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Showing 1-30 of 330 results for "WGA2" within Papers
Hajime Abe et al.
Toxicology and applied pharmacology, 280(3), 467-474 (2014-08-26)
Thioacetamide (TAA) has been used to develop a rodent model for hepatocarcinogenesis. To determine the genes with epigenetic modifications in early hepatocarcinogenesis, we did a genome-wide scan for hypermethylated promoter regions using CpG island microarrays in TAA-promoted rat liver tissue.
Saori Takahashi et al.
Nature genetics, 51(3), 529-540 (2019-02-26)
Here, we report a single-cell DNA replication sequencing method, scRepli-seq, a genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication-domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated
Jiachen Wang et al.
PLoS pathogens, 10(1), e1003830-e1003830 (2014-01-07)
Histone acetylation has been linked to developmental changes in gene expression and is a validated drug target of apicomplexan parasites, but little is known about the roles of individual histone modifying enzymes and how they are recruited to target genes.
Michael K Skinner et al.
PloS one, 8(7), e66318-e66318 (2013-07-23)
A number of environmental factors (e.g. toxicants) have been shown to promote the epigenetic transgenerational inheritance of disease and phenotypic variation. Transgenerational inheritance requires the germline transmission of altered epigenetic information between generations in the absence of direct environmental exposures.
Neerja Karnani et al.
Molecular biology of the cell, 21(3), 393-404 (2009-12-04)
DNA replication in metazoans initiates from multiple chromosomal loci called origins. Currently, there are two methods to purify origin-centered nascent strands: lambda exonuclease digestion and anti-bromodeoxyuridine immunoprecipitation. Because both methods have unique strengths and limitations, we purified nascent strands by
Steven R Eichten et al.
PLoS genetics, 8(12), e1003127-e1003127 (2012-12-29)
Transposable elements (TEs) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence
Ilona N Holcomb et al.
Cancer research, 69(19), 7793-7802 (2009-09-24)
Androgen deprivation is the mainstay of therapy for progressive prostate cancer. Despite initial and dramatic tumor inhibition, most men eventually fail therapy and die of metastatic castration-resistant (CR) disease. Here, we characterize the profound degree of genomic alteration found in
Rakesh Pathak et al.
Genetics, 209(3), 743-756 (2018-04-27)
Histone chaperones, chromatin remodelers, and histone modifying complexes play a critical role in alleviating the nucleosomal barrier for DNA-dependent processes. Here, we have examined the role of two highly conserved yeast (Saccharomyces cerevisiae) histone chaperones, facilitates chromatin transcription (FACT) and
Peter V Kharchenko et al.
Nature, 471(7339), 480-485 (2010-12-24)
Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on
Noemí García-Romero et al.
Oncotarget, 8(1), 1416-1428 (2016-12-03)
Tumor-cell-secreted extracellular vesicles (EVs) can cross the disrupted blood-brain barrier (BBB) into the bloodstream. However, in certain gliomas, the BBB remains intact, which might limit EVs release. To evaluate the ability of tumor-derived EVs to cross the BBB, we used
Alexandre Gaspar-Maia et al.
Nature, 460(7257), 863-868 (2009-07-10)
An open chromatin largely devoid of heterochromatin is a hallmark of stem cells. It remains unknown whether an open chromatin is necessary for the differentiation potential of stem cells, and which molecules are needed to maintain open chromatin. Here we
Liqing Wang et al.
Blood, 121(18), 3631-3639 (2013-02-28)
Protocols to use Foxp3+ T-regulatory (Treg) cells for cellular therapy, especially postallogeneic stem cell transplantation, are currently being developed and tested by various groups. Inhibitors of DNA methyltransferase (Dnmt) enzymes have been advocated as a means to promote and stabilize
Erwan Delbarre et al.
Molecular biology of the cell, 21(11), 1872-1884 (2010-04-09)
In contrast to canonical histones, histone variant H3.3 is incorporated into chromatin in a replication-independent manner. Posttranslational modifications of H3.3 have been identified; however, the epigenetic environment of incorporated H3.3 is unclear. We have investigated the genomic distribution of epitope-tagged
Xu Chen et al.
Cancer research, 72(9), 2294-2303 (2012-03-08)
NOTCH3 gene amplification plays an important role in the progression of many ovarian and breast cancers, but the targets of NOTCH3 signaling are unclear. Here, we report the use of an integrated systems biology approach to identify direct target genes
Caroline Brossas et al.
The EMBO journal, 39(21), e99520-e99520 (2020-09-17)
Vertebrate genomes replicate according to a precise temporal program strongly correlated with their organization into A/B compartments. Until now, the molecular mechanisms underlying the establishment of early-replicating domains remain largely unknown. We defined two minimal cis-element modules containing a strong
Juan Wang et al.
PloS one, 13(10), e0203155-e0203155 (2018-10-05)
Aberrant DNA methylation occurs frequently in cancer. The aim of this study was to identify novel methylation markers in lung cancer in Xuanwei, China, through integrated genome-wide DNA methylation and gene expression studies. Differentially methylated regions (DMRs) and differentially expressed
Savita Sankar et al.
