Genomes and Genes
Summary: Inorganic salts of sulfurous acid.
Publications240 found, 100 shown here
- Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applicationsFelix Krueger
Bioinformatics Group, The Babraham Institute, CB22 3AT, Cambridge, UK
Bioinformatics 27:1571-2. 2011..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...
- Principles and challenges of genomewide DNA methylation analysisPeter W Laird
USC Epigenome Center, University of Southern California, Keck School of Medicine, Los Angeles, 90089 9601, USA
Nat Rev Genet 11:191-203. 2010..This Review discusses the different approaches and their relative merits and introduces considerations for data analysis...
- Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterningShawn J Cokus
Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
Nature 452:215-9. 2008....
- DNA methylome analysis using short bisulfite sequencing dataFelix Krueger
Bioinformatics Group, The Babraham Institute, Cambridge, UK
Nat Methods 9:145-51. 2012..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...
- Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modificationsR Alan Harris
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
Nat Biotechnol 28:1097-105. 2010....
- Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profilingHongcang Gu
Broad Institute, Cambridge, Massachusetts, USA
Nat Protoc 6:468-81. 2011..The entire process of RRBS library construction takes ∼9 d...
- QUMA: quantification tool for methylation analysisYuichi Kumaki
Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN, 2 2 3 Minatojima minamimachi, Chuo Ku, Kobe 650 0047, Japan
Nucleic Acids Res 36:W170-5. 2008..It also provides a platform for consistent quality control of the analysis. The QUMA web server is available at http://quma.cdb.riken.jp/...
- BSMAP: whole genome bisulfite sequence MAPping programYuanxin Xi
Division of Biostatistics, Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
BMC Bioinformatics 10:232. 2009....
- BISMA--fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequencesChristian Rohde
School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28725 Bremen, Germany
BMC Bioinformatics 11:230. 2010..A region of interest is targeted by PCR and about 20-50 subcloned DNA molecules are usually analyzed, to determine the methylation status at single CpG sites and molecule resolution...
- BRAT-BW: efficient and accurate mapping of bisulfite-treated readsElena Y Harris
Department of Computer Science, University of California, Riverside, CA 92521, USA
Bioinformatics 28:1795-6. 2012..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...
- Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysisAlexander Meissner
Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA
Nucleic Acids Res 33:5868-77. 2005..Near-complete bisulfite conversion and largely unbiased representation of RRBS libraries suggest that random shotgun bisulfite sequencing can be scaled to a genome-wide approach...
- BS Seeker: precise mapping for bisulfite sequencingPao Yang Chen
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA
BMC Bioinformatics 11:203. 2010..It uses sequence tags to reduce mapping ambiguity. Post-processing of the alignments removes non-unique and low-quality mappings...
- BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencingPavlo Lutsik
Department of Genetics Epigenetics, Saarland University, 66123 Saarbrucken, Germany
Nucleic Acids Res 39:W551-6. 2011..In addition, it is useful for locus-specific visualization of genome-wide bisulfite sequencing data...
- Bisulfite genomic sequencing: systematic investigation of critical experimental parametersC Grunau
Institute of Molecular Biotechnology, Department of Genome Analysis, Beutenbergstrasse 11, 07745 Jena, Germany
Nucleic Acids Res 29:E65-5. 2001..The recognition rates for cytosine (>/=97%) and 5-methylcytosine (>/=94%) were found to be identical for both templates...
- Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouseNatasha Lane
Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge, UK
Genesis 35:88-93. 2003..In turn, this can result in the transgenerational inheritance of epigenetic states of IAPs, which could lead to heritable epimutations of neighbouring genes through influencing their transcriptional states...
- Comparison of alignment software for genome-wide bisulphite sequence dataAniruddha Chatterjee
Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand
Nucleic Acids Res 40:e79. 2012..This comparison highlights differences in methods for NGS data processing and provides guidance to advance sequence-based methylation data analysis for molecular biologists...
- DNA methylation: bisulphite modification and analysisSusan J Clark
Cancer Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia
Nat Protoc 1:2353-64. 2006..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...
- MethylCoder: software pipeline for bisulfite-treated sequencesBrent Pedersen
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
Bioinformatics 27:2435-6. 2011..It is more flexible than existing software and competitive in terms of speed and memory use...
- High-throughput bisulfite sequencing in mammalian genomesZachary D Smith
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
Methods 48:226-32. 2009..Contemporary sequencing and array-based technologies are compared against sample throughput and coverage, highlighting the variety of options available to investigate methylation on the genome-scale...
- The behaviour of 5-hydroxymethylcytosine in bisulfite sequencingYun Huang
Department of Pathology, Harvard Medical School and Immune Disease Institute, Boston, Massachusetts, United States of America
PLoS ONE 5:e8888. 2010..Since 5-hmC reacts with bisulfite to yield cytosine 5-methylenesulfonate (CMS), we asked how DNA containing 5-hmC behaves in bisulfite sequencing...
