1
|
Papadimitriou E, Thomaidou D. Post-transcriptional mechanisms controlling neurogenesis and direct neuronal reprogramming. Neural Regen Res 2024; 19:1929-1939. [PMID: 38227517 DOI: 10.4103/1673-5374.390976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/08/2023] [Indexed: 01/17/2024] Open
Abstract
Neurogenesis is a tightly regulated process in time and space both in the developing embryo and in adult neurogenic niches. A drastic change in the transcriptome and proteome of radial glial cells or neural stem cells towards the neuronal state is achieved due to sophisticated mechanisms of epigenetic, transcriptional, and post-transcriptional regulation. Understanding these neurogenic mechanisms is of major importance, not only for shedding light on very complex and crucial developmental processes, but also for the identification of putative reprogramming factors, that harbor hierarchically central regulatory roles in the course of neurogenesis and bare thus the capacity to drive direct reprogramming towards the neuronal fate. The major transcriptional programs that orchestrate the neurogenic process have been the focus of research for many years and key neurogenic transcription factors, as well as repressor complexes, have been identified and employed in direct reprogramming protocols to convert non-neuronal cells, into functional neurons. The post-transcriptional regulation of gene expression during nervous system development has emerged as another important and intricate regulatory layer, strongly contributing to the complexity of the mechanisms controlling neurogenesis and neuronal function. In particular, recent advances are highlighting the importance of specific RNA binding proteins that control major steps of mRNA life cycle during neurogenesis, such as alternative splicing, polyadenylation, stability, and translation. Apart from the RNA binding proteins, microRNAs, a class of small non-coding RNAs that block the translation of their target mRNAs, have also been shown to play crucial roles in all the stages of the neurogenic process, from neural stem/progenitor cell proliferation, neuronal differentiation and migration, to functional maturation. Here, we provide an overview of the most prominent post-transcriptional mechanisms mediated by RNA binding proteins and microRNAs during the neurogenic process, giving particular emphasis on the interplay of specific RNA binding proteins with neurogenic microRNAs. Taking under consideration that the molecular mechanisms of neurogenesis exert high similarity to the ones driving direct neuronal reprogramming, we also discuss the current advances in in vitro and in vivo direct neuronal reprogramming approaches that have employed microRNAs or RNA binding proteins as reprogramming factors, highlighting the so far known mechanisms of their reprogramming action.
Collapse
|
2
|
Moakley DF, Campbell M, Anglada-Girotto M, Feng H, Califano A, Au E, Zhang C. Reverse engineering neuron type-specific and type-orthogonal splicing-regulatory networks using single-cell transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.597128. [PMID: 38915499 PMCID: PMC11195221 DOI: 10.1101/2024.06.13.597128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Cell type-specific alternative splicing (AS) enables differential gene isoform expression between diverse neuron types with distinct identities and functions. Current studies linking individual RNA-binding proteins (RBPs) to AS in a few neuron types underscore the need for holistic modeling. Here, we use network reverse engineering to derive a map of the neuron type-specific AS regulatory landscape from 133 mouse neocortical cell types defined by single-cell transcriptomes. This approach reliably inferred the regulons of 350 RBPs and their cell type-specific activities. Our analysis revealed driving factors delineating neuronal identities, among which we validated Elavl2 as a key RBP for MGE-specific splicing in GABAergic interneurons using an in vitro ESC differentiation system. We also identified a module of exons and candidate regulators specific for long- and short-projection neurons across multiple neuronal classes. This study provides a resource for elucidating splicing regulatory programs that drive neuronal molecular diversity, including those that do not align with gene expression-based classifications.
Collapse
Affiliation(s)
- Daniel F Moakley
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Melissa Campbell
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Department of Neurosciences, University of California, San Diego, USA
| | - Miquel Anglada-Girotto
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Present address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Huijuan Feng
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Edmund Au
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
- Columbia Translational Neuroscience Initiative Scholar, New York, NY 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| |
Collapse
|
3
|
Patowary A, Zhang P, Jops C, Vuong CK, Ge X, Hou K, Kim M, Gong N, Margolis M, Vo D, Wang X, Liu C, Pasaniuc B, Li JJ, Gandal MJ, de la Torre-Ubieta L. Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. Science 2024; 384:eadh7688. [PMID: 38781356 DOI: 10.1126/science.adh7688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
RNA splicing is highly prevalent in the brain and has strong links to neuropsychiatric disorders; yet, the role of cell type-specific splicing and transcript-isoform diversity during human brain development has not been systematically investigated. In this work, we leveraged single-molecule long-read sequencing to deeply profile the full-length transcriptome of the germinal zone and cortical plate regions of the developing human neocortex at tissue and single-cell resolution. We identified 214,516 distinct isoforms, of which 72.6% were novel (not previously annotated in Gencode version 33), and uncovered a substantial contribution of transcript-isoform diversity-regulated by RNA binding proteins-in defining cellular identity in the developing neocortex. We leveraged this comprehensive isoform-centric gene annotation to reprioritize thousands of rare de novo risk variants and elucidate genetic risk mechanisms for neuropsychiatric disorders.
Collapse
Affiliation(s)
- Ashok Patowary
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Pan Zhang
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Connor Jops
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Celine K Vuong
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Xinzhou Ge
- Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kangcheng Hou
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Minsoo Kim
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Naihua Gong
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Margolis
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel Vo
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Institute for Precision Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jingyi Jessica Li
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Luis de la Torre-Ubieta
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
4
|
Ciampi L, Serrano L, Irimia M. Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States. Mol Syst Biol 2024; 20:296-310. [PMID: 38438733 PMCID: PMC10987577 DOI: 10.1038/s44320-024-00020-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 03/06/2024] Open
Abstract
Alternative Splicing (AS) programs serve as instructive signals of cell type specificity, particularly within the brain, which comprises dozens of molecularly and functionally distinct cell types. Among them, retinal photoreceptors stand out due to their unique transcriptome, making them a particularly well-suited system for studying how AS shapes cell type-specific molecular functions. Here, we use the Splicing Regulatory State (SRS) as a novel framework to discuss the splicing factors governing the unique AS pattern of photoreceptors, and how this pattern may aid in the specification of their highly specialized sensory cilia. In addition, we discuss how other sensory cells with ciliated structures, for which data is much scarcer, also rely on specific SRSs to implement a proteome specialized in the detection of sensory stimuli. By reviewing the general rules of cell type- and tissue-specific AS programs, firstly in the brain and subsequently in specialized sensory neurons, we propose a novel paradigm on how SRSs are established and how they can diversify. Finally, we illustrate how SRSs shape the outcome of mutations in splicing factors to produce cell type-specific phenotypes that can lead to various human diseases.
Collapse
Affiliation(s)
- Ludovica Ciampi
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Luis Serrano
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Manuel Irimia
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| |
Collapse
|
5
|
Hergenreder E, Minotti AP, Zorina Y, Oberst P, Zhao Z, Munguba H, Calder EL, Baggiolini A, Walsh RM, Liston C, Levitz J, Garippa R, Chen S, Ciceri G, Studer L. Combined small-molecule treatment accelerates maturation of human pluripotent stem cell-derived neurons. Nat Biotechnol 2024:10.1038/s41587-023-02031-z. [PMID: 38168993 DOI: 10.1038/s41587-023-02031-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/13/2023] [Indexed: 01/05/2024]
Abstract
The maturation of human pluripotent stem cell (hPSC)-derived neurons mimics the protracted timing of human brain development, extending over months to years for reaching adult-like function. Prolonged in vitro maturation presents a major challenge to stem cell-based applications in modeling and treating neurological disease. Therefore, we designed a high-content imaging assay based on morphological and functional readouts in hPSC-derived cortical neurons which identified multiple compounds that drive neuronal maturation including inhibitors of lysine-specific demethylase 1 and disruptor of telomerase-like 1 and activators of calcium-dependent transcription. A cocktail of four factors, GSK2879552, EPZ-5676, N-methyl-D-aspartate and Bay K 8644, collectively termed GENtoniK, triggered maturation across all parameters tested, including synaptic density, electrophysiology and transcriptomics. Maturation effects were further validated in cortical organoids, spinal motoneurons and non-neural lineages including melanocytes and pancreatic β-cells. The effects on maturation observed across a broad range of hPSC-derived cell types indicate that some of the mechanisms controlling the timing of human maturation might be shared across lineages.
Collapse
Affiliation(s)
- Emiliano Hergenreder
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
- Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
- Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Andrew P Minotti
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
- Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
- Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Yana Zorina
- Gene Editing and Screening Core Facility, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Polina Oberst
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
- Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Zeping Zhao
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Hermany Munguba
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
- Department of Psychiatry, Weill Cornell Medicine, New York, USA
| | - Elizabeth L Calder
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
- Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Arianna Baggiolini
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
- Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Ryan M Walsh
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
- Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Conor Liston
- Department of Psychiatry, Weill Cornell Medicine, New York, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Ralph Garippa
- Gene Editing and Screening Core Facility, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Gabriele Ciceri
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
- Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA.
- Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA.
| |
Collapse
|
6
|
Schweizer L, Krishnan R, Shimizu A, Metousis A, Kenny H, Mendoza R, Nordmann TM, Rauch S, Kelliher L, Heide J, Rosenberger FA, Bilecz A, Borrego SN, Strauss MT, Thielert M, Rodriguez E, Müller-Reif JB, Chen M, Yamada SD, Mund A, Lastra RR, Mann M, Lengyel E. Spatial proteo-transcriptomic profiling reveals the molecular landscape of borderline ovarian tumors and their invasive progression. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.13.23298409. [PMID: 38014221 PMCID: PMC10680885 DOI: 10.1101/2023.11.13.23298409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Serous borderline tumors (SBT) are epithelial neoplastic lesions of the ovaries that commonly have a good prognosis. In 10-15% of cases, however, SBT will recur as low-grade serous cancer (LGSC), which is deeply invasive and responds poorly to current standard chemotherapy1,2,3. While genetic alterations suggest a common origin, the transition from SBT to LGSC remains poorly understood4. Here, we integrate spatial proteomics5 with spatial transcriptomics to elucidate the evolution from SBT to LGSC and its corresponding metastasis at the molecular level in both the stroma and the tumor. We show that the transition of SBT to LGSC occurs in the epithelial compartment through an intermediary stage with micropapillary features (SBT-MP), which involves a gradual increase in MAPK signaling. A distinct subset of proteins and transcripts was associated with the transition to invasive tumor growth, including the neuronal splicing factor NOVA2, which was limited to expression in LGSC and its corresponding metastasis. An integrative pathway analysis exposed aberrant molecular signaling of tumor cells supported by alterations in angiogenesis and inflammation in the tumor microenvironment. Integration of spatial transcriptomics and proteomics followed by knockdown of the most altered genes or pharmaceutical inhibition of the most relevant targets confirmed their functional significance in regulating key features of invasiveness. Combining cell-type resolved spatial proteomics and transcriptomics allowed us to elucidate the sequence of tumorigenesis from SBT to LGSC. The approach presented here is a blueprint to systematically elucidate mechanisms of tumorigenesis and find novel treatment strategies.
