Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA editing targets in transcript 3'UTRs. Mus musculus

Apolipoprotein B-editing enzyme, catalytic polypeptide-1 (APOBEC1) is a cytidine deaminase, initially identified by its activity in converting a specific cytidine (C) to uridine (U) in apolipoprotein B (apoB) mRNA transcripts in the small intestine. Editing results in translation of a truncated apoB isoform with distinct functions in lipid transport. To address the possibility that APOBEC1 edits additional mRNAs, we developed a transcriptome-wide comparative RNA-Seq screen. We identified and validated 32 previously undescribed mRNA targets of APOBEC1 editing, all of which are located in AU-rich segments of transcript 3′ untranslated regions (3′ UTRs). Further analysis revealed several characteristic sequence features of editing targets, which were predictive for the identification of additional APOBEC1 substrates. The identification of multiple mRNA editing substrates for APOBEC1 suggests additional functions for this cytidine deaminase beyond its characterized role in lipid absorption. Overall design: Poly(A)+ RNA-Seq libraries were prepared from C57Bl6 Wild-type and congenic Apobec1-/- murine small intestinal epithelial cells (2 samples total).

载脂蛋白B编辑酶催化多肽1（Apolipoprotein B-editing enzyme, catalytic polypeptide-1，简称APOBEC1）是一种胞苷脱氨酶，最初因其在小肠内将载脂蛋白B（apolipoprotein B，apoB）mRNA转录本中特定胞苷（C）转化为尿苷（U）的活性而被鉴定。编辑过程会介导截短型载脂蛋白B同工型的翻译，该同工型在脂质转运中发挥独特功能。为探究APOBEC1是否可编辑其他mRNA的可能性，我们开发了全转录组范围的比较RNA测序（RNA-Seq）筛选策略。我们成功鉴定并验证了32个此前未被报道的APOBEC1编辑mRNA靶点，所有靶点均位于转录本3'非翻译区（3' UTR）的富AU序列片段中。进一步分析揭示了编辑靶点的若干特征性序列特征，这些特征可用于预测其他APOBEC1底物。对APOBEC1多种mRNA编辑底物的鉴定表明，该胞苷脱氨酶除已被证实的脂质吸收相关功能外，还存在其他额外生物学功能。整体实验设计：从C57Bl6野生型及同基因Apobec1敲除（Apobec1-/-）小鼠小肠上皮细胞中制备聚腺苷酸化RNA（Poly(A)+）测序文库，共包含2个样本。