Increased accuracy and speed in whole genome bisulfite read mapping using a two-letter alphabet

Range Of Functions ◽

Using Data

AbstractDNA methylation, characterized by the presence of methyl group at cytosines in a DNA sequence, is an important epigenomic mark with a wide range of functions across diverse organisms. Whole genome bisulfite sequencing (WGBS) has emerged as the gold standard to interrogate cytosine methylation. Accurately mapping WGBS reads to a reference genome allows reconstruction of tissue methylomes at single-base resolution. Algorithms used to map WGBS reads often encode the four-base DNA alphabet with three letters by reducing two bases to a common letter.We introduce another bisulfite mapping algorithm (abismal), based on the novel idea of encoding a four-letter DNA sequence as two letters, one for purines and one for pyrimidines. We show theoretically that this encoding benefits from higher uniformity and specificity when subsequences are selected from reads for filtration. In our implementation, this leads to a decreased mapping time relative to the three-letter encoding. We demonstrate, using data from multiple public studies, that the abismal software tool improves mapping accuracy at significantly lower mapping times compared to commonly used mappers, with most notable improvements observed in samples originating from the random priming post-bisulfite adapter tagging protocol.

Fast and memory-efficient mapping of short bisulfite sequencing reads using a two-letter alphabet

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqab115 ◽

2021 ◽

Vol 3 (4) ◽

Author(s):

Guilherme de Sena Brandine ◽

Andrew D Smith

Keyword(s):

Cytosine Methylation ◽

Bisulfite Sequencing ◽

Software Tool ◽

Read Mapping ◽

Mapping Algorithm ◽

Letter Alphabet ◽

Mapping Software ◽

Wide Range ◽

Range Of Functions ◽

Similar Accuracy

Abstract DNA cytosine methylation is an important epigenomic mark with a wide range of functions in many organisms. Whole genome bisulfite sequencing is the gold standard to interrogate cytosine methylation genome-wide. Algorithms used to map bisulfite-converted reads often encode the four-base DNA alphabet with three letters by reducing two bases to a common letter. This encoding substantially reduces the entropy of nucleotide frequencies in the resulting reference genome. Within the paradigm of read mapping by first filtering possible candidate alignments, reduced entropy in the sequence space can increase the required computing effort. We introduce another bisulfite mapping algorithm (abismal), based on the idea of encoding a four-letter DNA sequence as only two letters, one for purines and one for pyrimidines. We show that this encoding can lead to greater specificity compared to existing encodings used to map bisulfite sequencing reads. Through the two-letter encoding, the abismal software tool maps reads in less time and using less memory than most bisulfite sequencing read mapping software tools, while attaining similar accuracy. This allows in silico methylation analysis to be performed in a wider range of computing machines with limited hardware settings.

Dnmt3a and Dnmt3b-Decommissioned Fetal Enhancers are Linked to Kidney Disease

Journal of the American Society of Nephrology ◽

10.1681/asn.2019080797 ◽

2020 ◽

Vol 31 (4) ◽

pp. 765-782

Author(s):

Yuting Guan ◽

Hongbo Liu ◽

Ziyuan Ma ◽

Szu-Yuan Li ◽

Jihwan Park ◽

...

Keyword(s):

Kidney Disease ◽

Dna Methyltransferase ◽

Cytosine Methylation ◽

Bisulfite Sequencing ◽

Kidney Development ◽

Epigenetic Mark ◽

Whole Genome ◽

Tubule Cells

BackgroundCytosine methylation is an epigenetic mark that dictates cell fate and response to stimuli. The timing and establishment of methylation logic during kidney development remains unknown. DNA methyltransferase 3a and 3b are the enzymes capable of establishing de novo methylation.MethodsWe generated mice with genetic deletion of Dnmt3a and Dnmt3b in nephron progenitor cells (Six2CreDnmt3a/3b) and kidney tubule cells (KspCreDnmt3a/3b). We characterized KspCreDnmt3a/3b mice at baseline and after injury. Unbiased omics profiling, such as whole genome bisulfite sequencing, reduced representation bisulfite sequencing and RNA sequencing were performed on whole-kidney samples and isolated renal tubule cells.ResultsKspCreDnmt3a/3b mice showed no obvious morphologic and functional alterations at baseline. Knockout animals exhibited increased resistance to cisplatin-induced kidney injury, but not to folic acid–induced fibrosis. Whole-genome bisulfite sequencing indicated that Dnmt3a and Dnmt3b play an important role in methylation of gene regulatory regions that act as fetal-specific enhancers in the developing kidney but are decommissioned in the mature kidney. Loss of Dnmt3a and Dnmt3b resulted in failure to silence developmental genes. We also found that fetal-enhancer regions methylated by Dnmt3a and Dnmt3b were enriched for kidney disease genetic risk loci. Methylation patterns of kidneys from patients with CKD showed defects similar to those in mice with Dnmt3a and Dnmt3b deletion.ConclusionsOur results indicate a potential locus-specific convergence of genetic, epigenetic, and developmental elements in kidney disease development.

