sulfites

Summary

Summary: Inorganic salts of sulfurous acid.

Top Publications

  1. Diep D, Plongthongkum N, Gore A, Fung H, Shoemaker R, Zhang K. Library-free methylation sequencing with bisulfite padlock probes. Nat Methods. 2012;9:270-2 pubmed publisher
  2. Wang J, Jiang H, Ji G, Gao F, Wu M, Sun J, et al. High resolution profiling of human exon methylation by liquid hybridization capture-based bisulfite sequencing. BMC Genomics. 2011;12:597 pubmed publisher
    ..Thus, they are not practical for researchers to study multiple clinical samples in biomarker research...
  3. Prada D, Gonzalez R, Sánchez L, Castro C, Fabián E, Herrera L. Satellite 2 demethylation induced by 5-azacytidine is associated with missegregation of chromosomes 1 and 16 in human somatic cells. Mutat Res. 2012;729:100-5 pubmed publisher
    ..This change occurred in a non-specific pattern. Our study demonstrates an association between loss of satellite 2 DNA methylation and chromosome loss in human lymphocytes...
  4. Krueger F, Andrews S. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27:1571-2 pubmed publisher
    ..Its output discriminates between cytosines in CpG, CHG and CHH context and enables bench scientists to visualize and interpret their methylation data soon after the sequencing run is completed...
  5. Gu H, Smith Z, Bock C, Boyle P, Gnirke A, Meissner A. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc. 2011;6:468-81 pubmed publisher
    ..The entire process of RRBS library construction takes ?9 d...
  6. Ivanov M, Kals M, Kacevska M, Metspalu A, Ingelman Sundberg M, Milani L. In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes. Nucleic Acids Res. 2013;41:e72 pubmed publisher
  7. Su J, Yan H, Wei Y, Liu H, Liu H, Wang F, et al. CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. Nucleic Acids Res. 2013;41:e4 pubmed publisher
    ..CpG_MPs is the first user-friendly tool for identifying methylation patterns of genomic regions from bisulfite sequencing data, permitting further investigation of the biological functions of genome-scale methylation patterns...
  8. Wang L, Sun J, Wu H, Liu S, Wang J, Wu B, et al. Systematic assessment of reduced representation bisulfite sequencing to human blood samples: A promising method for large-sample-scale epigenomic studies. J Biotechnol. 2012;157:1-6 pubmed publisher
  9. Komori H, Lamere S, Torkamani A, Hart G, Kotsopoulos S, Warner J, et al. Application of microdroplet PCR for large-scale targeted bisulfite sequencing. Genome Res. 2011;21:1738-45 pubmed publisher
    ..The method was scaled to interrogate the methylation status of 77,674 CpGs in the promoter regions of 2100 genes in primary CD4 T cells. The 2100 gene library yielded 97% coverage of all targeted CpGs and 99% of the target amplicons...

More Information

Publications62

  1. Herrmann A, Haake A, Ammerpohl O, Martin Guerrero I, Szafranski K, Stemshorn K, et al. Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of hepitype evolution in tumors. PLoS ONE. 2011;6:e21332 pubmed publisher
  2. Robin S, Arese M, Forte E, Sarti P, Giuffrè A, Soulimane T. A sulfite respiration pathway from Thermus thermophilus and the key role of newly identified cytochrome c???. J Bacteriol. 2011;193:3988-97 pubmed publisher
    ..The description of the complete pathway reveals that electrons generated during sulfite oxidation by the SOR are funneled into the respiratory chain, participating in the energy production of T. thermophilus...
  3. Clark C, Palta P, Joyce C, Scott C, Grundberg E, Deloukas P, et al. A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(®) for methylome profiling. PLoS ONE. 2012;7:e50233 pubmed publisher
    ..In our study MeDIP-seq allowed the detection of 15,709 differentially methylated regions, nearly twice as many as the array-based method (8070), which may result in a more comprehensive study of the methylome...
