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Figure 1 | Genome Biology

Figure 1

From: Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver

Figure 1

RNA-seq identification of Apobec-1-dependent RNA-editing targets. (A) RNA-seq procedure and analyses of 3' UTR C-to-U calls identified in wild-type (WT) small intestine and liver. Five murine lines with distinctive Apobec-1 expression profiles were used for intestinal transcriptome analysis. Apobec-1-/- mice exhibit no intestinal or hepatic apoB RNA editing. Apobec-1Int/+, intestine-specific Apobec-1 transgenic mice [15], were crossed with Apobec-1-/- mice generating Apobec-1Int/OHi and Apobec-1Int/OLo transgenic mice, with high (Hi) and low (Lo) levels of Apobec-1 expression [15]. WT hepatic transcriptomes were compared to Apobec-1-/- mice. Apobec-1-/- + ad-Apobec-1 or ad-LacZ indicates Apobec-1-/- mice injected with adenovirus expressing Apobec-1 or Lac Z. Overexpression of Apobec-1 in the liver restores apoB RNA editing. Uniquely mapped reads were aligned to the C57BL/6 mouse genome (NCBI37/mm9) containing 23,334 reference genes. To minimize false positive calls, sites identified in both WT and Apobec-1-/- mice, known SNPs from dbSNP128 and sites lying outside the gene boundaries were excluded. The remaining sites were corrected for strand sense and qualified when supported by 3 minimum non-identical reads, a minimum frequency of 10% with a minimum coverage of 10 reads. An arbitrary cutoff of 30% editing frequency was set to sequence-validate calls identified in the intestine. Due to the low number of calls identified in WT liver, all calls (27) were sequenced. (B) Numbers of C-to-U editing events and RNAs Sanger-sequence-validated (SSV). Blue circles represent the 56 3' UTR C-to-U calls identified in 54 WT intestine RNAs. Red circles show the 22 validated C-to-U sites identified in 17 hepatic RNAs. The shaded regions represent the 11 C-to-U sites or RNAs identified in both small intestine and liver. Forty-five sites were specific to the intestine, 11 were liver-specific.

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