has an unexpected role in the biogenesis of ribosomal RNA (rRNA) and in haematopoiesis. The expression of kinase-dead DNA-PKcs abrogates cNHEJ2. However, most mice that both expressed kinase-dead DNA-PKcs and lacked the tumour suppressor TP53 developed myeloid disease, whereas all other previously characterized mice deficient in both cNHEJ and TP53 expression succumbed to pro-B cell lymphoma3. DNA-PK autophosphorylates DNA-PKcs, which is its best characterized substrate. Blocking the phosphorylation of DNA-PKcs at the T2609 cluster, but not the S2056 cluster, led to KU-dependent defects in 18S rRNA processing, compromised global protein synthesis in haematopoietic cells and caused bone marrow failure in mice. KU drives the assembly of DNA-PKcs on a wide range of cellular RNAs, including the U3 small nucleolar RNA, which is essential for processing of 18S rRNA4. U3 activates purified DNA-PK and triggers phosphorylation of DNA-PKcs at T2609. DNA-PK, but not other cNHEJ factors, resides in nucleoli in an rRNA-dependent manner and is co-purified with the small subunit processome. Together our data show that DNA-PK has RNA-dependent, cNHEJ-independent functions during ribosome biogenesis that require the kinase activity of DNA-PKcs and its phosphorylation at the T2609 cluster.
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Affiliation(s)
- Zhengping Shao
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Jennifer L Crowe
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Graduate Program of Pathobiology and Molecular Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Yimeng Zhu
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Jialiang Liang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wenxia Jiang
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Fardin Aryan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Patrick Aoude
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Verna M Estes
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Govind Bhagat
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Immunology and Microbiology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
- Department of Immunology and Microbiology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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28
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Esfahani MS, Lee LJ, Jeon YJ, Flynn RA, Stehr H, Hui AB, Ishisoko N, Kildebeck E, Newman AM, Bratman SV, Porteus MH, Chang HY, Alizadeh AA, Diehn M. Functional significance of U2AF1 S34F mutations in lung adenocarcinomas. Nat Commun 2019; 10:5712. [PMID: 31836708 PMCID: PMC6911043 DOI: 10.1038/s41467-019-13392-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 11/07/2019] [Indexed: 12/23/2022] Open
Abstract
The functional role of U2AF1 mutations in lung adenocarcinomas (LUADs) remains incompletely understood. Here, we report a significant co-occurrence of U2AF1 S34F mutations with ROS1 translocations in LUADs. To characterize this interaction, we profiled effects of S34F on the transcriptome-wide distribution of RNA binding and alternative splicing in cells harboring the ROS1 translocation. Compared to its wild-type counterpart, U2AF1 S34F preferentially binds and modulates splicing of introns containing CAG trinucleotides at their 3' splice junctions. The presence of S34F caused a shift in cross-linking at 3' splice sites, which was significantly associated with alternative splicing of skipped exons. U2AF1 S34F induced expression of genes involved in the epithelial-mesenchymal transition (EMT) and increased tumor cell invasion. Finally, S34F increased splicing of the long over the short SLC34A2-ROS1 isoform, which was also associated with enhanced invasiveness. Taken together, our results suggest a mechanistic interaction between mutant U2AF1 and ROS1 in LUAD.
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Affiliation(s)
- Mohammad S Esfahani
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Luke J Lee
- Stanford Cancer Institute, Stanford University, Stanford, USA
| | - Young-Jun Jeon
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Angela B Hui
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Noriko Ishisoko
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Eric Kildebeck
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Scott V Bratman
- Department of Radiation Oncology, Stanford University, Stanford, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA
- Department of Radiation Oncology, University of Toronto, Toronto, CA, USA
| | | | - Howard Y Chang
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, USA
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, USA.
- Division of Oncology, Department of Medicine, Stanford University, Stanford, USA.
- Division of Hematology, Department of Medicine, Stanford University, Stanford, USA.
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, USA.
- Department of Radiation Oncology, Stanford University, Stanford, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA.
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29
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Mumbach MR, Granja JM, Flynn RA, Roake CM, Satpathy AT, Rubin AJ, Qi Y, Jiang Z, Shams S, Louie BH, Guo JK, Gennert DG, Corces MR, Khavari PA, Atianand MK, Artandi SE, Fitzgerald KA, Greenleaf WJ, Chang HY. HiChIRP reveals RNA-associated chromosome conformation. Nat Methods 2019; 16:489-492. [PMID: 31133759 DOI: 10.1038/s41592-019-0407-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 04/05/2019] [Indexed: 12/25/2022]
Abstract
Modular domains of long non-coding RNAs can serve as scaffolds to bring distant regions of the linear genome into spatial proximity. Here, we present HiChIRP, a method leveraging bio-orthogonal chemistry and optimized chromosome conformation capture conditions, which enables interrogation of chromatin architecture focused around a specific RNA of interest down to approximately ten copies per cell. HiChIRP of three nuclear RNAs reveals insights into promoter interactions (7SK), telomere biology (telomerase RNA component) and inflammatory gene regulation (lincRNA-EPS).
