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Verena Beier et al.
Advances in biochemical engineering/biotechnology, 104, 1-11 (2007-02-13)
Methylation of cytosines at their carbon-5 position plays an important role both during development and in tumorgenesis. The methylation occurs almost exclusively in CpG dinucleotides. While the bulk of human genomic DNA is depleted in CpG sites, there are CpG-rich
Tatsuya Ohhata et al.
Molecular and cellular biology, 35(22), 3909-3920 (2015-09-16)
One of the two X chromosomes in female mammals is inactivated by the noncoding Xist RNA. In mice, X chromosome inactivation (XCI) is regulated by the antisense RNA Tsix, which represses Xist on the active X chromosome. In the absence
Hwan Young Lee et al.
International journal of legal medicine, 126(1), 55-62 (2011-06-01)
DNA analysis of various body fluid stains at crime scenes facilitates the identification of individuals but does not currently determine the type and origin of the biological material. Recent advances in whole genome epigenetic analysis indicate that chromosome pieces called
Lei Yuan et al.
Nature communications, 7, 10160-10160 (2016-01-09)
Previous studies have shown that biological noise may drive dynamic phenotypic mosaicism in isogenic unicellular organisms. However, there is no evidence for a similar mechanism operating in metazoans. Here we show that the endothelial-restricted gene, von Willebrand factor (VWF), is
Julian R Peat et al.
F1000Research, 6, 526-526 (2017-06-06)
Methylation of CG dinucleotides constitutes a critical system of epigenetic memory in bony vertebrates, where it modulates gene expression and suppresses transposon activity. The genomes of studied vertebrates are pervasively hypermethylated, with the exception of regulatory elements such as transcription
David E Condon et al.
BMC bioinformatics, 19(1), 31-31 (2018-02-07)
Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion. We developed a
In Young Moon et al.
Molecular medicine reports, 20(3), 2285-2293 (2019-07-02)
Methylation was suggested to suppress the transcriptional activity of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) in hepatocytes. This may be associated with its low replicative activity during the inactive stage of chronic HBV infection; however, the exact
Elena Ivanova et al.
Clinical epigenetics, 12(1), 64-64 (2020-05-13)
Preimplantation embryos experience profound resetting of epigenetic information inherited from the gametes. Genome-wide analysis at single-base resolution has shown similarities but also species differences between human and mouse preimplantation embryos in DNA methylation patterns and reprogramming. Here, we have extended
Will epigenetic allelic ratio analysis turn prenatal diagnosis of trisomy 18 on its EAR?
Diana W Bianchi
Clinical chemistry, 52(12), 2182-2183 (2006-12-02)
Nelly Olova et al.
Genome biology, 19(1), 33-33 (2018-03-17)
Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases and bisulfite conversion protocols. Although some steps in the procedure, such
Bradley J Toghill et al.
Clinical epigenetics, 10, 29-29 (2018-03-07)
Abdominal aortic aneurysm (AAA) is a deadly cardiovascular disease characterised by the gradual, irreversible dilation of the abdominal aorta. AAA is a complex genetic disease but little is known about the role of epigenetics. Our objective was to determine if
Sebastian Canovas et al.
International journal of molecular sciences, 22(12) (2021-07-03)
Assisted reproductive technologies impact transcriptome and epigenome of embryos and can result in long-term phenotypic consequences. Whole-genome DNA methylation profiles from individual bovine blastocysts in vivo- and in vitro-derived (using three sources of protein: reproductive fluids, blood serum and bovine
Suk Hang Cheng et al.
Blood, 109(5), 2089-2099 (2006-11-02)
In this study, we have elucidated the chromosomal imbalances in the multistep pathogenesis and delineated several critical tumor suppressor gene (TSG) loci in multiple myeloma (MM). By using comparative genomic hybridization, allelotyping, and multicolor interphase fluorescence in situ hybridization, 5
Heather J Lee et al.
Methods in molecular biology (Clifton, N.J.), 1712, 87-95 (2017-12-11)
DNA methylation is an epigenetic mark implicated in the regulation of key biological processes. Using high-throughput sequencing technologies and bisulfite-based approaches, it is possible to obtain comprehensive genome-wide maps of the mammalian DNA methylation landscape with a single-nucleotide resolution and
Sebastian Canovas et al.
eLife, 6 (2017-01-31)
The number of children born since the origin of Assisted Reproductive Technologies (ART) exceeds 5 million. The majority seem healthy, but a higher frequency of defects has been reported among ART-conceived infants, suggesting an epigenetic cost. We report the first
Matilde Y Follo et al.
