title: Contextual fear conditioning induces differential alternative splicing.
abstract: The process of memory consolidation requires transcription and translation to form long-term memories. Significant effort has been dedicated to understanding changes in hippocampal gene expression after contextual fear conditioning. However, alternative splicing by differential transcript regulation during this time period has received less attention. Here, we use RNA-seq to determine exon-level changes in expression after contextual fear conditioning and retrieval. Our work reveals that a short variant of Homer1, Ania-3, is regulated by contextual fear conditioning. The ribosome biogenesis regulator Las1l, small nucleolar RNA Snord14e, and the RNA-binding protein Rbm3 also change specific transcript usage after fear conditioning. The changes in Ania-3 and Las1l are specific to either the new context or the context-shock association, while the changes in Rbm3 occur after context or shock only. Our analysis revealed novel transcript regulation of previously undetected changes after learning, revealing the importance of high throughput sequencing approaches in the study of gene expression changes after learning.
authors.affiliation: Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA.
authors.forename: Shane G
authors.initials: SG
authors.lastname: Poplawski
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA, USA; Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA.
authors.forename: Lucia
authors.initials: L
authors.lastname: Peixoto
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
authors.forename: Giulia S
authors.initials: GS
authors.lastname: Porcari
authors.affiliation: Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA.
authors.forename: Mathieu E
authors.initials: ME
authors.lastname: Wimmer
authors.affiliation: Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA.
authors.forename: Anna G
authors.initials: AG
authors.lastname: McNally
authors.affiliation: Centre for the Cellular Basis of Behaviour, King's College London, London, UK.
authors.forename: Keiko
authors.initials: K
authors.lastname: Mizuno
authors.affiliation: Centre for the Cellular Basis of Behaviour, King's College London, London, UK.
authors.forename: K Peter
authors.initials: KP
authors.lastname: Giese
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
authors.forename: Snehajyoti
authors.initials: S
authors.lastname: Chatterjee
authors.affiliation: Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA.
authors.forename: John N
authors.initials: JN
authors.lastname: Koberstein
authors.affiliation: Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA.
authors.forename: Davide
authors.initials: D
authors.lastname: Risso
authors.affiliation: Department of Statistics, University of California, Berkeley, CA, USA; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Mathematics and Statistics, The University of Melbourne, Victoria, Australia.
authors.forename: Terence P
authors.initials: TP
authors.lastname: Speed
authors.affiliation: Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA, USA. Electronic address: abele@sas.upenn.edu.
authors.forename: Ted
authors.initials: T
authors.lastname: Abel
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D001522:Behavior, Animal / Q000502:physiology*; D003214:Conditioning, Classical / Q000502:physiology*; D005239:Fear; D015870:Gene Expression / Q000235:genetics*; D006624:Hippocampus / Q000378:metabolism*; D000072233:Homer Scaffolding Proteins / Q000235:genetics*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D020033:Protein Isoforms; D017423:Sequence Analysis, RNA
chemical_list: D000072233:Homer Scaffolding Proteins; C000606623:Homer1 protein, mouse; D020033:Protein Isoforms
keywords: Alternative splicing; Fear conditioning; Homer1; RNA-seq; Transcription