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Affiliation(s)
- Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Program in Biophysics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Caitlin M Roake
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yanyan Qi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhaozhao Jiang
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shadi Shams
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan H Louie
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jimmy K Guo
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - David G Gennert
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maninjay K Atianand
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven E Artandi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine A Fitzgerald
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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30
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Ang CE, Ma Q, Wapinski OL, Fan S, Flynn RA, Lee QY, Coe B, Onoguchi M, Olmos VH, Do BT, Dukes-Rimsky L, Xu J, Tanabe K, Wang L, Elling U, Penninger JM, Zhao Y, Qu K, Eichler EE, Srivastava A, Wernig M, Chang HY. The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders. eLife 2019; 8:41770. [PMID: 30628890 PMCID: PMC6380841 DOI: 10.7554/elife.41770] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/07/2019] [Indexed: 12/25/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been shown to act as important cell biological regulators including cell fate decisions but are often ignored in human genetics. Combining differential lncRNA expression during neuronal lineage induction with copy number variation morbidity maps of a cohort of children with autism spectrum disorder/intellectual disability versus healthy controls revealed focal genomic mutations affecting several lncRNA candidate loci. Here we find that a t(5:12) chromosomal translocation in a family manifesting neurodevelopmental symptoms disrupts specifically lnc-NR2F1. We further show that lnc-NR2F1 is an evolutionarily conserved lncRNA functionally enhances induced neuronal cell maturation and directly occupies and regulates transcription of neuronal genes including autism-associated genes. Thus, integrating human genetics and functional testing in neuronal lineage induction is a promising approach for discovering candidate lncRNAs involved in neurodevelopmental diseases.
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Affiliation(s)
- Cheen Euong Ang
- Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, United States.,Department of Bioengineering, Stanford University, Stanford, United States
| | - Qing Ma
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States.,Department of Dermatology, Stanford University, Stanford, United States.,Department of Genetics, Stanford University, Stanford, United States
| | - Orly L Wapinski
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States.,Department of Dermatology, Stanford University, Stanford, United States.,Department of Genetics, Stanford University, Stanford, United States
| | - ShengHua Fan
- JC Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, United States
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States.,Department of Dermatology, Stanford University, Stanford, United States.,Department of Genetics, Stanford University, Stanford, United States
| | - Qian Yi Lee
- Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, United States.,Department of Bioengineering, Stanford University, Stanford, United States
| | - Bradley Coe
- Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, United States
| | - Masahiro Onoguchi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States.,Department of Dermatology, Stanford University, Stanford, United States.,Department of Genetics, Stanford University, Stanford, United States
| | - Victor Hipolito Olmos
- Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, United States
| | - Brian T Do
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States
| | - Lynn Dukes-Rimsky
- JC Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, United States
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States
| | - Koji Tanabe
- Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, United States
| | - LiangJiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, United States
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter, Vienna, Austria
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter, Vienna, Austria
| | - Yang Zhao
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States
| | - Kun Qu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States.,Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter, Vienna, Austria
| | - Evan E Eichler
- Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, United States
| | - Anand Srivastava
- JC Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, United States.,Department of Genetics and Biochemistry, Clemson University, Clemson, United States
| | - Marius Wernig
- Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, United States
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States
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31
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Oh S, Flynn RA, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DTW, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, Marra MA, Malkin D, Lichter P, Doudna JA, Pfister SM, Taylor MD, Chang HY, Cho YJ. Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. Oncotarget 2018; 7:28169-82. [PMID: 27058758 PMCID: PMC5053718 DOI: 10.18632/oncotarget.8612] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 03/26/2016] [Indexed: 12/14/2022] Open
Abstract
DDX3X encodes a DEAD-box family RNA helicase (DDX3) commonly mutated in medulloblastoma, a highly aggressive cerebellar tumor affecting both children and adults. Despite being implicated in several facets of RNA metabolism, the nature and scope of DDX3′s interactions with RNA remain unclear. Here, we show DDX3 collaborates extensively with the translation initiation machinery through direct binding to 5′UTRs of nearly all coding RNAs, specific sites on the 18S rRNA, and multiple components of the translation initiation complex. Impairment of translation initiation is also evident in primary medulloblastomas harboring mutations in DDX3X, further highlighting DDX3′s role in this process. Arsenite-induced stress shifts DDX3 binding from the 5′UTR into the coding region of mRNAs concomitant with a general reduction of translation, and both the shift of DDX3 on mRNA and decreased translation are blunted by expression of a catalytically-impaired, medulloblastoma-associated DDX3R534H variant. Furthermore, despite the global repression of translation induced by arsenite, translation is preserved on select genes involved in chromatin organization in DDX3R534H-expressing cells. Thus, DDX3 interacts extensively with RNA and ribosomal machinery to help remodel the translation landscape in response to stress, while cancer-related DDX3 variants adapt this response to selectively preserve translation.
