title: Limited RNA editing in exons of mouse liver and adipose.
abstract: Several studies have investigated RNA-DNA differences (RDD), presumably due to RNA editing, with conflicting results. We report a rigorous analysis of RDD in exonic regions in mice, taking into account critical biases in RNA-Seq analysis. Using deep-sequenced F1 reciprocal inbred mice, we mapped 40 million RNA-Seq reads per liver sample and 180 million reads per adipose sample. We found 7300 apparent hepatic RDDs using a multiple-site mapping procedure, compared with 293 RDD found using a unique-site mapping procedure. After filtering for repeat sequence, splice junction proximity, undirectional strand, and extremity read bias, 63 RDD remained. In adipose tissue unique-site mapping identified 1667 RDD, and after applying the same four filters, 188 RDDs remained. In both tissues, the filtering procedure increased the proportion of canonical (A-to-I and C-to-U) editing events. The genomic DNA of 12 RDD sites among the potential 63 hepatic RDD was tested by Sanger sequencing, three of which proved to be due to unreferenced SNPs. We validated seven liver RDD with Sequenom technology, including two noncanonical, Gm5424 C-to-I(G) and Pisd I(G)-to-A RDD. Differences in diet, sex, or genetic background had very modest effects on RDD occurrence. Only a small number of apparent RDD sites overlapped between liver and adipose, indicating a high degree of tissue specificity. Our findings underscore the importance of properly filtering for bias in RNA-Seq investigations, including the necessity of confirming the DNA sequence to eliminate unreferenced SNPs. Based on our results, we conclude that RNA editing is likely limited to hundreds of events in exonic RNA in liver and adipose.
authors: Agrocampus Ouest, Unité Mixte de Recherche (UMR) 1348 Physiology, Environment and Genetics for the Animal and Livestock Systems (PEGASE), Animal Genetics Laboratory, F-35000 Rennes, France.
authors: Sandrine
authors: S
authors: Lagarrigue
authors: Farhad
authors: F
authors: Hormozdiari
authors: Lisa J
authors: LJ
authors: Martin
authors: Frédéric
authors: F
authors: Lecerf
authors: Yehudit
authors: Y
authors: Hasin
authors: Christoph
authors: C
authors: Rau
authors: Raffi
authors: R
authors: Hagopian
authors: Yu
authors: Y
authors: Xiao
authors: Jun
authors: J
authors: Yan
authors: Thomas A
authors: TA
authors: Drake
authors: Anatole
authors: A
authors: Ghazalpour
authors: Eleazar
authors: E
authors: Eskin
authors: Aldons J
authors: AJ
authors: Lusis
mesh_terms: D000273:Adipose Tissue / Q000378:metabolism*; D000818:Animals; D005091:Exons; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D008099:Liver / Q000378:metabolism*; D051379:Mice; D009928:Organ Specificity; D020641:Polymorphism, Single Nucleotide; D017393:RNA Editing; D017422:Sequence Analysis, DNA