Mapping epigenetic modifications by sequencing technologies

The “epigenetics” concept was first described in 1942. Thus far, chemical modifications on histones, DNA, and RNA have emerged as three important building blocks of epigenetic modifications. Many epigenetic modifications have been intensively studied and found to be involved in most essential biological processes as well as human diseases, including cancer. Precisely and quantitatively mapping over 100 [1], 17 [2], and 160 [3] different known types of epigenetic modifications in histone, DNA, and RNA is the key to understanding the role of epigenetic modifications in gene regulation in diverse biological processes. With the rapid development of sequencing technologies, scientists are able to detect specific epigenetic modifications with various quantitative, high-resolution, whole-genome/transcriptome approaches. Here, we summarize recent advances in epigenetic modification sequencing technologies, focusing on major histone, DNA, and RNA modifications in mammalian cells

Modular oxidation of cytosine modifications and their application in direct and quantitative sequencing of 5-hydroxymethylcytosine

Selective, efficient, and controllable oxidation of cytosine modifications is valuable for epigenetic analyses, yet only limited progress has been made. Here, we present two modular chemical oxidation reactions: conversion of 5-hydroxymethylcytosine (5hmC) into 5-formylcytosine (5fC) using 4-acetamido-2,2,6,6-tetramethylpiperidine-1-oxoammonium tetrafluoroborate (ACT+BF4–) and further transformation of 5fC into 5-carboxycytosine (5caC) through Pinnick oxidation. Both reactions are mild and efficient on double-stranded DNA. We integrated these two oxidations with borane reduction to develop chemical-assisted pyridine borane sequencing plus (CAPS+), for direct and quantitative mapping of 5hmC. Compared with CAPS, CAPS+ improved the conversion rate and false-positive rate. We applied CAPS+ to mouse embryonic stem cells, human normal brain, and glioblastoma DNA samples and demonstrated its superior sensitivity in analyzing the hydroxymethylome

Effects of the Zishen Yutai Pill compared with placebo on pregnancy outcomes among women in a fresh embryo transfer cycle: a Post Hoc subgroup analysis of a randomized controlled trial

ObjectiveTo assess whether the administration of Zishen Yutai Pill (ZYP) could improve the pregnancy outcomes in different subgroups of women undergoing fresh embryo transfer cycles.Materials and methodsThis is a post hoc analysis of a large scale, placebo-controlled, double blind, randomized clinical trial (RCT) regarding the use of ZYP during assisted reproductive technology (ART) treatment. The RCT was conducted at 19 in vitro fertilization (IVF) centers between April 2014 and June 2017. A total of 2265 women undergoing fresh embryo transfer cycles were randomly assigned in a 1:1 ratio to receive ZYP (n = 1131) or placebo (n = 1134). Post hoc logistic regression analyses were applied in this study to examine the between-group differences of ZYP and placebo on clinical pregnancy rate among different subgroups. Detailed analyses, both in intention-to-treat (ITT) and per-protocol population, were also conducted in specific subgroups with regards to rates of implantation, biochemical pregnancy, clinical pregnancy, live birth, pregnancy loss, as well as other neonatal indices.ResultsZYP showed a significantly higher clinical pregnancy rates than placebo in the ITT population. Detailed subgroup analyses were conducted in subgroup in advanced maternal age (AMA, ≥ 35 years old) and overweight/obese patients (BMI > 24), due to the clinical importance and statistical results. In these subgroups, baseline characteristics were similar between two arms (all P > 0.05). Significantly elevated clinical pregnancy rates were observed in ZYP cohort (both P < 0.05) compared with the placebo group. Results also showed that ZYP treatment resulted in significantly higher rates of implantation, biochemical pregnancy in AMA or overweight/obese patients in ITT analysis (all P < 0.05).ConclusionsThe current post hoc subgroup analysis suggested that AMA and overweight/obese women could experience clinical benefits when treated with ZYP in their fresh embryo transfer cycles. The study provides references for the use of ZYP in ART practices. However, further studies in specific subgroups should be examined in more rigorous clinical trial settings.Clinical trial registrationChictr.org.cn, ChictrTRC-14004494

SIRT5 promotes IDH2 desuccinylation and G6PD deglutarylation to enhance cellular antioxidant defense

Abstract Excess in mitochondrial reactive oxygen species (ROS) is considered as a major cause of cellular oxidative stress. NADPH, the main intracellular reductant, has a key role in keeping glutathione in its reduced form GSH, which scavenges ROS and thus protects the cell from oxidative damage. Here, we report that SIRT5 desuccinylates and deglutarylates isocitrate dehydrogenase 2 (IDH2) and glucose‐6‐phosphate dehydrogenase (G6PD), respectively, and thus activates both NADPH‐producing enzymes. Moreover, we show that knockdown or knockout of SIRT5 leads to high levels of cellular ROS. SIRT5 inactivation leads to the inhibition of IDH2 and G6PD, thereby decreasing NADPH production, lowering GSH, impairing the ability to scavenge ROS, and increasing cellular susceptibility to oxidative stress. Our study uncovers a SIRT5‐dependent mechanism that regulates cellular NADPH homeostasis and redox potential by promoting IDH2 desuccinylation and G6PD deglutarylation