Collapse
Affiliation(s)
- Lisa Schweizer
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Rahul Krishnan
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Aasa Shimizu
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Andreas Metousis
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Hilary Kenny
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Rachelle Mendoza
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Thierry M. Nordmann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sarah Rauch
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Lucy Kelliher
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Janna Heide
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Florian A. Rosenberger
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Agnes Bilecz
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Sanaa Nakad Borrego
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Maximillian T. Strauss
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marvin Thielert
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Edwin Rodriguez
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Johannes B. Müller-Reif
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Mengjie Chen
- Medicine/Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - S. Diane Yamada
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Andreas Mund
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ricardo R. Lastra
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Matthias Mann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| |
Collapse
|
7
|
Zhang H, Tian J, Ren S, Han B, Tian R, Zuo X, Liu H, Wang Z, Cui Y, Liu L, Guo H, Zhang F, Niu R. Comprehensively analysis of splicing factors to construct prognosis prediction classifier in prostate cancer. J Cell Mol Med 2023; 27:2684-2700. [PMID: 37559353 PMCID: PMC10494302 DOI: 10.1111/jcmm.17849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 08/11/2023] Open
Abstract
Splicing factors (SFs) are proteins that control the alternative splicing (AS) of RNAs, which have been recognized as new cancer hallmarks. Their dysregulation has been found to be involved in many biological processes of cancer, such as carcinogenesis, proliferation, metastasis and senescence. Dysregulation of SFs has been demonstrated to contribute to the progression of prostate cancer (PCa). However, a comprehensive analysis of the prognosis value of SFs in PCa is limited. In this work, we systematically analysed 393 SFs to deeply characterize the expression patterns, clinical relevance and biological functions of SFs in PCa. We identified 53 survival-related SFs that can stratify PCa into two de nove molecular subtypes with distinct mRNA expression and AS-event expression patterns and displayed significant differences in pathway activity and clinical outcomes. An SF-based classifier was established using LASSO-COX regression with six key SFs (BCAS1, LSM3, DHX16, NOVA2, RBM47 and SNRPN), which showed promising prognosis-prediction performance with a receiver operating characteristic (ROC) >0.700 in both the training and testing datasets, as well as in three external PCa cohorts (DKFZ, GSE70769 and GSE21035). CRISPR/CAS9 screening data and cell-level functional analysis suggested that LSM3 and DHX16 are essential factors for the proliferation and cell cycle progression in PCa cells. This study proposes that SFs and AS events are potential multidimensional biomarkers for the diagnosis, prognosis and treatment of PCa.
Collapse
Affiliation(s)
- He Zhang
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Jianfei Tian
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Sixin Ren
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Baoai Han
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Ruinan Tian
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Xiaoyan Zuo
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Hui Liu
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Zhiyong Wang
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Yanfen Cui
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Liming Liu
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Hui Guo
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Fei Zhang
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Ruifang Niu
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| |
Collapse
|
8
|
Verdile V, Riccioni V, Guerra M, Ferrante G, Sette C, Valle C, Ferri A, Paronetto MP. An impaired splicing program underlies differentiation defects in hSOD1 G93A neural progenitor cells. Cell Mol Life Sci 2023; 80:236. [PMID: 37524863 PMCID: PMC11072603 DOI: 10.1007/s00018-023-04893-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/02/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is an adult devastating neurodegenerative disease characterized by the loss of upper and lower motor neurons (MNs), resulting in progressive paralysis and death. Genetic animal models of ALS have highlighted dysregulation of synaptic structure and function as a pathogenic feature of ALS-onset and progression. Alternative pre-mRNA splicing (AS), which allows expansion of the coding power of genomes by generating multiple transcript isoforms from each gene, is widely associated with synapse formation and functional specification. Deciphering the link between aberrant splicing regulation and pathogenic features of ALS could pave the ground for novel therapeutic opportunities. Herein, we found that neural progenitor cells (NPCs) derived from the hSOD1G93A mouse model of ALS displayed increased proliferation and propensity to differentiate into neurons. In parallel, hSOD1G93A NPCs showed impaired splicing patterns in synaptic genes, which could contribute to the observed phenotype. Remarkably, master splicing regulators of the switch from stemness to neural differentiation are de-regulated in hSOD1G93A NPCs, thus impacting the differentiation program. Our data indicate that hSOD1G93A mutation impacts on neurogenesis by increasing the NPC pool in the developing mouse cortex and affecting their intrinsic properties, through the establishment of a specific splicing program.
Collapse
Affiliation(s)
- Veronica Verdile
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135, Rome, Italy
- Laboratory of Molecular and Cellular Neurobiology and of Neurochemistry, Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143, Rome, Italy
| | - Veronica Riccioni
- Laboratory of Molecular and Cellular Neurobiology and of Neurochemistry, Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143, Rome, Italy
| | - Marika Guerra
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gabriele Ferrante
- Laboratory of Molecular and Cellular Neurobiology and of Neurochemistry, Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143, Rome, Italy
| | - Claudio Sette
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, 00168, Rome, Italy
| | - Cristiana Valle
- Laboratory of Molecular and Cellular Neurobiology and of Neurochemistry, Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143, Rome, Italy
- Institute of Translational Pharmacology (IFT), Consiglio Nazionale delle Ricerche (CNR), 00133, Rome, Italy
| | - Alberto Ferri
- Laboratory of Molecular and Cellular Neurobiology and of Neurochemistry, Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143, Rome, Italy
- Institute of Translational Pharmacology (IFT), Consiglio Nazionale delle Ricerche (CNR), 00133, Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135, Rome, Italy.
- Laboratory of Molecular and Cellular Neurobiology and of Neurochemistry, Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143, Rome, Italy.
| |
Collapse
|
9
|
Ibrahim LA, Wamsley B, Alghamdi N, Yusuf N, Sevier E, Hairston A, Sherer M, Jaglin XH, Xu Q, Guo L, Khodadadi-Jamayran A, Favuzzi E, Yuan Y, Dimidschstein J, Darnell RB, Fishell G. Nova proteins direct synaptic integration of somatostatin interneurons through activity-dependent alternative splicing. eLife 2023; 12:e86842. [PMID: 37347149 PMCID: PMC10287156 DOI: 10.7554/elife.86842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/17/2023] [Indexed: 06/23/2023] Open
Abstract
Somatostatin interneurons are the earliest born population of cortical inhibitory cells. They are crucial to support normal brain development and function; however, the mechanisms underlying their integration into nascent cortical circuitry are not well understood. In this study, we begin by demonstrating that the maturation of somatostatin interneurons in mouse somatosensory cortex is activity dependent. We then investigated the relationship between activity, alternative splicing, and synapse formation within this population. Specifically, we discovered that the Nova family of RNA-binding proteins are activity-dependent and are essential for the maturation of somatostatin interneurons, as well as their afferent and efferent connectivity. Within this population, Nova2 preferentially mediates the alternative splicing of genes required for axonal formation and synaptic function independently from its effect on gene expression. Hence, our work demonstrates that the Nova family of proteins through alternative splicing are centrally involved in coupling developmental neuronal activity to cortical circuit formation.
Collapse
Affiliation(s)
- Leena Ali Ibrahim
- Department of Neurobiology, Harvard Medical SchoolBostonUnited States
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Stanley Center at the BroadCambridgeUnited States
| | - Brie Wamsley
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University School of MedicineNew YorkUnited States
| | - Norah Alghamdi
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Nusrath Yusuf
- Department of Neurobiology, Harvard Medical SchoolBostonUnited States
- Stanley Center at the BroadCambridgeUnited States
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University School of MedicineNew YorkUnited States
| | - Elaine Sevier
- Department of Neurobiology, Harvard Medical SchoolBostonUnited States
- Stanley Center at the BroadCambridgeUnited States
| | - Ariel Hairston
- Department of Neurobiology, Harvard Medical SchoolBostonUnited States
| | - Mia Sherer
- Department of Neurobiology, Harvard Medical SchoolBostonUnited States
- Stanley Center at the BroadCambridgeUnited States
| | - Xavier Hubert Jaglin
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University School of MedicineNew YorkUnited States
| | - Qing Xu
- Center for Genomics & Systems Biology, New York UniversityAbu DhabiUnited Arab Emirates
| | - Lihua Guo
- Center for Genomics & Systems Biology, New York UniversityAbu DhabiUnited Arab Emirates
| | - Alireza Khodadadi-Jamayran
- Genome Technology Center, Applied Bioinformatics Laboratories, NYU Langone Medical CenterNew YorkUnited States
| | - Emilia Favuzzi
- Department of Neurobiology, Harvard Medical SchoolBostonUnited States
- Stanley Center at the BroadCambridgeUnited States
| | - Yuan Yuan
- Laboratory of Molecular Neuro-Oncology, The Rockefeller UniversityNew YorkUnited States
| | | | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, The Rockefeller UniversityNew YorkUnited States
| | - Gordon Fishell
- Department of Neurobiology, Harvard Medical SchoolBostonUnited States
- Stanley Center at the BroadCambridgeUnited States
| |
Collapse
|
10
|
Rodrigues DC, Mufteev M, Yuki KE, Narula A, Wei W, Piekna A, Liu J, Pasceri P, Rissland OS, Wilson MD, Ellis J. Buffering of transcription rate by mRNA half-life is a conserved feature of Rett syndrome models. Nat Commun 2023; 14:1896. [PMID: 37019888 PMCID: PMC10076348 DOI: 10.1038/s41467-023-37339-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/13/2023] [Indexed: 04/07/2023] Open
Abstract
Transcriptional changes in Rett syndrome (RTT) are assumed to directly correlate with steady-state mRNA levels, but limited evidence in mice suggests that changes in transcription can be compensated by post-transcriptional regulation. We measure transcription rate and mRNA half-life changes in RTT patient neurons using RATEseq, and re-interpret nuclear and whole-cell RNAseq from Mecp2 mice. Genes are dysregulated by changing transcription rate or half-life and are buffered when both change. We utilized classifier models to predict the direction of transcription rate changes and find that combined frequencies of three dinucleotides are better predictors than CA and CG. MicroRNA and RNA-binding Protein (RBP) motifs are enriched in 3'UTRs of genes with half-life changes. Nuclear RBP motifs are enriched on buffered genes with increased transcription rate. We identify post-transcriptional mechanisms in humans and mice that alter half-life or buffer transcription rate changes when a transcriptional modulator gene is mutated in a neurodevelopmental disorder.
