Small and large RNA sequencing of mouse livers during development and after miR-122 exicision

miR-122 is a highly-expressed liver microRNA that is activated perinatally and aids in regulating cholesterol metabolism and promoting terminal differentiation of hepatocytes. Disrupting expression of miR-122 can re-activate embryo-expressed adult-silenced genes, ultimately leading to the development of hepatocellular carcinoma (HCC). We interrogated the liver transcriptome at various time points after genomic excision of miR-122 to determine the cellular consequences leading to oncogenesis. Loss of miR-122 led to specific and progressive increases in expression of imprinted clusters of microRNAs and mRNA transcripts at the Igf2 and Dlk1-Dio3 loci that could be curbed by re-introduction of exogenous miR-122. mRNA targets of other abundant hepatic microRNAs became functionally repressed leading to widespread hepatic transcriptional de-regulation. Together, this reveals a transcriptomic framework for the hepatic response to loss of miR-122 and the outcome on other microRNAs and their cognate gene targets. RNA sequencing of 14 liver samples of mice with LoxP sites surrounding mature miR-122. Triplicate of uninjected mice and mice harvested 21, and 45 days after receiving AAV-Cre and one mouse each 100 or 200 days after Cre. Triplicate liver samples of additional germline miR-122 knockout mice. Small RNA sequencing of the same liver samples along with additional time points after Cre removal of miR-122. Small RNA sequencing of livers of wildtype 129Sv/J mice at various stages of embryo and post-natal development.