Aberrant patterns in the epigenomic landscape have been closely associated with cancer. Deregulation of histone modifications silences tumor-suppressor genes, triggers genetic changes via aberrant DNA repair/replication, and contributes to tumor heterogeneity. Chromatin immunoprecipitation (ChIP) assay is the technique of choice for examining epigenetic mechanisms in vivo such as histone modifications. However, the technique in its conventional form suffers from serious limitations. The prevailing ChIP-seq protocol requires 107 cells per test, involves extensive manual handling of the samples, and takes 3-4 days to generate a sequencing library. The requirement of a large sample amount practically prevents the use of ChIP-seq on samples from scarce sources such as animal models and patients. We recently demonstrated a microfluidic technology (microfluidic-oscillatory-washing-based ChIP-seq or MOWChIP-seq) for profiling genome-wide histone modifications using as few as 100 cells. In this R33 project, we will develop the next-generation MOWChIP-seq technology by facilitating high throughput, improving the level of integration, and further validating the technology via testing mouse and human samples. The development will fully validate the use of MOWChIP- seq for high-throughput epigenomic profiling of a large number of samples in clinical research settings.
Aberrant patterns in the epigenomic landscape have been closely associated with cancer. We will develop the next-generation MOWChIP-seq (microfluidic-oscillatory-washing-based ChIP- seq) technology for mapping epigenomes with low input and high throughput.
| Sun, Chen; Lu, Chang (2018) Microfluidics-Based Chromosome Conformation Capture (3C) Technology for Examining Chromatin Organization with a Low Quantity of Cells. Anal Chem 90:3714-3719 |
| Murphy, Travis W; Hsieh, Yuan-Pang; Ma, Sai et al. (2018) Microfluidic Low-Input Fluidized-Bed Enabled ChIP-seq Device for Automated and Parallel Analysis of Histone Modifications. Anal Chem 90:7666-7674 |
| Ma, Sai; Hsieh, Yuan-Pang; Ma, Jian et al. (2018) Low-input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex. Sci Adv 4:eaar8187 |
| Murphy, Travis W; Zhang, Qiang; Naler, Lynette B et al. (2017) Recent advances in the use of microfluidic technologies for single cell analysis. Analyst 143:60-80 |