- High-throughput DNA methylation profiling using universal bead arraysMarina Bibikova
Illumina, Inc, San Diego, California 92121, USA
Genome Res 16:383-93. 2006..The technology should prove useful for DNA methylation analyses in large populations, with potential application to the classification and diagnosis of a broad range of cancers and other diseases...
- Whole genome DNA methylation analysis based on high throughput sequencing technologyNing Li
Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China
Methods 52:203-12. 2010....
- Identification and resolution of artifacts in bisulfite sequencingPeter M Warnecke
Sydney Cancer Centre, Kanematsu Laboratories, Royal Prince Alfred Hospital, Missenden Road, Camperdown, New South Wales 2050, Australia
Methods 27:101-7. 2002..We also include a brief summary of the experimental protocol for bisulfite treatment and tips for designing polymerase chain reaction (PCR) primers to amplify from bisulfite-treated DNA...
- Targeted and genome-scale strategies reveal gene-body methylation signatures in human cellsMadeleine P Ball
Department of Genetics, Harvard Medical School, Cambridge, MA, USA
Nat Biotechnol 27:361-8. 2009..Our observations highlight the usefulness of techniques that are not inherently or intentionally biased towards particular subsets like CpG islands or promoter regions...
- RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencingYuanxin Xi
Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Bioinformatics 28:430-2. 2012..In summary, RRBSMAP removes bioinformatic hurdles and reduces the computational burden of large-scale epigenome association studies performed with RRBS...
- A mostly traditional approach improves alignment of bisulfite-converted DNAMartin C Frith
Computational Biology Research Center, National Institute for Advanced Industrial Science and Technology AIST, 2 4 7 Aomi, Koto ku, Tokyo 135 0064, Japan
Nucleic Acids Res 40:e100. 2012..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...
- Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencingEun Joon Lee
GHSU Cancer Center, Department of Biochemistry and Molecular Biology, Georgia Health Sciences University, Augusta, GA 30912, USA
Nucleic Acids Res 39:e127. 2011..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...
- BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencingChristoph Bock
Max Planck Institut für Informatik Saarbrücken, Germany
Bioinformatics 21:4067-8. 2005..The BiQ Analyzer program is implemented in the Java programming language and runs on any platform for which a recent Java virtual machine is available...
- A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elementsAllen S Yang
Department of Leukemia, M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
Nucleic Acids Res 32:e38. 2004..This method can be used as a surrogate marker of genome-wide methylation changes. In addition, it is less labor intensive and requires less DNA than previous methods of assessing global DNA methylation...
- Acquisition of the H19 methylation imprint occurs differentially on the parental alleles during spermatogenesisT L Davis
Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
Genomics 58:18-28. 1999..The maternal allele becomes hypermethylated in this region during meiotic prophase. Thus, the parental H19 alleles acquire methylation differentially in the male germline...
- Sequence analysis and editing for bisulphite genomic sequencing projectsIan M Carr
Leeds Institute for Molecular Medicine, University of Leeds, Leeds, UK
Nucleic Acids Res 35:e79. 2007..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...
- Promoter hypermethylation profile of kidney cancerEssel Dulaimi
Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
Clin Cancer Res 10:3972-9. 2004..To gain insight into the role of epigenetic silencing of tumor suppressor and cancer genes in kidney tumorigenesis, we determined a hypermethylation profile of kidney cancer...
- Pyrosequencing assay to measure LINE-1 methylation level in esophageal squamous cell carcinomaShiro Iwagami
Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
Ann Surg Oncol 19:2726-32. 2012..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...
- DNA damaging effects of sulfur dioxide derivatives in cells from various organs of miceZiqiang Meng
Institute of Environmental Medicine and Toxicology, Research Center of Environmental Science and Engineering, Shanxi University, Taiyuan 030006, China
Mutagenesis 19:465-8. 2004..Taken together, these results suggest that SO2 and its derivatives are systemic toxic agents. However, further studies need to be performed before a definitive conclusion can be drawn...
- Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequenciesDiane P Genereux
Department of Biology, University of Washington, Seattle, WA 98195, USA
Nucleic Acids Res 36:e150. 2008....
- High resolution profiling of human exon methylation by liquid hybridization capture-based bisulfite sequencingJunwen Wang
Beijing Genomics Institute at Shenzhen, Beishan Road, Shenzhen 518000, China
BMC Genomics 12:597. 2011..Thus, they are not practical for researchers to study multiple clinical samples in biomarker research...
- A sulphite respiration system in the chemoheterotrophic human pathogen Campylobacter jejuniJonathan D Myers
Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
Microbiology 151:233-42. 2005..Sulphite respiration may be of importance for survival in environmental microaerobic niches and some foods, and may also provide a detoxification mechanism for this normally growth-inhibitory compound...
