BS-seq

Hybrids are always a focus of botanical research and have a high practical value in agricultural production. To better understand allele regulation and differences in DNA methylation in hybrids, we developed a phasing pipeline for hybrid rice based on two parental genomes (PP2PG), which is applicable for Iso-Seq, RNA-Seq, and Bisulfite sequencing (BS-Seq). Using PP2PG, we analyzed differences in gene transcription, alternative splicing, and DNA methylation in an allele-specific manner between parents and progeny or different progeny alleles...

SUMMARY: Bisulfite sequencing (BS-seq) is currently the gold standard for measuring genome-wide DNA methylation profiles at single-nucleotide resolution. Most analyses focus on mean CpG methylation and ignore methylation states on the same DNA fragments [DNA methylation haplotypes (mHaps)]. Here, we propose mHap, a simple DNA mHap format for storing DNA BS-seq data. This format reduces the size of a BAM file by 40- to 140-fold while retaining complete read-level CpG methylation information...

The generation of tools to study mammalian epigenetics is vital to understanding normal biological function and to identify how it is dysregulated in disease. The well-studied epigenetic DNA modification 5-methylcytosine can be enzymatically oxidized to 5-formylcytosine (5fC) in vivo. 5fC has been demonstrated to be an intermediate in demethylation, but recent evidence suggests that 5fC may have an epigenetic function of its own. We have developed reduced bisulfite sequencing (redBS-seq), which can quantitatively locate 5fC bases at single-base resolution in genomic DNA...

Epigenetic modifications play an important role in central nervous system disorders. As a widespread posttranscriptional RNA modification, the role of the m5 C modification in cerebral ischemia-reperfusion injury (IRI) remains poorly defined. Here, we successfully constructed a neuronal oxygen-glucose deprivation/reoxygenation (OGD/R) model and obtained an overview of the transcriptome-wide m5 C profiles using RNA-BS-seq. We discovered that the distribution of neuronal m5 C modifications was highly conserved, significantly enriched in CG-rich regions and concentrated in the mRNA translation initiation regions...

5-Methylcytosine (5mC) is an important type of epigenetic modification. Bisulfite sequencing (BS-seq) has limitations, such as severe DNA degradation. Using single molecule real-time sequencing, we developed a methodology to directly examine 5mC. This approach holistically examined kinetic signals of a DNA polymerase (including interpulse duration and pulse width) and sequence context for every nucleotide within a measurement window, termed the holistic kinetic (HK) model. The measurement window of each analyzed double-stranded DNA molecule comprised 21 nucleotides with a cytosine in a CpG site in the center...

DNA methylation plays crucial roles in cellular development and stress responses through gene regulation and genome stability control. Precise regulation of DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), the de novo Arabidopsis DNA methyltransferase, is crucial to maintain DNA methylation homeostasis to ensure genome integrity. Compared to the extensive studies on DRM2 targeting mechanisms, little is known regarding the quality control of DRM2 itself. Here, we conducted yeast two hybrid screen assay and identified an E3 ligase, COP9 INTERACTING F-BOX KELCH 1 (CFK1), as a novel DRM2-interacting partner and targets DRM2 for degradation via the ubiquitin-26S proteasome pathway in Arabidopsis thaliana...

Bisulfite sequencing (BS-seq) remains the gold standard technique to quantitively map DNA methylation at a single-base resolution. However, BS-seq cannot discriminate between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Oxidative bisulfite sequencing (oxBS-seq) was one of the first techniques that enabled absolute quantification of 5mC and 5hmC at single-base resolution. OxBS-seq uses chemical oxidation of 5hmC prior to bisulfite treatment to provide a direct readout of 5mC; comparison with BS-seq data can then be used to infer 5hmC levels...

Rice black-streaked dwarf virus (RBSDV) causes severe yield losses in rice ( Oryza sativa L.) in China. Studies have shown that the mechanisms of DNA methylation-mediated plant defense against DNA viruses and RNA viruses are different. However, in rice its function in response to infection of RBSDV, a double-stranded RNA virus, remains unclear. In this study, high-throughput single-base resolution bisulfite sequencing (BS-Seq) was carried out to analyze the distribution pattern and characteristics of cytosine methylation in RBSDV-infected rice...

BACKGROUND: A growing body of evidence suggests that certain epiphenotypes can be passed across generations via both the male and female germlines of mammals. These observations have been difficult to explain owing to a global loss of the majority of known epigenetic marks present in parental chromosomes during primordial germ cell development and after fertilization. RESULTS: By integrating previously published BS-seq, DNase-seq, ATAC-seq, and RNA-seq data collected during multiple stages of primordial germ cell and pre-implantation development, we find that the methylation status of the majority of CpGs genome-wide is restored after global de-methylation, despite the fact that global CpG methylation drops to 10% in primordial germ cells and 20% in the inner cell mass of the blastocyst...

MOTIVATION: Bisulfite sequencing (BS-seq) is a state-of-the-art technique for investigating methylation of the DNA to gain insights into the epigenetic regulation. Several algorithms have been published for identification of differentially methylated regions (DMRs). However, the performances of the individual methods remain unclear and it is difficult to optimally select an algorithm in application settings. RESULTS: We analyzed BS-seq data from four plants covering three taxonomic groups...

