A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

Irimia, Manuel, Weatheritt, Robert J., Ellis, Jonathan D., Parikshak, Neelroop N., Gonatopoulos-Pournatzis, Thomas, Babor, Mariana, Quesnel-Vallières, Mathieu, Tapial, Javier +9 more·2014·Cell

DOI 10.1016/j.cell.2014.11.035

Cited by (749)

Items 101–200 of 749

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Stromal Fat4 acts non-autonomously with Dachsous1/2 to restrict the nephron progenitor pool
Mazdak Bagherie-Lachidan, Antoine Reginensi, Hitisha P. Zaveri · 2015 · Development
The landscape of human mutually exclusive splicing
Klas Hatje, Raza‐Ur Rahman, Ramon Oliveira Vidal, Dominic Simm, Björn Hammesfahr, Vikas Bansal, Ashish Rajput, Michel‐Edwar Mickael, Ting Sun, Stefan Bonn et al. · 2017 · Molecular Systems Biology
Using Zebrafish to Model Autism Spectrum Disorder: A Comparison of ASD Risk Genes Between Zebrafish and Their Mammalian Counterparts
Victoria Rea, Terence J. Van Raay · 2020 · Frontiers in Molecular Neuroscience
An alternative splicing program promotes adipose tissue thermogenesis
Santiago Vernia, Yvonne J. K. Edwards, Myoung Sook Han, Julie Cavanagh, Tamera Barrett, Jason K. Kim, Roger J. Davis · 2016 · eLife
Genome‐wide association study of Alzheimer's disease endophenotypes at prediagnosis stages
Chung, Jaeyoon, Wang, Xulong, Maruyama, Toru, Ma, Yiyi, Zhang, Xiaoling, Mez, Jesse, Sherva, Richard, Takeyama, Haruko, The Alzheimer's Disease Neuroimaging Initiative, Lunetta, Kathryn L. et al. · 2018 · Alzheimer's & Dementia
Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders
David Zhang, Sebastian Guelfi, Sonia García-Ruiz, Beatrice Costa, Regina Hertfelder Reynolds, Karishma D’Sa, Wenfei Liu, Thomas Courtin, Amy Peterson, Andrew E. Jaffe et al. · 2020 · Science Advances
RNA on the brain: emerging layers of post‐transcriptional regulation in cerebral cortex development
Ashley L. Lennox, Hanqian Mao, Debra L. Silver · 2017 · Wiley Interdisciplinary Reviews Developmental Biology
Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians
Jordi Solana, Manuel Irimia, Salah Ayoub, Marta Rodriguez Orejuela, Vera Zywitza, Marvin Jens, Javier Tapial, Debashish Ray, Quaid Morris, Timothy R. Hughes et al. · 2016 · eLife
Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
Yen‐Ju Chen, Chia-Ying Chen, Te‐Lun Mai, Chih-Fan Chuang, Yu‐Chen Chen, Sachin Kumar Gupta, Laising Yen, Yi-Da Wang, Trees‐Juen Chuang · 2020 · Genome Research
The function of alternative splicing in the proteome: rewiring protein interactomes to put old functions into new contexts
Peter Kjer-Hansen, Robert J. Weatheritt · 2023 · Nature Structural & Molecular Biology
tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing
Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila, Héctor del Risco, Cristina Martí, Sonia Tarazona, Pedro Salguero, Raymond Scott, Alberto Lerma-Aguilera, Ana Alastrue‐Agudo et al. · 2020 · Genome biology
Alternative splicing controls teneurin-latrophilin interaction and synapse specificity by a shape-shifting mechanism
Jingxian Li, Yuan Xie, Shaleeka Cornelius, Xian Jiang, Richard C. Sando, Szymon P. Kordon, Man Pan, Katherine Leon, Thomas Christian Südhof, Minglei Zhao et al. · 2020 · Nature Communications
SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification
Manuel Tardáguila, Lorena de la Fuente, Cristina Martí et al. · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
Structural basis for adhesion G protein-coupled receptor Gpr126 function
Katherine Leon, Rebecca L. Cunningham, Joshua A. Riback, Ezra Feldman, Jingxian Li, Tobin R. Sosnick, Minglei Zhao, Kelly R. Monk, Demet Araç · 2020 · Nature Communications