Collapse
Affiliation(s)
- Deivid C Rodrigues
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Marat Mufteev
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Kyoko E Yuki
- Genetics & Genome Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Ashrut Narula
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Molecular Medicine, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Wei Wei
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Alina Piekna
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Jiajie Liu
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Peter Pasceri
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Olivia S Rissland
- Molecular Medicine, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- RNA Bioscience Initiative and Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Genetics & Genome Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - James Ellis
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| |
Collapse
|
11
|
Tajima Y, Ito K, Yuan Y, Frank MO, Saito Y, Darnell RB. NOVA1 acts on Impact to regulate hypothalamic function and translation in inhibitory neurons. Cell Rep 2023; 42:112050. [PMID: 36716149 PMCID: PMC10382602 DOI: 10.1016/j.celrep.2023.112050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/12/2022] [Accepted: 01/15/2023] [Indexed: 01/30/2023] Open
Abstract
We describe a patient haploinsufficient for the neuronal RNA binding protein NOVA1 who developed a behavioral motor hyperactivity disorder, suggesting a role of NOVA1 in postnatal motor inhibition. To investigate Nova1's action in adult Gad2+ inhibitory neurons, we generated a conditional Nova1-null mouse (Nova1-cKOGad2-cre). Strikingly, the phenotypes of these mice show many similarities to the NOVA1 haploinsufficient patient and identify a function of Nova1 in the hypothalamus. Molecularly, Nova1 loss in Gad2-positive neurons alters downstream expression of Impact mRNA, along with a subset of RNAs encoding electron transport chain-related factors and ribosomal proteins. NOVA1 stabilizes Impact mRNA by binding its 3' UTR, antagonizing the actions of miR-138 and miR-124. Together, these studies demonstrate actions of NOVA1 in adult hypothalamic neurons, mechanisms by which it functions in translation and metabolism, including through direct binding to Impact mRNA, and illuminate its role in human neurologic disease.
Collapse
Affiliation(s)
- Yoko Tajima
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Keiichi Ito
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Yuan Yuan
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Mayu O Frank
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Yuhki Saito
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
12
|
Traunmüller L, Schulz J, Ortiz R, Feng H, Furlanis E, Gomez AM, Schreiner D, Bischofberger J, Zhang C, Scheiffele P. A cell-type-specific alternative splicing regulator shapes synapse properties in a trans-synaptic manner. Cell Rep 2023; 42:112173. [PMID: 36862556 PMCID: PMC10066595 DOI: 10.1016/j.celrep.2023.112173] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/07/2022] [Accepted: 02/12/2023] [Indexed: 03/03/2023] Open
Abstract
The specification of synaptic properties is fundamental for the function of neuronal circuits. "Terminal selector" transcription factors coordinate terminal gene batteries that specify cell-type-specific properties. Moreover, pan-neuronal splicing regulators have been implicated in directing neuronal differentiation. However, the cellular logic of how splicing regulators instruct specific synaptic properties remains poorly understood. Here, we combine genome-wide mapping of mRNA targets and cell-type-specific loss-of-function studies to uncover the contribution of the RNA-binding protein SLM2 to hippocampal synapse specification. Focusing on pyramidal cells and somatostatin (SST)-positive GABAergic interneurons, we find that SLM2 preferentially binds and regulates alternative splicing of transcripts encoding synaptic proteins. In the absence of SLM2, neuronal populations exhibit normal intrinsic properties, but there are non-cell-autonomous synaptic phenotypes and associated defects in a hippocampus-dependent memory task. Thus, alternative splicing provides a critical layer of gene regulation that instructs specification of neuronal connectivity in a trans-synaptic manner.
Collapse
Affiliation(s)
| | - Jan Schulz
- Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
| | - Raul Ortiz
- Biozentrum of the University of Basel, 4056 Basel, Switzerland
| | - Huijuan Feng
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | | | - Andrea M Gomez
- Biozentrum of the University of Basel, 4056 Basel, Switzerland
| | | | | | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | | |
Collapse
|
13
|
MicroRNA-377: A therapeutic and diagnostic tumor marker. Int J Biol Macromol 2023; 226:1226-1235. [PMID: 36442575 DOI: 10.1016/j.ijbiomac.2022.11.236] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/15/2022] [Accepted: 11/18/2022] [Indexed: 11/26/2022]
Abstract
Cancer is considered as one of the main causes of human deaths globally. Despite the recent progresses in therapeutic modalities, there is still a high rate of mortality among cancer patients. Late diagnosis in advanced tumor stages is one of the main reasons for treatment failure in cancer patients. Therefore, it is required to suggest the novel strategies for the early tumor detection. MicroRNAs (miRNAs) have critical roles in neoplastic transformation by regulation of cell proliferation, migration, and apoptosis. They are always considered as non-invasive markers due to their high stability in body fluids. Since, all of the miRNAs have tissue-specific functions in different tumors as tumor suppressor or oncogene; it is required to investigate the molecular mechanisms of every miRNA in different tumors to introduce that as a suitable non-invasive diagnostic marker in cancer patients. For the first time in the present review, we discussed the role of miR-377 during tumor progression. It has been reported that miR-377 mainly functions as a tumor suppressor through the regulation of signaling pathways and transcription factors. This review is an important step toward introducing the miR-377 as a novel diagnostic marker as well as a therapeutic target in cancer patients.
Collapse
|
14
|
Fisher E, Feng J. RNA splicing regulators play critical roles in neurogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1728. [PMID: 35388651 DOI: 10.1002/wrna.1728] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Alternative RNA splicing increases transcript diversity in different cell types and under varying conditions. It is executed with the help of RNA splicing regulators (RSRs), which are operationally defined as RNA-binding proteins (RBPs) that regulate alternative splicing, but not directly catalyzing the chemical reactions of splicing. By systematically searching for RBPs and manually identifying those that regulate splicing, we curated 305 RSRs in the human genome. Surprisingly, most of the RSRs are involved in neurogenesis. Among these RSRs, we focus on nine families (PTBP, NOVA, RBFOX, ELAVL, CELF, DBHS, MSI, PCBP, and MBNL) that play essential roles in the neurogenic pathway. A better understanding of their functions will provide novel insights into the role of splicing in brain development, health, and disease. This comprehensive review serves as a stepping-stone to explore the diverse and complex set of RSRs as fundamental regulators of neural development. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Regulation/Alternative Splicing.
Collapse
Affiliation(s)
- Emily Fisher
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
| | - Jian Feng
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
| |
Collapse
|
15
|
Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R. Spatial profiling of chromatin accessibility in mouse and human tissues. Nature 2022; 609:375-383. [PMID: 35978191 PMCID: PMC9452302 DOI: 10.1038/s41586-022-05094-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/08/2022] [Indexed: 12/12/2022]
Abstract
Cellular function in tissue is dependent on the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context1. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping2-5, but the ability to capture spatial epigenetic information of tissue at the cellular level and genome scale is lacking. Here we describe a method for spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing (spatial-ATAC-seq) by combining in situ Tn5 transposition chemistry6 and microfluidic deterministic barcoding5. Profiling mouse embryos using spatial-ATAC-seq delineated tissue-region-specific epigenetic landscapes and identified gene regulators involved in the development of the central nervous system. Mapping the accessible genome in the mouse and human brain revealed the intricate arealization of brain regions. Applying spatial-ATAC-seq to tonsil tissue resolved the spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology progresses spatial biology by enabling spatially resolved chromatin accessibility profiling to improve our understanding of cell identity, cell state and cell fate decision in relation to epigenetic underpinnings in development and disease.
Collapse
Affiliation(s)
- Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Marek Bartosovic
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sai Ma
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Di Zhang
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Petra Kukanja
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yang Xiao
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Yang Liu
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Xiaoyu Qin
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Gorazd B Rosoklija
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Macedonian Academy of Sciences & Arts, Skopje, Republic of Macedonia
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Macedonian Academy of Sciences & Arts, Skopje, Republic of Macedonia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J John Mann
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Department of Radiology, Columbia University, New York, NY, USA
| | - Mina L Xu
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Joseph E Craft
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Maura Boldrini
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden.
