Technologies and applications of single-cell DNA methylation sequencing

DNA methylation is the most stable epigenetic modification. In mammals, it usually occurs at the cytosine of CpG dinucleotides. DNA methylation is essential for many physiological and pathological processes. Aberrant DNA methylation has been observed in human diseases, particularly cancer. Notably, conventional DNA methylation profiling technologies require a large amount of DNA, often from a heterogeneous cell population, and provide an average methylation level of many cells. It is often not realistic to collect sufficient numbers of cells, such as rare cells and circulating tumor cells in peripheral blood, for bulk sequencing assays. It is therefore essential to develop sequencing technologies that can accurately profile DNA methylation using small numbers of cells or even single cells. Excitingly, many single-cell DNA methylation sequencing and single-cell omics sequencing technologies have been developed, and applications of these methods have greatly expanded our understanding of the molecular mechanism of DNA methylation. Here, we summaries single-cell DNA methylation and multi-omics sequencing methods, delineate their applications in biomedical sciences, discuss technical challenges, and present our perspective on future research directions.

Automated summary

DNA methylation is a stable epigenetic modification occurring at CpG dinucleotides, playing essential roles in both physiological and pathological processes. In human diseases, especially cancer, aberrant DNA methylation has been observed. However, conventional methods for DNA methylation profiling require a large amount of DNA from heterogeneous cell populations, making it impractical for rare or circulating tumor cells. Therefore, the development of sequencing technologies that can accurately profile DNA methylation using small numbers of cells, or even single cells, is crucial. Excitingly, various single-cell DNA methylation sequencing and omics sequencing technologies have been developed, greatly advancing our understanding of the molecular mechanisms of DNA methylation. In this review, we summarize these methods, their applications in biomedical sciences, discuss technical challenges, and provide prospects for future research directions.