The Long Noncoding RNA Pnky Is a Trans-acting Regulator of Cortical Development In Vivo
Rebecca Andersen, Sung Jun Hong, Justin J. Lim, Miao Cui, Brock A. Harpur, Elizabeth E. Hwang, Ryan Nicholas Delgado, Alexander D. Ramos, Siyuan John Liu, Benjamin J. Blencowe et al. · 2019 · Developmental Cell
MTSplice predicts effects of genetic variants on tissue-specific splicing
Jun Cheng, Muhammed Hasan Çelik, Anshul Bharat Kundaje, Julien Gagneur · 2021 · Genome biology
Multi-Platform Sequencing Approach Reveals a Novel Transcriptome Profile in Pseudorabies Virus
Norbert Moldován, Dóra Tombácz, Attila László Szűcs · 2018 · Frontiers in Microbiology
Splicing regulation in brain and testis: common themes for highly specialized organs
Chiara Naro, Eleonora Cesari, Claudio Sette · 2021 · Cell Cycle
Postsynaptic autism spectrum disorder genes and synaptic dysfunction
Paola Bonsi, Antonella De Jaco, Laurent Fasano, Paolo Gubellini · 2021 · Neurobiology of Disease
Huntington’s disease-specific mis-splicing unveils key effector genes and altered splicing factors
Ainara Elorza, Yamile Márquez, Jorge Rubén Cabrera, Jose L. Sanchez‐Trincado, María Santos‐Galindo, Ivó H. Hernández, Sara Picó, Juan Ignacio Díaz‐Hernandéz, Ramón García‐Escudero, Manuel Irimia et al. · 2021 · Brain
Gomafu lncRNA knockout mice exhibit mild hyperactivity with enhanced responsiveness to the psychostimulant methamphetamine
Joanna Y. Y. Ip, Masamitsu Sone, Chieko Nashiki, Qun Pan, Kiyoyuki Kitaichi, Kaori Yanaka, Takaya Abe, Keizo Takao, Tsuyoshi Miyakawa, Benjamin J. Blencowe et al. · 2016 · Scientific Reports
Regulation of mRNA splicing by MeCP2 via epigenetic modifications in the brain
Tian‐Lin Cheng, Jingqi Chen, Huida Wan, Bin Tang, Weidong Tian, Lujian Liao, Zilong Qiu · 2017 · Scientific Reports
Loss of the fragile X syndrome protein FMRP results in misregulation of nonsense-mediated mRNA decay
Tatsuaki Kurosaki, Naoto Imamachi, Christoph Pröschel, Shuhei Mitsutomi, Rina Nagao, Nobuyoshi Akimitsu, Lynne E. Maquat · 2021 · Nature Cell Biology
Understanding aberrant RNA splicing to facilitate cancer diagnosis and therapy
Xuesen Dong, Ruiqi Chen · 2019 · Oncogene
Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus
Xi Wang, Xintian A. You, Julian D. Langer, Jingyi Hou, Fiona Rupprecht, Irena Vlatkovic, Claudia Quedenau, Georgi Tushev, Irina Epstein, Bernhard Schaefke et al. · 2019 · Nature Communications
Regulation of alternative polyadenylation by the C2H2-zinc-finger protein Sp1
Jingwen Song, Syed Nabeel‐Shah, Shuye Pu, Hyunmin Lee, Ulrich Braunschweig, Zuyao Ni, Nujhat Ahmed, Edyta Marcon, Guoqing Zhong, Debashish Ray et al. · 2022 · Molecular Cell
Central role of the p53 pathway in the noncoding-RNA response to oxidative stress
Paola Fuschi, Matteo Carrara, Christine Voellenkle, José Manuel García-Manteiga, Paolo Righini, Biagina Maimone, Elena Sangalli, Francesco Villa, Claudia Specchia, Mario Picozza et al. · 2017 · Aging
The alternative splicing factor Nova2 regulates vascular development and lumen formation
Costanza Giampietro, Gianluca Deflorian, Stefania Gallo, Anna Di Matteo, Davide Pradella, Serena Bonomi, Elisa Belloni, Daniel Nyqvist, Valeria Quaranta, Stefano Confalonieri et al. · 2015 · Nature Communications
Overlapping Activities of Two Neuronal Splicing Factors Switch the GABA Effect from Excitatory to Inhibitory by Regulating REST
Yoko Nakano, Susan C. Wiechert, Botond Bánfi · 2019 · Cell Reports
Mis-splicing of a neuronal microexon promotes CPEB4 aggregation in ASD
Carla Garcia‐Cabau, Anna Bartomeu, Giulio Tesei, Kai Chit Cheung, Julia Pose‐Utrilla, Sara Picó, Andreea Balaceanu, Berta Duran-Arqué, Marcos Fernández‐Alfara, Judit Martín et al. · 2024 · Nature
