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Abstract
In heterozygous genomes, allele-specific measurements can reveal biologically significant differences in DNA methylation between homologous alleles associated with local changes in genetic sequence. Current approaches for detecting such events from whole-genome bisulfite sequencing (WGBS) data perform statistically independent marginal analysis at individual cytosine-phosphate-guanine (CpG) sites, thus ignoring correlations in the methylation state, or carry-out a joint statistical analysis of methylation patterns at four CpG sites producing unreliable statistical evidence. Here, we employ the one-dimensional Ising model of statistical physics and develop a method for detecting allele-specific methylation (ASM) events within segments of DNA containing clusters of linked single-nucleotide polymorphisms (SNPs), called haplotypes. Comparisons with existing approaches using simulated and real WGBS data show that our method provides an improved fit to data, especially when considering large haplotypes. Importantly, the method employs robust hypothesis testing for detecting statistically significant imbalances in mean methylation level and methylation entropy, as well as for identifying haplotypes for which the genetic variant carries significant information about the methylation state. As such, our ASM analysis approach can potentially lead to biological discoveries with important implications for the genetics of complex human diseases.
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Affiliation(s)
- J Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Y Fang
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - A P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - J Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
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Domènech C, Abante J, Bozal FX, Mazo A, Cortés A, Bozal J. Microheterogeneity of the malate dehydrogenase from several sources. Biochem Biophys Res Commun 1987; 147:753-7. [PMID: 3632698 DOI: 10.1016/0006-291x(87)90994-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Different homogeneously purified cytosolic malate dehydrogenases gave, on isoelectric focusing, several active bands. The phenomenon could not be assigned to differences in their molecular weights or to alterations in the enzyme preparations during the purification procedure. Resolution of the multiple malate dehydrogenase active bands was achieved by chromatofocusing. The aged isolated subforms always yielded the original electrofocusing pattern. This fact suggests that conformational isomerism is a likely explanation for the charge heterogeneity of the enzymes studied.
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Fornós M, Bozal X, Abante J, Cortés A, Bozal J. Comparative analysis of the malate dehydrogenases isolated from the cytosolic fraction of several tissues of guinea-pig Cavia porcellus. Comp Biochem Physiol B 1987; 86:89-94. [PMID: 3829636 DOI: 10.1016/0305-0491(87)90179-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The specific activities of the malate dehydrogenase and lactate dehydrogenase present in the soluble fraction of several guinea-pig tissues are reported. The electrophoretic patterns showed always two forms (A and B) with malate dehydrogenase activity and the five isoenzymes of lactate dehydrogenase. Chromatography of the different soluble fractions through 5' AMP-Sepharose allowed both molecular forms of malate dehydrogenase to be separated and obtained free from lactate dehydrogenase. Comparative studies of the two forms of malate dehydrogenase evidenced that the A and B forms exhibited cytosolic and mitochondrial characteristics, respectively.
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