Table 1 Whole transcriptome mRNA editing screening studies in vertebrates
StudySpeciesCellsEdited Sites (N)Matched DNAaReplicatesbPotential Biases
(Ju et al. 2011)H. sapiensImmortalized B cells1809Yes2/17Splice, homopolymer, strand, extremity
(Li et al. 2011)H. sapiensImmortalized B cells28,766Yes2/27Splice, homopolymer, multimapping, strand, extremity
(Bahn et al. 2011)H. sapiensGlioblastoma cells10,000No2/2Splice, homopolymer, multimapping, strand, extremity
(Peng et al. 2012)H. sapiensImmortalized B cells22,688Yes1/1Splice, homopolymer, extremity
(Park et al. 2012)H. sapiens14 ENCODE cell lines5695No1/1Homopolymer, extremity, multimapping
(Kleinman et al. 2012)H. sapiensImmortalized B cells1503Yes1/2Homopolymer
(Ramaswami et al. 2012)H. sapiensENCODE cell lines150,865No1/2Strand, multimapping
(Picardi et al. 2012)H. sapiensSpinal cord cells15Yes (Exome)1/1Homopolymer, multimapping, strand
(Bazak et al. 2014)H. sapiens16 tissues1,586,270No1/1Homopolymer, multimapping, strand
(Chen 2013)H. sapiens7 ENCODE cell lines259,385No1/2Multimapping
(Chan et al. 2014)H. sapiensLiver cells20,007No1/3Splice, homopolymer, multimapping, strand, extremity
(Mo et al. 2014)H. sapiensProstate cancer cells16,194Yes2/10Homopolymer, multimapping, strand, extremity
(Sakurai et al. 2014)H. sapiensBrain cells19,791No1/1Splice, homopolymer, multimapping, strand, extremity
(Toung et al. 2014)H. sapiensImmortalized B cells5997No2/2Multimapping, strand, extremity
(Zhang and Xiao 2015)H. sapiensImmortalized B cells22,715No1/1Multimapping, extremity
(Hu et al. 2015)H. sapiensHepatocellular carcinoma cells900Yes6/6Splice, multimapping, strand
(Kang et al. 2015)H. sapiensLiver cells485,684Yes1/9Splice, multimapping, strand
(Danecek et al. 2012)M. musculusBrain cells7389No2/2Homopolymer, multimapping
(Gu et al. 2012)M. musculusLiver, adipose, and bone cells253No3/3Homopolymer, multimapping, extremity
(Lagarrigue et al. 2013)M. musculusLiver and adipose cells63 and 188No4/6Multimapping
(Cattenoz et al. 2013)M. musculusBrain cells665No1/1Splice, homopolymer, multimapping, strand, extremity
(Blanc et al. 2014)M. musculusIntestine and liver cells500No1/1Homopolymer, multimapping, extremity
(Chen et al. 2014)R. macaquePrefrontal cortex, cerebellum, muscle, kidney, heart, testis, and lung cells31,250Yes1/1Homopolymer, multimapping, extremity
Frésard et al. 2015G. gallusWhole embryo40Yes2/8
Roux et al. (The present study)G. gallusLiver and adipose cells11 and 17Yes3/8
  • a If “Yes”: individual genomic DNA information is used to account for potential private individual genomic polymorphisms. If “No”: potential private genomic polymorphisms are defined considering either genomic variant databases such as dbSNPs, or strain-specific consensus genomic sequence in the case of studies based on clonal mouse strains.

  • b Ratio between the number of biological replicates considered for reporting a candidate difference between DNA and mRNA as a true mRNA editing event and the total number of biological replicates available in the study for a given cell type.