A novel mechanism of SRRM4 in promoting neuroendocrine prostate cancer development via a pluripotency gene network
Ahn R. Lee, Yu Gan, Yuxin Tang, Xuesen Dong · 2018 · EBioMedicine
IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing
Yang Pan, John W. Phillips, Beatrice D. Zhang, Miyako Noguchi, Eric Kutschera, Jami McLaughlin, Pavlo A. Nesterenko, Zhiyuan Mao, Nathanael Joshua Bangayan, Robert Wang et al. · 2023 · Proceedings of the National Academy of Sciences
Common Genetic Variants Found in HLA and KIR Immune Genes in Autism Spectrum Disorder
Anthony Torres, Thayne L. Sweeten, Randall C. Johnson, Dennis Odell, Jonna B. Westover, Patricia Bray‐Ward, David C. Ward, Christopher J. Davies, Aaron J. Thomas, Lisa Croen et al. · 2016 · Frontiers in Neuroscience
Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome
Marina Reixachs‐Solé, Jorge Ruiz‐Orera, M. Mar Albà, Eduardo Eyras · 2020 · Nature Communications
The Tousled-like kinases regulate genome and epigenome stability: implications in development and disease
Sandra Segura‐Bayona, Travis H. Stracker · 2019 · Cellular and Molecular Life Sciences
Calcium regulation of mitochondrial carriers
Araceli del Arco, Laura Contreras, Beatriz Pardo, Jorgina Satrústegui · 2016 · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research
Cell environment shapes TDP-43 function with implications in neuronal and muscle disease
Urša Šušnjar, Neva Škrabar, Anna‐Leigh Brown, Yasmine Abbassi, Hemali P. Phatnani, Hemali P. Phatnani, Pietro Fratta, Justin Y. Kwan, Dhruv Sareen, James Riley Broach et al. · 2022 · Communications Biology
Antisense oligonucleotide rescue of CGG expansion–dependent FMR1 mis-splicing in fragile X syndrome restores FMRP
Sneha Shah, Kevin J. Sharp, Sithara Raju Ponny, Jonathan Wei Jie Lee, Jonathan K. Watts, Elizabeth Berry‐Kravis, Joel D. Richter · 2023 · Proceedings of the National Academy of Sciences
The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing
Evi Goulielmaki, Maria Tsekrekou, Nikos Batsiotos, Mariana Ascensão-Ferreira, Eleftheria Ledaki, Kalliopi Stratigi, Georgia Chatzinikolaou, Pantelis Topalis, Theodoros Kosteas, Janine Altmüller et al. · 2021 · Nature Communications
The RNA-binding profile of Acinus, a peripheral component of the exon junction complex, reveals its role in splicing regulation
Julie Rodor, Qun Pan, Benjamin J. Blencowe, Eduardo Eyras, Javier F. Cáceres · 2016 · RNA
Neuronal activity-regulated alternative mRNA splicing
Guido Hermey, Nils Blüthgen, Dietmar Kuhl · 2017 · The International Journal of Biochemistry & Cell Biology
Activity-dependent aberrations in gene expression and alternative splicing in a mouse model of Rett syndrome
Sivan Osenberg, Ariel Karten, Jialin Sun, Jin Li, Shaun V. Charkowick, Christy A. Felice, Mary F. Kritzer, Minh Vu Chuong Nguyen, Peng Yu, Nurit Ballas · 2018 · Proceedings of the National Academy of Sciences
LAR Receptor Tyrosine Phosphatase Family in Healthy and Diseased Brain
Francisca Cornejo, Bastián I. Cortés, Greg M. Findlay, Gonzalo I. Cancino · 2021 · Frontiers in Cell and Developmental Biology
NeuroLSD1: Splicing-Generated Epigenetic Enhancer of Neuroplasticity
Francesco Rusconi, Barbara Grillo, Emanuela Toffolo, Andrea Mattevi, Elena Battaglioli · 2016 · Trends in Neurosciences
Clustering by phenotype and genome-wide association study in autism
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Epigenetic Basis of Neuronal and Synaptic Plasticity
Nina N. Karpova, Amanda J. Sales, Sâmia R.L. Joca · 2016 · Current Topics in Medicinal Chemistry
FUS(1-359) transgenic mice as a model of ALS: pathophysiological and molecular aspects of the proteinopathy
