1
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Pollina EA, Gilliam DT, Landau AT, Lin C, Pajarillo N, Davis CP, Harmin DA, Yap EL, Vogel IR, Griffith EC, Nagy MA, Ling E, Duffy EE, Sabatini BL, Weitz CJ, Greenberg ME. A NPAS4-NuA4 complex couples synaptic activity to DNA repair. Nature 2023; 614:732-741. [PMID: 36792830 PMCID: PMC9946837 DOI: 10.1038/s41586-023-05711-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [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: 05/28/2021] [Accepted: 01/05/2023] [Indexed: 02/17/2023]
Abstract
Neuronal activity is crucial for adaptive circuit remodelling but poses an inherent risk to the stability of the genome across the long lifespan of postmitotic neurons1-5. Whether neurons have acquired specialized genome protection mechanisms that enable them to withstand decades of potentially damaging stimuli during periods of heightened activity is unknown. Here we identify an activity-dependent DNA repair mechanism in which a new form of the NuA4-TIP60 chromatin modifier assembles in activated neurons around the inducible, neuronal-specific transcription factor NPAS4. We purify this complex from the brain and demonstrate its functions in eliciting activity-dependent changes to neuronal transcriptomes and circuitry. By characterizing the landscape of activity-induced DNA double-strand breaks in the brain, we show that NPAS4-NuA4 binds to recurrently damaged regulatory elements and recruits additional DNA repair machinery to stimulate their repair. Gene regulatory elements bound by NPAS4-NuA4 are partially protected against age-dependent accumulation of somatic mutations. Impaired NPAS4-NuA4 signalling leads to a cascade of cellular defects, including dysregulated activity-dependent transcriptional responses, loss of control over neuronal inhibition and genome instability, which all culminate to reduce organismal lifespan. In addition, mutations in several components of the NuA4 complex are reported to lead to neurodevelopmental and autism spectrum disorders. Together, these findings identify a neuronal-specific complex that couples neuronal activity directly to genome preservation, the disruption of which may contribute to developmental disorders, neurodegeneration and ageing.
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Affiliation(s)
- Elizabeth A Pollina
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel T Gilliam
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Andrew T Landau
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Cindy Lin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Naomi Pajarillo
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - David A Harmin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ee-Lynn Yap
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ian R Vogel
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Eric C Griffith
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - M Aurel Nagy
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Emi Ling
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Erin E Duffy
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Bernardo L Sabatini
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Charles J Weitz
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
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2
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Duffy EE, Finander B, Choi G, Carter AC, Pritisanac I, Alam A, Luria V, Karger A, Phu W, Sherman MA, Assad EG, Pajarillo N, Khitun A, Crouch EE, Ganesh S, Chen J, Berger B, Sestan N, O'Donnell-Luria A, Huang EJ, Griffith EC, Forman-Kay JD, Moses AM, Kalish BT, Greenberg ME. Developmental dynamics of RNA translation in the human brain. Nat Neurosci 2022; 25:1353-1365. [PMID: 36171426 PMCID: PMC10198132 DOI: 10.1038/s41593-022-01164-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [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: 10/21/2021] [Accepted: 08/12/2022] [Indexed: 01/27/2023]
Abstract
The precise regulation of gene expression is fundamental to neurodevelopment, plasticity and cognitive function. Although several studies have profiled transcription in the developing human brain, there is a gap in understanding of accompanying translational regulation. In this study, we performed ribosome profiling on 73 human prenatal and adult cortex samples. We characterized the translational regulation of annotated open reading frames (ORFs) and identified thousands of previously unknown translation events, including small ORFs that give rise to human-specific and/or brain-specific microproteins, many of which we independently verified using proteomics. Ribosome profiling in stem-cell-derived human neuronal cultures corroborated these findings and revealed that several neuronal activity-induced non-coding RNAs encode previously undescribed microproteins. Physicochemical analysis of brain microproteins identified a class of proteins that contain arginine-glycine-glycine (RGG) repeats and, thus, may be regulators of RNA metabolism. This resource expands the known translational landscape of the human brain and illuminates previously unknown brain-specific protein products.