- Rapid quantification of DNA methylation by measuring relative peak heights in direct bisulfite-PCR sequencing tracesMinghong Jiang
State Key Laboratory of Genetic Engineering, School of Life Science and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
Lab Invest 90:282-90. 2010..Accordingly, this novel method is anticipated to be an efficient and economical alternative tool for rapid quantification of methylation patterns in screening large numbers of clinical samples across multiple genes...
- BRAT: bisulfite-treated reads analysis toolElena Y Harris
Department of Computer Science, University of California, Riverside, CA 92521, USA
Bioinformatics 26:572-3. 2010..The software package includes tools to end-trim low-quality bases of the reads and to report nucleotide counts for mapped reads on the reference genome...
- A rapid, quantitative, non-radioactive bisulfite-SNuPE- IP RP HPLC assay for methylation analysis at specific CpG sitesOsman El-Maarri
Institute of Experimental Haematology and Transfusion Medicine, Sigmund Freud Strasse 25, 53105 Bonn, Germany
Nucleic Acids Res 30:e25. 2002..The assay is linear, highly reproducible and several sites can be measured simultaneously in one reaction. It can be semi-automated and eliminates the need for cloning and sequencing of individual bisulfite PCR products...
- High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencingEmily Hodges
Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
Genome Res 19:1593-605. 2009..Methylation, along with specific histone marks, was enriched in exonic regions, suggesting that chromatin states can foreshadow the content of mature mRNAs...
- Establishment of the paternal methylation imprint of the human H19 and MEST/PEG1 genes during spermatogenesisA Kerjean
Laboratoire de Biologie de la Reproduction, Universite Paris V, hôpital Cochin Port Royal, Pavillon Cassini, 123 Boulevard de Port Royal, 75014 Paris, France
Hum Mol Genet 9:2183-7. 2000..The paternal-specific imprint is re-established only later, during spermatogonial differentiation in the adult testis...
- Enzymology and molecular biology of prokaryotic sulfite oxidationU Kappler
School of Molecular and Microbial Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
FEMS Microbiol Lett 203:1-9. 2001..In many pro- and also eukaryotes sulfite is formed as a degradative product from molecules containing sulfur as a heteroatom. In these organisms detoxification of sulfite is generally achieved by direct oxidation to sulfate...
- Fast and sensitive mapping of bisulfite-treated sequencing dataChristian Otto
Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Department of Computer Science, University Leipzig, 04107 Leipzig, Germany
Bioinformatics 28:1698-704. 2012..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...
- An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD SystemBrian D Ondov
National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, USA
Bioinformatics 26:1901-2. 2010....
- SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencingZhifu Sun
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
Bioinformatics 28:2180-1. 2012..This package facilitates a rapid transition from sequencing reads to a fully annotated CpG methylation report to biological interpretation...
- Epigenetic detection of human chromosome 14 uniparental disomyS K Murphy
Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
Hum Mutat 22:92-7. 2003....
- PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD readsDavide Campagna
CRIBI Biotechnology Centre, Universita di Padova, 35131 Padova, Italy
Bioinformatics 29:268-70. 2013..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...
- In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genesMaxim Ivanov
Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm 17177, Sweden
Nucleic Acids Res 41:e72. 2013....
- CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing dataJianzhong Su
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, People s Republic of China
Nucleic Acids Res 41:e4. 2013..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...
- Molecular cloning and functional characterization of a putative sulfite oxidase (SO) ortholog from Nicotiana benthamianaZongliang Xia
College of Life Science, Henan Agricultural University, Zhengzhou 450002, People s Republic of China
Mol Biol Rep 39:2429-37. 2012..benthamiana plants...
- Bacterial sulfite-oxidizing enzymesUlrike Kappler
Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia QLD 4072, Australia
Biochim Biophys Acta 1807:1-10. 2011....
- A sulfite respiration pathway from Thermus thermophilus and the key role of newly identified cytochrome c₅₅₀Sylvain Robin
Chemical and Environmental Science Department, Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
J Bacteriol 193:3988-97. 2011..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...
- A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(®) for methylome profilingChristine Clark
Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
PLoS ONE 7:e50233. 2012..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...
- Kismeth: analyzer of plant methylation states through bisulfite sequencingEyal Gruntman
BMC Bioinformatics 9:371. 2008..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)...
- Library-free methylation sequencing with bisulfite padlock probesDinh Diep
Department of Bioengineering, University of California at San Diego, La Jolla, California, USA
Nat Methods 9:270-2. 2012....
- Whole methylome analysis by ultra-deep sequencing using two-base encodingChristina A Bormann Chung
Life Technologies, Foster City, California, United States of America
PLoS ONE 5:e9320. 2010..Furthermore, the application of the SOLiD bisulfite sequencing to larger and more complex genomes is shown with preliminary in silico created bisulfite converted reads...
