Accumulating evidence suggests that the crosstalk between histone modification (HM) and DNA methylation (DM) may play important roles for establishing and maintaining the epigenomic landscape during development and disease. Conventionally, HM-DM crosstalk has been studied by examining HM and DM separately, using molecular assays such as ChIP-seq and whole- genome bisulfite sequencing (WGBS). These assays (in their conventional forms) require a large amount of sample input and are not practical with scarce primary samples from small lab animals and patients. This problem is particularly serious when multiple epigenomic marks are studied. In this project, we will develop novel microfluidic technology that permits low-input (1000 to single cells) sequential ChIP-MethylC treatment and examination of genome-wide HM- DM crosstalk using the same cell population. We will demonstrate the principle using H1 human embryonic stem cells (hESCs) and primary tissues (i.e. neuronal nuclei) isolated from frontal cortex of mouse brains. Our technology will pave the way for integrative analysis of multiple epigenomic marks based on scarce cell samples.
We will develop novel microfluidic technology that permits low-input (1000 to single cells) sequential ChIP-MethylC treatment and examination of genome-wide histone modification-DNA methylation crosstalk using the same cell population. Such genomic tool will help understand epigenomic regulations during development and disease.
|Ma, Sai; de la Fuente Revenga, Mario; Sun, Zhixiong et al. (2018) Cell-type-specific brain methylomes profiled via ultralow-input microfluidics. Nat Biomed Eng 2:183-194|
|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|
|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|