Humor and leadership style

Humor - International Journal of Humor Research ◽

10.1515/humor.2006.006 ◽

2006 ◽

Vol 19 (2) ◽

Cited By ~ 34

Author(s):

Janet Holmes ◽

Meredith Marra

Keyword(s):

Leadership Style ◽

Leadership Studies ◽

Workplace Interactions ◽

Effective Leaders ◽

Wide Range ◽

Range Of Functions ◽

Basic Distinction ◽

Using Data ◽

Creativity And Innovation ◽

And Task

AbstractDrawing on authentic workplace interactions, this paper examines the ways in which effective leaders use humor as a discursive resource to construct particular aspects of leadership style. The conventional wisdom in leadership studies suggests that humor is an important tool for “good” leaders who inspire and challenge their subordinates. The management studies literature suggests a basic distinction between a traditional transactional style, which is rule-driven and task focused, and a more favored transformational style, where leaders encourage creativity and innovation, and are characterized as inspirational. Using data collected in a range of New Zealand organizations, this paper explores and illustrates the wide range of functions served by humor, and the ways in which humor contributes to aspects of the construction of leadership styles. Our analysis supports recent proposals that many effective leaders combine aspects of both transactional and transformational styles of leadership.

Whole-genome bisulfite sequencing in systemic sclerosis provides novel targets to understand disease pathogenesis

BMC Medical Genomics ◽

10.1186/s12920-019-0602-8 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 2

Author(s):

Tianyuan Lu ◽

Kathleen Oros Klein ◽

Inés Colmegna ◽

Maximilien Lora ◽

Celia M. T. Greenwood ◽

...

Keyword(s):

Dna Methylation ◽

Genetic Variation ◽

Systemic Sclerosis ◽

Cytosine Methylation ◽

Bisulfite Sequencing ◽

Whole Genome ◽

Disease Pathogenesis ◽

Genome Wide ◽

Abstract Background Systemic sclerosis (SSc) is a rare autoimmune connective tissue disease whose pathogenesis remains incompletely understood. Increasing evidence suggests that both genetic susceptibilities and changes in DNA methylation influence pivotal biological pathways and thereby contribute to the disease. The role of DNA methylation in SSc has not been fully elucidated, because existing investigations of DNA methylation predominantly focused on nucleotide CpGs within restricted genic regions, and were performed on samples containing mixed cell types. Methods We performed whole-genome bisulfite sequencing on purified CD4+ T lymphocytes from nine SSc patients and nine controls in a pilot study, and then profiled genome-wide cytosine methylation as well as genetic variations. We adopted robust statistical methods to identify differentially methylated genomic regions (DMRs). We then examined pathway enrichment associated with genes located in these DMRs. We also tested whether changes in CpG methylation were associated with adjacent genetic variation. Results We profiled DNA methylation at more than three million CpG dinucleotides genome-wide. We identified 599 DMRs associated with 340 genes, among which 54 genes exhibited further associations with adjacent genetic variation. We also found these genes were associated with pathways and functions that are known to be abnormal in SSc, including Wnt/β-catenin signaling pathway, skin lesion formation and progression, and angiogenesis. Conclusion The CD4+ T cell DNA cytosine methylation landscape in SSc involves crucial genes in disease pathogenesis. Some of the methylation patterns are also associated with genetic variation. These findings provide essential foundations for future studies of epigenetic regulation and genome-epigenome interaction in SSc.