  4. Lutsik P, Feuerbach L, Arand J, Lengauer T, Walter J, Bock C. BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Res. 2011;39:W551-6 pubmed publisher
    ..In addition, it is useful for locus-specific visualization of genome-wide bisulfite sequencing data...
  5. Hansen K, Timp W, Bravo H, Sabunciyan S, Langmead B, McDonald O, et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet. 2011;43:768-75 pubmed publisher
    ..We suggest a model for cancer involving loss of epigenetic stability of well-defined genomic domains that underlies increased methylation variability in cancer that may contribute to tumor heterogeneity...
  6. Otto C, Stadler P, Hoffmann S. Fast and sensitive mapping of bisulfite-treated sequencing data. Bioinformatics. 2012;28:1698-704 pubmed publisher
    ..As a consequence, currently available read mapping software often fails to achieve high sensitivity and in many cases requires unrealistic computational resources to cope with large real-life datasets...
  7. Campagna D, Telatin A, Forcato C, Vitulo N, Valle G. PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads. Bioinformatics. 2013;29:268-70 pubmed publisher
    ..Here, we present an algorithm that efficiently aligns Bi-Seq reads obtained either from SOLiD or Illumina. An accompanying methylation-caller program creates a genomic view of methylated and unmethylated Cs on both DNA strands...
  8. Varley K, Gertz J, Bowling K, Parker S, Reddy T, Pauli Behn F, et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 2013;23:555-67 pubmed publisher
    ..This study provides an atlas of DNA methylation across diverse and well-characterized samples and enables new discoveries about DNA methylation and its role in gene regulation and disease...
  9. Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le J, et al. High density DNA methylation array with single CpG site resolution. Genomics. 2011;98:288-95 pubmed publisher
    ..Highly comparable DNA methylation profiles were generated by the array and sequencing methods (average R2 of 0.95). The ability to determine genome-wide methylation patterns will rapidly advance methylation research...
  10. Frith M, Mori R, Asai K. A mostly traditional approach improves alignment of bisulfite-converted DNA. Nucleic Acids Res. 2012;40:e100 pubmed publisher
    ..It also illustrates how to adapt general-purpose alignment methods to a special case with distorted base patterns: this should be informative for other special cases such as ancient DNA and AT-rich genomes...
  11. Brinkman A, Gu H, Bartels S, Zhang Y, Matarese F, Simmer F, et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 2012;22:1128-38 pubmed publisher
    ..Our strategy provides a unique way of investigating global interdependencies between DNA methylation and other chromatin features...
  12. Lee E, Pei L, Srivastava G, Joshi T, Kushwaha G, Choi J, et al. Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Res. 2011;39:e127 pubmed publisher
    ..Since all targets were captured and sequenced as a pool through a series of single-tube reactions, this method can be easily scaled up to deal with a large number of samples...
  13. Harris E, Ponts N, Le Roch K, Lonardi S. BRAT-BW: efficient and accurate mapping of bisulfite-treated reads. Bioinformatics. 2012;28:1795-6 pubmed publisher
    ..BRAT-BW is a part of a software suite for genome-wide single base-resolution methylation data analysis that supports single and paired-end reads and includes a tool for estimation of methylation level at each cytosine...
  14. Xia Z, Su X, Wu J, Wu K, Zhang H. Molecular cloning and functional characterization of a putative sulfite oxidase (SO) ortholog from Nicotiana benthamiana. Mol Biol Rep. 2012;39:2429-37 pubmed publisher
    ..benthamiana plants...
  15. Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, et al. SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics. 2012;28:2180-1 pubmed publisher
    ..This package facilitates a rapid transition from sequencing reads to a fully annotated CpG methylation report to biological interpretation...
