Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer

[1]  Qiang Liu,et al.  The mRNA Expression Signature and Prognostic Analysis of Multiple Fatty Acid Metabolic Enzymes in Clear Cell Renal Cell Carcinoma , 2019, Journal of Cancer.

[2]  Alla Slynko,et al.  Statistical methods for classification of 5hmC levels based on the Illumina Inifinium HumanMethylation450 (450k) array data, under the paired bisulfite (BS) and oxidative bisulfite (oxBS) treatment , 2019, PloS one.

[3]  Y. Ebenstein,et al.  Single-molecule quantification of 5-hydroxymethylcytosine for diagnosis of blood and colon cancers , 2017, Clinical Epigenetics.

[4]  I. Meza,et al.  IL-1β induces up-regulation of BIRC3, a gene involved in chemoresistance to doxorubicin in breast cancer cells. , 2017, Cancer letters.

[5]  M. Esteller,et al.  CHL1 hypermethylation as a potential biomarker of poor prognosis in breast cancer , 2017, Oncotarget.

[6]  P. Assumpção,et al.  Identification of IL11RA and MELK amplification in gastric cancer by comprehensive genomic profiling of gastric cancer cell lines , 2016, World journal of gastroenterology.

[7]  Qian Xu,et al.  Expression of semaphorin 6D and its receptor plexin-A1 in gastric cancer and their association with tumor angiogenesis. , 2016, Oncology letters.

[8]  G. Fuller,et al.  Analysis of the inhibitors of apoptosis identifies BIRC3 as a facilitator of malignant progression in glioma , 2016, Oncotarget.

[9]  G. Joksiċ,et al.  BIRC3 alterations in chronic and B-cell acute lymphocytic leukemia patients , 2016, Oncology letters.

[10]  J. Mulé,et al.  BIRC3 is a novel driver of therapeutic resistance in Glioblastoma , 2016, Scientific Reports.

[11]  G. Akkoyunlu,et al.  Dynamic expression of DNA methyltransferases (DNMTs) in oocytes and early embryos. , 2015, Biochimie.

[12]  Stephanie A. Tammen,et al.  Global DNA methylation and hydroxymethylation differ in hepatocellular carcinoma and cholangiocarcinoma and relate to survival rate , 2015, Hepatology.

[13]  H. Yoshioka,et al.  The dynamics of DNA methylation and hydroxymethylation during amelogenesis , 2015, Histochemistry and Cell Biology.

[14]  Mitsuyoshi Nakao,et al.  TET family proteins and 5-hydroxymethylcytosine in esophageal squamous cell carcinoma , 2015, Oncotarget.

[15]  A. Singh,et al.  Genetic alterations of DNA methylation machinery in human diseases. , 2015, Epigenomics.

[16]  J. Rinn,et al.  Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells , 2015, Nature Genetics.

[17]  S. Jeffrey,et al.  HIGD1A Regulates Oxygen Consumption, ROS Production, and AMPK Activity during Glucose Deprivation to Modulate Cell Survival and Tumor Growth. , 2015, Cell reports.

[18]  F. Tang,et al.  Genomic distribution and possible functions of DNA hydroxymethylation in the brain. , 2014, Genomics.

[19]  Claire L. Lill,et al.  Global changes in DNA methylation and hydroxymethylation in Alzheimer's disease human brain , 2014, Neurobiology of Aging.

[20]  K. Ayyanathan COX-2 Gene Expression in Colon Cancer Tissue Related to Regulating Factors and Promoter Methylation Status , 2014 .

[21]  Ruiqiang Li,et al.  Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain , 2014, Genome Biology.

[22]  T. Ishikawa,et al.  AHCYL2 (long‐IRBIT) as a potential regulator of the electrogenic Na+‐HCO3 − cotransporter NBCe1‐B , 2014, FEBS letters.

[23]  S. Powers,et al.  Genome-wide methylation analysis and epigenetic unmasking identify tumor suppressor genes in hepatocellular carcinoma. , 2013, Gastroenterology.

[24]  Howard Cedar,et al.  DNA methylation dynamics in health and disease , 2013, Nature Structural &Molecular Biology.

[25]  J. Ge,et al.  CHL1 is involved in human breast tumorigenesis and progression. , 2013, Biochemical and biophysical research communications.

[26]  Amit Verma,et al.  Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer , 2013, Nucleic acids research.

[27]  S. Jeffrey,et al.  Nuclear Localization of the Mitochondrial Factor HIGD1A during Metabolic Stress , 2013, PloS one.