Ultra-deep whole genome bisulfite sequencing reveals a single methylation hotspot in human brain mitochondrial DNA

10.1101/2021.03.30.437685 ◽

2021 ◽

Author(s):

Romain Guitton ◽

Christian Dölle ◽

Guido Alves ◽

Ole-Bjørn Tysnes ◽

Gonzalo S. Nido ◽

...

Keyword(s):

Gene Expression ◽

Parkinson’S Disease ◽

Mitochondrial Dna ◽

Prefrontal Cortex ◽

Cytosine Methylation ◽

Bisulfite Sequencing ◽

Whole Genome ◽

Low Levels

ABSTRACTWhile DNA methylation is established as a major regulator of gene expression in the nucleus, the existence of mitochondrial DNA (mtDNA) methylation remains controversial. Here, we characterised the mtDNA methylation landscape in the prefrontal cortex of neurological healthy individuals (n=26) and patients with Parkinson’s disease (n=27), using a combination of whole genome bisulfite sequencing (WGBS) and bisulfite-independent methods. Accurate mtDNA mapping from WGBS data required alignment to an mtDNA reference only, to avoid misalignment to nuclear mitochondrial pseudogenes. Once correctly aligned, WGBS data provided ultra-deep mtDNA coverage (16,723±7,711), and revealed overall very low levels of cytosine methylation. The highest methylation levels (5.49±0.97%) were found on CpG position m.545, located in the heavy-strand promoter 1 region. The m.545 methylation was validated using a combination of methylation-sensitive DNA digestion and quantitative PCR analysis. We detected no association between mtDNA methylation profile and Parkinson’s disease. Interestingly, m.545 methylation correlated with the levels of mtDNA transcripts, suggesting a putative role in regulating mtDNA gene expression. In addition, we propose a robust framework for methylation analysis of mtDNA from WGBS data, which is less prone to false-positive findings due to misalignment of nuclear mitochondrial pseudogene sequences.Graphical abstract of the analyses and main findingsFresh-frozen brain tissue was obtained from the prefrontal cortex (Brodmann area 9) of 53 individuals, comprising 27 patients with idiopathic PD and 26 healthy controls. Tissue from the same samples was used in three different downstream analyses. WGBS was conducted on all 53 samples and the data were analysed using three different alignment strategies. Alignment against an mtDNA reference only was clearly superior as it gave the highest and most even depth of coverage. WGBS analysis revealed that mtDNA harbours very low levels of cytosine methylation, with the exception of the CpG position m.545 within the HSP1 region (lower right inset). The m.545 methylation was confirmed by bisulfite- and sequencing-independent methods, employing methylation-specific MspJI DNA digestion, followed by quantification with qPCR or fluorescent PCR and capillary electrophoresis. Finally, mtDNA transcript levels were determined by RT-qPCR and correlated to m.545 methylation levels, showing a positive association.

Whole-genome bisulfite sequencing in systemic sclerosis provides novel targets to understand disease pathogenesis

10.21203/rs.2.12858/v3 ◽

2019 ◽

Author(s):

Tianyuan Lu ◽

Kathleen Oros Klein ◽

Inés Colmegna ◽

Maximilien Lora ◽

Celia M.T. Greenwood ◽

...

Keyword(s):

Dna Methylation ◽

Genetic Variation ◽

Systemic Sclerosis ◽

Cytosine Methylation ◽

Bisulfite Sequencing ◽

Whole Genome ◽

Disease Pathogenesis ◽

Genome Wide ◽

Abstract Background Systemic sclerosis (SSc) is a rare autoimmune connective tissue disease whose pathogenesis remains incompletely understood. Increasing evidence suggests that both genetic susceptibilities and changes in DNA methylation influence pivotal biological pathways and thereby contribute to the disease. The role of DNA methylation in SSc has not been fully elucidated, because existing investigations of DNA methylation predominantly focused on nucleotide CpGs within restricted genic regions, and were performed on samples containing mixed cell types. Methods We performed whole-genome bisulfite sequencing on purified CD4+ T lymphocytes from nine SSc patients and nine controls in a pilot study, and then profiled genome-wide cytosine methylation as well as genetic variations. We adopted robust statistical methods to identify differentially methylated genomic regions (DMRs). We then examined pathway enrichment associated with genes located in these DMRs. We also tested whether changes in CpG methylation were associated with adjacent genetic variation. Results We profiled DNA methylation at more than three million CpG dinucleotides genome-wide. We identified 599 DMRs associated with 340 genes, among which 54 genes exhibited further associations with adjacent genetic variation. We also found these genes were associated with pathways and functions that are known to be abnormal in SSc, including Wnt/-catenin signaling pathway, skin lesion formation and progression, and angiogenesis. Conclusion The CD4+ T cell DNA cytosine methylation landscape in SSc involves crucial genes in disease pathogenesis. Some of the methylation patterns are also associated with genetic variation. These findings provide essential foundations for future studies of epigenetic regulation and genome-epigenome interaction in SSc.