  16. Pedersen B, Hsieh T, Ibarra C, Fischer R. MethylCoder: software pipeline for bisulfite-treated sequences. Bioinformatics. 2011;27:2435-6 pubmed publisher
    ..MethylCoder requires only a python interpreter and a C compiler to run. Extensive documentation and the full source code are available under the MIT license at: https://github.com/brentp/methylcode. bpederse@gmail.com. ..
  17. Chatterjee A, Stockwell P, Rodger E, Morison I. Comparison of alignment software for genome-wide bisulphite sequence data. Nucleic Acids Res. 2012;40:e79 pubmed publisher
    ..This comparison highlights differences in methods for NGS data processing and provides guidance to advance sequence-based methylation data analysis for molecular biologists...
  18. Bibikova M, Le J, Barnes B, Saedinia Melnyk S, Zhou L, Shen R, et al. Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics. 2009;1:177-200 pubmed publisher
  19. Xi Y, Bock C, Müller F, Sun D, Meissner A, Li W. RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. Bioinformatics. 2012;28:430-2 pubmed publisher
    ..In summary, RRBSMAP removes bioinformatic hurdles and reduces the computational burden of large-scale epigenome association studies performed with RRBS...
  20. Iwagami S, Baba Y, Watanabe M, Shigaki H, Miyake K, Ida S, et al. Pyrosequencing assay to measure LINE-1 methylation level in esophageal squamous cell carcinoma. Ann Surg Oncol. 2012;19:2726-32 pubmed publisher
    ..The aim of this study is to assess the precision of sodium bisulfite conversion and polymerase chain reaction (PCR) pyrosequencing assay for evaluating LINE-1 methylation in ESCC...
  21. Krueger F, Kreck B, Franke A, Andrews S. DNA methylome analysis using short bisulfite sequencing data. Nat Methods. 2012;9:145-51 pubmed publisher
    ..We also explore the effect of sequencing errors and contaminants on inferred methylation levels and recommend the most appropriate way to analyze this type of data...
  22. Booth M, Branco M, Ficz G, Oxley D, Krueger F, Reik W, et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science. 2012;336:934-7 pubmed publisher
    ..Our results open new questions on 5hmC dynamics and sequence-specific targeting by TETs...
  23. Hiura H, Okae H, Miyauchi N, Sato F, Sato A, Van de Pette M, et al. Characterization of DNA methylation errors in patients with imprinting disorders conceived by assisted reproduction technologies. Hum Reprod. 2012;27:2541-8 pubmed publisher
    ..However, it is still unknown at what point(s) these imprinting errors arise, or the risk factors...
  24. Yu K, Roy D, Huang F, Lieber M. Detection and structural analysis of R-loops. Methods Enzymol. 2006;409:316-29 pubmed
    ..Our own lab has focused on class switch regions, where the R-loops can extend well over a kilobase in length. Here, methods are described for detection and analysis of R-loops in vitro and in vivo...
  25. Munson K, Clark J, Lamparska Kupsik K, Smith S. Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR. Nucleic Acids Res. 2007;35:2893-903 pubmed
  26. Weisenberger D, Trinh B, Campan M, Sharma S, Long T, Ananthnarayan S, et al. DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Res. 2008;36:4689-98 pubmed publisher
    ..Using digital MethyLight, we identified single-molecule, cancer-specific DNA hypermethylation events in the CpG islands of RUNX3, CLDN5 and FOXE1 present in plasma samples from breast cancer patients...
  27. Ehrich M, Zoll S, Sur S, van den Boom D. A new method for accurate assessment of DNA quality after bisulfite treatment. Nucleic Acids Res. 2007;35:e29 pubmed
    ..We also introduce a PCR-based assay, which allows ab initio assessment of the DNA quality after bisulfite treatment and can help to prevent inaccurate quantitative measurement resulting from poor bisulfite treatment...