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Affiliation(s)
- Sekyung Oh
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen N Floor
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - James Purzner
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Surgery, Division of Neurosurgery, University of Toronto, ON, Canada
| | - Lance Martin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Brian T Do
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Simone Schubert
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Dedeepya Vaka
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Sorana Morrissy
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Surgery, Division of Neurosurgery and Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Yisu Li
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC Canada
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Risch
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hans-Jörg Warnatz
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Christopher M Adams
- The Vincent Coates Foundation Mass Spectrometry Laboratory, Stanford University, Stanford, CA, USA
| | - Ryan D Leib
- The Vincent Coates Foundation Mass Spectrometry Laboratory, Stanford University, Stanford, CA, USA
| | - Marcus Breese
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC Canada
| | - David Malkin
- Cancer Genetic Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,Department of Chemistry, University of California, Berkeley, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Surgery, Division of Neurosurgery and Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, ON, Canada
| | - Howard Y Chang
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Yoon-Jae Cho
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA.,Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA.,Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
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32
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Tomlin F, Gerling-Driessen UIM, Liu YC, Flynn RA, Vangala JR, Lentz CS, Clauder-Muenster S, Jakob P, Mueller WF, Ordoñez-Rueda D, Paulsen M, Matsui N, Foley D, Rafalko A, Suzuki T, Bogyo M, Steinmetz LM, Radhakrishnan SK, Bertozzi CR. Inhibition of NGLY1 Inactivates the Transcription Factor Nrf1 and Potentiates Proteasome Inhibitor Cytotoxicity. ACS Cent Sci 2017; 3:1143-1155. [PMID: 29202016 PMCID: PMC5704294 DOI: 10.1021/acscentsci.7b00224] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Indexed: 05/06/2023]
Abstract
Proteasome inhibitors are used to treat blood cancers such as multiple myeloma (MM) and mantle cell lymphoma. The efficacy of these drugs is frequently undermined by acquired resistance. One mechanism of proteasome inhibitor resistance may involve the transcription factor Nuclear Factor, Erythroid 2 Like 1 (NFE2L1, also referred to as Nrf1), which responds to proteasome insufficiency or pharmacological inhibition by upregulating proteasome subunit gene expression. This "bounce-back" response is achieved through a unique mechanism. Nrf1 is constitutively translocated into the ER lumen, N-glycosylated, and then targeted for proteasomal degradation via the ER-associated degradation (ERAD) pathway. Proteasome inhibition leads to accumulation of cytosolic Nrf1, which is then processed to form the active transcription factor. Here we show that the cytosolic enzyme N-glycanase 1 (NGLY1, the human PNGase) is essential for Nrf1 activation in response to proteasome inhibition. Chemical or genetic disruption of NGLY1 activity results in the accumulation of misprocessed Nrf1 that is largely excluded from the nucleus. Under these conditions, Nrf1 is inactive in regulating proteasome subunit gene expression in response to proteasome inhibition. Through a small molecule screen, we identified a cell-active NGLY1 inhibitor that disrupts the processing and function of Nrf1. The compound potentiates the cytotoxicity of carfilzomib, a clinically used proteasome inhibitor, against MM and T cell-derived acute lymphoblastic leukemia (T-ALL) cell lines. Thus, NGLY1 inhibition prevents Nrf1 activation and represents a new therapeutic approach for cancers that depend on proteasome homeostasis.
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Affiliation(s)
- Frederick
M. Tomlin
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | | | - Yi-Chang Liu
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Ryan A. Flynn
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Janakiram R. Vangala
- Department
of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Christian S. Lentz
- Department
of Pathology, Stanford University School
of Medicine, 300 Pasteur
Drive, Stanford, California 94305, United States
| | - Sandra Clauder-Muenster
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Petra Jakob
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - William F. Mueller
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Diana Ordoñez-Rueda
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Malte Paulsen
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Naoko Matsui
- Glycomine,
Inc., 953 Indiana Street, San Francisco, California 94107, United States
| | - Deirdre Foley
- Glycomine,
Inc., 953 Indiana Street, San Francisco, California 94107, United States
| | - Agnes Rafalko
- Glycomine,
Inc., 953 Indiana Street, San Francisco, California 94107, United States
| | - Tadashi Suzuki
- Glycometabolome
Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Matthew Bogyo
- Department
of Pathology, Stanford University School
of Medicine, 300 Pasteur
Drive, Stanford, California 94305, United States
- Department
of Microbiology and Immunology, Stanford
University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Lars M. Steinmetz
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
- Department
of Genetics, School of Medicine, Stanford
University, Stanford, California 94305, United States
| | - Senthil K. Radhakrishnan
- Department
of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Carolyn R. Bertozzi
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
- E-mail:
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33
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Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY. Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nat Genet 2017; 49:1602-1612. [PMID: 28945252 DOI: 10.1038/ng.3963] [Citation(s) in RCA: 305] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/01/2017] [Indexed: 12/14/2022]
Abstract
The challenge of linking intergenic mutations to target genes has limited molecular understanding of human diseases. Here we show that H3K27ac HiChIP generates high-resolution contact maps of active enhancers and target genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naive T cells into T helper 17 cells or regulatory T cells creates subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to putative gene targets. Target genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact genes beyond the nearest gene in the linear genome, leading to a fourfold increase in the number of potential target genes for autoimmune and cardiovascular diseases.
