E-GEOD-44384 - Transcription profiling by high throughput sequencing of HEK293 cells transfected with siRNA against Nsun2

Released on 23 July 2013, last updated on 12 April 2016
Homo sapiens
Samples (8)
Protocols (3)
Autosomal-recessive loss of the NSUN2 gene has been recently identified as a causative link to intellectual disability disorders in humans. NSun2 is an RNA methyltransferase modifying cytosine-5 in transfer RNAs (tRNA). Whether NSun2 methylates additional RNA species is currently debated. Here, we adapted the individual-nucleotide resolution UV cross-linking and immunoprecipitation method (iCLIP) to identify NSun2-mediated methylation in RNA transcriptome. We confirm site-specific methylation in tRNA and identify messenger and non-coding RNAs as potential methylation targets for NSun2. Using RNA bisulfite sequencing we establish Vault non-coding RNAs as novel substrates for NSun2 and identified six cytosine-5 methylated sites. Furthermore, we show that loss of cytosine-5 methylation in Vault RNAs causes aberrant processing into argonaute-associating small RNA fragments (svRNA). Thus, impaired Vault non-coding RNA processing may be an important contributor to the etiology of NSUN2-deficieny human disorders. mRNA-seq in Embryonic kidney (HEK293) cells transfected with siRNA against Nsun2 vs control
Experiment type
RNA-seq of coding RNA 
Shobbir Hussain
NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs. Hussain S, Sajini AA, Blanco S, Dietmann S, Lombard P, Sugimoto Y, Paramor M, Gleeson JG, Odom DT, Ule J, Frye M. , Europe PMC 23871666
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-44384.idf.txt
Sample and data relationshipE-GEOD-44384.sdrf.txt
Processed data (1)E-GEOD-44384.processed.1.zip