BACKGROUND: The Metarhizium genus harbors important entomopathogenic fungi. These species have been widely explored as biological control agents, and strategies to improve the fungal virulence are under investigation. Thus, the interaction between Metarhizium species and susceptible hosts have been explored employing different methods in order to characterize putative virulence determinants. However, the impact of epigenetic modulation on the infection cycle of Metarhizium is still an open topic...

Aim: To comprehensively identify allele-specific DNA methylation (ASM) at the genome-wide level. Methods: Here, we propose a new method, called GeneASM, to identify ASM using high-throughput bisulfite sequencing data in the absence of haplotype information. Results: A total of 2194 allele-specific DNA methylated genes were identified in the GM12878 lymphocyte lineage using GeneASM. These genes are mainly enriched in cell cytoplasm function, subcellular component movement or cellular linkages. GM12878 methylated DNA immunoprecipitation sequencing, and methylation sensitive restriction enzyme sequencing data were used to evaluate ASM...

MOTIVATION: DNA methylation plays an important role in regulating gene expression. DNA methylation is commonly analyzed using bisulfite sequencing (BS-seq)-based designs, such as whole-genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and oxidative bisulfite sequencing (oxBS-seq). Furthermore, there has been growing interest in investigating the roles that genetic variants play in changing the methylation levels (i.e., methylation quantitative trait loci or meQTLs), how methylation regulates the imprinting of gene expression (i...

We conducted genome-wide identification of R-loops followed by integrative analyses of R-loops with relation to gene expression and epigenetic signatures in the rice genome. We found that the correlation between gene expression levels and profiled R-loop peak levels was dependent on the positions of R-loops within gene structures (hereafter named "genic position"). Both antisense only (ASO)-R-loops and sense/antisense (S/AS)-R-loops sharply peaked around transcription start sites (TSSs), and these peak levels corresponded positively with transcript levels of overlapping genes...

Neonicotinoids are effective insecticides used on many important arable and horticultural crops. They are nicotinic acetylcholine receptor agonists which disrupt the function of insect neurons and cause paralysis and death. In addition to direct mortality, there are numerous sublethal effects of low doses of neonicotinoids on bees. We hypothesize that some of these large array of effects could be a consequence of epigenetic changes in bees induced by neonicotinoids. We compared whole methylome (BS-seq) and RNA-seq libraries of the brains of buff-tailed bumblebee Bombus terrestris workers exposed to field-realistic doses of the neonicotinoid imidacloprid to libraries from control workers...

Chromatin features are characterized by genome-wide assays for nucleosome location, protein binding sites, three-dimensional interactions, and modifications to histones and DNA. For example, assay for transposase accessible chromatin sequencing (ATAC-seq) identifies nucleosome-depleted (open) chromatin, which harbors potentially active gene regulatory sequences; and bisulfite sequencing (BS-seq) quantifies DNA methylation. When two distinct chromatin features like these are assayed separately in populations of cells, it is impossible to determine, with certainty, where the features are coincident in the genome by simply overlaying data sets...

MOTIVATION: Single-cell bisulfite sequencing (BS-seq) techniques have been developed for DNA methylation heterogeneity detection and studies with limited materials. However, the data deficiency such as low read mapping ratio is still a critical issue. RESULTS: We comprehensively characterize single-cell BS-seq data and reveal chimerical molecules to be the major source of alignment failures. These chimerical molecules are produced by recombination of genomic proximal sequences with microhomology regions (MR) after bisulfite conversion...

BACKGROUND: Fruit peel colour is an important agronomic trait for fruit quality. Cytosine methylation plays an important role in gene regulation. Although the DNA methylation level of a single gene is important to affect the phenotype of mutation, there are large unknown of difference of the DNA methylation in plant and its mutants. RESULTS: Using bisulfite sequencing (BS-Seq) and RNA-sequencing (RNA-Seq), we analysed three deep-red-skinned apple (Malus × domestica) mutants (Yanfu 3, YF3; Yanfu 8, YF8; Shannonghong, SNH) and their lighter-skinned parents (Nagafu 2, NF2; Yanfu 3, YF3; Ralls, RL) to explore the different changes in methylation patterns associated with anthocyanin concentrations...

BACKGROUND: DNA methylation plays crucial roles in most eukaryotic organisms. Bisulfite sequencing (BS-Seq) is a sequencing approach that provides quantitative cytosine methylation levels in genome-wide scope and single-base resolution. However, genomic variations such as insertions and deletions (indels) affect methylation calling, and the alignment of reads near/across indels becomes inaccurate in the presence of polymorphisms. Hence, the simultaneous detection of DNA methylation and indels is important for exploring the mechanisms of functional regulation in organisms...

In recent years, there have been many studies utilizing DNA methylome data to answer fundamental biological questions. Bisulfite sequencing (BS-seq) has enabled measurement of a genome-wide absolute level of DNA methylation at single-nucleotide resolution. However, due to the ambiguity introduced by bisulfite-treatment, the aligning process especially in large-scale epigenetic research is still considered a huge burden. We present Cloud-BS, an efficient BS-seq aligner designed for parallel execution on a distributed environment...