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

Area of Science:

• Epigenetics
• Genomics
• Cell Biology

Background:

• Polycystic liver disease (PLD) is a hereditary disorder causing liver cysts and reduced quality of life.
• Current PLD treatments are insufficient, highlighting the need for new therapeutic approaches.
• Epigenetic regulation's role in PLD is poorly understood, partly due to challenges in obtaining primary cholangiocytes for traditional profiling.

Purpose of the Study:

• To optimize low-input epigenetic profiling techniques for primary cholangiocytes.
• To enable the study of chromatin accessibility and histone modifications in PLD with minimal cell input.
• To facilitate the exploration of epigenetic mechanisms in biliary diseases and other low-input cell contexts.

Main Methods:

• Optimized low-input ChIP-seq (Chromatin Immunoprecipitation sequencing) using micrococcal nuclease (MNase).
• Optimized low-input ATAC-seq (Assay for Transposase-Accessible Chromatin sequencing) using Tn5 transposase.
• Applied these multi-omics techniques to primary cholangiocytes for chromatin state analysis.

Main Results:

• Successfully adapted ChIP-seq and ATAC-seq for low cell numbers, enabling detailed epigenetic analysis.
• These methods provide insights into chromatin dynamics in cholangiocytes relevant to PLD.
• The optimized protocols are versatile and applicable to other primary cell types with limited sample availability.

Conclusions:

• Developed robust low-input epigenetic assays for studying PLD and other biliary diseases.
• These techniques overcome cell number limitations in primary cell research.
• This work supports the development of novel epigenetic-based therapeutic strategies for PLD.