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Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism

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  • Neelroop N. Parikshak

    (Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles
    David Geffen School of Medicine, University of California Los Angeles)

  • Vivek Swarup

    (Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles
    David Geffen School of Medicine, University of California Los Angeles)

  • T. Grant Belgard

    (Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles
    David Geffen School of Medicine, University of California Los Angeles)

  • Manuel Irimia

    (Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST)
    Universitat Pompeu Fabra (UPF))

  • Gokul Ramaswami

    (Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles
    David Geffen School of Medicine, University of California Los Angeles)

  • Michael J. Gandal

    (Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles
    David Geffen School of Medicine, University of California Los Angeles)

  • Christopher Hartl

    (Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles
    David Geffen School of Medicine, University of California Los Angeles)

  • Virpi Leppa

    (Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles)

  • Luis de la Torre Ubieta

    (Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles
    David Geffen School of Medicine, University of California Los Angeles)

  • Jerry Huang

    (Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles
    David Geffen School of Medicine, University of California Los Angeles)

  • Jennifer K. Lowe

    (Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles)

  • Benjamin J. Blencowe

    (Donnelly Centre, University of Toronto
    University of Toronto)

  • Steve Horvath

    (David Geffen School of Medicine, University of California
    David Geffen School of Medicine, University of California)

  • Daniel H. Geschwind

    (Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles
    David Geffen School of Medicine, University of California Los Angeles
    David Geffen School of Medicine, University of California)

Abstract

Gene expression analysis in brain tissue from individuals with and without autism spectrum disorder (ASD) suggests that the transcription factor SOX5 contributes to an ASD-associated reduction in transcriptional differences between brain areas and indicates that common transcriptomic changes occur in different forms of ASD.

Suggested Citation

  • Neelroop N. Parikshak & Vivek Swarup & T. Grant Belgard & Manuel Irimia & Gokul Ramaswami & Michael J. Gandal & Christopher Hartl & Virpi Leppa & Luis de la Torre Ubieta & Jerry Huang & Jennifer K. Lo, 2016. "Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism," Nature, Nature, vol. 540(7633), pages 423-427, December.
    • Handle: RePEc:nat:nature:v:540:y:2016:i:7633:d:10.1038_nature20612
    DOI: 10.1038/nature20612
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    Cited by:

    1. Elaine T. Lim & Yingleong Chan & Pepper Dawes & Xiaoge Guo & Serkan Erdin & Derek J. C. Tai & Songlei Liu & Julia M. Reichert & Mannix J. Burns & Ying Kai Chan & Jessica J. Chiang & Katharina Meyer & , 2022. "Orgo-Seq integrates single-cell and bulk transcriptomic data to identify cell type specific-driver genes associated with autism spectrum disorder," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Gavin J. Sutton & Daniel Poppe & Rebecca K. Simmons & Kieran Walsh & Urwah Nawaz & Ryan Lister & Johann A. Gagnon-Bartsch & Irina Voineagu, 2022. "Comprehensive evaluation of deconvolution methods for human brain gene expression," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    3. Iva Salamon & Yongkyu Park & Terezija Miškić & Janja Kopić & Paul Matteson & Nicholas F. Page & Alfonso Roque & Geoffrey W. McAuliffe & John Favate & Marta Garcia-Forn & Premal Shah & Miloš Judaš & Ja, 2023. "Celf4 controls mRNA translation underlying synaptic development in the prenatal mammalian neocortex," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    4. Marco Pagani & Noemi Barsotti & Alice Bertero & Stavros Trakoshis & Laura Ulysse & Andrea Locarno & Ieva Miseviciute & Alessia De Felice & Carola Canella & Kaustubh Supekar & Alberto Galbusera & Vinod, 2021. "mTOR-related synaptic pathology causes autism spectrum disorder-associated functional hyperconnectivity," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    5. Takeshi Kaizuka & Takehiro Suzuki & Noriyuki Kishi & Kota Tamada & Manfred W. Kilimann & Takehiko Ueyama & Masahiko Watanabe & Tomomi Shimogori & Hideyuki Okano & Naoshi Dohmae & Toru Takumi, 2024. "Remodeling of the postsynaptic proteome in male mice and marmosets during synapse development," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    6. Hillary M. Heiling & Douglas R. Wilson & Naim U. Rashid & Wei Sun & Joseph G. Ibrahim, 2023. "Estimating cell type composition using isoform expression one gene at a time," Biometrics, The International Biometric Society, vol. 79(2), pages 854-865, June.

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