scholarly journals Mirror bisulfite sequencing — a method for single-base resolution of hydroxymethylcytosine

2015 ◽  
Author(s):  
Xueguang Sun ◽  
Darany Tan ◽  
Tzu Hung Chung ◽  
Xi-Yu Jia
Keyword(s):  
Bisulfite Sequencing ◽  
Biological Role ◽  
Human Tissues ◽  
Bisulfite Conversion ◽  
Single Base ◽  
Cpg Site ◽  
Genome Wide ◽  
Single Base Resolution ◽  
Dna Strand

While the role of 5-methylcytosine has been well studied, the biological role of 5-hydroxymethylcytosine still remains unclear due to the limited methods available for single-base detection of 5-hydroxymethylcytosine (5hmC). Here, we present Mirror bisulfite sequencing detects 5-hydroxymethylcytosines at a single CpG site by synthesizing a DNA strand to mirror the parental strand. This semi-conservative duplex is sequentially treated with β-glucosyltransferase and M.SssI methylase. A glucosyl-5hmCpG in the parental strand inhibits methylation of the mirroring CpG site, and after bisulfite conversion, a thymine in the mirroring strand indicates a 5hmCpG site in the parental strand whereas a cytosine indicates a non-5hmC site. Using this method, the 5hmC levels of various human tissues and paired liver tissues were mapped genome-wide.

scholarly journals Mirror Bisulfite Sequencing: A Method for Single-Base Resolution of Hydroxymethylcytosine

2018 ◽  
Vol 90 (22) ◽  
pp. 13200-13206
Author(s):  
Darany Tan ◽  
Tzu Hung Chung ◽  
Xueguang Sun ◽  
Xi-Yu Jia
Keyword(s):  
Bisulfite Sequencing ◽  
Single Base ◽  
Single Base Resolution

scholarly journals Bacterial Epigenomics: Coming of Age

mSystems ◽  
2021 ◽  
Author(s):  
Pedro H. Oliveira
Keyword(s):  
Dna Methylation ◽  
Coming Of Age ◽  
Innate Immune ◽  
Physiological Significance ◽  
Single Base ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Single Base Resolution

Epigenetic DNA methylation in bacteria has been traditionally studied in the context of antiparasitic defense and as part of the innate immune discrimination between self and nonself DNA. However, sequencing advances that allow genome-wide analysis of DNA methylation at the single-base resolution are nowadays expanding and have propelled a modern epigenomic revolution in our understanding of the extent, evolution, and physiological significance of methylation.

scholarly journals Timing Polymerase Pausing with TV-PRO-seq

2018 ◽  
Author(s):  
Jie Zhang ◽  
Massimo Cavallaro ◽  
Daniel Hebenstreit
Keyword(s):  
High Resolution ◽  
Human Cells ◽  
Rrna Genes ◽  
Dna Motifs ◽  
Single Base ◽  
Chromatin States ◽  
Genome Wide ◽  
A Genome ◽  
Single Base Resolution ◽  
Polymerase Pausing

Transcription of many genes in metazoans is subject to polymerase pausing, which corresponds to the transient arrest of transcriptionally engaged polymerase. It occurs mainly at promoter proximal regions and is not well understood. In particular, a genome-wide measurement of pausing times at high resolution has been lacking.We present here an extension of PRO-seq, time variant PRO-seq (TV-PRO-seq), that allowed us to estimate genome-wide pausing times at single base resolution. Its application to human cells reveals that promoter proximal pausing is surprisingly short compared to other regions and displays an intricate pattern. We also find precisely conserved pausing profiles at tRNA and rRNA genes and identified DNA motifs associated with pausing time. Finally, we show how chromatin states reflect differences in pausing times.

scholarly journals Retraction Note: DNA methylome profiling at single-base resolution through bisulfite sequencing of 5mC-immunoprecipitated DNA

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhen Jia ◽  
Yueyi Shi ◽  
Lei Zhang ◽  
Yipeng Ren ◽  
Tong Wang ◽  
...  
Keyword(s):  
Bisulfite Sequencing ◽  
Single Base ◽  
Dna Methylome ◽  
Single Base Resolution

scholarly journals EM-seq: Detection of DNA Methylation at Single Base Resolution from Picograms of DNA

2019 ◽  
Author(s):  
Romualdas Vaisvila ◽  
V. K. Chaithanya Ponnaluri ◽  
Zhiyi Sun ◽  
Bradley W. Langhorst ◽  
Lana Saleh ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Nucleotide Composition ◽  
Whole Genome ◽  
Sequencing Data ◽  
Genomic Features ◽  
Single Base ◽  
Bisulfite Treatment ◽  
Genome Bisulfite Sequencing ◽  
Single Base Resolution

