Increased reactive oxygen species levels in the mitochondrial matrix can induce Parkin-dependent mitophagy, which selectively degrades dysfunctional mitochondria via the autolysosome pathway. Phosphorylated mitofusin-2 (MFN2), a receptor of parkin RBR E3 ubiquitin-protein ligase (Parkin), interacts with Parkin to promote the ubiquitination of mitochondrial proteins; meanwhile, the mitophagy receptors Optineurin (OPTN) and nuclear dot protein 52 (NDP52) are recruited to damaged mitochondria to promote mitophagy. However, previous studies have not investigated changes in the levels of OPTN, MFN2, and NDP52 during Parkin-mediated mitophagy. Here, we show that mild and sustained hydrogen peroxide (H2O2) stimulation induces Parkin-dependent mitophagy accompanied by downregulation of the mitophagy-associated proteins OPTN, NDP52, and MFN2. We further demonstrate that H2O2 promotes the expression of the miR-106b-93-25 cluster and that miR-106b and miR-93 synergistically inhibit the translation of OPTN, NDP52, and MFN2 by targeting their 3’ untranslated regions. We further reveal that compromised phosphorylation of MYC proto-oncogene protein (c-Myc) at threonine 58 (T58) (producing an unstable form of c-Myc) caused by reduced nuclear glycogen synthase kinase-3 beta (GSK3β) levels contributes to the promotion of miR-106b-93-25 cluster expression upon H2O2 induction. Furthermore, miR-106b-mediated and miR-93-mediated inhibition of mitophagy-associated proteins (OPTN, MFN2, and NDP52) restrains cell death by controlling excessive mitophagy. Our data suggest that microRNAs (miRNAs) targeting mitophagy-associated proteins maintain cell survival, which is a novel mechanism of mitophagy control. Thus, our findings provide mechanistic insight into how miRNA-mediated regulation alters the biological process of mitophagy.

Bacterial epigenetic modifications play key roles in cellular processes such as stress responses, DNA replication, segregation, antimicrobial resistance, etc. In recent years, emerging new sequencing technologies, including single-molecule real-time (SMRT) sequencing, and nanopore sequencing, have enabled the directed reading of epigenetic modifications without pre-treatment of DNA or DNA amplification. The applications of SMRT and nanopore sequencing open the door for the identification of more diverse epigenetic modifications of DNA bases and backbones and potentially facilitate the understanding of the novel functions of these epigenetic markers in cell physiology. With ongoing improvements in throughput and accuracy, new-generation sequencing has become a contender as an alternative to second-generation sequencing technologies. Here, the authors review recent advances in bacterial epigenetic analysis using SMRT sequencing and nanopore sequencing to provide insights regarding the detection and analysis of DNA epigenetic modifications in bacterial genomes.

In this study, we observed that deletion of CD226 on regulatory T cells (Tregs) precedes renal fibrosis in a mouse unilateral ureteral obstruction (UUO) model. First, we generated Treg‐specific CD226 gene knockout mice (CD226fl/fl Foxp3YFP‐Cre). Next, CD226fl/fl Foxp3YFP‐Cre mice and Foxp3YFP‐Cre control mice were subjected to UUO surgery. Pathologic analysis and Sirius red and Masson's trichrome staining showed that the kidneys of CD226fl/fl Foxp3YFP‐Cre mice following UUO showed much more severe interstitial fibrosis than Foxp3YFP‐Cre control mice at days 10 and 20. Additionally, CD226fl/fl Foxp3YFP‐Cre mice showed increased fibronectin expression, as demonstrated by immunohistochemistry (IHC) staining. Although Treg cell‐restricted CD226 deficiency showed increased Foxp3+ expression, expression of the cell surface functional molecule CD103 was significantly reduced, indicating impaired homeostasis in the Tregs of CD226fl/fl Foxp3YFP‐Cre mice. To better understand CD226 function, RNA sequencing (RNA‐Seq) analysis was conducted in Tregs isolated from CD226fl/fl Foxp3YFP‐Cre and Foxp3YFP‐Cre mice. RNA‐Seq data showed that the helper T cell (Th) 2‐related cytokines IL‐4 and IL‐10 were significantly up‐regulated in CD226 deficient Tregs. In addition, mRNA analysis of kidney samples from the mice following UUO by qPCR also showed increased IL‐4 and IL‐10 expression in CD226fl/fl Foxp3YFP‐Cre mice, as well as elevated TGF‐β1 levels, indicating that CD226 deficiency in Tregs resulted in the acquisition of the ability to produce Th2 cytokines. Finally, we found that microRNA‐340 (miR‐340), which was down‐regulated in Tregs isolated from CD226fl/fl Foxp3YFP‐Cre mice, directly regulated IL‐4 gene expression in vitro. These data suggest that the promotion of CD226 signaling on Tregs is a therapeutic target for renal disease.