ATAC-seq Analysis in Control and Mier1 KO Mice Liver at 0 h and 24 h after 70% Partial Hepatectomy

To explore how Mier1 affects liver regeneration, we specifically knocked out Mier1 in mouse liver through adeno-associated virus (AAV). The mice we used were knocked in a Cre-induced Cas9 expression cassette. Through tail vein injection, we delivered the AAV expressing Cre-recombinase under TBG promoter, and sgRNA targeting Mier1 (AAV-Mier1 sgRNA), into the adult Cas9 knockin mice to knock out the Mier1 gene in liver. AAV vectors with no sgRNA inserted (AAV-Cre) were used in control animals. To assess the role of MIER1 in liver regeneration, we performed 70% partial hepatectomy, 3 weeks after AAV injection. We then performed ATAC-seq in Control and Mier1 liver-sepcific knockout mice liver tissues at 0 h and 24 h after PHx to explore the influence of Mier1 on the chromation opening during liver regeneration. Overall design: For the ATAC-seq analysis, nuclei were extracted from frozen liver tissues. 30mg frozen liver tissue from 3 different samples was added into a pre-chilled 1mL Dounce with 1mL cold homogenization buffer, then dounce with loose pestle for 10 strokes and dounce with tight pestle for 25 strokes. After centrifugation to remove larger cellular debris from the homogenized liver fluid, the supernatant containing the nuclei was further purified by gradient density centrifugation. 50,000 purified nuclei were used to generated ATAC-seq libraries by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501). Final libraries were purified and size selected using VAHTS DNA Clean Beads (Vazyme, N411). ATAC libraries were sequenced using 2×150bp Illumina HiSeq. Liver tissues were collected for analysis at 0 h and 24 h after 70% partial hepatectomy in WT and Mier1 KO mice.