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Affiliation(s)
- Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Evan A Boyle
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Chao Dai
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin G Gowen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Michelle L Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Katelynn R Kazane
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Trieu Nguyen
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Peyton G Greenside
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Josh Tycko
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Dimitre R Simeonov
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Nabeela Suliman
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Alexander Marson
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Applied Physics, Stanford University, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
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34
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Simsek D, Tiu GC, Flynn RA, Byeon GW, Leppek K, Xu AF, Chang HY, Barna M. The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity. Cell 2017; 169:1051-1065.e18. [PMID: 28575669 PMCID: PMC5548193 DOI: 10.1016/j.cell.2017.05.022] [Citation(s) in RCA: 242] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 03/13/2017] [Accepted: 05/14/2017] [Indexed: 11/19/2022]
Abstract
During eukaryotic evolution, ribosomes have considerably increased in size, forming a surface-exposed ribosomal RNA (rRNA) shell of unknown function, which may create an interface for yet uncharacterized interacting proteins. To investigate such protein interactions, we establish a ribosome affinity purification method that unexpectedly identifies hundreds of ribosome-associated proteins (RAPs) from categories including metabolism and cell cycle, as well as RNA- and protein-modifying enzymes that functionally diversify mammalian ribosomes. By further characterizing RAPs, we discover the presence of ufmylation, a metazoan-specific post-translational modification (PTM), on ribosomes and define its direct substrates. Moreover, we show that the metabolic enzyme, pyruvate kinase muscle (PKM), interacts with sub-pools of endoplasmic reticulum (ER)-associated ribosomes, exerting a non-canonical function as an RNA-binding protein in the translation of ER-destined mRNAs. Therefore, RAPs interconnect one of life's most ancient molecular machines with diverse cellular processes, providing an additional layer of regulatory potential to protein expression.
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Affiliation(s)
- Deniz Simsek
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Gerald C Tiu
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gun W Byeon
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kathrin Leppek
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Adele F Xu
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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35
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Chan D, Feng C, Zhen Y, Flynn RA, Spitale RC. Comparative Analysis Reveals Furoyl in Vivo Selective Hydroxyl Acylation Analyzed by Primer Extension Reagents Form Stable Ribosyl Ester Adducts. Biochemistry 2017; 56:1811-1814. [PMID: 28319368 PMCID: PMC10884885 DOI: 10.1021/acs.biochem.7b00128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
RNA molecules depend on structural elements that are critical for cellular function. Chemical methods for probing RNA structure have emerged as a necessary component of characterizing RNA function. As such, understanding the limitations and idiosyncrasies of these methods is essential for their utility. Selective hydroxyl acylation has emerged as a common method for analyzing RNA structure. Ester products as a result of 2'-hydroxyl acylation can then be identified through reverse transcription or mutational enzyme profiling. The central aspect of selective hydroxyl acylation analyzed by primer extension (SHAPE) experiments is the fact that stable ester adducts are formed on the 2'-hydroxyl. Despite its importance, there has not been a direct comparison of SHAPE electrophiles for their ability to make stable RNA adducts. Herein, we conduct a systematic analysis of hydrolysis stability experiments to demonstrate that furoyl imidazole SHAPE reagents form stable ester adducts even at elevated temperatures. We also demonstrate that the acylation reaction with the furoyl acylimidaole SHAPE reagent can be controlled with dithiothreitol quenching, even in live cells. These results are important for our understanding of the biochemical details of the SHAPE experiment.
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Affiliation(s)
- Dalen Chan
- Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
| | - Chao Feng
- Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
| | - Yuran Zhen
- Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
| | - Ryan A Flynn
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
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36
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Lee B, Flynn RA, Kadina A, Guo JK, Kool ET, Chang HY. Comparison of SHAPE reagents for mapping RNA structures inside living cells. RNA 2017; 23:169-174. [PMID: 27879433 PMCID: PMC5238792 DOI: 10.1261/rna.058784.116] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/20/2016] [Indexed: 05/10/2023]
Abstract
Recent advances in SHAPE technology have converted the classic primer extension method to next-generation sequencing platforms, allowing transcriptome-level analysis of RNA secondary structure. In particular, icSHAPE and SHAPE-MaP, using NAI-N3 and 1M7 reagents, respectively, are methods that claim to measure in vivo structure with high-throughput sequencing. However, these compounds have not been compared on an unbiased, raw-signal level. Here, we directly compare several in vivo SHAPE acylation reagents using the simple primer extension assay. We conclude that while multiple SHAPE technologies are effective at measuring purified RNAs in vitro, acylimidazole reagents NAI and NAI-N3 give markedly greater signals with lower background than 1M7 for in vivo measurement of the RNA structurome.