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA.
| |
Collapse
|
16
|
Scala M, Drouot N, MacLennan SC, Wessels MW, Krygier M, Pavinato L, Telegrafi A, de Man SA, van Slegtenhorst M, Iacomino M, Madia F, Scudieri P, Uva P, Giacomini T, Nobile G, Mancardi MM, Balagura G, Galloni GB, Verrotti A, Umair M, Khan A, Liebelt J, Schmidts M, Langer T, Brusco A, Lipska-Ziętkiewicz BS, Saris JJ, Charlet-Berguerand N, Zara F, Striano P, Piton A. De novo truncating NOVA2 variants affect alternative splicing and lead to heterogeneous neurodevelopmental phenotypes. Hum Mutat 2022; 43:1299-1313. [PMID: 35607920 PMCID: PMC9543825 DOI: 10.1002/humu.24414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 05/02/2022] [Accepted: 05/22/2022] [Indexed: 11/10/2022]
Abstract
Alternative splicing (AS) is crucial for cell-type specific gene transcription and plays a critical role in neuronal differentiation and synaptic plasticity. De novo frameshift variants in NOVA2, encoding a neuron-specific key splicing factor, have been recently associated with a new neurodevelopmental disorder (NDD) with hypotonia, neurological features, and brain abnormalities. We investigated eight unrelated individuals by exome sequencing (ES) and identified seven novel pathogenic NOVA2 variants, including two with a novel localization at the KH1 and KH3 domains. In addition to a severe NDD phenotype, novel clinical features included psychomotor regression, attention deficit-hyperactivity disorder (ADHD), dyspraxia, and urogenital and endocrinological manifestations. To test the effect of the variants on splicing regulation, we transfected HeLa cells with wildtype and mutant NOVA2 cDNA. The novel variants NM_002516.4: c.754_756delCTGinsTT p.(Leu252Phefs*144) and c.1329dup p.(Lys444Glnfs*82) all negatively affected AS events. The distal p.(Lys444Glnfs*82) variant, causing a partial removal of the KH3 domain, had a milder functional effect leading to an intermediate phenotype. Our findings expand the molecular and phenotypic spectrum of NOVA2-related NDD, supporting the pathogenic role of AS disruption by truncating variants and suggesting that this is a heterogeneous condition with variable clinical course. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Nathalie Drouot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, 67400, France.,Université de Strasbourg, Illkirch, 67400, France
| | - Suzanna C MacLennan
- Department of Paediatric Neurology, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Marja W Wessels
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Magdalena Krygier
- Department of Developmental Neurology, Medical University of Gdańsk, ul. Dębinki 7 80-952, Gdańsk, Poland
| | - Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy.,Center for Molecular Medicine Cologne, Institute of Human Genetics, University of Cologne, 50931, Cologne, Germany
| | - Aida Telegrafi
- Clinical Genomics Program, GeneDx, Gaithersburg, MD, USA
| | - Stella A de Man
- Department of Pediatrics, Amphia Hospital, Breda, The Netherlands
| | | | - Michele Iacomino
- Unit of Medical Genetics, IRCCS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Francesca Madia
- Unit of Medical Genetics, IRCCS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Paolo Scudieri
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Unit of Medical Genetics, IRCCS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Paolo Uva
- Clinical Bioinformatics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Thea Giacomini
- Unit of Child Neuropsychiatry, IRCCS Istituto Giannina Gaslini, Genoa, Italy, DINOGMI, University of Genoa, Genoa, Italy
| | - Giulia Nobile
- Unit of Child Neuropsychiatry, IRCCS Istituto Giannina Gaslini, Genoa, Italy, DINOGMI, University of Genoa, Genoa, Italy
| | - Maria Margherita Mancardi
- Unit of Child Neuropsychiatry, IRCCS Istituto Giannina Gaslini, Genoa, Italy, DINOGMI, University of Genoa, Genoa, Italy
| | - Ganna Balagura
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Giovanni Battista Galloni
- Struttura Complessa Neuropsichiatria Infantile Sud, Azienda Sanitaria Locale Città di Torino, Torino, Italy
| | | | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Amjad Khan
- Faculty of Biological Science, Department of Zoology, University of Lakki Marwat, Lakki Marwat, Pakistan
| | - Jan Liebelt
- South Australian Clinical Genetics Service, Women's and Children's Hospital, Adelaide, SA, Australia
| | - Miriam Schmidts
- Department of General Pediatrics and Adolescent Medicine, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thorsten Langer
- Department of Neuropediatrics and Muscle Disorders, Center for Pediatrics, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy.,Unit of Medical Genetics, "Città della Salute e della Scienza" University Hospital, 10126, Turin, Italy
| | - Beata S Lipska-Ziętkiewicz
- Clinical Genetics Unit, Department of Biology and Medical Genetics, Medical University of Gdańsk, Gdańsk, Poland.,27Centre for Rare Diseases, Medical University of Gdańsk, Gdańsk, Poland
| | - Jasper J Saris
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Nicolas Charlet-Berguerand
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, 67400, France.,Université de Strasbourg, Illkirch, 67400, France
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Unit of Medical Genetics, IRCCS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Amélie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, 67400, France.,Université de Strasbourg, Illkirch, 67400, France.,Laboratory of Genetic Diagnostic, Hôpitaux Universitaires de Strasbourg, Strasbourg, 67000, France.,Institut Universitaire de France, Paris, Île-de-France, France
| |
Collapse
|
17
|
Hauser D, Behr K, Konno K, Schreiner D, Schmidt A, Watanabe M, Bischofberger J, Scheiffele P. Targeted proteoform mapping uncovers specific Neurexin-3 variants required for dendritic inhibition. Neuron 2022; 110:2094-2109.e10. [PMID: 35550065 PMCID: PMC9275415 DOI: 10.1016/j.neuron.2022.04.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 02/05/2022] [Accepted: 04/15/2022] [Indexed: 12/21/2022]
Abstract
The diversification of cell adhesion molecules by alternative splicing is proposed to underlie molecular codes for neuronal wiring. Transcriptomic approaches mapped detailed cell-type-specific mRNA splicing programs. However, it has been hard to probe the synapse-specific localization and function of the resulting protein splice isoforms, or “proteoforms,” in vivo. We here apply a proteoform-centric workflow in mice to test the synapse-specific functions of the splice isoforms of the synaptic adhesion molecule Neurexin-3 (NRXN3). We uncover a major proteoform, NRXN3 AS5, that is highly expressed in GABAergic interneurons and at dendrite-targeting GABAergic terminals. NRXN3 AS5 abundance significantly diverges from Nrxn3 mRNA distribution and is gated by translation-repressive elements. Nrxn3 AS5 isoform deletion results in a selective impairment of dendrite-targeting interneuron synapses in the dentate gyrus without affecting somatic inhibition or glutamatergic perforant-path synapses. This work establishes cell- and synapse-specific functions of a specific neurexin proteoform and highlights the importance of alternative splicing regulation for synapse specification. Translational regulation guides alternative Neurexin proteoform expression NRXN3 AS5 proteoforms are concentrated at dendrite-targeting interneuron synapses A proteome-centric workflow uncovers NRXN3 AS5 interactors in vivo Loss of NRXN3 AS5 leads to selective impairments in dendritic inhibition
Collapse
Affiliation(s)
- David Hauser
- Biozentrum of the University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Katharina Behr
- Department of Biomedicine, University of Basel, Pestalozzistrasse 20, 4056 Basel, Switzerland
| | - Kohtarou Konno
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Dietmar Schreiner
- Biozentrum of the University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Alexander Schmidt
- Biozentrum of the University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Josef Bischofberger
- Department of Biomedicine, University of Basel, Pestalozzistrasse 20, 4056 Basel, Switzerland
| | - Peter Scheiffele
- Biozentrum of the University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
| |
Collapse
|
18
|
Saito Y, Hawley BR, Puno MR, Sarathy SN, Lima CD, Jaffrey SR, Darnell RB, Keeney S, Jain D. YTHDC2 control of gametogenesis requires helicase activity but not m 6A binding. Genes Dev 2022; 36:180-194. [PMID: 35058317 PMCID: PMC8887132 DOI: 10.1101/gad.349190.121] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/05/2022] [Indexed: 11/30/2022]
Abstract
Mechanisms regulating meiotic progression in mammals are poorly understood. The N6-methyladenosine (m6A) reader and 3' → 5' RNA helicase YTHDC2 switches cells from mitotic to meiotic gene expression programs and is essential for meiotic entry, but how this critical cell fate change is accomplished is unknown. Here, we provide insight into its mechanism and implicate YTHDC2 in having a broad role in gene regulation during multiple meiotic stages. Unexpectedly, mutation of the m6A-binding pocket of YTHDC2 had no detectable effect on gametogenesis and mouse fertility, suggesting that YTHDC2 function is m6A-independent. Supporting this conclusion, CLIP data defined YTHDC2-binding sites on mRNA as U-rich and UG-rich motif-containing regions within 3' UTRs and coding sequences, distinct from the sites that contain m6A during spermatogenesis. Complete loss of YTHDC2 during meiotic entry did not substantially alter translation of its mRNA binding targets in whole-testis ribosome profiling assays but did modestly affect their steady-state levels. Mutation of the ATPase motif in the helicase domain of YTHDC2 did not affect meiotic entry, but it blocked meiotic prophase I progression, causing sterility. Our findings inform a model in which YTHDC2 binds transcripts independent of m6A status and regulates gene expression during multiple stages of meiosis by distinct mechanisms.
Collapse
Affiliation(s)
- Yuhki Saito
- Laboratory of Molecular Neuro-oncology, Howard Hughes Medical Institute, Rockefeller University, New York, New York 10065, USA
| | - Ben R Hawley
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - M Rhyan Puno
- Structural Biology Program, Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Shreya N Sarathy
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Christopher D Lima
- Structural Biology Program, Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology, Howard Hughes Medical Institute, Rockefeller University, New York, New York 10065, USA
| | - Scott Keeney
- Molecular Biology Program, Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Devanshi Jain
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey 08854, USA
| |
Collapse
|
19
|
Wright DJ, Hall NAL, Irish N, Man AL, Glynn W, Mould A, Angeles ADL, Angiolini E, Swarbreck D, Gharbi K, Tunbridge EM, Haerty W. Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes. BMC Genomics 2022; 23:42. [PMID: 35012468 PMCID: PMC8744310 DOI: 10.1186/s12864-021-08261-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/15/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Alternative splicing is a key mechanism underlying cellular differentiation and a driver of complexity in mammalian neuronal tissues. However, understanding of which isoforms are differentially used or expressed and how this affects cellular differentiation remains unclear. Long read sequencing allows full-length transcript recovery and quantification, enabling transcript-level analysis of alternative splicing processes and how these change with cell state. Here, we utilise Oxford Nanopore Technologies sequencing to produce a custom annotation of a well-studied human neuroblastoma cell line SH-SY5Y, and to characterise isoform expression and usage across differentiation. RESULTS We identify many previously unannotated features, including a novel transcript of the voltage-gated calcium channel subunit gene, CACNA2D2. We show differential expression and usage of transcripts during differentiation identifying candidates for future research into state change regulation. CONCLUSIONS Our work highlights the potential of long read sequencing to uncover previously unknown transcript diversity and mechanisms influencing alternative splicing.