  28. Ehrich M, Nelson M, Stanssens P, Zabeau M, Liloglou T, Xinarianos G, et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci U S A. 2005;102:15785-90 pubmed
  29. Luo D, Zhang B, Lv L, Xiang S, Liu Y, Ji J, et al. Methylation of CpG islands of p16 associated with progression of primary gastric carcinomas. Lab Invest. 2006;86:591-8 pubmed
    ..In conclusion, the present data indicates that p16 methylation correlates with progression of GCs significantly...
  30. Arányi T, Tusnady G. BiSearch: ePCR tool for native or bisulfite-treated genomic template. Methods Mol Biol. 2007;402:385-402 pubmed
    ..This option is currently available on four native or bisulfite-treated mammalian genomes...
  31. Dronov R, Kurth D, Mohwald H, Spricigo R, Leimkuhler S, Wollenberger U, et al. Layer-by-layer arrangement by protein-protein interaction of sulfite oxidase and cytochrome c catalyzing oxidation of sulfite. J Am Chem Soc. 2008;130:1122-3 pubmed publisher
  32. Kumaki Y, Oda M, Okano M. QUMA: quantification tool for methylation analysis. Nucleic Acids Res. 2008;36:W170-5 pubmed publisher
    ..It also provides a platform for consistent quality control of the analysis. The QUMA web server is available at http://quma.cdb.riken.jp/...
  33. Deng J, Shoemaker R, Xie B, Gore A, LeProust E, Antosiewicz Bourget J, et al. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol. 2009;27:353-60 pubmed publisher
    ..We found 288 regions methylated differently in fibroblasts and pluripotent cells. This targeted approach should be particularly useful for analyzing DNA methylation in large genomes...
  34. Feng C, Tollin G, Enemark J. Sulfite oxidizing enzymes. Biochim Biophys Acta. 2007;1774:527-39 pubmed
  35. Wong I. Qualitative and quantitative polymerase chain reaction-based methods for DNA methylation analyses. Methods Mol Biol. 2006;336:33-43 pubmed
    ..After enzyme digestion, PCR products are obtained if the enzyme does not digest the methylated CpG sites within the specified DNA region. COBRA, Ms-SNuPE, and quantitative real-time MSP allow the quantitative analyses of DNA methylation...
  36. Korshunova Y, Maloney R, Lakey N, Citek R, Bacher B, Budiman A, et al. Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA. Genome Res. 2008;18:19-29 pubmed
    ..Importantly, by establishing the methylation landscape within circulating DNA, this study has better defined the development challenges facing DNA methylation-based cancer-detection tests...
  37. Varley K, Mitra R. Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. Genome Res. 2010;20:1279-87 pubmed publisher
    ..This method is broadly applicable for studying DNA methylation across large numbers of patient samples using next-generation sequencing...
  38. Laird P. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet. 2010;11:191-203 pubmed publisher
    ..This Review discusses the different approaches and their relative merits and introduces considerations for data analysis...
  39. Dietrich D, Lesche R, Tetzner R, Krispin M, Dietrich J, Haedicke W, et al. Analysis of DNA methylation of multiple genes in microdissected cells from formalin-fixed and paraffin-embedded tissues. J Histochem Cytochem. 2009;57:477-89 pubmed publisher
    ..For most genes, increased DNA methylation in invasive and intraductal carcinoma cells compared with other tissue components was observed. For TFF1, decreased methylation levels were observed in tumor cells...
  40. Carr I, Valleley E, Cordery S, Markham A, Bonthron D. Sequence analysis and editing for bisulphite genomic sequencing projects. Nucleic Acids Res. 2007;35:e79 pubmed
    ..The program then also collates and presents data derived from independent templates (e.g. separate clones). This results in a considerable reduction in the time required for completion of a detailed genomic methylation project...
  41. Taylor K, Kramer R, Davis J, Guo J, Duff D, Xu D, et al. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res. 2007;67:8511-8 pubmed
    ..This new generation of methylome sequencing will provide digital profiles of aberrant DNA methylation for individual human cancers and offers a robust method for the epigenetic classification of tumor subtypes...