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Affiliation(s)
- Byron Lee
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Anastasia Kadina
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Jimmy K Guo
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
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37
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Mumbach MR, Rubin AJ, Flynn RA, Dai C, Khavari PA, Greenleaf WJ, Chang HY. HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat Methods 2016; 13:919-922. [PMID: 27643841 PMCID: PMC5501173 DOI: 10.1038/nmeth.3999] [Citation(s) in RCA: 646] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/10/2016] [Indexed: 12/19/2022]
Abstract
Genome conformation is central to gene control but challenging to interrogate. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the yield of conformation-informative reads by over 10-fold and lowers the input requirement over 100-fold relative to that of ChIA-PET. HiChIP of cohesin reveals multiscale genome architecture with greater signal-to-background ratios than those of in situ Hi-C.
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Affiliation(s)
- Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Chao Dai
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Applied Physics, Stanford University, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
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38
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Schmitt AM, Garcia JT, Hung T, Flynn RA, Shen Y, Qu K, Payumo AY, Peres-da-Silva A, Broz DK, Baum R, Guo S, Chen JK, Attardi LD, Chang HY. An inducible long noncoding RNA amplifies DNA damage signaling. Nat Genet 2016; 48:1370-1376. [PMID: 27668660 PMCID: PMC5083181 DOI: 10.1038/ng.3673] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/22/2016] [Indexed: 12/17/2022]
Abstract
Long noncoding RNAs (lncRNAs) are prevalent genes with frequently precise regulation but mostly unknown functions. Here we demonstrate that lncRNAs guide the organismal DNA damage response. DNA damage activated transcription of the DINO (Damage Induced Noncoding) lncRNA via p53. DINO was required for p53-dependent gene expression, cell cycle arrest and apoptosis in response to DNA damage, and DINO expression was sufficient to activate damage signaling and cell cycle arrest in the absence of DNA damage. DINO bound to p53 protein and promoted its stabilization, mediating a p53 auto-amplification loop. Dino knockout or promoter inactivation in mice dampened p53 signaling and ameliorated acute radiation syndrome in vivo. Thus, inducible lncRNA can create a feedback loop with its cognate transcription factor to amplify cellular signaling networks.
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Affiliation(s)
- Adam M Schmitt
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Julia T Garcia
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Tiffany Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Ying Shen
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Kun Qu
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Alexander Y Payumo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Ashwin Peres-da-Silva
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | | | - Rachel Baum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Shuling Guo
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Laura D Attardi
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
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39
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Tan JL, Fogley RD, Flynn RA, Ablain J, Yang S, Saint-André V, Fan ZP, Do BT, Laga AC, Fujinaga K, Santoriello C, Greer CB, Kim YJ, Clohessy JG, Bothmer A, Pandell N, Avagyan S, Brogie JE, van Rooijen E, Hagedorn EJ, Shyh-Chang N, White RM, Price DH, Pandolfi PP, Peterlin BM, Zhou Y, Kim TH, Asara JM, Chang HY, Young RA, Zon LI. Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma. Mol Cell 2016; 62:34-46. [PMID: 27058786 DOI: 10.1016/j.molcel.2016.03.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 02/02/2016] [Accepted: 03/10/2016] [Indexed: 12/29/2022]
Abstract
Studying cancer metabolism gives insight into tumorigenic survival mechanisms and susceptibilities. In melanoma, we identify HEXIM1, a transcription elongation regulator, as a melanoma tumor suppressor that responds to nucleotide stress. HEXIM1 expression is low in melanoma. Its overexpression in a zebrafish melanoma model suppresses cancer formation, while its inactivation accelerates tumor onset in vivo. Knockdown of HEXIM1 rescues zebrafish neural crest defects and human melanoma proliferation defects that arise from nucleotide depletion. Under nucleotide stress, HEXIM1 is induced to form an inhibitory complex with P-TEFb, the kinase that initiates transcription elongation, to inhibit elongation at tumorigenic genes. The resulting alteration in gene expression also causes anti-tumorigenic RNAs to bind to and be stabilized by HEXIM1. HEXIM1 plays an important role in inhibiting cancer cell-specific gene transcription while also facilitating anti-cancer gene expression. Our study reveals an important role for HEXIM1 in coupling nucleotide metabolism with transcriptional regulation in melanoma.