Collapse
Affiliation(s)
- David J Wright
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Nicola A L Hall
- Department of Psychiatry, Medical Sciences Division, University of Oxford, Oxfordshire, OX3 3JX, UK
- Oxford Health, NHS Foundation Trust, Oxford, Oxfordshire, OX3 7JX, UK
| | - Naomi Irish
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Angela L Man
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Will Glynn
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Arne Mould
- Department of Psychiatry, Medical Sciences Division, University of Oxford, Oxfordshire, OX3 3JX, UK
- Oxford Health, NHS Foundation Trust, Oxford, Oxfordshire, OX3 7JX, UK
| | - Alejandro De Los Angeles
- Department of Psychiatry, Medical Sciences Division, University of Oxford, Oxfordshire, OX3 3JX, UK
- Oxford Health, NHS Foundation Trust, Oxford, Oxfordshire, OX3 7JX, UK
| | - Emily Angiolini
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Karim Gharbi
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Elizabeth M Tunbridge
- Department of Psychiatry, Medical Sciences Division, University of Oxford, Oxfordshire, OX3 3JX, UK
- Oxford Health, NHS Foundation Trust, Oxford, Oxfordshire, OX3 7JX, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK.
| |
Collapse
|
20
|
Xu SJ, Lombroso SI, Fischer DK, Carpenter MD, Marchione DM, Hamilton PJ, Lim CJ, Neve RL, Garcia BA, Wimmer ME, Pierce RC, Heller EA. Chromatin-mediated alternative splicing regulates cocaine-reward behavior. Neuron 2021; 109:2943-2966.e8. [PMID: 34480866 PMCID: PMC8454057 DOI: 10.1016/j.neuron.2021.08.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/14/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022]
Abstract
Neuronal alternative splicing is a key gene regulatory mechanism in the brain. However, the spliceosome machinery is insufficient to fully specify splicing complexity. In considering the role of the epigenome in activity-dependent alternative splicing, we and others find the histone modification H3K36me3 to be a putative splicing regulator. In this study, we found that mouse cocaine self-administration caused widespread differential alternative splicing, concomitant with the enrichment of H3K36me3 at differentially spliced junctions. Importantly, only targeted epigenetic editing can distinguish between a direct role of H3K36me3 in splicing and an indirect role via regulation of splice factor expression elsewhere on the genome. We targeted Srsf11, which was both alternatively spliced and H3K36me3 enriched in the brain following cocaine self-administration. Epigenetic editing of H3K36me3 at Srsf11 was sufficient to drive its alternative splicing and enhanced cocaine self-administration, establishing the direct causal relevance of H3K36me3 to alternative splicing of Srsf11 and to reward behavior.
Collapse
Affiliation(s)
- Song-Jun Xu
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sonia I Lombroso
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Delaney K Fischer
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marco D Carpenter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dylan M Marchione
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter J Hamilton
- Department of Brain and Cognitive Sciences, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Carissa J Lim
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rachel L Neve
- Gene Delivery Technology Core, Massachusetts General Hospital, Cambridge, MA 02139, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mathieu E Wimmer
- Department of Psychology, Temple University, Philadelphia, PA 19121, USA
| | - R Christopher Pierce
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Elizabeth A Heller
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA,19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
21
|
Transcriptome programs involved in the development and structure of the cerebellum. Cell Mol Life Sci 2021; 78:6431-6451. [PMID: 34406416 PMCID: PMC8558292 DOI: 10.1007/s00018-021-03911-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/02/2021] [Indexed: 12/23/2022]
Abstract
In the past two decades, mounting evidence has modified the classical view of the cerebellum as a brain region specifically involved in the modulation of motor functions. Indeed, clinical studies and engineered mouse models have highlighted cerebellar circuits implicated in cognitive functions and behavior. Furthermore, it is now clear that insults occurring in specific time windows of cerebellar development can affect cognitive performance later in life and are associated with neurological syndromes, such as Autism Spectrum Disorder. Despite its almost homogenous cytoarchitecture, how cerebellar circuits form and function is not completely elucidated yet. Notably, the apparently simple neuronal organization of the cerebellum, in which Purkinje cells represent the only output, hides an elevated functional diversity even within the same neuronal population. Such complexity is the result of the integration of intrinsic morphogenetic programs and extracellular cues from the surrounding environment, which impact on the regulation of the transcriptome of cerebellar neurons. In this review, we briefly summarize key features of the development and structure of the cerebellum before focusing on the pathways involved in the acquisition of the cerebellar neuron identity. We focus on gene expression and mRNA processing programs, including mRNA methylation, trafficking and splicing, that are set in motion during cerebellar development and participate to its physiology. These programs are likely to add new layers of complexity and versatility that are fundamental for the adaptability of cerebellar neurons.
Collapse
|
22
|
Complexity and graded regulation of neuronal cell-type-specific alternative splicing revealed by single-cell RNA sequencing. Proc Natl Acad Sci U S A 2021; 118:2013056118. [PMID: 33674385 DOI: 10.1073/pnas.2013056118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The enormous cellular diversity in the mammalian brain, which is highly prototypical and organized in a hierarchical manner, is dictated by cell-type-specific gene-regulatory programs at the molecular level. Although prevalent in the brain, the contribution of alternative splicing (AS) to the molecular diversity across neuronal cell types is just starting to emerge. Here, we systematically investigated AS regulation across over 100 transcriptomically defined neuronal types of the adult mouse cortex using deep single-cell RNA-sequencing data. We found distinct splicing programs between glutamatergic and GABAergic neurons and between subclasses within each neuronal class. These programs consist of overlapping sets of alternative exons showing differential splicing at multiple hierarchical levels. Using an integrative approach, our analysis suggests that RNA-binding proteins (RBPs) Celf1/2, Mbnl2, and Khdrbs3 are preferentially expressed and more active in glutamatergic neurons, while Elavl2 and Qk are preferentially expressed and more active in GABAergic neurons. Importantly, these and additional RBPs also contribute to differential splicing between neuronal subclasses at multiple hierarchical levels, and some RBPs contribute to splicing dynamics that do not conform to the hierarchical structure defined by the transcriptional profiles. Thus, our results suggest graded regulation of AS across neuronal cell types, which may provide a molecular mechanism to specify neuronal identity and function that are orthogonal to established classifications based on transcriptional regulation.
Collapse
|
23
|
Abstract
Autism is a common and complex neurologic disorder whose scientific underpinnings have begun to be established in the past decade. The essence of this breakthrough has been a focus on families, where genetic analyses are strongest, versus large-scale, case-control studies. Autism genetics has progressed in parallel with technology, from analyses of copy number variation to whole-exome sequencing (WES) and whole-genome sequencing (WGS). Gene mutations causing complete loss of function account for perhaps one-third of cases, largely detected through WES. This limitation has increased interest in understanding the regulatory variants of genes that contribute in more subtle ways to the disorder. Strategies combining biochemical analysis of gene regulation, WGS analysis of the noncoding genome, and machine learning have begun to succeed. The emerging picture is that careful control of the amounts of transcription, mRNA, and proteins made by key brain genes-stoichiometry-plays a critical role in defining the clinical features of autism.
Collapse
Affiliation(s)
- Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA;
| |
Collapse
|
24
|
Knupp D, Cooper DA, Saito Y, Darnell RB, Miura P. NOVA2 regulates neural circRNA biogenesis. Nucleic Acids Res 2021; 49:6849-6862. [PMID: 34157123 PMCID: PMC8266653 DOI: 10.1093/nar/gkab523] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 05/03/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are highly expressed in the brain and their expression increases during neuronal differentiation. The factors regulating circRNAs in the developing mouse brain are unknown. NOVA1 and NOVA2 are neural-enriched RNA-binding proteins with well-characterized roles in alternative splicing. Profiling of circRNAs from RNA-seq data revealed that global circRNA levels were reduced in embryonic cortex of Nova2 but not Nova1 knockout mice. Analysis of isolated inhibitory and excitatory cortical neurons lacking NOVA2 revealed an even more dramatic reduction of circRNAs and establishes a widespread role for NOVA2 in enhancing circRNA biogenesis. To investigate the cis-elements controlling NOVA2-regulation of circRNA biogenesis, we generated a backsplicing reporter based on the Efnb2 gene. We found that NOVA2-mediated backsplicing of circEfnb2 was impaired when YCAY clusters located in flanking introns were mutagenized. CLIP (cross-linking and immunoprecipitation) and additional reporter analyses demonstrated the importance of NOVA2 binding sites located in both flanking introns of circRNA loci. NOVA2 is the first RNA-binding protein identified to globally promote circRNA biogenesis in the developing brain.
Collapse
Affiliation(s)
- David Knupp
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, USA
| | - Daphne A Cooper
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, USA
| | - Yuhki Saito
- Laboratory of Molecular Neuro-oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Pedro Miura
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, USA
| |
Collapse
|
25
|
McKenna JT, Yang C, Bellio T, Anderson-Chernishof MB, Gamble MC, Hulverson A, McCoy JG, Winston S, Hodges E, Katsuki F, McNally JM, Basheer R, Brown RE. Characterization of basal forebrain glutamate neurons suggests a role in control of arousal and avoidance behavior. Brain Struct Funct 2021; 226:1755-1778. [PMID: 33997911 PMCID: PMC8340131 DOI: 10.1007/s00429-021-02288-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 05/05/2021] [Indexed: 12/25/2022]
Abstract
The basal forebrain (BF) is involved in arousal, attention, and reward processing but the role of individual BF neuronal subtypes is still being uncovered. Glutamatergic neurons are the least well-understood of the three main BF neurotransmitter phenotypes. Here we analyzed the distribution, size, calcium-binding protein content and projections of the major group of BF glutamatergic neurons expressing the vesicular glutamate transporter subtype 2 (vGluT2) and tested the functional effect of activating them. Mice expressing Cre recombinase under the control of the vGluT2 promoter were crossed with a reporter strain expressing the red fluorescent protein, tdTomato, to generate vGluT2-cre-tdTomato mice. Immunohistochemical staining for choline acetyltransferase and a cross with mice expressing green fluorescent protein selectively in GABAergic neurons confirmed that cholinergic, GABAergic and vGluT2+ neurons represent distinct BF subpopulations. Subsets of BF vGluT2+ neurons expressed the calcium-binding proteins calbindin or calretinin, suggesting that multiple subtypes of BF vGluT2+ neurons exist. Anterograde tracing using adeno-associated viral vectors expressing channelrhodopsin2-enhanced yellow fluorescent fusion proteins revealed major projections of BF vGluT2+ neurons to neighboring BF cholinergic and parvalbumin neurons, as well as to extra-BF areas involved in the control of arousal or aversive/rewarding behavior such as the lateral habenula and ventral tegmental area. Optogenetic activation of BF vGluT2+ neurons elicited a striking avoidance of the area where stimulation was given, whereas stimulation of BF parvalbumin or cholinergic neurons did not. Together with previous optogenetic findings suggesting an arousal-promoting role, our findings suggest that BF vGluT2 neurons play a dual role in promoting wakefulness and avoidance behavior.