Whole-genome bisulfite sequencing in systemic sclerosis provides novel targets to understand disease pathogenesis

10.21203/rs.2.12858/v1 ◽

2019 ◽

Author(s):

Tianyuan Lu ◽

Kathleen Oros Klein ◽

Inés Colmegna ◽

Maximilien Lora ◽

Celia M.T. Greenwood ◽

...

Keyword(s):

Dna Methylation ◽

Genetic Variation ◽

Systemic Sclerosis ◽

Cytosine Methylation ◽

Bisulfite Sequencing ◽

Whole Genome ◽

Disease Pathogenesis ◽

Genome Wide ◽

Abstract Background Systemic sclerosis (SSc) is a rare autoimmune connective tissue disease whose pathogenesis remains incompletely understood. Increasing evidence suggests that both genetic susceptibilities and changes in DNA methylation influence pivotal biological pathways and thereby contribute to the disease. The role of DNA methylation in SSc has not been fully elucidated, because existing investigations of DNA methylation predominantly focused on nucleotide CpGs within restricted genic regions, and were performed on samples containing mixed cell types. Methods We performed whole-genome bisulfite sequencing on purified CD4+ T lymphocytes from nine SSc patients and nine controls in a pilot study, and then profiled genome-wide cytosine methylation as well as genetic variations. We adopted robust statistical methods to identify differentially methylated genomic regions (DMRs). We then examined pathway enrichment associated with genes located in these DMRs. We also tested whether changes in CpG methylation were associated with adjacent genetic variation. Results We profiled DNA methylation at more than three million CpG dinucleotides genome-wide. We identified 599 DMRs associated with 340 genes, among which 54 genes exhibited further associations with adjacent genetic variation. We also found these genes were associated with pathways and functions that are known to be abnormal in SSc, including Wnt/-catenin signaling pathway, skin lesion formation and progression, and angiogenesis. Conclusion The CD4+ T cell DNA cytosine methylation landscape in SSc involves crucial genes in disease pathogenesis. Some of the methylation patterns are also associated with genetic variation. These findings provide essential foundations for future studies of epigenetic regulation and genome-epigenome interaction in SSc.

Whole-genome bisulfite sequencing in systemic sclerosis provides novel targets to understand disease pathogenesis

10.21203/rs.2.12858/v2 ◽

2019 ◽

Author(s):

Tianyuan Lu ◽

Kathleen Oros Klein ◽

Inés Colmegna ◽

Maximilien Lora ◽

Celia M.T. Greenwood ◽

...

Keyword(s):

Dna Methylation ◽

Genetic Variation ◽

Systemic Sclerosis ◽

Cytosine Methylation ◽

Bisulfite Sequencing ◽

Whole Genome ◽

Disease Pathogenesis ◽

Genome Wide ◽

Abstract Background Systemic sclerosis (SSc) is a rare autoimmune connective tissue disease whose pathogenesis remains incompletely understood. Increasing evidence suggests that both genetic susceptibilities and changes in DNA methylation influence pivotal biological pathways and thereby contribute to the disease. The role of DNA methylation in SSc has not been fully elucidated, because existing investigations of DNA methylation predominantly focused on nucleotide CpGs within restricted genic regions, and were performed on samples containing mixed cell types. Methods We performed whole-genome bisulfite sequencing on purified CD4+ T lymphocytes from nine SSc patients and nine controls in a pilot study, and then profiled genome-wide cytosine methylation as well as genetic variations. We adopted robust statistical methods to identify differentially methylated genomic regions (DMRs). We then examined pathway enrichment associated with genes located in these DMRs. We also tested whether changes in CpG methylation were associated with adjacent genetic variation. Results We profiled DNA methylation at more than three million CpG dinucleotides genome-wide. We identified 599 DMRs associated with 340 genes, among which 54 genes exhibited further associations with adjacent genetic variation. We also found these genes were associated with pathways and functions that are known to be abnormal in SSc, including Wnt/-catenin signaling pathway, skin lesion formation and progression, and angiogenesis. Conclusion The CD4+ T cell DNA cytosine methylation landscape in SSc involves crucial genes in disease pathogenesis. Some of the methylation patterns are also associated with genetic variation. These findings provide essential foundations for future studies of epigenetic regulation and genome-epigenome interaction in SSc.