Scientific reports, 6, 37412-37412 (2016-11-25)
Neural cell fate acquisition is mediated by transcription factors expressed in nascent neuroectoderm, including Geminin and members of the Zic transcription factor family. However, regulatory networks through which this occurs are not well defined. Here, we identified Geminin-associated chromatin locations
Madapura M Pradeepa et al.
Nucleic acids research, 42(14), 9021-9032 (2014-07-25)
Trithorax and polycomb group proteins are generally thought to antagonize one another. The trithorax family member MLL (myeloid/lymphoid or mixed-lineage leukemia) is presumed to activate Hox expression, counteracting polycomb-mediated repression. PC4 and SF2 interacting protein 1 (PSIP1)/p75, also known as
Camilla Nylund et al.
PloS one, 7(9), e45382-e45382 (2012-10-03)
Cancer-testis (CT) antigens are predominantly expressed in testis or placenta, but absent in most adult tissues. During malignant transformation CT genes are often activated. CT antigen 16 (CT16, PAGE5) is frequently expressed in advanced melanoma but its biological function has
Anne Y Lai et al.
The Journal of experimental medicine, 207(9), 1939-1950 (2010-08-25)
Aberrant DNA methylation commonly occurs in cancer cells where it has been implicated in the epigenetic silencing of tumor suppressor genes. Additional roles for DNA methylation, such as transcriptional activation, have been predicted but have yet to be clearly demonstrated.
Sarah Brasa et al.
Clinical epigenetics, 8, 15-15 (2016-02-09)
Fragile X syndrome (FXS) is the most common form of inherited intellectual disability, resulting from the loss of function of the fragile X mental retardation 1 (FMR1) gene. The molecular pathways associated with FMR1 epigenetic silencing are still elusive, and
Jürg E Frey et al.
PloS one, 17(7), e0270897-e0270897 (2022-07-26)
The unintentional movement of agronomic pests and pathogens is steadily increasing due to the intensification of global trade. Being able to identify accurately and rapidly early stages of an invasion is critical for developing successful eradication or management strategies. For
John P Thomson et al.
Nucleic acids research, 41(11), 5639-5654 (2013-04-20)
Aberrant DNA methylation is a common feature of neoplastic lesions, and early detection of such changes may provide powerful mechanistic insights and biomarkers for carcinogenesis. Here, we investigate dynamic changes in the mouse liver DNA methylome associated with short (1
Susan M Gribble et al.
PloS one, 8(4), e60482-e60482 (2013-04-19)
Down syndrome (DS) is caused by trisomy of chromosome 21 (Hsa21) and presents a complex phenotype that arises from abnormal dosage of genes on this chromosome. However, the individual dosage-sensitive genes underlying each phenotype remain largely unknown. To help dissect
Hui Li et al.
BMC neuroscience, 22(1), 24-24 (2021-04-08)
Methamphetamine (METH) is one of the most widely abused illicit substances worldwide; unfortunately, its addiction mechanism remains unclear. Based on accumulating evidence, changes in gene expression and chromatin modifications might be related to the persistent effects of METH on the
Ricco Lindner et al.
Scientific data, 1, 140038-140038 (2014-01-01)
The regulatory mechanisms responsible for the gene expression pattern associated with axotomy-dependent signaling affecting the neuronal phenotype, including the axonal regenerative program, remain unclear. To further this understanding, we recently performed DNA methylation temporal profiling in lumbar dorsal root ganglia
Yu Wu et al.
The Journal of molecular diagnostics : JMD, 18(1), 131-143 (2015-11-27)
Circulating tumor cells and disseminated tumor cells (DTCs) are of great interest because they provide a minimally invasive window for assessing aspects of cancer biology, including tumor heterogeneity, a means to discover biomarkers of disease behavior, and a way to
John Arne Dahl et al.
Genome biology, 10(2), R13-R13 (2009-02-12)
Genome-wide location analysis of histone modifications and transcription factor binding relies on chromatin immunoprecipitation (ChIP) assays. These assays are, however, time-consuming and require large numbers of cells, hindering their application to the analysis of many interesting cell types. We report
Amit Sharma et al.
Clinical epigenetics, 7, 76-76 (2015-07-30)
Abnormal sex chromosome numbers in humans are observed in Turner (45,X) and Klinefelter (47,XXY) syndromes. Both syndromes are associated with several clinical phenotypes, whose molecular mechanisms are obscure, and show a range of inter-individual penetrance. In order to understand the
Muy-Teck Teh et al.
PloS one, 7(3), e34329-e34329 (2012-03-31)
The oncogene FOXM1 has been implicated in all major types of human cancer. We recently showed that aberrant FOXM1 expression causes stem cell compartment expansion resulting in the initiation of hyperplasia. We have previously shown that FOXM1 regulates HELLS, a
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