- Systematic assessment of reduced representation bisulfite sequencing to human blood samples: A promising method for large-sample-scale epigenomic studiesLi Wang
BGI Shenzhen, Shenzhen, Guangdong, China
J Biotechnol 157:1-6. 2012....
- Application of microdroplet PCR for large-scale targeted bisulfite sequencingH Kiyomi Komori
Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
Genome Res 21:1738-45. 2011..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...
- SIRPH analysis: SNuPE with IP-RP-HPLC for quantitative measurements of DNA methylation at specific CpG sitesOsman El-Maarri
Institute of Experimental Haematology and Transfusion Medicine, Bonn, Germany
Methods Mol Biol 287:195-205. 2004..The ratio of the ddCTP to the ddTTP gives the fraction of the methylated cytosines at that specific CpG site...
- Satellite 2 demethylation induced by 5-azacytidine is associated with missegregation of chromosomes 1 and 16 in human somatic cellsDiddier Prada
Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología Instituto de Investigaciones Biomédicas, Universidad Nacional Autonoma de Mexico UNAM, Mexico, D F, Mexico
Mutat Res 729:100-5. 2012..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...
- Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNAYulia Korshunova
Orion Genomics, LLC, St Louis, Missouri 63108, USA
Genome Res 18:19-29. 2008..Importantly, by establishing the methylation landscape within circulating DNA, this study has better defined the development challenges facing DNA methylation-based cancer-detection tests...
- Mechanism of sulfite cytotoxicity in isolated rat hepatocytesHossein Niknahad
Department of Pharmacology and Toxicology, Faculty of Pharmacy, and Pharmaceutical Research Center, Shiraz University of Medical Sciences, Isfahan Road, Akbarabad, Shiraz 71345 1583, Iran
Chem Biol Interact 174:147-54. 2008..Restoring GSH content of the cell or protein-SH groups by DTT can prevent sulfite cytotoxicity...
- PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCROwen J Marshall
Murdoch Childrens Research Institute, Royal Childrens Hospital, Flemington Road, Parkville, Vic, 3052, Australia
Bioinformatics 20:2471-2. 2004..It aims to automate and simplify the process of primer design...
- De novo quantitative bisulfite sequencing using the pyrosequencing technologyJean Michel Dupont
Laboratoire d Histologie Embryologie Cytogénétique, CHU Cochin Port Royal, AP HP Université Paris 5, 75014 Paris, France
Anal Biochem 333:119-27. 2004..This allowed accurate and quantitative de novo sequencing of the methylation state of each CpG, showing reproducible variations of methylation state in contiguous CpGs, and proved to be a useful adjunct to current technologies...
- DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLightDaniel J Weisenberger
Department of Surgery, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
Nucleic Acids Res 36:4689-98. 2008..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...
- Methylation of p16 CpG islands associated with malignant transformation of gastric dysplasia in a population-based studyYu Sun
Peking University School of Oncology and Beijing Institute for Cancer Research, Beijing, People s Republic of China
Clin Cancer Res 10:5087-93. 2004..The aim of this study is to investigate the relationship between p16 methylation and malignant transformation of human gastric dysplasia (DYS) based on follow-up endoscopic screening in a high-risk population...
- Sulfite oxidizing enzymesChangjian Feng
College of Pharmacy, University of New Mexico, Albuquerque, NM 87131, USA
Biochim Biophys Acta 1774:527-39. 2007....
- Precision of pyrosequencing assay to measure LINE-1 methylation in colon cancer, normal colonic mucosa, and peripheral blood cellsNatsumi Irahara
Molecular Oncologic Pathology, Dana Farber Cancer Institute, Brigham and Women s Hospital, Harvard Medical School, 44 Binney St, Room JF 215C, Boston, MA 02115, USA
J Mol Diagn 12:177-83. 2010..9) in leukocyte DNA. In conclusion, bisulfite conversion and PCR-pyrosequencing assay can measure LINE-1 methylation in macrodissected colon cancer, normal colon, and blood DNA, and may be useful in clinical and research settings...
- A global disorder of imprinting in the human female germ lineHannah Judson
University of Leeds, Molecular Medicine Unit, St James s University Hospital, UK
Nature 416:539-42. 2002..This disorder offers a genetic route to the identification of trans-acting oocyte factors that mediate maternal imprint establishment...
- Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosineSeung Gi Jin
Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
Nucleic Acids Res 38:e125. 2010..Selective mapping of 5hmC will require the development of unique tools for the detection of this modified base...
- Degradation of DNA by bisulfite treatmentKazuo Tanaka
Frontier Research System, RIKEN The Institute of Physical and Chemical Research, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
Bioorg Med Chem Lett 17:1912-5. 2007..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...