S. Yu. Funikov, Alexander P. Rezvykh, Pavel Mazin, Alexey V. Morozov, Andrey V. Maltsev, Maria M. Chicheva, Ekaterina A. Vikhareva, Михаил Б. Евгеньев, A. A. Ustyugov · 2018 · Neurogenetics
The contribution of alternative splicing to genetic risk for psychiatric disorders
Emma Reble, Aidan Dineen, Cathy L. Barr · 2017 · Genes Brain & Behavior
Epigenetic Delay in the Neurodevelopmental Trajectory of DNA Methylation States in Autism Spectrum Disorders
Michael J. Corley, Naurú Idalia Vargas-Maya, Alina P.S. Pang, Annette Lum‐Jones, Dongmei Li, Vedbar S. Khadka, Răzvan Sultana, D. Caroline Blanchard, Alika K. Maunakea · 2019 · Frontiers in Genetics
A developmentally programmed splicing failure contributes to DNA damage response attenuation during mammalian zygotic genome activation
Christopher D. R. Wyatt, Bárbara Pernaute, André Gohr, Marta Miret-Cuesta, Lucía Goyeneche, Quirze Rovira, Marion Claudia Salzer, Elvan Böke, Ozren Bogdanović, Sophie Bonnal et al. · 2022 · Science Advances
Alternative Splicing Shapes the Phenotype of a Mutation in BBS8 To Cause Nonsyndromic Retinitis Pigmentosa
Daniel Murphy, Ratnesh Kumar Singh, Saravanan Kolandaivelu, Visvanathan Ramamurthy, Peter Stoilov · 2015 · Molecular and Cellular Biology
Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice
Yoshida, Tomoyuki, Yamagata, Atsushi, Imai, Ayako, Kim, Juhyon, Izumi, Hironori, Nakashima, Shogo, Shiroshima, Tomoko, Maeda, Asami, Iwasawa-Okamoto, Shiho, Azechi, Kenji et al. · 2021 · Nature Communications
psichomics: graphical application for alternative splicing quantification and analysis
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SRRM4-dependent neuron-specific alternative splicing of protrudin transcripts regulates neurite outgrowth
Takafumi Ohnishi, Michiko Shirane, Keiichi I. Nakayama · 2017 · Scientific Reports
Steering research on mRNA splicing in cancer towards clinical translation
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Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates
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Full-length isoform transcriptome of the developing human brain provides further insights into autism
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ELAV/Hu RNA binding proteins determine multiple programs of neural alternative splicing
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A comprehensive benchmarking of differential splicing tools for RNA-seq analysis at the event level
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Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes
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Specialization of the photoreceptor transcriptome by Srrm3 -dependent microexons is required for outer segment maintenance and vision
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Mechanisms of Neuronal Alternative Splicing and Strategies for Therapeutic Interventions
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Tissue- and stage-specific landscape of the mouse translatome
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Rescue of spinal muscular atrophy mouse models with AAV9-Exon-specific U1 snRNA
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Identification of small molecule modulators of HIV-1 Tat and Rev protein accumulation
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P2X7 Receptor Upregulation in Huntington’s Disease Brains
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The Many Faces of Microbiota-Gut-Brain Axis in Autism Spectrum Disorder
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Alternative microexon splicing by RBFOX2 and PTBP1 is associated with metastasis in colorectal cancer