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Affiliation(s)
- Erin E Duffy
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
| | | | - GiHun Choi
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ava C Carter
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Iva Pritisanac
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Aqsa Alam
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Amir Karger
- IT-Research Computing, Harvard Medical School, Boston, MA, USA
| | - William Phu
- Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Maxwell A Sherman
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Elena G Assad
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Naomi Pajarillo
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Alexandra Khitun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Elizabeth E Crouch
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Sanika Ganesh
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Jin Chen
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Anne O'Donnell-Luria
- Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eric J Huang
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Pathology Service 113B, San Francisco Veterans Affairs Healthcare System, San Francisco, CA, USA
| | - Eric C Griffith
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Julie D Forman-Kay
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Alan M Moses
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Brian T Kalish
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
- Department of Paediatrics, Division of Neonatology, Hospital for Sick Children, Toronto, ON, Canada.
- Program in Neuroscience and Mental Health, SickKids Research Institute, Toronto, ON, Canada.
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3
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Kalish BT, Kim E, Finander B, Duffy EE, Kim H, Gilman CK, Yim YS, Tong L, Kaufman RJ, Griffith EC, Choi GB, Greenberg ME, Huh JR. Maternal immune activation in mice disrupts proteostasis in the fetal brain. Nat Neurosci 2021; 24:204-213. [PMID: 33361822 PMCID: PMC7854524 DOI: 10.1038/s41593-020-00762-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [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: 04/13/2020] [Accepted: 11/18/2020] [Indexed: 12/21/2022]
Abstract
Maternal infection and inflammation during pregnancy are associated with neurodevelopmental disorders in offspring, but little is understood about the molecular mechanisms underlying this epidemiologic phenomenon. Here, we leveraged single-cell RNA sequencing to profile transcriptional changes in the mouse fetal brain in response to maternal immune activation (MIA) and identified perturbations in cellular pathways associated with mRNA translation, ribosome biogenesis and stress signaling. We found that MIA activates the integrated stress response (ISR) in male, but not female, MIA offspring in an interleukin-17a-dependent manner, which reduced global mRNA translation and altered nascent proteome synthesis. Moreover, blockade of ISR activation prevented the behavioral abnormalities as well as increased cortical neural activity in MIA male offspring. Our data suggest that sex-specific activation of the ISR leads to maternal inflammation-associated neurodevelopmental disorders.
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Affiliation(s)
- Brian T Kalish
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
| | - Eunha Kim
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Benjamin Finander
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Erin E Duffy
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Hyunju Kim
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Casey K Gilman
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Yeong Shin Yim
- The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lilin Tong
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Randal J Kaufman
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Eric C Griffith
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Gloria B Choi
- The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael E Greenberg
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Jun R Huh
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
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4
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Canzio D, Nwakeze CL, Horta A, Rajkumar SM, Coffey EL, Duffy EE, Duffié R, Monahan K, O'Keeffe S, Simon MD, Lomvardas S, Maniatis T. Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice. Cell 2019; 177:639-653.e15. [PMID: 30955885 DOI: 10.1016/j.cell.2019.03.008] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 11/08/2018] [Accepted: 03/04/2019] [Indexed: 11/15/2022]
Abstract
Stochastic activation of clustered Protocadherin (Pcdh) α, β, and γ genes generates a cell-surface identity code in individual neurons that functions in neural circuit assembly. Here, we show that Pcdhα gene choice involves the activation of an antisense promoter located in the first exon of each Pcdhα alternate gene. Transcription of an antisense long noncoding RNA (lncRNA) from this antisense promoter extends through the sense promoter, leading to DNA demethylation of the CTCF binding sites proximal to each promoter. Demethylation-dependent CTCF binding to both promoters facilitates cohesin-mediated DNA looping with a distal enhancer (HS5-1), locking in the transcriptional state of the chosen Pcdhα gene. Uncoupling DNA demethylation from antisense transcription by Tet3 overexpression in mouse olfactory neurons promotes CTCF binding to all Pcdhα promoters, resulting in proximity-biased DNA looping of the HS5-1 enhancer. Thus, antisense transcription-mediated promoter demethylation functions as a mechanism for distance-independent enhancer/promoter DNA looping to ensure stochastic Pcdhα promoter choice.
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Affiliation(s)
- Daniele Canzio
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Chiamaka L Nwakeze
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Adan Horta
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Sandy M Rajkumar
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Eliot L Coffey
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Erin E Duffy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06516, USA
| | - Rachel Duffié
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Kevin Monahan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Sean O'Keeffe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06516, USA
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; New York Genome Center, New York, NY 10013, USA.