  42. Cokus S, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild C, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008;452:215-9 pubmed publisher
  43. Gruntman E, Qi Y, Slotkin R, Roeder T, Martienssen R, Sachidanandam R. Kismeth: analyzer of plant methylation states through bisulfite sequencing. BMC Bioinformatics. 2008;9:371 pubmed publisher
    ..However, in contrast to the situation in animals, there aren't many tools that analyze bisulfite data in plants, which can exhibit methylation of cytosines in a variety of sequence contexts (CG, CHG, and CHH)...
  44. Wilson J, Kappler U. Sulfite oxidation in Sinorhizobium meliloti. Biochim Biophys Acta. 2009;1787:1516-25 pubmed publisher
    ..Phylogenetic analysis of SorT-related SOEs and enzymes of taurine degradation indicate that there is no link between the two processes...
  45. Di Salle A, D Errico G, La Cara F, Cannio R, Rossi M. A novel thermostable sulfite oxidase from Thermus thermophilus: characterization of the enzyme, gene cloning and expression in Escherichia coli. Extremophiles. 2006;10:587-98 pubmed
    ..The identified gene was PCR amplified on T. thermophilus AT62 genome, expressed in Escherichia coli and the recombinant protein identified and characterized...
  46. Clark S, Statham A, Stirzaker C, Molloy P, Frommer M. DNA methylation: bisulphite modification and analysis. Nat Protoc. 2006;1:2353-64 pubmed
    ..Bisulphite conversion of DNA, in either single tubes or in a 96-well format, can be performed in a minimum of 8 h and a maximum of 18 h, depending on the amount and quality of starting DNA...
  47. Kilgore J, Hoose S, Gustafson T, Porter W, Kladde M. Single-molecule and population probing of chromatin structure using DNA methyltransferases. Methods. 2007;41:320-32 pubmed
    ..This application of MAP-IT provides the first means to simultaneously determine CpG methylation of mammalian genes and their overlying chromatin structure in the same single DNA molecule...
  48. Park H, Hwang Y. Genome-wide transcriptional responses to sulfite in Saccharomyces cerevisiae. J Microbiol. 2008;46:542-8 pubmed publisher
    ..Cells treated with sulfite generated more than 70% of acetaldehyde than untreated cells, suggesting that the increased acetaldehyde production is correlated with the induction of PDC1 gene encoding pyruvate decarboxylase...
  49. Jin S, Kadam S, Pfeifer G. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res. 2010;38:e125 pubmed publisher
    ..Selective mapping of 5hmC will require the development of unique tools for the detection of this modified base...
  50. Rohde C, Zhang Y, Jurkowski T, Stamerjohanns H, Reinhardt R, Jeltsch A. Bisulfite sequencing Data Presentation and Compilation (BDPC) web server--a useful tool for DNA methylation analysis. Nucleic Acids Res. 2008;36:e34 pubmed publisher
    ..v) A condensed file, containing all primary data in simplified format for further downstream data analysis and (vi) a custom track file for display of the results in the UCSC genome browser...
  51. Ondov B, Cochran C, Landers M, Meredith G, Dudas M, Bergman N. An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System. Bioinformatics. 2010;26:1901-2 pubmed publisher
  52. Tanaka K, Okamoto A. Degradation of DNA by bisulfite treatment. Bioorg Med Chem Lett. 2007;17:1912-5 pubmed
    ..The depyrimidination proceeded via addition of bisulfite to pyrimidines in DNA. The quantification with real-time PCR after conventional bisulfite treatment showed a large decrease in the amount of full-length DNA...
  53. Yang Y, Wang W, Li Y, Tu J, Bai Y, Xiao P, et al. Identification of methylated regions with peak search based on Poisson model from massively parallel methylated DNA immunoprecipitation-sequencing data. Electrophoresis. 2010;31:3537-44 pubmed publisher
    ..92). It suggests that this method provides a reliable and high-throughput strategy for whole genome methylation identification...