Proceedings of the National Academy of Sciences of the United States of America, 106(39), 16811-16816 (2009-10-07)
Lipid signaling pathways are involved in cell growth, differentiation, and apoptosis, and could have a role in the progression of myelodysplastic syndromes (MDS) into acute myeloid leukemia (AML). Indeed, recent studies showed that phosphoinositide-phospholipase (PI-PL)Cbeta1 mono-allelic deletion correlates with a
Priyadarshini Kachroo et al.
Epigenomics, 10(2), 133-147 (2018-01-16)
To determine whether methylation differences between mostly fatal TCF3-HLF and curable TCF3-PBX1 pediatric acute lymphoblastic leukemia subtypes can be associated with differential gene expression and remission. Five (extremely rare) TCF3-HLF versus five (very similar) TCF3-PBX1 patients were sampled before and
Giuseppe Leone et al.
Haematologica, 87(12), 1324-1341 (2002-12-24)
Methylation of DNA is a common epigenetic modification that plays an important role in the control of gene expression in mammalian cells. This process involves CpG dinucleotide sequences and is catalyzed by DNA-methyltransferase enzymes. Under physiological conditions, methylated CpG sites
Eduardo Portillo Del Campo et al.
Biomedical reports, 2(1), 101-104 (2014-03-22)
Estrogens play a key role in breast cancer, with 60-70% of the cases expressing estrogen receptors (ERs), which are encoded by the ESR1 gene. CTCFL, a paralogue of the chromatin organizer CTCF, is a potential biomarker of breast cancer, but
Masoumeh Afzali et al.
Iranian biomedical journal, 17(2), 77-83 (2013-04-10)
The protein of Niemann-pick type C1 (NPC1) gene promotes the egress of cholesterol from late endosomes and lysosomes to other cellular compartments and contributes to a process known as reverse cholesterol transport. This study aimed to examine whether promoter methylation
Vijayalakshmi Nandakumar et al.
Carcinogenesis, 32(4), 597-604 (2010-12-28)
Overexposure of the human skin to solar ultraviolet (UV) radiation is the major etiologic factor for development of skin cancers. Here, we report the results of epigenetic modifications in UV-exposed skin and skin tumors in a systematic manner. The skin
Hernán G Hernández et al.
BioTechniques, 55(4), 181-197 (2013-10-11)
Comprehensive analysis of DNA methylation patterns is critical for understanding the molecular basis of many human diseases. While hundreds of PCR-based DNA methylation studies are published every year, the selection and implementation of appropriate methods for these studies can be
The elephant shark methylome reveals conservation of epigenetic regulation across jawed vertebrates
Peat JR, et al.
F1000Research (2017)
Optimizing annealing temperature overcomes bias in bisulfite PCR methylation analysis.
Lanlan Shen et al.
BioTechniques, 42(1), 48-48 (2007-02-03)
Kay Ka Wai Li et al.
International journal of cancer, 120(4), 947-950 (2006-12-26)
The epithelial membrane protein 3 (EMP3) gene located on chromosome 19q13 has been implicated as a candidate tumor suppressor gene (TSG) in neuroblastomas and gliomas. The aim of this study was to investigate whether EMP3 is involved in oligodendroglial tumors
Sanjida H Rangwala et al.
Genome biology, 10(9), R100-R100 (2009-09-24)
While LINE1 (L1) retroelements comprise nearly 20% of the human genome, the majority are thought to have been rendered transcriptionally inactive, due to either mutation or epigenetic suppression. How many L1 elements 'escape' these forms of repression and contribute to
Sarah Rose Huffman et al.
Methods in molecular biology (Clifton, N.J.), 925, 201-209 (2012-08-22)
Researchers whose experimental models are mammalian oocytes and preimplantation embryos are often limited by the yield of nucleic acids that can be isolated from such a small sample size. In addition, the limited number of cells from these types of
Julian R Peat et al.
Methods in molecular biology (Clifton, N.J.), 1708, 161-169 (2017-12-11)
The epigenetic mark 5-methylcytosine confers heritable regulation of gene expression that can be dynamically modulated during transitions in cell fate. With the development of high-throughput sequencing technologies, it is now possible to obtain comprehensive genome-wide maps of the mammalian DNA
Susanne Edelmann et al.
Methods in molecular biology (Clifton, N.J.), 1675, 45-60 (2017-10-21)
Bisulfite sequencing (BS-seq) enables the detection of DNA methylation at cytosine residues (5mC) at single-nucleotide resolution. For many applications, a limiting factor of conventional BS-seq protocols is the high amount of DNA required, since the treatment with bisulfite causes severe
M Y Follo et al.
Leukemia, 26(5), 943-950 (2011-10-29)
Phosphoinositide-phospholipase C (PI-PLC) beta1 can be considered a specific target for demethylating therapy in high-risk myelodysplastic syndrome (MDS) patients, as azacitidine treatment has been associated with a PI-PLCbeta1-specific promoter demethylation, and induction of PI-PLCbeta1 gene and protein expression. However, little
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