WT1 Recruits TET2 to Regulate Its Target Gene Expression and Suppress Leukemia Cell Proliferation

The TET2 DNA dioxygenase regulates cell identity and suppresses tumorigenesis by modulating DNA methylation and expression of a large number of genes. How TET2, like most other chromatin modifying enzymes, is recruited to specific genomic sites is unknown. Here we report that WT1, a sequence-specific transcription factor, is mutated in a mutually exclusive manner with TET2, IDH1 and IDH2 in acute myeloid leukemia (AML). WT1 physically interacts with and recruits TET2 to its target genes to activate their expression. The interaction between WT1 and TET2 is disrupted by multiple AML-derived TET2 mutations. TET2 suppresses leukemia cell proliferation and colony formation in a manner dependent on WT1. These results provide a mechanism for targeting TET2 to specific DNA sequence in the genome. Our results also provide an explanation for the mutual exclusivity of WT1 and TET2 mutations in AML and suggest an IDH1/2-TET2-WT1 pathway in suppressing AML

Additional file 3 of A comprehensive assessment of fungal communities in various habitats from an ice-free area of maritime Antarctica: diversity, distribution, and ecological trait

Additional file 3. Table S3. Information on the 17,236 fungal ASVs in the 213 samples collected from the Fildes Region (maritime Antarctica)

Additional file 1 of A comprehensive assessment of fungal communities in various habitats from an ice-free area of maritime Antarctica: diversity, distribution, and ecological trait

Additional file 1. Table S1. Information on the 213 samples collected from the Fildes Region (maritime Antarctica). Table S5. An overview of potentially pathogenic fungi found in the eleven habitats from the Fildes Region (maritime Antarctica). Fig. S1. Dendrogram showing fungal communities in the 202 samples of eleven habitats from the Fildes Region (maritime Antarctica). Fig. S2. LEfSe analysis showing the fungal phyla that are significantly different among the eleven habitats in the Fildes Region (maritime Antarctica). Significant phyla are ranked by their LDA scores (x-axis). The right heatmap shows whether the relative abundances of phyla are higher (red) or lower (blue). Fig. S3. LEfSe analysis showing the fungal classes that are significantly different among the eleven habitats in the Fildes Region (maritime Antarctica). Significant classes are ranked by their LDA scores (x-axis). The right heatmap shows whether the relative abundances of classes are higher (red) or lower (blue). Fig. S4. LEfSe analysis showing the fungal families that are significantly different among the eleven habitats in the Fildes Region (maritime Antarctica). Significant families are ranked by their LDA scores (x-axis). The right heatmap shows whether the relative abundances of families are higher (red) or lower (blue)

Additional file 2 of A comprehensive assessment of fungal communities in various habitats from an ice-free area of maritime Antarctica: diversity, distribution, and ecological trait

Additional file 2. Table S2. Representative sequence of fungal ASV detected in the 213 samples

Additional file 4 of A comprehensive assessment of fungal communities in various habitats from an ice-free area of maritime Antarctica: diversity, distribution, and ecological trait

Additional file 4. Table S4. Information on the 14,814 fungal ASVs in the 202 samples collected from the Fildes Region (maritime Antarctica)

Regulatory effects of Zishen Yutai Pill on endometrial epithelial response in vitro in immunology microenvironment

Objective: Zishen Yutai Pill (ZYP) is a frequently used traditional Chinese medicine (TCM) preparation in women’s health. However, the effects of ZYP on endometrial epithelial response have not been fully explored. Herein, uterine natural killer cell (uNK) secretion medium was used to mimic the uterine microenvironment. Thereafter, an endometrial epithelial cell line (Ishikawa cells) was treated with ZYP-containing serum to elucidate the effects of ZYP on endometrial receptivity.Methods: uNK cells were isolated from decidual tissues of pregnant women undergoing pregnancy termination surgery, and thereafter, uNK secretion medium was collected. ZYP-containing serum was collected from rats after intragastrical administration of ZYP. Ishikawa cells were divided into three groups, one treated with blank control (control group), one treated with uNK secretion medium (uNK group), and one treated with both uNK secretion medium and ZYP-containing serum (ZYP + uNK group). Total RNAs were extracted. Gene expression profiles of Ishikawa in different groups were determined through microarray analysis. mRNA expressions of selected genes were determined through quantitative real-time polymerase chain reaction (qRT-PCR). Expression of intercellular cell adhesion molecule-1 (ICAM-1) was determined using Western blotting (WB). Results: Compared with the uNK group, the gene expressions of ZYP group with a total of 1117 genes were significantly altered, among which 510 genes were upregulated and 607 genes were downregulated. Compared with uNK group, expressions of CSF1, CSF2, SPP1, and ICAM1 were upregulated (P < 0.05). Up-regulation of ICAM-1 expression after treatment of ZYP was further confirmed by WB analysis. Conclusion: In brief, in the presence of uNK cell medium, ZYP could improve the expressions of ICAM1, CSF1, CSF2, TNF, SPP1, etc. However, further exploration should be carried out in in vivo experiments for the validation of the mechanisms of ZYP on endometrial epithelial response