Insight Between the Epigenetics and Transcription Responding of Cotton Hypocotyl Cellular Elongation Under Salt-Alkaline Stress

Frontiers in Plant Science ◽

10.3389/fpls.2021.772123 ◽

2021 ◽

Vol 12 ◽

Author(s):

Cun Rui ◽

Yuexin Zhang ◽

Yapeng Fan ◽

Mingge Han ◽

Maohua Dai ◽

...

Keyword(s):

Dna Methylation ◽

Growth Regulation ◽

Cytosine Methylation ◽

Alkali Treatment ◽

Regulation Mechanism ◽

Alkaline Stress ◽

Whole Genome ◽

Three Samples ◽

Relationship Of

Gossypium barbadense is a cultivated cotton not only known for producing superior fiber but also for its salt and alkaline resistance. Here, we used Whole Genome Bisulfite Sequencing (WGBS) technology to map the cytosine methylation of the whole genome of the G. barbadense hypocotyl at single base resolution. The methylation sequencing results showed that the mapping rates of the three samples were 75.32, 77.54, and 77.94%, respectively. In addition, the Bisulfite Sequence (BS) conversion rate was 99.78%. Approximately 71.03, 53.87, and 6.26% of the cytosine were methylated at CG, CHG, and CHH sequence contexts, respectively. A comprehensive analysis of DNA methylation and transcriptome data showed that the methylation level of the promoter region was a positive correlation in the CHH context. Saline-alkaline stress was related to the methylation changes of many genes, transcription factors (TFs) and transposable elements (TEs), respectively. We explored the regulatory mechanism of DNA methylation in response to salt and alkaline stress during cotton hypocotyl elongation. Our data shed light into the relationship of methylation regulation at the germination stage of G. barbadense hypocotyl cell elongation and salt-alkali treatment. The results of this research help understand the early growth regulation mechanism of G. barbadense in response to abiotic stress.

Structure, Function and Interactions of Tau: Particular Focus on Potential Drug Targets for the Treatment of Tauopathies

CNS & Neurological Disorders - Drug Targets ◽

10.2174/1871527317666180525112008 ◽

2018 ◽

Vol 17 (5) ◽

pp. 325-337 ◽

Cited By ~ 2

Author(s):

Hojjat Borna ◽

Kasim Assadoulahei ◽

Gholamhossein Riazi ◽

Asghar Beigi Harchegani ◽

Alireza Shahriary

Keyword(s):

Tau Protein ◽

Drug Targets ◽

Brain Injuries ◽

Potential Drug ◽

Microtubule Network ◽

Wide Range ◽

Potential Risk Factors ◽

Range Of Functions ◽

Potential Drug Targets

Background & Objective: Neurodegenrative diseases are among the most widespread lifethreatening disorders around the world in elderly ages. The common feature of a group of neurodegenerative disorders, called tauopathies, is an accumulation of microtubule associated protein tau inside the neurons. The exact mechanism underlying tauopathies is not well-understood but several factors such as traumatic brain injuries and genetics are considered as potential risk factors. Although tau protein is well-known for its key role in stabilizing and organization of axonal microtubule network, it bears a broad range of functions including DNA protection and participation in signaling pathways. Moreover, the flexible unfolded structure of tau facilitates modification of tau by a wide range of intracellular enzymes which in turn broadens tau function and interaction spectrum. The distinctive properties of tau protein concomitant with the crucial role of tau interaction partners in the progression of neurodegeneration suggest tau and its binding partners as potential drug targets for the treatment of neurodegenerative diseases. Conclusion: This review aims to give a detailed description of structure, functions and interactions of tau protein in order to provide insight into potential therapeutic targets for treatment of tauopathies.