An Epigenome-Wide DNA Methylation Map of Testis in Pigs for Study of Complex Traits
Frontiers in Genetics, 2019 Epigenetic changes are important for understanding complex trait variation and inheritance in pigs that are also a valuable biomedical model for human health research.
Xiao Wang, Haja N. Kadarmideen
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Nucleosomes correlate with in vivo progression pattern of de novo methylation of p16 CpG islands in human gastric carcinogenesis. [PDF]
PLoS ONE, 2012 BACKGROUND: The exact relationship between nucleosome positioning and methylation of CpG islands in human pathogenesis is unknown. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we characterized the nucleosome position within the p16 CpG island ...
Zhe-Ming Lu +9 more
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BMC Medical Genomics, 2008 Background Hypermethylation of promoter CpG islands with associated loss of gene expression, and hypomethylation of CpG-rich repetitive elements that may destabilize the genome are common events in most, if not all, epithelial cancers.
DeGeest Koen +5 more
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Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. [PDF]
PLoS Genetics, 2007 The role of CpG island methylation in normal development and cell differentiation is of keen interest, but remains poorly understood. We performed comprehensive DNA methylation profiling of promoter regions in normal peripheral blood by methylated CpG ...
Lanlan Shen +9 more
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Locating regions in a sequence under density constraints [PDF]
SIAM Journal on Computing 42 (2013), no. 3, 1201-1215, 2011 Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence matching. Mathematically, this corresponds to searching a string of 0s and 1s for a substring whose relative proportion ...
arxiv +1 more source
Fish species lifespan prediction from promoter cytosine‐phosphate‐guanine density
Molecular Ecology Resources, EarlyView., 2023 Abstract Lifespan is a key attribute of a species' life cycle and varies extensively among major lineages of animals. In fish, lifespan varies by several orders of magnitude, with reported values ranging from less than 1 year to approximately 400 years.
Alyssa M. Budd +3 more
wiley +1 more source
Beyond Structure: Methylation Fine‐Tunes Stability and Folding Kinetics of bcl2Mid G‐Quadruplex
Angewandte Chemie, EarlyView.The introduction of a single 5‐methylcytosine into a G‐rich sequence originating from the B‐cell lymphoma 2 (BCL2) gene promoter affects both the folding kinetics and thermodynamics of the two G4 structures and thus plays a crucial role in regulating G4 folding pathways, which has significant implications for the control of gene expression.
Nataša Medved +5 more
wiley +2 more sources
Permissive transcriptional activity at the centromere through pockets of DNA hypomethylation. [PDF]
PLoS Genetics, 2006 DNA methylation is a hallmark of transcriptional silencing, yet transcription has been reported at the centromere. To address this apparent paradox, we employed a fully sequence-defined ectopic human centromere (or neocentromere) to investigate the ...
Nicholas C Wong +7 more
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Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. [PDF]
PLoS Genetics, 2012 We have developed an enhanced form of reduced representation bisulfite sequencing with extended genomic coverage, which resulted in greater capture of DNA methylation information of regions lying outside of traditional CpG islands.
Altuna Akalin +21 more
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Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements [PDF]
, 2013 Background: Recent assays for individual-specific genome-wide DNA methylation profiles have enabled epigenome-wide association studies to identify specific CpG sites associated with a phenotype. Computational prediction of CpG site-specific methylation levels is important, but current approaches tackle average methylation within a genomic locus and are
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