[28]  M. Fraga,et al.  The role of genetics in the establishment and maintenance of the epigenome , 2013, Cellular and Molecular Life Sciences.

[29]  A. H. Smits,et al.  Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives , 2013, Cell.

[30]  N. Heintz,et al.  MeCP2 binds to 5hmc enriched within active genes and accessible chromatin in the nervous system , 2012, Cell.

[31]  A. Goel,et al.  Epigenetics of colorectal cancer. , 2012, Gastroenterology.

[32]  H. Kimura,et al.  Chromosome-wide regulation of euchromatin-specific 5mC to 5hmC conversion in mouse ES cells and female human somatic cells , 2012, Chromosome Research.

[33]  U. Schüller,et al.  Low values of 5‐hydroxymethylcytosine (5hmC), the “sixth base,” are associated with anaplasia in human brain tumors , 2012, International journal of cancer.

[34]  Abraham J. Khorasani,et al.  Loss of 5-Hydroxymethylcytosine Is an Epigenetic Hallmark of Melanoma , 2012, Cell.

[35]  N. Dalay,et al.  Promoter and histone methylation and p16INK4A gene expression in colon cancer , 2012, Experimental and therapeutic medicine.

[36]  Peter A. Jones,et al.  Cancer genetics and epigenetics: two sides of the same coin? , 2012, Cancer cell.

[37]  M. Dawson,et al.  Cancer Epigenetics: From Mechanism to Therapy , 2012, Cell.

[38]  G. Hon,et al.  Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome , 2012, Cell.

[39]  Y. Shi,et al.  Tet family proteins and 5-hydroxymethylcytosine in development and disease , 2012, Development.

[40]  P. Hof,et al.  Age-related increase in levels of 5-hydroxymethylcytosine in mouse hippocampus is prevented by caloric restriction. , 2012, Current Alzheimer research.

[41]  S. Balasubramanian,et al.  Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution , 2012, Science.

[42]  H. Aburatani,et al.  Loss of 5‐hydroxymethylcytosine is accompanied with malignant cellular transformation , 2012, Cancer science.

[43]  Jianhong Zhou,et al.  Estrogen Receptor Alpha Interacts with Mitochondrial Protein HADHB and Affects Beta-Oxidation Activity* , 2012, Molecular & Cellular Proteomics.

[44]  Huanming Yang,et al.  An atlas of DNA methylomes in porcine adipose and muscle tissues , 2012, Nature Communications.

[45]  C. Iacobuzio-Donahue,et al.  Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers , 2011, Oncotarget.

[46]  W. Reik,et al.  Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation , 2011, Nature.

[47]  George S. Krasnov,et al.  Differential Expression of CHL1 Gene during Development of Major Human Cancers , 2011, PloS one.

[48]  G. Pfeifer,et al.  Genomic mapping of 5-hydroxymethylcytosine in the human brain , 2011, Nucleic acids research.

[49]  A. Lichtenstein Cancer: evolutionary, genetic and epigenetic aspects , 2010, Clinical Epigenetics.

[50]  Swati Kadam,et al.  Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine , 2010, Nucleic acids research.

[51]  C. Ki,et al.  Two novel HADHB gene mutations in a Korean patient with mitochondrial trifunctional protein deficiency. , 2009, Annals of clinical and laboratory science.

[52]  A. Feinberg,et al.  Genome-wide methylation analysis of human colon cancer reveals similar hypo- and hypermethylation at conserved tissue-specific CpG island shores , 2008, Nature Genetics.

[53]  Lin Chen,et al.  Expression of semaphorin 6D in gastric carcinoma and its significance. , 2006, World journal of gastroenterology.

[54]  Matthew C Lorincz,et al.  Dynamics, stability and inheritance of somatic DNA methylation imprints. , 2006, Journal of theoretical biology.

[55]  W. Lam,et al.  Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells , 2005, Nature Genetics.

[56]  A. Koong,et al.  Epigenetic Regulation of Gene Expression in Cervical Cancer Cells by the Tumor Microenvironment 1 , 2000 .

[57]  J. Claverie,et al.  The significance of digital gene expression profiles. , 1997, Genome research.

[58]  H. Galehdari,et al.  Identification of a Novel HADHB Gene Mutation in an Iranian Patient with Mitochondrial Trifunctional Protein Deficiency. , 2017, Archives of Iranian medicine.

[59]  S. Pradhan,et al.  Ten eleven translocation enzymes and 5-hydroxymethylation in mammalian development and cancer. , 2013, Advances in experimental medicine and biology.

[60]  M. Roizen,et al.  Hallmarks of Cancer: The Next Generation , 2012 .