title: RNA-sequencing of a mouse-model of spinal muscular atrophy reveals tissue-wide changes in splicing of U12-dependent introns.
abstract: Spinal Muscular Atrophy (SMA) is a neuromuscular disorder caused by insufficient levels of the Survival of Motor Neuron (SMN) protein. SMN is expressed ubiquitously and functions in RNA processing pathways that include trafficking of mRNA and assembly of snRNP complexes. Importantly, SMA severity is correlated with decreased snRNP assembly activity. In particular, the minor spliceosomal snRNPs are affected, and some U12-dependent introns have been reported to be aberrantly spliced in patient cells and animal models. SMA is characterized by loss of motor neurons, but the underlying mechanism is largely unknown. It is likely that aberrant splicing of genes expressed in motor neurons is involved in SMA pathogenesis, but increasing evidence indicates that pathologies also exist in other tissues. We present here a comprehensive RNA-seq study that covers multiple tissues in an SMA mouse model. We show elevated U12-intron retention in all examined tissues from SMA mice, and that U12-dependent intron retention is induced upon siRNA knock-down of SMN in HeLa cells. Furthermore, we show that retention of U12-dependent introns is mitigated by ASO treatment of SMA mice and that many transcriptional changes are reversed. Finally, we report on missplicing of several Ca2+channel genes that may explain disrupted Ca2+homeostasis in SMA and activation of Cdk5.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.|The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark.
authors.forename: Thomas Koed
authors.initials: TK
authors.lastname: Doktor
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
authors.forename: Yimin
authors.initials: Y
authors.lastname: Hua
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.|The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark.
authors.forename: Henriette Skovgaard
authors.initials: HS
authors.lastname: Andersen
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.|The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Brøner
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
authors.forename: Ying Hsiu
authors.initials: YH
authors.lastname: Liu
authors.affiliation: Department of Gamete and Embryo Biology, Division of Reproductive Biology, Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, 10-243 Olsztyn, Poland.
authors.forename: Anna
authors.initials: A
authors.lastname: Wieckowska
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.|The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark.
authors.forename: Maja
authors.initials: M
authors.lastname: Dembic
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.|The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark.
authors.forename: Gitte Hoffmann
authors.initials: GH
authors.lastname: Bruun
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
authors.forename: Adrian R
authors.initials: AR
authors.lastname: Krainer
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark bragea@bmb.sdu.dk.|The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark.
authors.forename: Brage Storstein
authors.initials: BS
authors.lastname: Andresen
mesh_terms: D000818:Animals; D002118:Calcium / Q000378:metabolism; D015220:Calcium Channels / Q000172:deficiency / Q000235:genetics; D004195:Disease Models, Animal; D005260:Female; D006367:HeLa Cells; D006801:Humans; D007438:Introns; D008297:Male; D051379:Mice; D009046:Motor Neurons / Q000378:metabolism / Q000473:pathology; D009134:Muscular Atrophy, Spinal / Q000235:genetics* / Q000378:metabolism / Q000473:pathology / Q000628:therapy; D016376:Oligonucleotides, Antisense / Q000008:administration & dosage / Q000235:genetics / Q000378:metabolism; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D017411:Ribonucleoproteins, Small Nuclear / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013116:Spinal Cord / Q000378:metabolism / Q000473:pathology; D055533:Survival of Motor Neuron 1 Protein / Q000037:antagonists & inhibitors / Q000235:genetics* / Q000378:metabolism; D055540:Survival of Motor Neuron 2 Protein / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism
chemical_list: D015220:Calcium Channels; D016376:Oligonucleotides, Antisense; D012333:RNA, Messenger; D017411:Ribonucleoproteins, Small Nuclear; C526471:SMN1 protein, human; C526477:SMN2 protein, human; D055533:Survival of Motor Neuron 1 Protein; D055540:Survival of Motor Neuron 2 Protein; C552126:U11-U12 small nuclear ribonucleoprotein; D002118:Calcium