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5
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Duffy EE, Schofield JA, Simon MD. Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine. Wiley Interdiscip Rev RNA 2018; 10:e1513. [PMID: 30370679 DOI: 10.1002/wrna.1513] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022]
Abstract
Cellular RNA levels are the result of a juggling act between RNA transcription, processing, and degradation. By tuning one or more of these parameters, cells can rapidly alter the available pool of transcripts in response to stimuli. While RNA sequencing (RNA-seq) is a vital method to quantify RNA levels genome-wide, it is unable to capture the dynamics of different RNA populations at steady-state or distinguish between different mechanisms that induce changes to the steady-state (i.e., altered rate of transcription vs. degradation). The dynamics of different RNA populations can be studied by targeted incorporation of noncanonical nucleosides. 4-Thiouridine (s4 U) is a commonly used and versatile RNA metabolic label that allows the study of many properties of RNA metabolism from synthesis to degradation. Numerous experimental strategies have been developed that leverage the power of s4 U to label newly transcribed RNA in whole cells, followed by enrichment with activated disulfides or chemistry to induce C mutations at sites of s4 U during sequencing. This review presents existing methods to study RNA population dynamics genome-wide using s4 U metabolic labeling, as well as a discussion of considerations and challenges when designing s4 U metabolic labeling experiments. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Erin E Duffy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Jeremy A Schofield
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
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6
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Duffy EE, Canzio D, Maniatis T, Simon MD. Solid phase chemistry to covalently and reversibly capture thiolated RNA. Nucleic Acids Res 2018; 46:6996-7005. [PMID: 29986098 PMCID: PMC6101502 DOI: 10.1093/nar/gky556] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 02/23/2018] [Revised: 06/04/2018] [Accepted: 06/14/2018] [Indexed: 12/26/2022] Open
Abstract
Here, we describe an approach to enrich newly transcribed RNAs from primary mouse neurons using 4-thiouridine (s4U) metabolic labeling and solid phase chemistry. This one-step enrichment procedure captures s4U-RNA by using highly efficient methane thiosulfonate (MTS) chemistry in an immobilized format. Like solution-based methods, this solid-phase enrichment can distinguish mature RNAs (mRNA) with differential stability, and can be used to reveal transient RNAs such as enhancer RNAs (eRNAs) and primary microRNAs (pri-miRNAs) from short metabolic labeling. Most importantly, the efficiency of this solid-phase chemistry made possible the first large scale measurements of RNA polymerase II (RNAPII) elongation rates in mouse cortical neurons. Thus, our approach provides the means to study regulation of RNA metabolism in specific tissue contexts as a means to better understand gene expression in vivo.
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Affiliation(s)
- Erin E Duffy
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Daniele Canzio
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
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7
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Schofield JA, Duffy EE, Kiefer L, Sullivan MC, Simon MD. TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding. Nat Methods 2018; 15:221-225. [PMID: 29355846 PMCID: PMC5831505 DOI: 10.1038/nmeth.4582] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [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: 05/15/2017] [Accepted: 12/14/2017] [Indexed: 12/18/2022]
Abstract
RNA sequencing (RNA-seq) offers a snapshot of cellular RNA populations, but not temporal information about the sequenced RNA. Here we report TimeLapse-seq, which uses oxidative-nucleophilic-aromatic substitution to convert 4-thiouridine into cytidine analogs, yielding apparent U-to-C mutations that mark new transcripts upon sequencing. TimeLapse-seq is a single-molecule approach that is adaptable to many applications and reveals RNA dynamics and induced differential expression concealed in traditional RNA-seq.
