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 Precision methylome and in vivo methylation kinetics characterization of Klebsiella pneumoniae

2020 ◽  
Author(s):  
Jing Fu ◽  
Ju Zhang ◽  
Li Yang ◽  
Nan Ding ◽  
Liya Yue ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Replication Initiation ◽  
Epigenetic Mechanism ◽  
Single Base ◽  
Genome Wide ◽  
A Genome ◽  
Intergenic Regions ◽  
Wide Scale ◽  
Single Base Resolution

Klebsiella pneumoniae (K. pneumonia) is an important pathogen that can cause severe hospital-/community-acquired infections. To panoramically analyze K. pneumoniae's methylation features, we completed the whole genome sequences of 14 K. pneumoniae strains covering various serotypes, multilocus-sequence typings (MLSTs), clonal groups (CG), viscosity/virulence and drug-resistances, and further characterized their methylomes using Pacbio-SMRT and bisulfite technologies. We identified 15 methylation motifs (13 6mA and two 5mC motifs), among which eight were novel ones. Their corresponding MTases were further validated. Additionally, we analyzed the genomic distribution of GATC and CCWGG methylation motifs shared by all strains, and identified differential distributive patterns of some hemi/un-methylated GATC motifs tending to locate in the intergenic regions (IGRs). Specifically, we characterized the in vivo methylation kinetics at single-base resolution on a genome-wide scale by simulating the dynamic processes of replication-mediated passive demethylation and MTase-catalyzed re-methylation. The slower methylation-rates of the GATC motifs in the replication origins (oriC) and IGRs suggest an epigenetic mechanism implicated in the regulation of replication-initiation and transcription. Our findings illustrate the first comprehensive dynamic methylome map of K. pneumonia at single base resolution, and provide an efficient means and important reference for a better understanding of epigenetic regulation in bacteria.

Clinical Relevance of Plasma DNA Methylation in Colorectal Cancer Patients Identified by Using a Genome-Wide High-Resolution Array

2014 ◽  
Vol 22 (S3) ◽  
pp. 1419-1427 ◽  
Author(s):  
Pei-Ching Lin ◽  
Jen-Kou Lin ◽  
Chien-Hsing Lin ◽  
Hung-Hsin Lin ◽  
Shung-Haur Yang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Dna Methylation ◽  
High Resolution ◽  
Cancer Patients ◽  
Clinical Relevance ◽  
Plasma Dna ◽  
Genome Wide ◽  
A Genome ◽  
Colorectal Cancer Patients

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 A genome‐wide screen identifies IRF2 as a key regulator of caspase‐4 in human cells

EMBO Reports ◽  
2019 ◽  
Vol 20 (9) ◽  
Author(s):  
Sacha Benaoudia ◽  
Amandine Martin ◽  
Marta Puig Gamez ◽  
Gabrielle Gay ◽  
Brice Lagrange ◽  
...  
Keyword(s):  
Human Cells ◽  
Genome Wide ◽  
A Genome

scholarly journals The Antisense Transcriptomes of Human Cells

Science ◽  
2008 ◽  
Vol 322 (5909) ◽  
pp. 1855-1857 ◽  
Author(s):  
Yiping He ◽  
Bert Vogelstein ◽  
Victor E. Velculescu ◽  
Nickolas Papadopoulos ◽  
Kenneth W. Kinzler
Keyword(s):  
Mammalian Cells ◽  
Cell Types ◽  
Human Cells ◽  
Antisense Transcripts ◽  
Genome Wide ◽  
Human Genes ◽  
A Genome ◽  
Dna Strand ◽  
The Relationship ◽  
Rna Transcript

Transcription in mammalian cells can be assessed at a genome-wide level, but it has been difficult to reliably determine whether individual transcripts are derived from the plus or minus strands of chromosomes. This distinction can be critical for understanding the relationship between known transcripts (sense) and the complementary antisense transcripts that may regulate them. Here, we describe a technique that can be used to (i) identify the DNA strand of origin for any particular RNA transcript, and (ii) quantify the number of sense and antisense transcripts from expressed genes at a global level. We examined five different human cell types and in each case found evidence for antisense transcripts in 2900 to 6400 human genes. The distribution of antisense transcripts was distinct from that of sense transcripts, was nonrandom across the genome, and differed among cell types. Antisense transcripts thus appear to be a pervasive feature of human cells, which suggests that they are a fundamental component of gene regulation.

scholarly journals A Genome-Wide High-Resolution Array-CGH Analysis of Cutaneous Melanoma and Comparison of Array-CGH to FISH in Diagnostic Evaluation

2013 ◽  
Vol 15 (5) ◽  
pp. 581-591 ◽  
Author(s):  
Lu Wang ◽  
Mamta Rao ◽  
Yuqiang Fang ◽  
Meera Hameed ◽  
Agnes Viale ◽  
...  
Keyword(s):  
High Resolution ◽  
Cutaneous Melanoma ◽  
Array Cgh ◽  
Diagnostic Evaluation ◽  
Genome Wide ◽  
A Genome

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 MRLR: unraveling high-resolution meiotic recombination by linked reads

2019 ◽  
Vol 36 (1) ◽  
pp. 10-16
Author(s):  
Peng Xu ◽  
Timothy Kennell ◽  
Min Gao ◽  
Robert P Kimberly ◽  
Zechen Chong ◽  
...  
Keyword(s):  
High Resolution ◽  
Meiotic Recombination ◽  
Genetic Material ◽  
Supplementary Information ◽  
Genomic Features ◽  
Homologous Chromosomes ◽  
Related Family ◽  
Genome Wide ◽  
A Genome ◽  
Eukaryotic Organisms

Abstract Motivation Meiotic recombination facilitates the transmission of exchanged genetic material between homologous chromosomes and plays a crucial role in increasing the genetic variations in eukaryotic organisms. In humans, thousands of crossover events have been identified by genotyping related family members. However, most of these crossover regions span tens to hundreds of kb, which is not sufficient resolution to accurately identify the crossover breakpoints in a typical trio family. Results We have developed MRLR, a software using 10X linked reads to identify crossover events at a high resolution. By reconstructing the gamete genome, MRLR only requires a trio family dataset and can efficiently discover the crossover events. Using MRLR, we revealed a fine-scale pattern of crossover regions in six human families. From the two closest heterozygous alleles around the crossovers, we determined that MRLR achieved a median resolution 4.5 kb. This method can delineate a genome-wide landscape of crossover events at a precise scale, which is important for both functional and genomic features analysis of meiotic recombination. Availability and implementation MRLR is freely available at https://github.com/ChongLab/MRLR, implemented in Perl. Supplementary information Supplementary data are available at Bioinformatics online.

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