Collapse
Affiliation(s)
- James T McKenna
- Laboratory of Neuroscience, Dept. of Psychiatry, VA Boston Healthcare System and Harvard Medical School, 1400 VFW Parkway, West Roxbury, MA, 02132, USA
| | - Chun Yang
- Laboratory of Neuroscience, Dept. of Psychiatry, VA Boston Healthcare System and Harvard Medical School, 1400 VFW Parkway, West Roxbury, MA, 02132, USA
| | - Thomas Bellio
- Laboratory of Neuroscience, Dept. of Psychiatry, VA Boston Healthcare System and Harvard Medical School, 1400 VFW Parkway, West Roxbury, MA, 02132, USA
- Stonehill College, Easton, MA, 02357, USA
| | - Marissa B Anderson-Chernishof
- Laboratory of Neuroscience, Dept. of Psychiatry, VA Boston Healthcare System and Harvard Medical School, 1400 VFW Parkway, West Roxbury, MA, 02132, USA
| | - Mackenzie C Gamble
- Laboratory of Neuroscience, Dept. of Psychiatry, VA Boston Healthcare System and Harvard Medical School, 1400 VFW Parkway, West Roxbury, MA, 02132, USA
- Stonehill College, Easton, MA, 02357, USA
| | - Abigail Hulverson
- Laboratory of Neuroscience, Dept. of Psychiatry, VA Boston Healthcare System and Harvard Medical School, 1400 VFW Parkway, West Roxbury, MA, 02132, USA
- Stonehill College, Easton, MA, 02357, USA
| | - John G McCoy
- Laboratory of Neuroscience, Dept. of Psychiatry, VA Boston Healthcare System and Harvard Medical School, 1400 VFW Parkway, West Roxbury, MA, 02132, USA
- Stonehill College, Easton, MA, 02357, USA
| | - Stuart Winston
- Laboratory of Neuroscience, Dept. of Psychiatry, VA Boston Healthcare System and Harvard Medical School, 1400 VFW Parkway, West Roxbury, MA, 02132, USA
| | - Erik Hodges
- Laboratory of Neuroscience, Dept. of Psychiatry, VA Boston Healthcare System and Harvard Medical School, 1400 VFW Parkway, West Roxbury, MA, 02132, USA
| | - Fumi Katsuki
- Laboratory of Neuroscience, Dept. of Psychiatry, VA Boston Healthcare System and Harvard Medical School, 1400 VFW Parkway, West Roxbury, MA, 02132, USA
| | - James M McNally
- Laboratory of Neuroscience, Dept. of Psychiatry, VA Boston Healthcare System and Harvard Medical School, 1400 VFW Parkway, West Roxbury, MA, 02132, USA
| | - Radhika Basheer
- Laboratory of Neuroscience, Dept. of Psychiatry, VA Boston Healthcare System and Harvard Medical School, 1400 VFW Parkway, West Roxbury, MA, 02132, USA
| | - Ritchie E Brown
- Laboratory of Neuroscience, Dept. of Psychiatry, VA Boston Healthcare System and Harvard Medical School, 1400 VFW Parkway, West Roxbury, MA, 02132, USA.
| |
Collapse
|
26
|
Alternative splicing of GluN1 gates glycine site-dependent nonionotropic signaling by NMDAR receptors. Proc Natl Acad Sci U S A 2021; 118:2026411118. [PMID: 34187890 PMCID: PMC8271567 DOI: 10.1073/pnas.2026411118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
N-methyl-D-aspartate receptors (NMDARs), which are critical in the brain, are increasingly being shown to signal without ion flux (i.e., “metabotropically”). What controls the metabotropic function of NMDARs is unknown. We discovered that a form of metabotropic signaling—glycine priming—is controlled by alternative splicing of the mRNA encoding one NMDAR subunit, GluN1. Our discovery was surprising because the spliced exon encodes a peptide cassette in the extracellular region of GluN1 far from the plasma membrane, and yet, metabotropic function requires signaling across the neuronal membrane. Moreover, we found that this metabotropic function of NMDARs is neuron cell–type specific: excitatory neurons show glycine priming, whereas inhibitory neurons do not. These findings have widespread implications for NMDARs in health and disease. N-methyl-D-aspartate (NMDA) receptors (NMDARs), a principal subtype of excitatory neurotransmitter receptor, are composed as tetrameric assemblies of two glycine-binding GluN1 subunits and two glutamate-binding GluN2 subunits. NMDARs can signal nonionotropically through binding of glycine alone to its cognate site on GluN1. A consequence of this signaling by glycine is that NMDARs are primed such that subsequent gating, produced by glycine and glutamate, drives receptor internalization. The GluN1 subunit contains eight alternatively spliced isoforms produced by including or excluding the N1 and the C1, C2, or C2’ polypeptide cassettes. Whether GluN1 alternative splicing affects nonionotropic signaling by NMDARs is a major outstanding question. Here, we discovered that glycine priming of recombinant NMDARs critically depends on GluN1 isoforms lacking the N1 cassette; glycine priming is blocked in splice variants containing N1. On the other hand, the C-terminal cassettes—C1, C2, or C2’—each permit glycine signaling. In wild-type mice, we found glycine-induced nonionotropic signaling at synaptic NMDARs in CA1 hippocampal pyramidal neurons. This nonionotropic signaling by glycine to synaptic NMDARs was prevented in mice we engineered, such that GluN1 obligatorily contained N1. We discovered in wild-type mice that, in contrast to pyramidal neurons, synaptic NMDARs in CA1 inhibitory interneurons were resistant to glycine priming. But we recapitulated glycine priming in inhibitory interneurons in mice engineered such that GluN1 obligatorily lacked the N1 cassette. Our findings reveal a previously unsuspected molecular function for alternative splicing of GluN1 in controlling nonionotropic signaling of NMDARs by activating the glycine site.
Collapse
|
27
|
Herbrechter R, Hube N, Buchholz R, Reiner A. Splicing and editing of ionotropic glutamate receptors: a comprehensive analysis based on human RNA-Seq data. Cell Mol Life Sci 2021; 78:5605-5630. [PMID: 34100982 PMCID: PMC8257547 DOI: 10.1007/s00018-021-03865-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/12/2021] [Accepted: 05/22/2021] [Indexed: 12/11/2022]
Abstract
Ionotropic glutamate receptors (iGluRs) play key roles for signaling in the central nervous system. Alternative splicing and RNA editing are well-known mechanisms to increase iGluR diversity and to provide context-dependent regulation. Earlier work on isoform identification has focused on the analysis of cloned transcripts, mostly from rodents. We here set out to obtain a systematic overview of iGluR splicing and editing in human brain based on RNA-Seq data. Using data from two large-scale transcriptome studies, we established a workflow for the de novo identification and quantification of alternative splice and editing events. We detected all canonical iGluR splice junctions, assessed the abundance of alternative events described in the literature, and identified new splice events in AMPA, kainate, delta, and NMDA receptor subunits. Notable events include an abundant transcript encoding the GluA4 amino-terminal domain, GluA4-ATD, a novel C-terminal GluD1 (delta receptor 1) isoform, GluD1-b, and potentially new GluK4 and GluN2C isoforms. C-terminal GluN1 splicing may be controlled by inclusion of a cassette exon, which shows preference for one of the two acceptor sites in the last exon. Moreover, we identified alternative untranslated regions (UTRs) and species-specific differences in splicing. In contrast, editing in exonic iGluR regions appears to be mostly limited to ten previously described sites, two of which result in silent amino acid changes. Coupling of proximal editing/editing and editing/splice events occurs to variable degree. Overall, this analysis provides the first inventory of alternative splicing and editing in human brain iGluRs and provides the impetus for further transcriptome-based and functional investigations.
Collapse
Affiliation(s)
- Robin Herbrechter
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Nadine Hube
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Raoul Buchholz
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Andreas Reiner
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany.
| |
Collapse
|
28
|
Hafner M, Katsantoni M, Köster T, Marks J, Mukherjee J, Staiger D, Ule J, Zavolan M. CLIP and complementary methods. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00018-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
29
|
Abstract
The function of neuronal circuits relies on the properties of individual neuronal cells and their synapses. We propose that a substantial degree of synapse formation and function is instructed by molecular codes resulting from transcriptional programmes. Recent studies on the Neurexin protein family and its ligands provide fundamental insight into how synapses are assembled and remodelled, how synaptic properties are specified and how single gene mutations associated with neurodevelopmental and psychiatric disorders might modify the operation of neuronal circuits and behaviour. In this Review, we first summarize insights into Neurexin function obtained from various model organisms. We then discuss the mechanisms and logic of the cell type-specific regulation of Neurexin isoforms, in particular at the level of alternative mRNA splicing. Finally, we propose a conceptual framework for how combinations of synaptic protein isoforms act as 'senders' and 'readers' to instruct synapse formation and the acquisition of cell type-specific and synapse-specific functional properties.
Collapse
|
30
|
Koterniak B, Pilaka PP, Gracida X, Schneider LM, Pritišanac I, Zhang Y, Calarco JA. Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans. Genome Res 2020; 30:1766-1780. [PMID: 33127752 PMCID: PMC7706725 DOI: 10.1101/gr.267328.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/28/2020] [Indexed: 12/27/2022]
Abstract
Alternative splicing plays a major role in shaping tissue-specific transcriptomes. Among the broad tissue types present in metazoans, the central nervous system contains some of the highest levels of alternative splicing. Although many documented examples of splicing differences between broad tissue types exist, there remains much to be understood about the splicing factors and the cis sequence elements controlling tissue and neuron subtype-specific splicing patterns. By using translating ribosome affinity purification coupled with deep-sequencing (TRAP-seq) in Caenorhabditis elegans, we have obtained high coverage profiles of ribosome-associated mRNA for three broad tissue classes (nervous system, muscle, and intestine) and two neuronal subtypes (dopaminergic and serotonergic neurons). We have identified hundreds of splice junctions that exhibit distinct splicing patterns between tissue types or within the nervous system. Alternative splicing events differentially regulated between tissues are more often frame-preserving, are more highly conserved across Caenorhabditis species, and are enriched in specific cis regulatory motifs, when compared with other types of exons. By using this information, we have identified a likely mechanism of splicing repression by the RNA-binding protein UNC-75/CELF via interactions with cis elements that overlap a 5′ splice site. Alternatively spliced exons also overlap more frequently with intrinsically disordered peptide regions than constitutive exons. Moreover, regulated exons are often shorter than constitutive exons but are flanked by longer intron sequences. Among these tissue-regulated exons are several highly conserved microexons <27 nt in length. Collectively, our results indicate a rich layer of tissue-specific gene regulation at the level of alternative splicing in C. elegans that parallels the evolutionary forces and constraints observed across metazoa.
