Methylation profiling by bisulfite sequencing analysis of the mtDNA Non-Coding Region in replicative and senescent Endothelial Cells

Mitochondrion ◽  
2016 ◽  
Vol 27 ◽  
pp. 40-47 ◽  
Author(s):  
Valentina Bianchessi ◽  
Maria Cristina Vinci ◽  
Patrizia Nigro ◽  
Valeria Rizzi ◽  
Floriana Farina ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Bisulfite Sequencing ◽  
Sequencing Analysis ◽  
Coding Region ◽  
Bisulfite Sequencing Analysis ◽  
Methylation Profiling

scholarly journals BiSulfite Bolt: A bisulfite sequencing analysis platform

GigaScience ◽  
2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Colin Farrell ◽  
Michael Thompson ◽  
Anela Tosevska ◽  
Adewale Oyetunde ◽  
Matteo Pellegrini
Keyword(s):  
Data Aggregation ◽  
Bisulfite Sequencing ◽  
Low Complexity ◽  
Sequencing Analysis ◽  
Command Line ◽  
Sequencing Data ◽  
Bisulfite Sequencing Data ◽  
Analysis Platform ◽  
Python Package ◽  
Bisulfite Sequencing Analysis

Abstract Background Bisulfite sequencing is commonly used to measure DNA methylation. Processing bisulfite sequencing data is often challenging owing to the computational demands of mapping a low-complexity, asymmetrical library and the lack of a unified processing toolset to produce an analysis-ready methylation matrix from read alignments. To address these shortcomings, we have developed BiSulfite Bolt (BSBolt), a fast and scalable bisulfite sequencing analysis platform. BSBolt performs a pre-alignment sequencing read assessment step to improve efficiency when handling asymmetrical bisulfite sequencing libraries. Findings We evaluated BSBolt against simulated and real bisulfite sequencing libraries. We found that BSBolt provides accurate and fast bisulfite sequencing alignments and methylation calls. We also compared BSBolt to several existing bisulfite alignment tools and found BSBolt outperforms Bismark, BSSeeker2, BISCUIT, and BWA-Meth based on alignment accuracy and methylation calling accuracy. Conclusion BSBolt offers streamlined processing of bisulfite sequencing data through an integrated toolset that offers support for simulation, alignment, methylation calling, and data aggregation. BSBolt is implemented as a Python package and command line utility for flexibility when building informatics pipelines. BSBolt is available at https://github.com/NuttyLogic/BSBolt under an MIT license.

scholarly journals Ultradeep Bisulfite Sequencing Analysis of DNA Methylation Patterns in Multiple Gene Promoters by 454 Sequencing

2007 ◽  
Vol 67 (18) ◽  
pp. 8511-8518 ◽  
Author(s):  
Kristen H. Taylor ◽  
Robin S. Kramer ◽  
J. Wade Davis ◽  
Juyuan Guo ◽  
Deiter J. Duff ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
454 Sequencing ◽  
Sequencing Analysis ◽  
Gene Promoters ◽  
Multiple Gene ◽  
Methylation Patterns ◽  
Bisulfite Sequencing Analysis

scholarly journals BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform

2020 ◽  
Author(s):  
Colin Farrell ◽  
Michael Thompson ◽  
Anela Tosevska ◽  
Adewale Oyetunde ◽  
Matteo Pellegrini
Keyword(s):  
Data Aggregation ◽  
Bisulfite Sequencing ◽  
Low Complexity ◽  
Sequencing Analysis ◽  
Command Line ◽  
Sequencing Data ◽  
Bisulfite Sequencing Data ◽  
Analysis Platform ◽  
Python Package ◽  
Bisulfite Sequencing Analysis

AbstractBackgroundBisulfite sequencing is commonly employed to measure DNA methylation. Processing bisulfite sequencing data is often challenging due to the computational demands of mapping a low complexity, asymmetrical library and the lack of a unified processing toolset to produce an analysis ready methylation matrix from read alignments. To address these shortcomings, we have developed BiSulfite Bolt (BSBolt); a fast and scalable bisulfite sequencing analysis platform.FindingsWe evaluated BSBolt against simulated and real bisulfite sequencing libraries. We found that BSBolt provides accurate and fast bisulfite sequencing alignments and methylation calls. We also compared BSBolt to several existing bisulfite alignment tools and found BSBolt outperforms Bismark, BSSeeker2, BISCUIT, and BWA-Meth based on alignment accuracy and methylation calling accuracy.ConclusionBSBolt offers streamlined processing of bisulfite sequencing data through an integrated toolset that offers support for simulation, alignment, methylation calling, and data aggregation. BSBolt is implemented as a python package and command line utility for flexibility when building informatics pipelines. BSBolt is available at https://github.com/NuttyLogic/BSBolt under a MIT license.

scholarly journals 25-Hydroxycholesterol 3-Sulfate Recovers Acetaminophen Induced Acute Liver Injury via Stabilizing Mitochondria in Mouse Models