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Affiliation(s)
- Justin L Tan
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Rachel D Fogley
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Julien Ablain
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Song Yang
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Violaine Saint-André
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Zi Peng Fan
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Brian T Do
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alvaro C Laga
- Department of Pathology, Brigham & Women's Hospital, Boston, MA 02215, USA
| | - Koh Fujinaga
- Departments of Medicine, Microbiology, and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cristina Santoriello
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Celeste B Greer
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Yoon Jung Kim
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - John G Clohessy
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, and Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Bothmer
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, and Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole Pandell
- Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Serine Avagyan
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - John E Brogie
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Ellen van Rooijen
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Elliott J Hagedorn
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Ng Shyh-Chang
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Richard M White
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY 10065, USA
| | - David H Price
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, and Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - B Matija Peterlin
- Departments of Medicine, Microbiology, and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yi Zhou
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Tae Hoon Kim
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - John M Asara
- Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Leonard I Zon
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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40
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Huang W, Thomas B, Flynn RA, Gavzy SJ, Wu L, Kim SV, Hall JA, Miraldi ER, Ng CP, Rigo F, Meadows S, Montoya NR, Herrera NG, Domingos AI, Rastinejad F, Myers RM, Fuller-Pace FV, Bonneau R, Chang HY, Acuto O, Littman DR. Corrigendum: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions. Nature 2016; 533:130. [PMID: 26789242 PMCID: PMC11078536 DOI: 10.1038/nature16968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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41
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Flynn RA, Do BT, Rubin AJ, Calo E, Lee B, Kuchelmeister H, Rale M, Chu C, Kool ET, Wysocka J, Khavari PA, Chang HY. 7SK-BAF axis controls pervasive transcription at enhancers. Nat Struct Mol Biol 2016; 23:231-8. [PMID: 26878240 PMCID: PMC4982704 DOI: 10.1038/nsmb.3176] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 01/20/2016] [Indexed: 01/08/2023]
Abstract
RNA functions at enhancers remain mysterious. Here we show that the 7SK small nuclear RNA (snRNA) inhibits enhancer transcription by modulating nucleosome position. 7SK occupies enhancers and super enhancers genome-wide in mouse and human cells, and 7SK is required to limit eRNA initiation and synthesis in a manner distinct from promoter pausing. Clustered elements at super enhancers uniquely require 7SK to prevent convergent transcription and DNA damage signaling. 7SK physically interacts with the BAF chromatin remodeling complex, recruit BAF to enhancers, and inhibits enhancer transcription by modulating chromatin structure. In turn, 7SK occupancy at enhancers coincides with Brd4 and is exquisitely sensitive to the bromodomain inhibitor JQ1. Thus, 7SK employs distinct mechanisms to counteract diverse consequences of pervasive transcription that distinguish super enhancers, enhancers, and promoters.
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Affiliation(s)
- Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Brian T Do
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Eliezer Calo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Byron Lee
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | | | - Michael Rale
- The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Ci Chu
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
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42
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Mazumdar C, Shen Y, Xavy S, Zhao F, Reinisch A, Li R, Corces MR, Flynn RA, Buenrostro JD, Chan SM, Thomas D, Koenig JL, Hong WJ, Chang HY, Majeti R. Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation. Cell Stem Cell 2015; 17:675-688. [PMID: 26607380 PMCID: PMC4671831 DOI: 10.1016/j.stem.2015.09.017] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/24/2015] [Accepted: 09/23/2015] [Indexed: 01/14/2023]
Abstract
Recurrent mutations in cohesin complex proteins have been identified in pre-leukemic hematopoietic stem cells and during the early development of acute myeloid leukemia and other myeloid malignancies. Although cohesins are involved in chromosome separation and DNA damage repair, cohesin complex functions during hematopoiesis and leukemic development are unclear. Here, we show that mutant cohesin proteins block differentiation of human hematopoietic stem and progenitor cells (HSPCs) in vitro and in vivo and enforce stem cell programs. These effects are restricted to immature HSPC populations, where cohesin mutants show increased chromatin accessibility and likelihood of transcription factor binding site occupancy by HSPC regulators including ERG, GATA2, and RUNX1, as measured by ATAC-seq and ChIP-seq. Epistasis experiments show that silencing these transcription factors rescues the differentiation block caused by cohesin mutants. Together, these results show that mutant cohesins impair HSPC differentiation by controlling chromatin accessibility and transcription factor activity, possibly contributing to leukemic disease.
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Affiliation(s)
- Claire Mazumdar
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ying Shen
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seethu Xavy
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Feifei Zhao
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andreas Reinisch
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - M Ryan Corces
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jason D Buenrostro
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven M Chan
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel Thomas
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Julie L Koenig
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wan-Jen Hong
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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43
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Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. Erratum: Structural imprints in vivo decode RNA regulatory mechanisms. Nature 2015; 527:264. [PMID: 26416736 DOI: 10.1038/nature15717] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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44
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Abstract
In recent years, long noncoding RNAs (lncRNAs) have emerged as an important class of regulators of gene expression. lncRNAs exhibit several distinctive features that confer unique regulatory functions, including exquisite cell- and tissue-specific expression and the capacity to transduce higher-order spatial information. Here we review evidence showing that lncRNAs exert critical functions in adult tissue stem cells, including skin, brain, and muscle, as well as in developmental patterning and pluripotency. We highlight new approaches for ascribing lncRNA functions and discuss mammalian dosage compensation as a classic example of an lncRNA network coupled to stem cell differentiation.
