title: Position-specific binding of FUS to nascent RNA regulates mRNA length.
abstract: More than half of all human genes produce prematurely terminated polyadenylated short mRNAs. However, the underlying mechanisms remain largely elusive. CLIP-seq (cross-linking immunoprecipitation [CLIP] combined with deep sequencing) of FUS (fused in sarcoma) in neuronal cells showed that FUS is frequently clustered around an alternative polyadenylation (APA) site of nascent RNA. ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing) of RNA polymerase II (RNAP II) demonstrated that FUS stalls RNAP II and prematurely terminates transcription. When an APA site is located upstream of an FUS cluster, FUS enhances polyadenylation by recruiting CPSF160 and up-regulates the alternative short transcript. In contrast, when an APA site is located downstream from an FUS cluster, polyadenylation is not activated, and the RNAP II-suppressing effect of FUS leads to down-regulation of the alternative short transcript. CAGE-seq (cap analysis of gene expression [CAGE] combined with deep sequencing) and PolyA-seq (a strand-specific and quantitative method for high-throughput sequencing of 3' ends of polyadenylated transcripts) revealed that position-specific regulation of mRNA lengths by FUS is operational in two-thirds of transcripts in neuronal cells, with enrichment in genes involved in synaptic activities.
authors.affiliation: Division of Neurogenetics, Center for Neurological Diseases and Cancer, Showa-ku, Nagoya 466-8550, Japan;
authors.forename: Akio
authors.initials: A
authors.lastname: Masuda
authors.affiliation: Division of Neurogenetics, Center for Neurological Diseases and Cancer, Showa-ku, Nagoya 466-8550, Japan;
authors.forename: Jun-ichi
authors.initials: J
authors.lastname: Takeda
authors.affiliation: Division of Neurogenetics, Center for Neurological Diseases and Cancer, Showa-ku, Nagoya 466-8550, Japan;
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Okuno
authors.affiliation: Division of Neurogenetics, Center for Neurological Diseases and Cancer, Showa-ku, Nagoya 466-8550, Japan;
authors.forename: Takaaki
authors.initials: T
authors.lastname: Okamoto
authors.affiliation: Division of Neurogenetics, Center for Neurological Diseases and Cancer, Showa-ku, Nagoya 466-8550, Japan;
authors.forename: Bisei
authors.initials: B
authors.lastname: Ohkawara
authors.affiliation: Division of Neurogenetics, Center for Neurological Diseases and Cancer, Showa-ku, Nagoya 466-8550, Japan;
authors.forename: Mikako
authors.initials: M
authors.lastname: Ito
authors.affiliation: Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan.
authors.forename: Shinsuke
authors.initials: S
authors.lastname: Ishigaki
authors.affiliation: Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan.
authors.forename: Gen
authors.initials: G
authors.lastname: Sobue
authors.affiliation: Division of Neurogenetics, Center for Neurological Diseases and Cancer, Showa-ku, Nagoya 466-8550, Japan; ohnok@med.nagoya-u.ac.jp.
authors.forename: Kinji
authors.initials: K
authors.lastname: Ohno
mesh_terms: D000818:Animals; D045744:Cell Line, Tumor; D039223:Cleavage And Polyadenylation Specificity Factor / Q000378:metabolism; D005786:Gene Expression Regulation; D055785:Gene Knockdown Techniques; D057809:HEK293 Cells; D006801:Humans; D051379:Mice; D026723:Polyadenylation; D011485:Protein Binding; D012313:RNA / Q000378:metabolism*; D012319:RNA Polymerase II / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism*; D034702:RNA-Binding Protein FUS / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D039223:Cleavage And Polyadenylation Specificity Factor; D012333:RNA, Messenger; D034702:RNA-Binding Protein FUS; D012313:RNA; D012319:RNA Polymerase II
keywords: CLIP; FUS; RNA polymerase II; alternative polyadenylation; mRNA length