BackgroundSingle-cell transcriptome and single-cell methylome technologies have become powerful tools to study RNA and DNA methylation profiles of single cells at a genome-wide scale. A major challenge has been to understand the direct correlation of DNA methylation and gene expression within single-cells. Due to large cell-to-cell variability and the lack of direct measurements of transcriptome and methylome of the same cell, the association is still unclear.ResultsHere, we describe a novel method (scMT-seq) that simultaneously profiles both DNA methylome and transcriptome from the same cell. In sensory neurons, we consistently identify transcriptome and methylome heterogeneity among single cells but the majority of the expression variance is not explained by proximal promoter methylation, with the exception of genes that do not contain CpG islands. By contrast, gene body methylation is positively associated with gene expression for only those genes that contain a CpG island promoter. Furthermore, using single nucleotide polymorphism patterns from our hybrid mouse model, we also find positive correlation of allelic gene body methylation with allelic expression.ConclusionsOur method can be used to detect transcriptome, methylome, and single nucleotide polymorphism information within single cells to dissect the mechanisms of epigenetic gene regulation.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0950-z) contains supplementary material, which is available to authorized users.

Summary Purpose:  Increasing evidence indicates that neuroinflammation plays a critical role in the pathogenesis of mesial temporal lobe epilepsy (MTLE). The aim of this study was to investigate the dynamic expression of interleukin (IL)–1β as a proinflammatory cytokine and microRNA (miR)‐146a as a posttranscriptional inflammation‐associated microRNA (miRNA) in the hippocampi of an immature rat model and children with MTLE. Methods:  To study the expression of IL‐1β and miR‐146a, we performed a reverse transcription polymerase chain reaction, Western blot, and real‐time quantitative PCR on the hippocampi of immature rats at 11 days of age. Expression was monitored in the acute, latent, and chronic stages of disease (2 h and 3 and 8 weeks after induction of lithium‐pilocarpine status epilepticus, respectively), and in control hippocampal tissues corresponding to the same timeframes. Similar expression methods were applied to hippocampi obtained from children with MTLE and normal controls. Key Findings:  The expression of IL‐1β and miR‐146a in both children and immature rats with MTLE differs according to the stage of MTLE development. Both IL‐1β and miR‐146a are significantly up‐regulated, but in opposite ways: IL‐1β expression is highest in the acute stage, when expression of miR‐146a is at its lowest level; miR‐146a expression is highest in the latent stage, when IL‐1β expression is at its lowest level. Both IL‐1β and miR‐146a are up‐regulated in the chronic stage, but not as much as in the other stages. Significance:  Our study is the first to focus on the expression of miR‐146a in the immature rat model of lithium‐pilocarpine MTLE and in children with MTLE. We have detected that the expression of proinflammatory cytokine IL‐1β and posttranscriptional inflammation‐associated miR‐146a is variable depending on the disease stage. Furthermore, both IL‐1β and miR‐146a are up‐regulated in immature rats and children with MTLE. Our findings elucidate the role of inflammation in the pathogenesis of MTLE in the immature rat model and children. Therefore, modulation of the IL‐1β–miR‐146a axis may be a novel therapeutic target in the treatment of MTLE.

Bioelectrical impulses intrinsically generated within the sinoatrial node (SAN) trigger the contraction of the heart in mammals. Though discovered over a century ago, the molecular and cellular features of the SAN that underpin its critical function in the heart are uncharted territory. Here, we identify four distinct transcriptional clusters by single-cell RNA sequencing in the mouse SAN. Functional analysis of differentially expressed genes identifies a core cell cluster enriched in the electrogenic genes. The similar cellular features are also observed in the SAN from both rabbit and cynomolgus monkey. Notably, Vsnl1, a core cell cluster marker in mouse, is abundantly expressed in SAN, but is barely detectable in atrium or ventricle, suggesting that Vsnl1 is a potential SAN marker. Importantly, deficiency of Vsnl1 not only reduces the beating rate of human induced pluripotent stem cell - derived cardiomyocytes (hiPSC-CMs) but also the heart rate of mice. Furthermore, weighted gene co-expression network analysis (WGCNA) unveiled the core gene regulation network governing the function of the SAN in mice. Overall, these findings reveal the whole transcriptome profiling of the SAN at single-cell resolution, representing an advance toward understanding of both the biology and the pathology of SAN.

No abstract