Multi-omics Techniques for Profiling Chromatin State Transitions in Low-input Primary Mouse Cholangiocytes

Polycystic liver disease (PLD) is a hereditary disorder characterized by the formation of fluid-filled cysts derived from cholangiocytes, leading to progressive disease and a significant reduction in patients' quality of life. Current treatments for PLD are inadequate, emphasizing the need for novel therapeutic strategies. The role of epigenetic regulation in PLD progression, particularly chromatin accessibility and histone modifications, remains underexplored. Traditional epigenetic profiling techniques, such as ChIP-seq and DNase-seq, require large numbers of cells, which are difficult to obtain from primary cholangiocytes. To address this, we optimized low-input ChIP-seq and ATAC-seq protocols for low numbers of primary cholangiocytes. These approaches allow for the analysis of histone modifications and chromatin accessibility with minimal cell input. Low-input ChIP-seq utilizes micrococcal nuclease (MNase) for DNA fragmentation, while ATAC-seq employs Tn5 transposase to capture open chromatin regions. These multi-omics techniques provide valuable insights into chromatin state dynamics during cholangiocyte fate transitions in PLD and other biliary diseases. Importantly, the optimized protocols are confidently applicable to other low-input primary cells, enabling the exploration of epigenetic mechanisms across various cellular contexts. This work presents a systematic approach for studying chromatin state alterations, contributing to the development of epigenetic-based therapeutic strategies for PLD and related diseases.