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Affiliation(s)
- Ryan A Flynn
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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45
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Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. Structural imprints in vivo decode RNA regulatory mechanisms. Nature 2015; 519:486-90. [PMID: 25799993 PMCID: PMC4376618 DOI: 10.1038/nature14263] [Citation(s) in RCA: 517] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 01/26/2015] [Indexed: 01/08/2023]
Abstract
Visualizing the physical basis for molecular behavior inside living cells is a grand challenge in biology. RNAs are central to biological regulation, and RNA’s ability to adopt specific structures intimately controls every step of the gene expression program1. However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles view only two of four nucleotides that make up RNA2,3. Here we present a novel biochemical approach, In Vivo Click SHAPE (icSHAPE), that enables the first global view of RNA secondary structures of all four bases in living cells. icSHAPE of mouse embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguishes different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved from in vitro, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA binding proteins or RNA modification sites that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N6-methyladenosine (m6A) modification genome-wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.
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Affiliation(s)
- Robert C Spitale
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ryan A Flynn
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Qiangfeng Cliff Zhang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Pete Crisalli
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Byron Lee
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jong-Wha Jung
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | - Pedro J Batista
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Eduardo A Torre
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Howard Y Chang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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46
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Flynn RA, Martin L, Spitale RC, Do BT, Sagan SM, Zarnegar B, Qu K, Khavari PA, Quake SR, Sarnow P, Chang HY. Dissecting noncoding and pathogen RNA-protein interactomes. RNA 2015; 21:135-143. [PMID: 25411354 PMCID: PMC4274633 DOI: 10.1261/rna.047803.114] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/27/2014] [Indexed: 05/30/2023]
Abstract
RNA-protein interactions are central to biological regulation. Cross-linking immunoprecipitation (CLIP)-seq is a powerful tool for genome-wide interrogation of RNA-protein interactomes, but current CLIP methods are limited by challenging biochemical steps and fail to detect many classes of noncoding and nonhuman RNAs. Here we present FAST-iCLIP, an integrated pipeline with improved CLIP biochemistry and an automated informatic pipeline for comprehensive analysis across protein coding, noncoding, repetitive, retroviral, and nonhuman transcriptomes. FAST-iCLIP of Poly-C binding protein 2 (PCBP2) showed that PCBP2-bound CU-rich motifs in different topologies to recognize mRNAs and noncoding RNAs with distinct biological functions. FAST-iCLIP of PCBP2 in hepatitis C virus-infected cells enabled a joint analysis of the PCBP2 interactome with host and viral RNAs and their interplay. These results show that FAST-iCLIP can be used to rapidly discover and decipher mechanisms of RNA-protein recognition across the diversity of human and pathogen RNAs.
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Affiliation(s)
- Ryan A Flynn
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lance Martin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, USA
| | - Brian T Do
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Brian Zarnegar
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kun Qu
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA Department of Applied Physics, Stanford University, Stanford, California 94305, USA Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Peter Sarnow
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Howard Y Chang
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
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47
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Calo E, Flynn RA, Martin L, Spitale RC, Chang HY, Wysocka J. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature 2014; 518:249-53. [PMID: 25470060 DOI: 10.1038/nature13923] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 10/06/2014] [Indexed: 12/19/2022]
Abstract
DEAD-box RNA helicases are vital for the regulation of various aspects of the RNA life cycle, but the molecular underpinnings of their involvement, particularly in mammalian cells, remain poorly understood. Here we show that the DEAD-box RNA helicase DDX21 can sense the transcriptional status of both RNA polymerase (Pol) I and II to control multiple steps of ribosome biogenesis in human cells. We demonstrate that DDX21 widely associates with Pol I- and Pol II-transcribed genes and with diverse species of RNA, most prominently with non-coding RNAs involved in the formation of ribonucleoprotein complexes, including ribosomal RNA, small nucleolar RNAs (snoRNAs) and 7SK RNA. Although broad, these molecular interactions, both at the chromatin and RNA level, exhibit remarkable specificity for the regulation of ribosomal genes. In the nucleolus, DDX21 occupies the transcribed rDNA locus, directly contacts both rRNA and snoRNAs, and promotes rRNA transcription, processing and modification. In the nucleoplasm, DDX21 binds 7SK RNA and, as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, is recruited to the promoters of Pol II-transcribed genes encoding ribosomal proteins and snoRNAs. Promoter-bound DDX21 facilitates the release of the positive transcription elongation factor b (P-TEFb) from the 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes. Our results uncover the multifaceted role of DDX21 in multiple steps of ribosome biogenesis, and provide evidence implicating a mammalian RNA helicase in RNA modification and Pol II elongation control.