- Assessing loss of imprint methylation in sperm from subfertile men using novel methylation polymerase chain reaction Luminex analysisAkiko Sato
Department of Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
Fertil Steril 95:129-34, 134.e1-4. 2011..To assess the clinical value of bisulfite polymerase chain reaction Luminex (BPL), an automated, high-throughput procedure for the detection of alterations in DNA methylation...
- Sulfite oxidation in Sinorhizobium melilotiJeremy J Wilson
Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
Biochim Biophys Acta 1787:1516-25. 2009..Phylogenetic analysis of SorT-related SOEs and enzymes of taurine degradation indicate that there is no link between the two processes...
- Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of hepitype evolution in tumorsAlexander Herrmann
Institute of Internal Medicine I, Christian Albrechts University, Kiel, Germany
PLoS ONE 6:e21332. 2011....
- Accurate genome-scale percentage DNA methylation estimates from microarray dataMartin J Aryee
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University and Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21231, USA
Biostatistics 12:197-210. 2011..We illustrate the method on data generated to detect methylation differences between tissues and between normal and tumor colon samples...
- Rapid analysis of CpG methylation patterns using RNase T1 cleavage and MALDI-TOFPhilipp Schatz
Epigenomics AG, Science Department, Kleine Präsidentenstrasse 1, D 10178 Berlin, Germany
Nucleic Acids Res 32:e167. 2004..The applicability for the analysis of both PCR products and cloned PCR products is demonstrated. The observed methylation patterns were confirmed by bisulfite sequencing...
- Genome-wide analysis of DNA methylation patternsDaniel Zilberman
University of California, 211 Koshland Hall, Berkeley, CA 94720, USA
Development 134:3959-65. 2007..Here we discuss recent developments and future directions for identifying and mapping methylation, in an effort to help colleagues to identify the approaches that best serve their research interests...
- Transgenerational inheritance of epigenetic states at the murine Axin(Fu) allele occurs after maternal and paternal transmissionVardhman K Rakyan
School of Molecular and Microbial Biosciences, University of Sydney, New South Wales 2006, Australia
Proc Natl Acad Sci U S A 100:2538-43. 2003..Finally, we show that epigenetic inheritance is influenced by strain background. These findings enable us to propose a model for transgenerational epigenetic inheritance in mammals...
- Genome-wide high throughput analysis of DNA methylation in eukaryotesKyle R Pomraning
Center for Genome Research and Biocomputing and Department of Biochemistry and Biophysics, Oregon State University, 2011 ALS Building, Corvallis, OR 97331 7305, USA
Methods 47:142-50. 2009....
- Circulating methylated DNAJames G Herman
Department of Oncology, Evelyn Grollman Glick Scholar, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland 21231, USA
Ann N Y Acad Sci 1022:33-9. 2004..These factors are presented and their impact on the detection of methylated DNA circulating in the bloodstream is demonstrated...
- Bisulfite conversion of genomic DNA for methylation analysis: protocol simplification with higher recovery applicable to limited samples and increased throughputVictoria L Boyd
Applied Biosystems, 850 Lincoln Centre Drive, Foster City, CA 94404, USA
Anal Biochem 326:278-80. 2004
- Accurate quantification of DNA methylation using combined bisulfite restriction analysis coupled with the Agilent 2100 Bioanalyzer platformRomulo Martin Brena
Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
Nucleic Acids Res 34:e17. 2006....
- Mapping of the methylation pattern of the MUC2 promoter in pancreatic cancer cell lines, using bisulfite genomic sequencingTomofumi Hamada
Department of Human Pathology, Field of Oncology, Kagoshima University Graduate School of Medical and Dental Sciences, 8 35 1 Sakuragaoka, Kagoshima 890 8544, Japan
Cancer Lett 227:175-84. 2005..Our mapping data provide an essential basis for further studies of methylation-regulated MUC2 inactivation...
- Identification of methylated regions with peak search based on Poisson model from massively parallel methylated DNA immunoprecipitation-sequencing dataYao Yang
State Key Laboratory of Bioelectronics, Southeast University, Nanjing, PR China
Electrophoresis 31:3537-44. 2010..92). It suggests that this method provides a reliable and high-throughput strategy for whole genome methylation identification...
- Use of sulfite resistance in Saccharomyces cerevisiae as a dominant selectable markerH Park
Department of Food Science and Technology, Oregon State University, Corvallis 97331 6602, USA
Curr Genet 36:339-44. 1999..5 x 10(7)/plate. In two ura3 laboratory strains where selection for URA3 was applied independently of that for sulfite, the transformation efficiency for sulfite resistance was about 50% that for uracil prototrophy...
- Bisulfite genomic sequencing of microdissected cellsA Kerjean
Institut Cochin de Genetique Moleculaire, Laboratoire de Biologie de la Reproduction, Hopital Cochin, 75014 Paris, France
Nucleic Acids Res 29:E106-6. 2001..We report here our results on the methylation status of the androgen receptor gene studied by bisulfite genomic sequencing on purified cells isolated from human testis...