AbstractBisulfite sequencing is widely used to detect 5mC and 5hmC at single base resolution. However, bisulfite treatment damages DNA resulting in fragmentation, loss of DNA and biased sequencing data. To overcome this, we developed Enzymatic Methyl-seq (EM-seq), an enzymatic based approach that uses as little as 100 pg of DNA. EM-seq outperformed bisulfite converted libraries in all metrics examined including coverage, duplication, sensitivity and nucleotide composition. EM-seq libraries displayed even GC distribution, improved correlation across input amounts as well as increased representation of genomic features. These data indicate that EM-seq is more accurate and reliable than whole genome bisulfite sequencing (WGBS).

scholarly journals DNA Methylation and Transcriptomic Features are Preserved Throughout Disease Recurrence and Chemoresistance in High Grade Serous Ovarian Cancers

2022 ◽  
Author(s):  
Nicole Gull ◽  
Michell Jones ◽  
Pei-Chen Peng ◽  
Simon Coetzee ◽  
Tiago Silva ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Disease Recurrence ◽  
High Grade ◽  
Chemotherapy Treatment ◽  
Recurrent Tumors ◽  
Genome Wide ◽  
Genome Bisulfite Sequencing

Abstract Background Little is known about the role of global DNA methylation in recurrence and chemoresistance of high grade serous ovarian cancer (HGSOC). We performed whole genome bisulfite sequencing and transcriptome sequencing in 62 primary and recurrent tumors from 28 patients with stage III/IV HGSOC, of which 11 patients carried germline, pathogenic BRCA1 and/or BRCA2 mutations. Results Landscapes of genome-wide methylation (on average 24.2 million CpGs per tumor) and transcriptomes in primary and recurrent tumors showed extensive heterogeneity between patients but were highly preserved in tumors from the same patient. We identified significant differences in the burden of differentially methylated regions (DMRs) in tumors from BRCA1/2 compared to non-BRCA1/2 carriers (mean 659 DMRs and 388 DMRs in paired comparisons respectively). We identified overexpression of immune pathways in BRCA1/2 carriers compared to non-carriers, implicating an increased immune response in improved survival (P=0.006) in these BRCA1/2 carriers. Conclusions These findings indicate methylome and gene expression programs established in the primary tumor are conserved throughout disease progression, even extensive chemotherapy treatment, and that changes in methylation and gene expression are unlikely to serve as drivers for chemoresistance in HGSOC.

scholarly journals BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues

2017 ◽  
Author(s):  
Luli S. Zou ◽  
Michael R. Erdos ◽  
D. Leland Taylor ◽  
Peter S. Chines ◽  
Arushi Varshney ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Gradient Boosting ◽  
Whole Genome ◽  
Human Tissues ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Bisulfite Sequencing ◽  
Boosting Algorithm ◽  
Multiple Samples

AbstractBisulfite sequencing is widely employed to study the role of DNA methylation in disease; however, the data suffer from biases due to coverage depth variability. Here we describe BoostMe, a method for imputing low quality DNA methylation estimates within whole-genome bisulfite sequencing (WGBS) data. BoostMe uses a gradient boosting algorithm, XGBoost, and leverages information from multiple samples for prediction. We find that BoostMe outperforms existing algorithms in speed and accuracy when applied to WGBS of human tissues. We also show that imputation improves concordance between WGBS and the MethylationEPIC array at low WGBS depth, suggesting improved WGBS accuracy after imputation.

scholarly journals The landscape of human mutually exclusive splicing

2017 ◽  
Author(s):  
Klas Hatje ◽  
Ramon O. Vidal ◽  
Raza-Ur Rahman ◽  
Dominic Simm ◽  
Björn Hammesfahr ◽  
...  
Keyword(s):  
Strong Evidence ◽  
Human Disease ◽  
Biological Role ◽  
Rna Seq ◽  
Timothy Syndrome ◽  
Temporal Expression ◽  
Genome Wide ◽  
Spatio Temporal ◽  
Organismal Development

AbstractMutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genome-wide estimate of the extent and biological role of mutually exclusive splicing in humans we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA-seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than five-fold. The data provides strong evidence for the existence of large and multi-cluster MXEs in higher vertebrates and offers new insights into MXE splicing mechanics and evolution. Finally, MXEs are significantly enriched in pathogenic mutations and their spatio-temporal expression predicts human disease pathology.

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