Transcriptomics,Genomics

Dataset Information

91

DsRNAs expressed in C. elegans development


ABSTRACT: Cellular RNAs containing double-stranded RNA (dsRNA) structures are subject to A-to-I RNA editing by the adenosine deaminases that act on RNA (ADARs). While A-to-I editing can alter mRNA coding potential, most editing is observed in non-coding sequences, the function of which remains poorly characterized. Using a dsRNA immunoprecipitation and high-thoughput sequencing (dsRIP-Seq) approach, we identify 1523 expressed A-to-I edited regions and characterize their expression during Caenorhabditis elegans development. We observe that edited regions are highly expressed in early development and are closely associated with protein-coding genes. Edited dsRNA structures give rise to abundant small interfering RNAs (siRNAs) that are negatively correlated with ADAR expression and regulate the developmental expression of associated genes. Overall design: RNA-Seq of total RNA and RNA immunoprecipitated with a dsRNA-specific antibody (dsRIP) from whole C. elegans at four stages of development: embryos, early stage larvae (L1-L2), late stage larvae (L3-L4), and young adults.

INSTRUMENT(S): Illumina HiSeq 2000 (Caenorhabditis elegans)

SUBMITTER: Brenda L Bass  

PROVIDER: GSE79375 | GEO | 2018-02-23

REPOSITORIES: GEO

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Publications

C. elegans ADARs antagonize silencing of cellular dsRNAs by the antiviral RNAi pathway.

Reich Daniel P DP   Tyc Katarzyna M KM   Bass Brenda L BL  

Genes & development 20180226 3-4


Cellular dsRNAs are edited by adenosine deaminases that act on RNA (ADARs). While editing can alter mRNA-coding potential, most editing occurs in noncoding sequences, the function of which is poorly understood. Using dsRNA immunoprecipitation (dsRIP) and RNA sequencing (RNA-seq), we identified 1523 regions of clustered A-to-I editing, termed editing-enriched regions (EERs), in four stages of Caenorhabditis elegans development, often with highest expression in embryos. Analyses of small RNA-seq d  ...[more]

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