- Genome-wide transcriptional responses to sulfite in Saccharomyces cerevisiaeHoon Park
Division of Applied Biological Sciences, SunMoon University, Asan 336 708, Republic of Korea
J Microbiol 46:542-8. 2008..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...
- Detection and structural analysis of R-loopsKefei Yu
Department of Pathology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, USA
Methods Enzymol 409:316-29. 2006..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...
- Determination of total sulfite in wine by ion chromatography after in-sample oxidationMatthias Koch
BAM Federal Institute for Materials Research and Testing, Richard Willstaetter Strasse 11, D 12489 Berlin, Germany
J Agric Food Chem 58:9463-7. 2010Sulfur dioxide (SO2) or sulfites are the most common preservatives used in winemaking. The level of total SO2 is subject to regulation...
- Role of the promoter in maintaining transcriptionally active chromatin structure and DNA methylation patterns in vivoSung Hae Lee Kang
Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
Mol Cell Biol 23:4150-61. 2003..These findings suggest that the promoter and active transcription play a relatively limited role in maintaining transcriptionally potentiated epigenetic states...
- Epoxides, cyclic sulfites, and sulfate from natural pentacyclic triterpenoids: theoretical calculations and chemical transformationsAndrés García-Granados
Departamento de Quimica Organica, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
J Org Chem 68:4833-44. 2003..The reactivities of sulfites, sulfate, and epoxides in these triterpene compounds were investigated under different reaction conditions...
- Final report on the safety assessment of sodium sulfite, potassium sulfite, ammonium sulfite, sodium bisulfite, ammonium bisulfite, sodium metabisulfite and potassium metabisulfiteBindu Nair
Int J Toxicol 22:63-88. 2003..Although Ammonium Sulfite is not in current use, the others are widely used in hair care products. Sulfites that enter mammals via ingestion, inhalation, or injection are metabolized by sulfite oxidase to sulfate...
- Determination of sulfite by pervaporation-flow injection with amperometric detection using copper hexacyanoferrate-carbon nanotube modified carbon paste electrodeLori Shayne T Alamo
Department of Chemistry, Faculty of Science, Maejo University, Sansai, Chiang Mai, Thailand
Talanta 81:1793-9. 2010..The results agreed well with those obtained through the officially recommended differential pulse polarographic method...
- Bioenergetics of the alkaliphilic sulfate-reducing bacterium Desulfonatronovibrio hydrogenovoransUlrike Sydow
Institut für Chemie und Biologie des Meeres, Universitat Oldenburg, D 26111 Oldenburg, Germany
Microbiology 148:853-60. 2002..It is concluded that energy conservation in D. hydrogenovorans depends on a proton-translocating ATPase, whereas electron transport appears to be coupled to sodium ion translocation...
- Sulfites--a food and drug administration review of recalls and reported adverse eventsBabgaleh Timbo
Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland 20740 3835, USA
J Food Prot 67:1806-11. 2004Sulfite-sensitive individuals can experience adverse reactions after consuming foods containing sulfiting agents (sulfites), and some of these reactions may be severe. In the 1980s and 1990s, the U.S...
- Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samplesKatherine Elena Varley
Department of Genetics, Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
Genome Res 20:1279-87. 2010..This method is broadly applicable for studying DNA methylation across large numbers of patient samples using next-generation sequencing...
- Development of a new analytical method for the determination of sulfites in fresh meats and shrimps by ion-exchange chromatography with conductivity detectionMarco Iammarino
Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71100 Foggia, Italy
Anal Chim Acta 672:61-5. 2010..and suppressed conductivity detection, has been developed and validated for the quantitative determination of sulfites in fresh meats and shrimps...
- Transposable elements: targets for early nutritional effects on epigenetic gene regulationRobert A Waterland
Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
Mol Cell Biol 23:5293-300. 2003..These findings suggest that dietary supplementation, long presumed to be purely beneficial, may have unintended deleterious influences on the establishment of epigenetic gene regulation in humans...
- Sulfate assimilation in higher plants characterization of a stable intermediate in the adenosine 5'-phosphosulfate reductase reactionM Weber
Institute of Plant Physiology, Bern, Switzerland
Eur J Biochem 267:3647-53. 2000....
- Layer-by-layer arrangement by protein-protein interaction of sulfite oxidase and cytochrome c catalyzing oxidation of sulfiteRoman Dronov
Max Planck Institute of Colloids and Interfaces, D 14424 Golm Potsdam, Germany
J Am Chem Soc 130:1122-3. 2008
- Regulation of BER Gene Expression by Folate DeficiencyDIANE CABELOF; Fiscal Year: 2006..The loss of the BER response to DNA damage when folate is deficient would establish a mechanism by which diet can alter susceptibility to environmental exposure. [unreadable] [unreadable] [unreadable]..
