Cell-type-specific brain methylomes profiled via ultralow-input microfluidics

Sai Ma, Mario De La Fuente Revenga, Zhixiong Sun, Chen Sun, Travis W. Murphy, Hehuang Xie, Javier González-Maeso, Chang Lu

Research output: Contribution to journalArticlepeer-review

30 Scopus citations


Methylomic analyses typically require substantial amounts of DNA, thus hindering studies involving scarce samples. Here, we show that microfluidic diffusion-based reduced representation bisulfite sequencing (MID-RRBS) permits high-quality methylomic profiling with nanogram-to-single-cell quantities of starting DNA. We used the microfluidic device, which allows for efficient bisulfite conversion with high DNA recovery, to analyse genome-wide DNA methylation in cell nuclei isolated from mouse brains and sorted into NeuN+ (primarily neuronal) and NeuN- (primarily glial) fractions, and to establish cell-type-specific methylomes. Genome-wide methylation and methylation in low-CpG-density promoter regions showed distinct patterns for NeuN+ and NeuN- fractions from the mouse cerebellum. The identification of substantial variations in the methylomic landscapes of the NeuN+ fraction of the frontal cortex of mice chronically treated with an atypical antipsychotic drug suggests that this technology can be broadly used for cell-type-specific drug profiling and for the study of drug-methylome interactions.

Original languageEnglish
Pages (from-to)183-194
Number of pages12
JournalNature Biomedical Engineering
Issue number3
StatePublished - 1 Mar 2018
Externally publishedYes


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