Yasushi Mochizuki, Ryo Funayama, Matsuyuki Shirota, Yuna Kikukawa, Masahiro Ohira, Hideaki Karasawa, Minoru Kobayashi, Shinobu Ohnuma, Michiaki Unno, Keiko Nakayama · 2021 · International Journal of Cancer
Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases
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Striking circadian neuron diversity and cycling of Drosophila alternative splicing
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Single-cell long-read sequencing in human cerebral organoids uncovers cell-type-specific and autism-associated exons
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A systematic survey of human tissue-specific gene expression and splicing reveals new opportunities for therapeutic target identification and evaluation
Robert Yang, Jie Quan, Reza Sodaei, François Aguet, Ayellet V. Segrè, John Allen, Thomas A. Lanz, Veronica Reinhart, Matthew E. Crawford, Samuel A. Hasson et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2
Haissi Cui, Jolene K. Diedrich, Douglas C. Wu, Justin J. Lim, Ryan M. Nottingham, James J. Moresco, John R. Yates, Benjamin J. Blencowe, Alan M. Lambowitz, PAUL R. SCHIMMEL · 2023 · Nature Cell Biology
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Jennie J. Lin, Yu Hu, Sara Núñez, Andrea S. Foulkes, Benjamin Walter Cieply, Chenyi Xue, Mark Gerelus, Wenjun Li, Hanrui Zhang, Daniel James Rader et al. · 2016 · Arteriosclerosis Thrombosis and Vascular Biology
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MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development
Guillermo E. Parada, Roberto Munita, Ilias Georgakopoulos‐Soares, Hugo J. R. Fernandes, Veronika R. Kedlian, Emmanouil Metzakopian, Marı́a Estela Andrés, Eric Alexander Miska, Martin Hemberg · 2021 · Genome biology
A Novel Alternative Splicing Mechanism That Enhances Human 5-HT1A Receptor RNA Stability Is Altered in Major Depression
Brice Le François, Lei Zhang, Gouri Mahajan, Craig A. Stockmeier, Eitan Friedman, Paul R. Albert · 2018 · Journal of Neuroscience
QUAKING Regulates Microexon Alternative Splicing of the Rho GTPase Pathway and Controls Microglia Homeostasis
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When one becomes many—Alternative splicing in β‐cell function and failure
Maria Inês Alvelos, Jonàs Juan‐Mateu, Máikel L. Colli, Jean‐Valéry Turatsinze, Decio Laks Eizirik · 2018 · Diabetes Obesity and Metabolism
Alternative RNA splicing of the MEAF6 gene facilitates neuroendocrine prostate cancer progression
Ahn R. Lee, Yinan Li, Ning Xie · 2017 · Oncotarget
A single-nucleotide exon found in Arabidopsis
Lei Guo, Chunming Liu · 2015 · Scientific Reports
The Alter Retina: Alternative Splicing of Retinal Genes in Health and Disease
Izarbe Aísa-Marín, Rocío García-Arroyo, Serena Mirra, Gemma Marfany · 2021 · International Journal of Molecular Sciences
Temporal regulation of axonal repulsion by alternative splicing of a conserved microexon in mammalian Robo1 and Robo2
Verity R. Johnson, Harald J. Junge, Zhe Chen · 2019 · eLife
Spliceosomal component PRP-40 is a central regulator of microexon splicing
Bikash C. Choudhary, Olivia M. Marx, Adam D. Norris · 2021 · Cell Reports
Nanopore long-read sequencing of circRNAs
Karim Rahimi, Anne Færch Nielsen, Morten Trillingsgaard Venø · 2021 · Methods
How alternative splicing affects membrane-trafficking dynamics
R. Eric Blue, Ennessa G. Curry, Nichlas M. Engels, Eunice Y. Lee, Jimena Giudice · 2018 · Journal of Cell Science
Decoding mixed messages in the developing cortex: translational regulation of neural progenitor fate
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