title: RNA targets of TDP-43 identified by UV-CLIP are deregulated in ALS.
abstract: TDP-43 is a predominantly nuclear DNA/RNA binding protein involved in transcriptional regulation and RNA processing. TDP-43 is also a component of the cytoplasmic inclusion bodies characteristic of amyotrophic lateral sclerosis (ALS) and of frontotemporal lobar degeneration with ubiquitinated inclusions (FTLD-U). We have investigated the premise that abnormalities of TDP-43 in disease would be reflected by changes in processing of its target RNAs. To this end, we have firstly identified RNA targets of TDP-43 using UV-Cross-Linking and Immunoprecipitation (UV-CLIP) of SHSY5Y cells, a human neuroblastoma cell line. We used conventional cloning strategies to identify, after quality control steps, 127 targets. Results show that TDP-43 binds mainly to introns at UG/TG repeat motifs (49%) and polypyrimidine rich sequences (17.65%). To determine if the identified RNA targets of TDP-43 were abnormally processed in ALS versus control lumbar spinal cord RNA, we performed RT-PCR using primers designed according to the location of TDP-43 binding within the gene, and prior evidence of alternative splicing of exons adjacent to this site. Of eight genes meeting these criteria, five were differentially spliced in ALS versus control. This supports the premise that abnormalities of TDP-43 in ALS are reflected in changes of RNA processing.
authors.affiliation: Centre for Research in Neurodegenerative Diseases, Department of Laboratory Medicine and Pathobiology, University of Toronto, 6 Queen's Park Crescent West, Toronto, Ontario, Canada M5S 3H2.
authors.forename: Shangxi
authors.initials: S
authors.lastname: Xiao
authors.forename: Teresa
authors.initials: T
authors.lastname: Sanelli
authors.forename: Samar
authors.initials: S
authors.lastname: Dib
authors.forename: David
authors.initials: D
authors.lastname: Sheps
authors.forename: Joseph
authors.initials: J
authors.lastname: Findlater
authors.forename: Juan
authors.initials: J
authors.lastname: Bilbao
authors.forename: Julia
authors.initials: J
authors.lastname: Keith
authors.forename: Lorne
authors.initials: L
authors.lastname: Zinman
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Rogaeva
authors.forename: Janice
authors.initials: J
authors.lastname: Robertson
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D000690:Amyotrophic Lateral Sclerosis / Q000235:genetics / Q000378:metabolism*; D045744:Cell Line, Tumor; D019976:Cloning, Organism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D005260:Female; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods; D008297:Male; D008875:Middle Aged; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D012326:RNA Splicing; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D013116:Spinal Cord / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D016601:RNA-Binding Proteins; D012313:RNA