Identification of dysregulated genes after deletion of miR-1-1 and miR-1-2
Purpose: The goals of this study are to identify dysregulated mRNAs in the heart after deletion of miR-1-1 and miR-1-2.  Methods: Total RNAs were extracted from hearts at embryonic E15.5 (E15.5) or postnatal 2.5 days (P2.5) of miR-1s dHET and miR-1s dKO mice. mRNAs were purified using a poly-A selection approach and sequenced using Illumina HiSeq 2000. The sequence reads were aligned to the mouse reference genome (NCBI Build 37/mm9) using TopHat program (Bowtie algorithm). Transcript assembles and identification of differentially expressed genes were achieved using Cufflinks package. To account for expression bias due to transcript length, each sample transcript expression was normalized by using cufflinks algorithm with a FDR of 0.05.  Results: Using 1.5-fold change as a cutoff, 997 and 653 transcripts were found to be upregulated and downregulated, respectively, in miR-1s dKO heart at P2.5. 423 transcripts were found to be upregulated and 653 were down-regulated in miR-1s dKO heart at E15.5. Many upregulated genes are directly involved in a fetal gene program.  Conclusions: miR-1 directly represses a fetal gene program. Overall design: We performed RNA deep-seq using postnatal 2.5 days (P2.5) heart from miR-1-1 and miR-1-2 double knockout mice and compared it to that of littermate control.