Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications

DNA methylation is a crucial epigenetic regulatory mechanism in eukaryotes, and its dysregulation is closely associated with numerous diseases. Recent advances in long-read sequencing (LRS) have transformed the ability to comprehensively characterize the methylation modifications in DNA, including the technically difficult genomic regions. However, the translation of this technological potential into reliable biological insights relies heavily on accurate computational analysis of raw signal data. Currently, a growing number of bioinformatic tools have emerged, demonstrating superior performance in LRS-based methylation detection. Our review first briefly describes the detection principles and technological improvement of LRS, and then provides a comprehensive overview of the existing LRS-based methylation detection tools and related benchmarking studies. We further explore the applications in biomedical research, the current challenges, and the future perspective of LRS-based methylation detection. By highlighting the research progress and key issues in the field, this review aims to provide researchers with an essential framework to advance the further development and application of LRS-based methylation detection.