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Affiliation(s)
- Jeremy A Schofield
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Erin E Duffy
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Lea Kiefer
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Meaghan C Sullivan
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut, USA
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8
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Li HB, Tong J, Zhu S, Batista PJ, Duffy EE, Zhao J, Bailis W, Cao G, Kroehling L, Chen Y, Wang G, Broughton JP, Chen YG, Kluger Y, Simon MD, Chang HY, Yin Z, Flavell RA. m 6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways. Nature 2017; 548:338-342. [PMID: 28792938 PMCID: PMC5729908 DOI: 10.1038/nature23450] [Citation(s) in RCA: 584] [Impact Index Per Article: 83.4] [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: 10/03/2016] [Accepted: 06/30/2017] [Indexed: 12/28/2022]
Abstract
N6 -methyladenosine (m6A) is the most common and abundant messenger RNA modification, modulated by ‘writers’, ‘erasers’ and ‘readers’ of this mark 1,2. In vitro data have shown that m6A influences all fundamental aspects of mRNA metabolism, mainly mRNA stability, to determine stem cell fates 3,4. However, its in vivo physiological function in mammals and adult mammalian cells is still unknown. Here we show that deletion of m6A ‘writer’ protein METTL3 in mouse T cells disrupts T cell homeostasis and differentiation. In a lymphopenic mouse adoptive transfer model, naive Mettl3 deficient T cells failed to undergo homeostatic expansion and remarkably remained in the naïve state up through 12 weeks, thereby preventing colitis. Consistent with these observations, the mRNAs of SOCS family genes encoding STAT- signaling inhibitory proteins, Socs1, Socs3 and Cish, were marked by m6A, exhibited slower mRNA decay and increased mRNAs and protein expression levels in Mettl3 deficient naïve T cells. This increased SOCS family activity consequently inhibited IL-7 mediated STAT5 activation and T cell homeostatic proliferation and differentiation. We also found that m6A plays important roles for inducible degradation of Socs mRNAs in response to IL-7 signaling in order to reprogram Naïve T cells for proliferation and differentiation. Our study elucidates for the first time the in vivo biological role of m6A modification in T cell mediated pathogenesis and reveals a novel mechanism of T cell homeostasis and signal-dependent induction of mRNA degradation.
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Affiliation(s)
- Hua-Bing Li
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Jiyu Tong
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,The First Affiliated Hospital, Biomedical Translational Research Institute and Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Shu Zhu
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Pedro J Batista
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Erin E Duffy
- Department of Molecular Biophysics &Biochemistry, Yale University, New Haven, Connecticut 06511, USA.,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Jun Zhao
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Will Bailis
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Guangchao Cao
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,The First Affiliated Hospital, Biomedical Translational Research Institute and Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Lina Kroehling
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Yuanyuan Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Institute of Surgical Research, Daping Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Geng Wang
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - James P Broughton
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Y Grace Chen
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Matthew D Simon
- Department of Molecular Biophysics &Biochemistry, Yale University, New Haven, Connecticut 06511, USA.,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Howard Y Chang
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Zhinan Yin
- The First Affiliated Hospital, Biomedical Translational Research Institute and Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789, USA
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9
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Abstract
Metabolic labeling of cellular RNA is a useful approach to study RNA biology. 4-Thiouridine (s4 U) is a convenient nucleoside for metabolic labeling because it is cell permeable and is incorporated into newly transcribed RNA, and the sulfur moiety provides a handle for biochemical purification. However, a critical step in the purification of s4 U-RNA is the efficiency of the chemistry used to enrich s4 U-RNA. Here, we present a protocol for s4 U-RNA enrichment that includes efficient and reversible covalent chemistry to biotinylate s4 U-RNA using the activated disulfide methane thiosulfonate conjugated to biotin (MTS-biotin), followed by enrichment on streptavidin beads. The efficiency of this chemistry reduces enrichment bias and requires less starting material, thereby expanding the utility of s4 U to study RNA biology. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Erin E Duffy
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut
| | - Matthew D Simon
- Chemical Biology Institute, Yale University, West Haven, Connecticut
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10
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Duffy EE, Rutenberg-Schoenberg M, Stark CD, Kitchen RR, Gerstein MB, Simon MD. Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry. Mol Cell 2015; 59:858-66. [PMID: 26340425 DOI: 10.1016/j.molcel.2015.07.023] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 06/11/2015] [Accepted: 07/20/2015] [Indexed: 12/21/2022]
Abstract
We describe a chemical method to label and purify 4-thiouridine (s(4)U)-containing RNA. We demonstrate that methanethiosulfonate (MTS) reagents form disulfide bonds with s(4)U more efficiently than the commonly used HPDP-biotin, leading to higher yields and less biased enrichment. This increase in efficiency allowed us to use s(4)U labeling to study global microRNA (miRNA) turnover in proliferating cultured human cells without perturbing global miRNA levels or the miRNA processing machinery. This improved chemistry will enhance methods that depend on tracking different populations of RNA, such as 4-thiouridine tagging to study tissue-specific transcription and dynamic transcriptome analysis (DTA) to study RNA turnover.
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Affiliation(s)
- Erin E Duffy
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Michael Rutenberg-Schoenberg
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Catherine D Stark
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Robert R Kitchen
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Mark B Gerstein
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA.
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Duffy EE, Penn DJ, Botton ML, Brockmann HJ, Loveland RE. Eye and clasper damage influence male mating tactics in the horseshoe crab, Limulus polyphemus. J ETHOL 2005. [DOI: 10.1007/s10164-005-0163-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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