Epigenetic processes such as histone modification and DNA methylation have profound influence on gene expression by altering chromatin structures and creating binding sites for effector proteins, without changing the DNA sequence. Profiling epigenetic modifications at the genome level (i.e. an epigenomic study) has always been conducted with a huge number of cells (>1-10 million). Although there has been effort on increasing the sensitivity of these assays, no current technology comes close to profiling epigenomes of single cells. In this project, taking advantage of new methods we recently developed for multi-step analysis of nucleic acids and immunoprecipitation based on functionalized reactor surface, we will develop a drastically simple microfluidic array system that captures and lyses single cells, conducts microfluidic chromatin immunoprecipitation (ChIP) and whole genome amplification, and eventually permits sequencing of ChIP DNA for epigenomic profiling of single cells. Furthermore, we will develop a novel approach to quantify the technical noise in single-cell ChIP-Seq data in order to accurately measure true biological variations in the epigenome. We will demonstrate our technology by profiling histone modifications at the genome level with single hematopoietic stem cells isolated from mice during their fate specification. Upon the completion of this project, we will lay the groundwork for single-cell epigenomic research, which is entirely out of reach at this moment.
We will develop a microfluidic array system and associated data analysis methods for profiling epigenomes of single cells in parallel. This novel tool will yield unique insights into the molecular mechanisms involved in important processes such as stem cell differentiation, inflammation and cancer.
| 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 |
| Ma, Sai; Murphy, Travis W; Lu, Chang (2017) Microfluidics for genome-wide studies involving next generation sequencing. Biomicrofluidics 11:021501 |
| 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 |
| Cao, Zhenning; Lu, Chang (2016) A Microfluidic Device with Integrated Sonication and Immunoprecipitation for Sensitive Epigenetic Assays. Anal Chem 88:1965-72 |