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Affiliation(s)
- Eliezer Calo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ryan A Flynn
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lance Martin
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Robert C Spitale
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Howard Y Chang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Joanna Wysocka
- 1] Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA [2] Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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48
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Batista PJ, Molinie B, Wang J, Qu K, Zhang J, Li L, Bouley DM, Lujan E, Haddad B, Daneshvar K, Carter AC, Flynn RA, Zhou C, Lim KS, Dedon P, Wernig M, Mullen AC, Xing Y, Giallourakis CC, Chang HY. m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 2014; 15:707-19. [PMID: 25456834 DOI: 10.1016/j.stem.2014.09.019] [Citation(s) in RCA: 871] [Impact Index Per Article: 87.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 08/14/2014] [Accepted: 09/30/2014] [Indexed: 12/21/2022]
Abstract
N6-methyl-adenosine (m(6)A) is the most abundant modification on messenger RNAs and is linked to human diseases, but its functions in mammalian development are poorly understood. Here we reveal the evolutionary conservation and function of m(6)A by mapping the m(6)A methylome in mouse and human embryonic stem cells. Thousands of messenger and long noncoding RNAs show conserved m(6)A modification, including transcripts encoding core pluripotency transcription factors. m(6)A is enriched over 3' untranslated regions at defined sequence motifs and marks unstable transcripts, including transcripts turned over upon differentiation. Genetic inactivation or depletion of mouse and human Mettl3, one of the m(6)A methylases, led to m(6)A erasure on select target genes, prolonged Nanog expression upon differentiation, and impaired ESC exit from self-renewal toward differentiation into several lineages in vitro and in vivo. Thus, m(6)A is a mark of transcriptome flexibility required for stem cells to differentiate to specific lineages.
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Affiliation(s)
- Pedro J Batista
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Benoit Molinie
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jinkai Wang
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kun Qu
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jiajing Zhang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lingjie Li
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Donna M Bouley
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ernesto Lujan
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bahareh Haddad
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kaveh Daneshvar
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ava C Carter
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ryan A Flynn
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chan Zhou
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kok-Seong Lim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alan C Mullen
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Cosmas C Giallourakis
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| | - Howard Y Chang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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49
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Spitale RC, Flynn RA, Torre EA, Kool ET, Chang HY. RNA structural analysis by evolving SHAPE chemistry. Wiley Interdiscip Rev RNA 2014; 5:867-81. [PMID: 25132067 DOI: 10.1002/wrna.1253] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/17/2014] [Accepted: 06/02/2014] [Indexed: 12/19/2022]
Abstract
RNA is central to the flow of biological information. From transcription to splicing, RNA localization, translation, and decay, RNA is intimately involved in regulating every step of the gene expression program, and is thus essential for health and understanding disease. RNA has the unique ability to base-pair with itself and other nucleic acids to form complex structures. Hence the information content in RNA is not simply its linear sequence of bases, but is also encoded in complex folding of RNA molecules. A general chemical functionality that all RNAs have is a 2'-hydroxyl group in the ribose ring, and the reactivity of the 2'-hydroxyl in RNA is gated by local nucleotide flexibility. In other words, the 2'-hydroxyl is reactive at single-stranded and conformationally flexible positions but is unreactive at nucleotides constrained by base-pairing. Recent efforts have been focused on developing reagents that modify RNA as a function of RNA 2' hydroxyl group reactivity. Such RNA structure probing techniques can be read out by primer extension in experiments termed RNA SHAPE (selective 2'- hydroxyl acylation and primer extension). Herein, we describe the efforts devoted to the design and utilization of SHAPE probes for characterizing RNA structure. We also describe current technological advances that are being applied to utilize SHAPE chemistry with deep sequencing to probe many RNAs in parallel. The merging of chemistry with genomics is sure to open the door to genome-wide exploration of RNA structure and function.
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Affiliation(s)
- Robert C Spitale
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
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50
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Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY. Landscape and variation of RNA secondary structure across the human transcriptome. Nature 2014; 505:706-9. [PMID: 24476892 PMCID: PMC3973747 DOI: 10.1038/nature12946] [Citation(s) in RCA: 389] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 12/16/2013] [Indexed: 02/01/2023]
Abstract
In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure. RNA structure influences practically every step in the gene expression program1. Yet the nature of most RNA structures or effects of sequence variation on structure are not known. Here we report the initial landscape and variation of RNA secondary structures (RSS) in a human family Trio, providing a comprehensive RSS map of human coding and noncoding RNAs. We identify unique RSS signatures that demarcate open reading frames, splicing junctions, and define authentic microRNA binding sites. Comparison of native deproteinized RNA isolated from cells versus refolded purified RNA suggests that the majority of the RSS information is encoded within RNA sequence. Over 1900 transcribed single nucleotide variants (~15% of all transcribed SNVs) alter local RNA structure. We discover simple sequence and spacing rules that determine the ability of point mutations to impact RSS. Selective depletion of RiboSNitches versus structurally synonymous variants at precise locations suggests selection for specific RNA shapes at thousands of sites, including 3’UTRs, binding sites of miRNAs and RNA binding proteins genome-wide. These results highlight the potentially broad contribution of RNA structure and its variation to gene regulation.
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Affiliation(s)
- Yue Wan
- 1] Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA [2] Stem Cell and Development, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672 [3]
| | - Kun Qu
- 1] Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA [2]
| | - Qiangfeng Cliff Zhang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ryan A Flynn
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ohad Manor
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovet 76100, Israel
| | - Zhengqing Ouyang
- 1] Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA [2] The Jackson Laboratory for Genomic Medicine, 263 Farmington Avenue, ASB Call Box 901 Farmington, Connecticut 06030, USA
| | - Jiajing Zhang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Robert C Spitale
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovet 76100, Israel
| | - Howard Y Chang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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