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 3027
Author(s):  
Yaping Wang ◽  
William M. Pandak ◽  
Edward J. Lesnefsky ◽  
Phillip B. Hylemon ◽  
Shunlin Ren
Keyword(s):  
Liver Injury ◽  
Signaling Pathways ◽  
Mouse Models ◽  
Bisulfite Sequencing ◽  
Acute Liver Injury ◽  
Sequencing Analysis ◽  
Oxygen Species ◽  
Promoter Regions ◽  
Genome Bisulfite Sequencing ◽  
Bisulfite Sequencing Analysis

Acetaminophen (APAP) overdose is one of the most frequent causes of acute liver failure (ALF). N-acetylcysteine (NAC) is currently being used as part of the standard care in the clinic but its usage has been limited in severe cases, in which liver transplantation becomes the only treatment option. Therefore, there still is a need for a specific and effective therapy for APAP induced ALF. In the current study, we have demonstrated that treatment with 25-Hydroxycholesterol 3-Sulfate (25HC3S) not only significantly reduced mortality but also decreased the plasma levels of liver injury markers, including LDH, AST, and ALT, in APAP overdosed mouse models. 25HC3S also decreased the expression of those genes involved in cell apoptosis, stabilized mitochondrial polarization, and significantly decreased the levels of oxidants, malondialdehyde (MDA), and reactive oxygen species (ROS). Whole genome bisulfite sequencing analysis showed that 25HC3S increased demethylation of 5mCpG in key promoter regions and thereby increased the expression of those genes involved in MAPK-ERK and PI3K-Akt signaling pathways. We concluded that 25HC3S may alleviate APAP induced liver injury via up-regulating the master signaling pathways and maintaining mitochondrial membrane polarization. The results suggest that 25HC3S treatment facilitates the recovery and significantly decreases the mortality of APAP induced acute liver injury and has a synergistic effect with NAC in propylene glycol (PG) for the injury.

scholarly journals GIMAP5 maintains liver endothelial cell homeostasis and prevents portal hypertension

2021 ◽  
Vol 218 (7) ◽  
Author(s):  
Kaela Drzewiecki ◽  
Jungmin Choi ◽  
Joseph Brancale ◽  
Michael A. Leney-Greene ◽  
Sinan Sari ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Portal Hypertension ◽  
Liver Disease ◽  
Endothelial Cell ◽  
Sequencing Analysis ◽  
Major Contributor ◽  
Liver Sinusoidal Endothelial Cells ◽  
Cell Homeostasis ◽  
Liver Endothelial Cell ◽  
Insight Into

Portal hypertension is a major contributor to decompensation and death from liver disease, a global health problem. Here, we demonstrate homozygous damaging mutations in GIMAP5, a small organellar GTPase, in four families with unexplained portal hypertension. We show that GIMAP5 is expressed in hepatic endothelial cells and that its loss in both humans and mice results in capillarization of liver sinusoidal endothelial cells (LSECs); this effect is also seen when GIMAP5 is selectively deleted in endothelial cells. Single-cell RNA-sequencing analysis in a GIMAP5-deficient mouse model reveals replacement of LSECs with capillarized endothelial cells, a reduction of macrovascular hepatic endothelial cells, and places GIMAP5 upstream of GATA4, a transcription factor required for LSEC specification. Thus, GIMAP5 is a critical regulator of liver endothelial cell homeostasis and, when absent, produces portal hypertension. These findings provide new insight into the pathogenesis of portal hypertension, a major contributor to morbidity and mortality from liver disease.

scholarly journals Genome-Wide DNA Methylation Profiling in the Lotus (Nelumbo nucifera) Flower Showing its Contribution to the Stamen Petaloid

Plants ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 135 ◽  
Author(s):  
Zhongyuan Lin ◽  
Meihui Liu ◽  
Rebecca Njeri Damaris ◽  
Tonny Maraga Nyong’a ◽  
Dingding Cao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Epigenetic Modification ◽  
Nelumbo Nucifera ◽  
Flower Formation ◽  
Relationship Analysis ◽  
Genome Wide ◽  
Dna Methylation Profiling ◽  
Methylation Profiling

DNA methylation is a vital epigenetic modification. Methylation has a significant effect on the gene expression influencing the regulation of different physiological processes. Current studies on DNA methylation have been conducted on model plants. Lotus (Nelumbo nucifera) is a basic eudicot exhibiting variations during development, especially in flower formation. DNA methylation profiling was conducted on different flower tissues of lotuses through whole genome bisulfite sequencing (WGBS) to investigate the effects of DNA methylation on its stamen petaloid. A map of methylated cytosines at the single base pair resolution for the lotus was constructed. When the stamen was compared with the stamen petaloid, the DNA methylation exhibited a global decrease. Genome-wide relationship analysis between DNA methylation and gene expression identified 31 different methylation region (DMR)-associated genes, which might play crucial roles in floral organ formation, especially in the stamen petaloid. One out of 31 DMR-associated genes, NNU_05638 was homolog with Plant U-box 33 (PUB33). The DNA methylation status of NNU_05638 promoter was distinct in three floral organs, which was confirmed by traditional bisulfite sequencing. These results provide further insights about the regulation of stamen petaloids at the epigenetic level in lotus.

