Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

Krueger, Felix; Andrews, Simon

doi:10.1093/bioinformatics/btr167

Cited by 4,216 publications

(3,606 citation statements)

References 9 publications

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“…Our data provide a ~20-fold coverage of the E. coli genome per sample. Using Bismark software 36 , we mapped fully bisulfite-converted forward and reverse read (C-> T and G-> A conversions of the forward strand) to similarly converted versions of the reference genome; the best of the four possible alignments was compared with the normal reference sequence to enable calls on the methylation state of all cytosine positions in the read. To our knowledge, this is the first genome-wide base-resolution study of cytosine methylation in any bacterium.…”

Section: Resultsmentioning

confidence: 99%

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

et al. 2012

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DnA cytosine methylation regulates gene expression in mammals. In bacteria, its role in gene expression and genome architecture is less understood. Here we perform high-throughput sequencing of bisulfite-treated genomic DnA from Escherichia coli K12 to describe, for the first time, the extent of cytosine methylation of bacterial DnA at single-base resolution. Whereas most target sites (C m CWGG) are fully methylated in stationary phase cells, many sites with an extended CC m CWGG motif are only partially methylated in exponentially growing cells. We speculate that these partially methylated sites may be selected, as these are slightly correlated with the risk of spontaneous, non-synonymous conversion of methylated cytosines to thymines. microarray analysis in a cytosine methylation-deficient mutant of E. coli shows increased expression of the stress response sigma factor Rpos and many of its targets in stationary phase. Thus, DnA cytosine methylation is a regulator of stationary phase gene expression in E. coli.

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Section: Resultsmentioning

confidence: 99%

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

et al. 2012

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“…The human reference genome (GRCh38) was in silico bisulphite converted before aligning trimmed reads with Bismark v0.10.1 and bowtie2 (v2.1.0) as previously described(Krueger & Andrews, 2011; Langmead & Salzberg, 2012). PCR bias was removed by a deduplication step.…”

Section: Methodsmentioning

confidence: 99%

A molecular signature for delayed graft function

et al. 2018

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Chronic kidney disease and associated comorbidities (diabetes, cardiovascular diseases) manifest with an accelerated ageing phenotype, leading ultimately to organ failure and renal replacement therapy. This process can be modulated by epigenetic and environmental factors which promote loss of physiological function and resilience to stress earlier, linking biological age with adverse outcomes post‐transplantation including delayed graft function (DGF). The molecular features underpinning this have yet to be fully elucidated. We have determined a molecular signature for loss of resilience and impaired physiological function, via a synchronous genome, transcriptome and proteome snapshot, using human renal allografts as a source of healthy tissue as an in vivo model of ageing in humans. This comprises 42 specific transcripts, related through IFNγ signalling, which in allografts displaying clinically impaired physiological function (DGF) exhibited a greater magnitude of change in transcriptional amplitude and elevated expression of noncoding RNAs and pseudogenes, consistent with increased allostatic load. This was accompanied by increased DNA methylation within the promoter and intragenic regions of the DGF panel in preperfusion allografts with immediate graft function. Pathway analysis indicated that an inability to sufficiently resolve inflammatory responses was enabled by decreased resilience to stress and resulted in impaired physiological function in biologically older allografts. Cross‐comparison with publically available data sets for renal pathologies identified significant transcriptional commonality for over 20 DGF transcripts. Our data are clinically relevant and important, as they provide a clear molecular signature for the burden of “wear and tear” within the kidney and thus age‐related physiological capability and resilience.

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“…Trimmed paired reads were joined with the fastq‐join option of ea‐utils, v1.1.2–537. The reads were aligned to the human genome reference sequence hg19 UCSC with Bismark, v0.14.3 and Bowtie2, v2.2.6 17, 18. Read alignments were processed with SAMtools v1 19.…”

Section: Methodsmentioning

confidence: 99%

Single CpG hypermethylation, allele methylation errors, and decreased expression of multiple tumor suppressor genes in normal body cells of mutation‐negative early‐onset and high‐risk breast cancer patients

Böck

Appenzeller

Haertle

et al. 2018

Intl Journal of Cancer

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To evaluate the role of constitutive epigenetic changes in normal body cells of BRCA1/BRCA2‐mutation negative patients, we have developed a deep bisulfite sequencing assay targeting the promoter regions of 8 tumor suppressor (TS) genes (BRCA1, BRCA2, RAD51C, ATM, PTEN, TP53, MLH1, RB1) and the estrogene receptor gene (ESR1), which plays a role in tumor progression. We analyzed blood samples of two breast cancer (BC) cohorts with early onset (EO) and high risk (HR) for a heterozygous mutation, respectively, along with age‐matched controls. Methylation analysis of up to 50,000 individual DNA molecules per gene and sample allowed quantification of epimutations (alleles with >50% methylated CpGs), which are associated with epigenetic silencing. Compared to ESR1, which is representative for an average promoter, TS genes were characterized by a very low (< 1%) average methylation level and a very low mean epimutation rate (EMR; < 0.0001% to 0.1%). With exception of BRCA1, which showed an increased EMR in BC (0.31% vs. 0.06%), there was no significant difference between patients and controls. One of 36 HR BC patients exhibited a dramatically increased EMR (14.7%) in BRCA1, consistent with a disease‐causing epimutation. Approximately one third (15 of 44) EO BC patients exhibited increased rates of single CpG methylation errors in multiple TS genes. Both EO and HR BC patients exhibited global underexpression of blood TS genes. We propose that epigenetic abnormalities in normal body cells are indicative of disturbed mechanisms for maintaining low methylation and appropriate expression levels and may be associated with an increased BC risk.

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Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

Cited by 4,216 publications

References 9 publications

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

A molecular signature for delayed graft function

Single CpG hypermethylation, allele methylation errors, and decreased expression of multiple tumor suppressor genes in normal body cells of mutation‐negative early‐onset and high‐risk breast cancer patients

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