- GENOMIC IMPRINTING AND THE CLONING OF MICERudolf Jaenisch; Fiscal Year: 2008..This program attempts to define the biological parameters which limit the nuclear cloning approach. ..
- Regulation of the Reelin GeneDennis Grayson; Fiscal Year: 2006....
- Epigenetics of Dietary and Body Fat in DrosophilaDouglas Ruden; Fiscal Year: 2006..abstract_text> ..
- SPORE in Head and Neck CancerDavid Sidransky; Fiscal Year: 2006..Goodman). The Career Development Program (Dr.Forastiere) aids the emergence of new investigators and the Research Developmental Program (Dr. David Sidransky) provides rapid funding of innovative directions. ..
- Molecular Epigenetic Studies of Major DepressionART PETRONIS; Fiscal Year: 2009..controls in both within and between all the listed comparisons. If the null hypotheses cannot be rejected, the study will provide a new perspective on the fundamental issues in MDD and other complex diseases. ..
- Cell Death Society Symposium on Targeting Cell Death Pathways for Human DiseasesZahra Zakeri; Fiscal Year: 2008..Our meeting will address the idea of how to go from basic research to development of methods for therapeutic interventions and targeting cell death pathways for human diseases. [unreadable] [unreadable] [unreadable]..
- DNA Methylation Markers in Ovarian CancerPETER LAIRD; Fiscal Year: 2006..Finally, we propose to use the most promising biomarkers to evaluate the capacity to detect preclinical relapse of disease, as a function of time before clinical diagnosis of relapse. ..
- Scientific Meeting: Mechanisms of Cell DeathZahra Zakeri; Fiscal Year: 2006..We are currently negotiating publication arrangements. NIH funds will be used to support speakers and facilities. Future meetings in France and China are planned. [unreadable] [unreadable] [unreadable]..
- SUPPRESSION OF NEOPLASIA BY DNA HYPOMETHYLATIONPETER LAIRD; Fiscal Year: 2007..abstract_text> ..
- Shotgun Hairpin-Bisulfite PCR Reveals Genome Methylation and Sequence VariationCharles Laird; Fiscal Year: 2008..Our innovative strategy will initiate a more systematic characterization of combined epigenetic and genetic variations in normal and diseased cells. [unreadable] [unreadable] [unreadable]..
- In Vitro Reprogramming of Somatic Cells into Pluripotent ES-like CellsRudolf Jaenisch; Fiscal Year: 2008....
- CHFR Methylation for Predicting Taxane Sensitivity in Lung and Esophageal CancerJames Herman; Fiscal Year: 2007..We will further develop a test for CHFR methylation and determine whether CHFR methylation can be used to predict which patients will respond to taxane based chemotherapies. ..
- The Role of MicroRNA in HepatocarcinogenesisKalpana Ghoshal; Fiscal Year: 2007..Further, this proposal fits well with the mission/goals set forth by multiple institutes that include NCI, NIDDK and NIAAA n the etiology, prevention and treatment of hepatocellular carcinomas. [unreadable] [unreadable] [unreadable]..
- P38, G2 Arrest, and Temozolomide Resistance in GliomasRUSSELL PIEPER; Fiscal Year: 2008....
- STRUCTURAL MODELS FOR MOLYBDOENZYMESJohn H Enemark; Fiscal Year: 2011..The rates of intramolecular electron transfer between the molybdenum and iron centers of SO will be investigated by flash photolysis and theoretical modeling. ..
- REGULATION OF INTESTINE-SPECIFIC GENE TRANSCRIPTIONEunran Suh; Fiscal Year: 2006..abstract_text> ..
- EPS Markers in the Early Detection of Prostate CancerSteven Smith; Fiscal Year: 2006..unreadable] [unreadable] [unreadable]..
- Contributions of Akt to Glioblastoma FormationRUSSELL PIEPER; Fiscal Year: 2006..Defining Akt function may help identify targets useful in GBM therapy. ..
- REGULATION OF CDX GENE EXPRESSION IN COLON CANCEREunran Suh; Fiscal Year: 2002..This will provide the basis for understanding the network of cellular pathways that control these important cell specific transcription factors and how they are altered in neoplasia. ..
- TRIGGERING OF ABERRANT CPG ISLAND METHYLATIONRuss Pieper; Fiscal Year: 2002..These studies represent a first step in understanding the gene silencing process and will ultimately contribute to the development of therapies addressed at controlling gene expression. ..
- DNA Methylation in Early Detection of Prostate CancerSteven Smith; Fiscal Year: 2002..We will combined the methylation results with the results of the EPS telomerase in patients with prostatic cancer and then compare this EPS profile to the stage and grade of the disease. ..
