Advances in the Profiling of Single‐Cell DNA Modifications

Abstract

Epigenetic modifications on DNA include canonical 5‐methylcytosine (5mC) and its iteratively oxidized derivatives mediated by TET dioxygenase: 5‐hydroxymethylcytosine (5hmC), 5‐formylcytosine (5fC), and 5‐carboxycytosine (5caC). All of them have been recognized to play important roles in gene expression regulation and to be indispensable for normal mammalian reproduction and development. In order to understand the mechanisms underlying these roles, over the past few decades, technical advances have been made to comprehensively profile the distribution pattern of bulk epigenetic modifications in genomic DNA. Recently, single‐cell methods have identified the epigenetic patterns even within an individual cell. This review focuses on single‐cell DNA epigenetic modifications sequencing technologies and their applications, and gives prospects on the development of single‐cell methods based on bisulfite‐free strategy.

The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms

“…Plant methylation is divided into two types: Cytosine methylation (C-methylation) and Adenine methylation (A-methylation) [82]. Joint-snhmC-seq is a novel technique for accurately determining 5-methylcytosine (5mC) and 5-hydroxylmethylcytosine (5hmC) levels in DNA at the single-cell level, offering advantages of low sample input, high accuracy, and simultaneous detection of both modifications [83]. Recently developed software, such as DeepSignal-plant (version 1.2.0), combines deep learning and nanopore sequencing to detect methylation information in plant genomes [84].…”

Advances in single-cell multi-omics profiling

“…Since the first performance of single-cell RNA-seq in 2009, 1 many other single-cell sequencing methodologies have been developed for the individual profiling of multiple “omics.” 2 …”

Facile Clamp-Assisted Ligation Strategy for Direct Discrimination and Background-Free Quantification of Site-Specific 5-Formylcytosine

“…Balasubramanian and He groups have respectively developed reduced bisulfite sequencing and 5fC-assisted bisulfite sequencing methods to map 5fC in genomic DNA. Nevertheless, such strategies require harsh bisulfite treatment, where the acidic and thermal conditions may result in some DNA degradation. − Quite recently, the Yi group has reported the elegant bisulfite-free strategies by specifically label 5fC with some functional compounds, , which could map 5fC under mild conditions. However, as for sensitively detecting known 5fC sites of biomedical interest, deep sequencing is costly and time-consuming, prohibiting its routine clinical use. , Although great efforts toward simple and accurate detection of site-specific 5fC have been made, − there still remains two roadblocks on the way toward this goal.…”