title: HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism.
abstract: The RNA binding proteins Rbfox1/2/3 regulate alternative splicing in the nervous system, and disruption of Rbfox1 has been implicated in autism. However, comprehensive identification of functional Rbfox targets has been challenging. Here, we perform HITS-CLIP for all three Rbfox family members in order to globally map, at a single-nucleotide resolution, their in vivo RNA interaction sites in the mouse brain. We find that the two guanines in the Rbfox binding motif UGCAUG are critical for protein-RNA interactions and crosslinking. Using integrative modeling, these interaction sites, combined with additional datasets, define 1,059 direct Rbfox target alternative splicing events. Over half of the quantifiable targets show dynamic changes during brain development. Of particular interest are 111 events from 48 candidate autism-susceptibility genes, including syndromic autism genes Shank3, Cacna1c, and Tsc2. Alteration of Rbfox targets in some autistic brains is correlated with downregulation of all three Rbfox proteins, supporting the potential clinical relevance of the splicing-regulatory network.
authors.affiliation: Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA.
authors.forename: Sebastien M
authors.initials: SM
authors.lastname: Weyn-Vanhentenryck
authors.affiliation: Howard Hughes Medical Institute, Laboratory of Molecular Neuro-Oncology, Rockefeller University, New York, NY 10065, USA.
authors.forename: Aldo
authors.initials: A
authors.lastname: Mele
authors.affiliation: Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA.
authors.forename: Qinghong
authors.initials: Q
authors.lastname: Yan
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Shuying
authors.initials: S
authors.lastname: Sun
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Natalie
authors.initials: N
authors.lastname: Farny
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Merck Research Laboratories, Merck & Co., Inc., Rahway, NJ 07065, USA.
authors.forename: Zuo
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
authors.forename: Chenghai
authors.initials: C
authors.lastname: Xue
authors.affiliation: Howard Hughes Medical Institute, Laboratory of Molecular Neuro-Oncology, Rockefeller University, New York, NY 10065, USA.
authors.forename: Margaret
authors.initials: M
authors.lastname: Herre
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Pamela A
authors.initials: PA
authors.lastname: Silver
authors.affiliation: Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA; Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China.
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
authors.forename: Adrian R
authors.initials: AR
authors.lastname: Krainer
authors.affiliation: Howard Hughes Medical Institute, Laboratory of Molecular Neuro-Oncology, Rockefeller University, New York, NY 10065, USA. Electronic address: darnelr@rockefeller.edu.
authors.forename: Robert B
authors.initials: RB
authors.lastname: Darnell
authors.affiliation: Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA. Electronic address: cz2294@columbia.edu.
authors.forename: Chaolin
authors.initials: C
authors.lastname: Zhang
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001321:Autistic Disorder / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D001921:Brain / Q000254:growth & development* / Q000378:metabolism; D005091:Exons; D053263:Gene Regulatory Networks; D020022:Genetic Predisposition to Disease; D006801:Humans; D047468:Immunoprecipitation; D051379:Mice; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012313:RNA / Q000235:genetics* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D016601:RNA-Binding Proteins; D012097:Repressor Proteins; D012313:RNA