- MOLECULAR PROGRESSION MODEL FOR HNSCCDavid Sidransky; Fiscal Year: 2002..Thus, the studies outlined in this proposal are aimed at developing a comprehensive genetic model of SCC progression and ultimately new transnational clinical approaches. ..
- DNA METHYLOME STUDY IN TYPE 1 DIABETESART PETRONIS; Fiscal Year: 2009..This effort may have a major impact on our understanding of autoimmune mechanisms in T1D and lead to new strategies in diagnostics and treatment of the disease. ..
- Imprinted PEG3 domain at 19q13.4 and carcinogenesisSusan Murphy; Fiscal Year: 2002..These studies will help clarify the role of the human PEG3 isoforms in the control of cellular growth, and may further contribute potential diagnostic and therapeutic targets for ovarian cancer. ..
- Toxicogenomics of Lead, Mercury, and CadmiumDouglas Ruden; Fiscal Year: 2003....
- Dominant Mutation that Affect EGF-R Signal TransductionDouglas Ruden; Fiscal Year: 2003..It is important to understand regulators of RTK signaling because Ras-Raf dependent neoplasia accounts for as many as one-fifth of all human cancers. ..
- GLUTAMATE BIOSYNTHESIS MUTANTS AND ALCOHOL SENSITIVITYDouglas Ruden; Fiscal Year: 2003..This genetic approach would eventually lead to a better understanding to a better understanding of the genetic influences that underlie risk for alcoholism. ..
- Epigenetics, Stem Cells, and CancerRudolf Jaenisch; Fiscal Year: 2010..Aim 3 will use nuclear transplantation as a criterion to define the genetic and epigenetic alterations of the cancer cell genome that interfere with reversion to pluripotency. ..
- Meeting: Mechanisms of Cell DeathZahra Zakeri; Fiscal Year: 2004..We expect that this meeting will lead to further publications. ..
- UPGRADE OF VARIABLE FREQUENCY PULSED EPR FACILITYJOHN ENEMARK; Fiscal Year: 2005....
- IMMUNOGENETIC MECHANISMS OF VACCINE RESPONSEGregory A Poland; Fiscal Year: 2010..The knowledge gained from these studies will enable us to design new strategies and new vaccines to protect human health against viral diseases. ..
- The Role of P40 in Squamous Cell CarcinomasDavid Sidransky; Fiscal Year: 2009..abstract_text> ..
- UNDERSTANDING TRAIL SENSITIVITY IN HUMAN GLIOMARussell O Pieper; Fiscal Year: 2010..This work has relevance to public health in that it will provide the ways to identify TRAIL-sensitive brain tumors and also to make TRAIL-resistant tumors sensitive to TRAIL-induced killing. ..
- Environmental EpigenomicsPETER LAIRD; Fiscal Year: 2004..At the end of the planning period, they intend to submit an application to establish a Center for Environmental Epigenomics, to be affiliated with the Environmental Genome Project. ..
- EXPRESSION AND SILENCING OF CPG ISLAND-CONTAINING GENESRuss Pieper; Fiscal Year: 2001....
- MOLECULAR GENETICS AND EPIGENETICS OF FRAGILE X SYNDROMECharles Laird; Fiscal Year: 2004..Finally they will further develop and use a technique called "boomerang PCR" to determine the direction of DNA synthesis in relation to methylation. ..
- DNA Methylation Markers in Esophageal AdenocarcinomaPETER LAIRD; Fiscal Year: 2006..We will also investigate whether factors known to increase the risk of adenocarcinoma of the esophagus, increase the risk of DNA methylation in normal tissue, or in the resulting adenocarcinoma. [unreadable] [unreadable]..
- MGB Eclipse Probe Detection of Category A OrganismsIrina Afonina; Fiscal Year: 2003..In Phase II, we will expand the number of Category A organisms and improve throughput by multiplexing. In addition, commercial prototype MGB Eclipse(TM) probe assays will be developed for each of these organisms. ..
- Archaeal gene recruitment by the ChlamydialesDavid Graham; Fiscal Year: 2008..Results from these experiments will support future microbiological studies of the role of this system in chlamydial infection and survival in the host cell. [unreadable] [unreadable] [unreadable]..
- MECHANISMS OF SULFATE TRANSPORT AND REGULATIONMichael Jennings; Fiscal Year: 2007..abstract_text> ..
- Immune Complex Stimulation of TNFalphaKathleen Sullivan; Fiscal Year: 2007..In the third aim, we will define the role of chromatin in the regulation of responses to immune complexes. ..
- TNF Alpha In InflammationKathleen Sullivan; Fiscal Year: 2008..Overall, this proposal will define the mechanisms underlying repression of the TNF alpha locus. [unreadable] [unreadable]..
- Body Plan Formation in Early Mouse EmbryoYusuke Marikawa; Fiscal Year: 2004....