Molecular characterization of the Na-K-Cl cotransporter of bovine aortic endothelial cells

1997 ◽  
Vol 273 (1) ◽  
pp. C188-C197 ◽  
Author(s):  
T. R. Yerby ◽  
C. R. Vibat ◽  
D. Sun ◽  
J. A. Payne ◽  
M. E. O'Donnell
Keyword(s):  
Endothelial Cells ◽  
Endothelial Cell ◽  
Amino Acid ◽  
Blot Analysis ◽  
Cdna Probe ◽  
Bovine Aortic Endothelial Cell ◽  
Coding Region ◽  
Cerebral Microvessels ◽  
Aortic Endothelial Cells ◽  
Aortic Endothelial

The Na-K-Cl cotransporter is an important regulator of endothelial cell volume and may also contribute to flux of Na and Cl across the endothelium of the blood-brain barrier. To date, two Na-K-Cl cotransport isoforms have been identified, the cotransporter in secretory epithelia, NKCC1, and that in absorptive renal epithelia, NKCC2. Our previous studies showed that a monoclonal antibody to the cotransporter of human colonic T84 epithelial cells, an NKCC1 isoform, recognizes a 170-kDa glycoprotein from endothelial cells. The molecular identity of the Na-K-Cl cotransporter present in endothelial cells, however, has been unknown. In addition, although evidence has been provided that phosphorylation of the endothelial cotransporter plays a role in regulating its activity, little is known about potential sites for protein kinase interaction with the cotransporter. The present study was conducted to determine the molecular structure of the endothelial Na-K-Cl cotransporter. Using a 1.0-kilobase (kb) cDNA fragment from a conserved region of the T84 cell cotransporter, we screened a bovine aortic endothelial cell cDNA library and subsequently identified and sequenced two overlapping clones that together spanned the entire coding region. The endothelial cotransporter is a 1,201-amino acid protein with 12 putative transmembrane segments and large amino and carboxy termini, each containing several consensus sites for phosphorylation by protein kinases. Comparison of the endothelial cotransporter amino acid sequence with known NKCC1 and NKCC2 sequences revealed a 96% identity with NKCC1. Northern blot analysis using a cDNA probe from the endothelial cotransporter revealed high expression of approximately 7.5-kb transcripts in a number of bovine tissues. Finally, a prominent expression of Na-K-Cl cotransporter was found by Western blot analysis in both cultured and freshly isolated endothelial cells of bovine aorta and cerebral microvessels.

scholarly journals Novel PITX2 Mutations including a Mutation Causing an Unusual Ophthalmic Phenotype of Axenfeld-Rieger Syndrome

2019 ◽  
Vol 2019 ◽  
pp. 1-10
Author(s):  
Liqin Huang ◽  
Yong Meng ◽  
Xiangming Guo
Keyword(s):  
Genomic Dna ◽  
Anterior Segment ◽  
Dominant Negative ◽  
Chinese Patients ◽  
Dominant Negative Effect ◽  
Sequencing Analysis ◽  
Coding Region ◽  
Direct Dna Sequencing ◽  
Rieger Syndrome ◽  
Pitx2 Gene

Purpose. The aims of this study were to examine novel mutations in PITX2 and FOXC1 in Chinese patients with anterior segment dysgenesis (ASD) and to compare the clinical presentations of these mutations with previously reported associated phenotypes. Methods. Twenty-six unrelated patients with different forms of ASD were enrolled from our paediatric and genetic eye clinic. The ocular manifestations of both eyes of each patient were recorded. Genomic DNA was prepared from venous leukocytes. All coding exons of PITX2 and FOXC1 were amplified by polymerase chain reaction (PCR) from genomic DNA and subjected to direct DNA sequencing. Analysis of mutations in control subjects was performed by heteroduplex single-strand conformation polymorphism (SSCP) analysis. Results. Sequence analysis of the PITX2 gene revealed four mutations, including c.475_476delCT (P.L159VfsX39), c.64C > T (P.Q22X), c.296delG (P.R99PfsX56), and c.206G > A (P.R69H). The first three mutations were found to be novel. The c.475_476delCT (P.L159VfsX39) mutation, located at the 3′ end of the PITX2-coding region, was identified in a Chinese Axenfeld-Rieger syndrome (ARS) patient who presented with an unusual severe phenotype of bilateral aniridia. The clinical characteristics, including the severity and manifestations of the patient’s phenotype, were compared with reported PITX2-associated aniridia phenotypes of ARS in the literature. Conclusions. These results expand the mutation spectrum of the PITX2 gene in patients with ARS. The PITX2 gene may be responsible for a significant portion of ARS with additional systemic defects in the Chinese population. This is the first reported case of a mutation at the 3′ end of the PITX2-coding region extending the phenotypic consequences to bilateral aniridia. The traits of ARS could display tremendous variability in severity and manifestations due to the dominant-negative effect of PITX2. Our results further emphasize the importance of careful clinical and genetic analysis in determining mutation-disease associations and may lead to a better understanding of the role of PITX2 in ocular development.

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