Collapse
Affiliation(s)
- Bina Koterniak
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Pallavi P Pilaka
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Xicotencatl Gracida
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Lisa-Marie Schneider
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada.,Department of Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Iva Pritišanac
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada.,Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Yun Zhang
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - John A Calarco
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| |
Collapse
|
31
|
Nedoluzhko A, Gruzdeva N, Sharko F, Rastorguev S, Zakharova N, Kostyuk G, Ushakov V. The Biomarker and Therapeutic Potential of Circular Rnas in Schizophrenia. Cells 2020; 9:E2238. [PMID: 33020462 PMCID: PMC7601372 DOI: 10.3390/cells9102238] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are endogenous, single-stranded, most frequently non-coding RNA (ncRNA) molecules that play a significant role in gene expression regulation. Circular RNAs can affect microRNA functionality, interact with RNA-binding proteins (RBPs), translate proteins by themselves, and directly or indirectly modulate gene expression during different cellular processes. The affected expression of circRNAs, as well as their targets, can trigger a cascade of events in the genetic regulatory network causing pathological conditions. Recent studies have shown that altered circular RNA expression patterns could be used as biomarkers in psychiatric diseases, including schizophrenia (SZ); moreover, circular RNAs together with other cell molecules could provide new insight into mechanisms of this disorder. In this review, we focus on the role of circular RNAs in the pathogenesis of SZ and analyze their biomarker and therapeutic potential in this disorder.
Collapse
Affiliation(s)
- Artem Nedoluzhko
- Faculty of Biosciences and Aquaculture, Nord University, PB 1490. 8049 Bodø, Norway
- Mental-Health Clinic No. 1 Named after N.A. Alexeev, Moscow Healthcare Department, Zagorodnoye Highway, 2, 115191 Moscow, Russia; (N.Z.); (G.K.); (V.U.)
| | - Natalia Gruzdeva
- National Research Center “Kurchatov Institute”, 1st Akademika Kurchatova Square, 123182 Moscow, Russia; (N.G.); (F.S.); (S.R.)
| | - Fedor Sharko
- National Research Center “Kurchatov Institute”, 1st Akademika Kurchatova Square, 123182 Moscow, Russia; (N.G.); (F.S.); (S.R.)
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospect 33/2, 119071 Moscow, Russia
| | - Sergey Rastorguev
- National Research Center “Kurchatov Institute”, 1st Akademika Kurchatova Square, 123182 Moscow, Russia; (N.G.); (F.S.); (S.R.)
| | - Natalia Zakharova
- Mental-Health Clinic No. 1 Named after N.A. Alexeev, Moscow Healthcare Department, Zagorodnoye Highway, 2, 115191 Moscow, Russia; (N.Z.); (G.K.); (V.U.)
| | - Georgy Kostyuk
- Mental-Health Clinic No. 1 Named after N.A. Alexeev, Moscow Healthcare Department, Zagorodnoye Highway, 2, 115191 Moscow, Russia; (N.Z.); (G.K.); (V.U.)
| | - Vadim Ushakov
- Mental-Health Clinic No. 1 Named after N.A. Alexeev, Moscow Healthcare Department, Zagorodnoye Highway, 2, 115191 Moscow, Russia; (N.Z.); (G.K.); (V.U.)
- Institute for Advanced Brain Studies, Lomonosov Moscow State University, Leninskiye Gory, 119899 Moscow, Russia
| |
Collapse
|
32
|
Schieweck R, Ninkovic J, Kiebler MA. RNA-binding proteins balance brain function in health and disease. Physiol Rev 2020; 101:1309-1370. [PMID: 33000986 DOI: 10.1152/physrev.00047.2019] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Posttranscriptional gene expression including splicing, RNA transport, translation, and RNA decay provides an important regulatory layer in many if not all molecular pathways. Research in the last decades has positioned RNA-binding proteins (RBPs) right in the center of posttranscriptional gene regulation. Here, we propose interdependent networks of RBPs to regulate complex pathways within the central nervous system (CNS). These are involved in multiple aspects of neuronal development and functioning, including higher cognition. Therefore, it is not sufficient to unravel the individual contribution of a single RBP and its consequences but rather to study and understand the tight interplay between different RBPs. In this review, we summarize recent findings in the field of RBP biology and discuss the complex interplay between different RBPs. Second, we emphasize the underlying dynamics within an RBP network and how this might regulate key processes such as neurogenesis, synaptic transmission, and synaptic plasticity. Importantly, we envision that dysfunction of specific RBPs could lead to perturbation within the RBP network. This would have direct and indirect (compensatory) effects in mRNA binding and translational control leading to global changes in cellular expression programs in general and in synaptic plasticity in particular. Therefore, we focus on RBP dysfunction and how this might cause neuropsychiatric and neurodegenerative disorders. Based on recent findings, we propose that alterations in the entire regulatory RBP network might account for phenotypic dysfunctions observed in complex diseases including neurodegeneration, epilepsy, and autism spectrum disorders.
Collapse
Affiliation(s)
- Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Jovica Ninkovic
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Michael A Kiebler
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| |
Collapse
|
33
|
Microexons: at the nexus of nervous system development, behaviour and autism spectrum disorder. Curr Opin Genet Dev 2020; 65:22-33. [PMID: 32535349 DOI: 10.1016/j.gde.2020.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022]
Abstract
The discovery and characterization of a network of highly conserved neuronal microexons has provided fundamental new insight into mechanisms underlying nervous system development and function, as well as an important basis for pathway convergence in autism spectrum disorder. In the past few years, considerable progress has been made in comprehensively determining the repertoires of factors that control neuronal microexons. These results have illuminated molecular mechanisms that activate the splicing of microexons, including those that control gene expression programs critical for neurogenesis, as well as synaptic protein translation and neuronal activity. Remarkably, individual disruption of specific microexons in these pathways results in autism-like phenotypes and cognitive impairment in mice. This review discusses these findings and their implications for delivering new therapeutic strategies for neurological disorders.
Collapse
|
34
|
Meldolesi J. Alternative Splicing by NOVA Factors: From Gene Expression to Cell Physiology and Pathology. Int J Mol Sci 2020; 21:ijms21113941. [PMID: 32486302 PMCID: PMC7312376 DOI: 10.3390/ijms21113941] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/24/2022] Open
Abstract
NOVA1 and NOVA2, the two members of the NOVA family of alternative splicing factors, bind YCAY clusters of pre-mRNAs and assemble spliceosomes to induce the maintenance/removal of introns and exons, thus governing the development of mRNAs. Members of other splicing families operate analogously. Activity of NOVAs accounts for up to 700 alternative splicing events per cell, taking place both in the nucleus (co-transcription of mRNAs) and in the cytoplasm. Brain neurons express high levels of NOVAs, with NOVA1 predominant in cerebellum and spinal cord, NOVA2 in the cortex. Among brain physiological processes NOVAs play critical roles in axon pathfinding and spreading, structure and function of synapses, as well as the regulation of surface receptors and voltage-gated channels. In pathology, NOVAs contribute to neurodegenerative diseases and epilepsy. In vessel endothelial cells, NOVA2 is essential for angiogenesis, while in adipocytes, NOVA1 contributes to regulation of thermogenesis and obesity. In many cancers NOVA1 and also NOVA2, by interacting with specific miRNAs and by additional mechanisms, activate oncogenic roles promoting cell proliferation, colony formation, migration, and invasion. In conclusion, NOVAs regulate cell functions of physiological and pathological nature. Single cell identification and distinction, and new therapies addressed to NOVA targets might be developed in the near future.
Collapse
Affiliation(s)
- Jacopo Meldolesi
- Department of Neuroscience, San Raffaele Institute and San Raffaele University, via Olgettina 58, 20132 Milan, Italy
| |
Collapse
|
35
|
Mattioli F, Hayot G, Drouot N, Isidor B, Courraud J, Hinckelmann MV, Mau-Them FT, Sellier C, Goldman A, Telegrafi A, Boughton A, Gamble C, Moutton S, Quartier A, Jean N, Van Ness P, Grotto S, Nambot S, Douglas G, Si YC, Chelly J, Shad Z, Kaplan E, Dineen R, Golzio C, Charlet-Berguerand N, Mandel JL, Piton A. De Novo Frameshift Variants in the Neuronal Splicing Factor NOVA2 Result in a Common C-Terminal Extension and Cause a Severe Form of Neurodevelopmental Disorder. Am J Hum Genet 2020; 106:438-452. [PMID: 32197073 DOI: 10.1016/j.ajhg.2020.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 02/18/2020] [Indexed: 12/13/2022] Open
Abstract
The neuro-oncological ventral antigen 2 (NOVA2) protein is a major factor regulating neuron-specific alternative splicing (AS), previously associated with an acquired neurologic condition, the paraneoplastic opsoclonus-myoclonus ataxia (POMA). We report here six individuals with de novo frameshift variants in NOVA2 affected with a severe neurodevelopmental disorder characterized by intellectual disability (ID), motor and speech delay, autistic features, hypotonia, feeding difficulties, spasticity or ataxic gait, and abnormal brain MRI. The six variants lead to the same reading frame, adding a common proline rich C-terminal part instead of the last KH RNA binding domain. We detected 41 genes differentially spliced after NOVA2 downregulation in human neural cells. The NOVA2 variant protein shows decreased ability to bind target RNA sequences and to regulate target AS events. It also fails to complement the effect on neurite outgrowth induced by NOVA2 downregulation in vitro and to rescue alterations of retinotectal axonal pathfinding induced by loss of NOVA2 ortholog in zebrafish. Our results suggest a partial loss-of-function mechanism rather than a full heterozygous loss-of-function, although a specific contribution of the novel C-terminal extension cannot be excluded.
Collapse
Affiliation(s)
- Francesca Mattioli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France
| | - Gaelle Hayot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France
| | - Nathalie Drouot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes 44093, France
| | - Jérémie Courraud
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France
| | - Maria-Victoria Hinckelmann
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France
| | - Frederic Tran Mau-Them
- Laboratoire de Génétique Moléculaire, UF Innovation en diagnostic génomique des maladies rares, Plateau Technique de Biologie, Centre Hospitalier Universitaire de Dijon, Dijon 21070, France; INSERM U1231, LNC UMR1231 GAD, Burgundy University, Dijon 21070, France
| | - Chantal Sellier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France
| | - Alica Goldman
- Department of Neurology, Neurophysiology Section, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | - Sebastien Moutton
- INSERM U1231, LNC UMR1231 GAD, Burgundy University, Dijon 21070, France; Centre de Génétique et Centre de référence "Anomalies du Développement et Syndromes Malformatifs," Hôpital d'Enfants, Centre Hospitalier Universitaire de Dijon, Dijon 21070, France
| | - Angélique Quartier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France
| | - Nolwenn Jean
- INSERM U1231, LNC UMR1231 GAD, Burgundy University, Dijon 21070, France; Centre de Génétique et Centre de référence "Anomalies du Développement et Syndromes Malformatifs," Hôpital d'Enfants, Centre Hospitalier Universitaire de Dijon, Dijon 21070, France
| | - Paul Van Ness
- Department of Neurology, Neurophysiology Section, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Grotto
- Service de Génétique Médicale, AP-HP Robert-Debré, Paris 75019, France
| | - Sophie Nambot
- INSERM U1231, LNC UMR1231 GAD, Burgundy University, Dijon 21070, France; Centre de Génétique et Centre de référence "Anomalies du Développement et Syndromes Malformatifs," Hôpital d'Enfants, Centre Hospitalier Universitaire de Dijon, Dijon 21070, France
| | | | | | - Jamel Chelly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France; Laboratory of Genetic Diagnostic, Hôpitaux Universitaires de Strasbourg, Strasbourg 67000, France
| | - Zohra Shad
- Department of Genetics, University of Illinois College of Medicine, Chicago, IL 60607, USA
| | - Elisabeth Kaplan
- Department of Genetics, University of Illinois College of Medicine, Chicago, IL 60607, USA
| | - Richard Dineen
- Department of Genetics, University of Illinois College of Medicine, Chicago, IL 60607, USA
| | - Christelle Golzio
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France
| | - Nicolas Charlet-Berguerand
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France
| | - Jean-Louis Mandel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France; University of Strasbourg Institute of Advanced Studies, Strasbourg 67000, France
| | - Amélie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France; Laboratory of Genetic Diagnostic, Hôpitaux Universitaires de Strasbourg, Strasbourg 67000, France.
| |
Collapse
|
36
|
Abstract
High-throughput sequencing-based methods and their applications in the study of transcriptomes have revolutionized our understanding of alternative splicing. Networks of functionally coordinated and biologically important alternative splicing events continue to be discovered in an ever-increasing diversity of cell types in the context of physiologically normal and disease states. These studies have been complemented by efforts directed at defining sequence codes governing splicing and their cognate trans-acting factors, which have illuminated important combinatorial principles of regulation. Additional studies have revealed critical roles of position-dependent, multivalent protein-RNA interactions that direct splicing outcomes. Investigations of evolutionary changes in RNA binding proteins, splice variants, and associated cis elements have further shed light on the emergence, mechanisms, and functions of splicing networks. Progress in these areas has emphasized the need for a coordinated, community-based effort to systematically address the functions of individual splice variants associated with normal and disease biology.
Collapse
|
37
|
Zhang P, Southey BR, Rodriguez-Zas SL. Co-expression networks uncover regulation of splicing and transcription markers of disease. PROCEEDINGS OF THE ... ANNUAL INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 2020; 70:119-128. [PMID: 35047432 DOI: 10.29007/rl4h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Gene co-expression networks based on gene expression data are usually used to capture biologically significant patterns, enabling the discovery of biomarkers and interpretation of regulatory relationships. However, the coordination of numerous splicing changes within and across genes can exert a substantial impact on the function of these genes. This is particularly impactful in studies of the properties of the nervous system, which can be masked in the networks that only assess the correlation between gene expression levels. A bioinformatics approach was developed to uncover the role of alternative splicing and associated transcriptional networks using RNA-seq profiles. Data from 40 samples, including control and two treatments associated with sensitivity to stimuli across two central nervous system regions that can present differential splicing, were explored. The gene expression and relative isoform levels were integrated into a transcriptome-wide matrix, and then Graphical Lasso was applied to capture the interactions between genes and isoforms. Next, functional enrichment analysis enabled the discovery of pathways dysregulated at the isoform or gene levels and the interpretation of these interactions within a central nervous region. In addition, a Bayesian biclustering strategy was used to reconstruct treatment-specific networks from gene expression profile, allowing the identification of hub molecules and visualization of highly connected modules of isoforms and genes in specific conditions. Our bioinformatics approach can offer comparable insights into the discovery of biomarkers and therapeutic targets for a wide range of diseases and conditions.
Collapse
Affiliation(s)
- Pan Zhang
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL, the U.S.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, the U.S
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, the U.S
| | - Sandra L Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, the U.S.,Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, the U.S.,Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, the U.S
| |
Collapse
|
38
|
Licatalosi DD, Ye X, Jankowsky E. Approaches for measuring the dynamics of RNA-protein interactions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1565. [PMID: 31429211 PMCID: PMC7006490 DOI: 10.1002/wrna.1565] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/20/2019] [Accepted: 07/25/2019] [Indexed: 12/17/2022]
Abstract
RNA-protein interactions are pivotal for the regulation of gene expression from bacteria to human. RNA-protein interactions are dynamic; they change over biologically relevant timescales. Understanding the regulation of gene expression at the RNA level therefore requires knowledge of the dynamics of RNA-protein interactions. Here, we discuss the main experimental approaches to measure dynamic aspects of RNA-protein interactions. We cover techniques that assess dynamics of cellular RNA-protein interactions that accompany biological processes over timescales of hours or longer and techniques measuring the kinetic dynamics of RNA-protein interactions in vitro. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Evolution and Genomics > Ribonomics.
Collapse
Affiliation(s)
- Donny D Licatalosi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Xuan Ye
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| |
Collapse
|
39
|
Sawicka K, Hale CR, Park CY, Fak JJ, Gresack JE, Van Driesche SJ, Kang JJ, Darnell JC, Darnell RB. FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory. eLife 2019; 8:e46919. [PMID: 31860442 PMCID: PMC6924960 DOI: 10.7554/elife.46919] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 12/02/2019] [Indexed: 12/14/2022] Open
Abstract
Loss of the RNA binding protein FMRP causes Fragile X Syndrome (FXS), the most common cause of inherited intellectual disability, yet it is unknown how FMRP function varies across brain regions and cell types and how this contributes to disease pathophysiology. Here we use conditional tagging of FMRP and CLIP (FMRP cTag CLIP) to examine FMRP mRNA targets in hippocampal CA1 pyramidal neurons, a critical cell type for learning and memory relevant to FXS phenotypes. Integrating these data with analysis of ribosome-bound transcripts in these neurons revealed CA1-enriched binding of autism-relevant mRNAs, and CA1-specific regulation of transcripts encoding circadian proteins. This contrasted with different targets in cerebellar granule neurons, and was consistent with circadian defects in hippocampus-dependent memory in Fmr1 knockout mice. These findings demonstrate differential FMRP-dependent regulation of mRNAs across neuronal cell types that may contribute to phenotypes such as memory defects and sleep disturbance associated with FXS.
Collapse
Affiliation(s)
- Kirsty Sawicka
- Laboratory of Molecular Neuro-OncologyThe Rockefeller UniversityNew YorkUnited States
| | - Caryn R Hale
- Laboratory of Molecular Neuro-OncologyThe Rockefeller UniversityNew YorkUnited States
| | - Christopher Y Park
- Laboratory of Molecular Neuro-OncologyThe Rockefeller UniversityNew YorkUnited States
| | - John J Fak
- Laboratory of Molecular Neuro-OncologyThe Rockefeller UniversityNew YorkUnited States
| | - Jodi E Gresack
- Laboratory of Molecular and Cellular NeuroscienceThe Rockefeller UniversityNew YorkUnited States
| | - Sarah J Van Driesche
- Laboratory of Molecular Neuro-OncologyThe Rockefeller UniversityNew YorkUnited States
| | - Jin Joo Kang
- Laboratory of Molecular Neuro-OncologyThe Rockefeller UniversityNew YorkUnited States
| | - Jennifer C Darnell
- Laboratory of Molecular Neuro-OncologyThe Rockefeller UniversityNew YorkUnited States
| | - Robert B Darnell
- Laboratory of Molecular Neuro-OncologyThe Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| |
Collapse
|
40
|
Furlanis E, Traunmüller L, Fucile G, Scheiffele P. Landscape of ribosome-engaged transcript isoforms reveals extensive neuronal-cell-class-specific alternative splicing programs. Nat Neurosci 2019; 22:1709-1717. [PMID: 31451803 PMCID: PMC6763336 DOI: 10.1038/s41593-019-0465-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 07/09/2019] [Indexed: 01/21/2023]
Abstract
Nervous system function relies on complex assemblies of distinct neuronal cell types that have unique anatomical and functional properties instructed by molecular programs. Alternative splicing is a key mechanism for the expansion of molecular repertoires, and protein splice isoforms shape neuronal cell surface recognition and function. However, the logic of how alternative splicing programs are arrayed across neuronal cells types is poorly understood. We systematically mapped ribosome-associated transcript isoforms in genetically defined neuron types of the mouse forebrain. Our dataset provides an extensive resource of transcript diversity across major neuron classes. We find that neuronal transcript isoform profiles reliably distinguish even closely related classes of pyramidal cells and inhibitory interneurons in the mouse hippocampus and neocortex. These highly specific alternative splicing programs selectively control synaptic proteins and intrinsic neuronal properties. Thus, transcript diversification via alternative splicing is a central mechanism for the functional specification of neuronal cell types and circuits.
Collapse
Affiliation(s)
| | | | - Geoffrey Fucile
- Center for Scientific Computing (sciCORE), University of Basel, Basel, Switzerland
| | | |
Collapse
|