Genome-wide analysis of DNA 5-hmC in peripheral blood of uremia by hMeDIP-chip

References

• Shalhoub V, Shatzen EM, Ward SC, et al. FGF23 neutralization improves chronic kidney disease-associated hyperparathyroidism yet increases mortality. J Clin Invest. 2012;122(7):2543–2553
   PubMed Web of Science ®Google Scholar
• Haddy FJ, Meyer TW, Hostetter TH. Uremia. N Engl J Med. 2008;358(1):95 . doi: 10.1056/NEJMc073016
   PubMed Web of Science ®Google Scholar
• Girndt M. Clinical issues with uremia. Internist (Berl). 2012;53(7):817–822
   PubMed Web of Science ®Google Scholar
• Gernsheimer T, James AH, Stasi R. How I treat thrombocytopenia in pregnancy. Blood. 2013;121(1):38–47
   PubMed Web of Science ®Google Scholar
• Liakopoulos V, Georgianos PI, Eleftheriadis T, Sarafidis PA. Epigenetic mechanisms and kidney diseases. Curr Med Chem. 2011;18(9):1733–1739
   PubMedGoogle Scholar
• Zawada AM, Rogacev KS, Heine GH. Clinical relevance of epigenetic dysregulation in chronic kidney disease-associated cardiovascular disease. Nephrol Dial Transplant. 2013;28(7):1663–1671
   Google Scholar
• Stenvinkel P, Ekström TJ. Epigenetics and the uremic phenotype: a matter of balance. Contrib Nephrol. 2008;161:55–62
   PubMed Web of Science ®Google Scholar
• Zawada AM, Rogacev KS, Hummel B, et al. SuperTAG methylation-specific digital karyotyping reveals uremia-induced epigenetic dysregulation of atherosclerosis-related genes. Circ Cardiovasc Genet. 2012;5(6):611–620
   PubMedGoogle Scholar
• Ingrosso D, Perna AF. Epigenetics in hyperhomocysteinemic states. A special focus on uremia. Biochim Biophys Acta. 2009;1790(9):892–899
   PubMed Web of Science ®Google Scholar
• Tahiliani M, Koh KP, Shen Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009;324(5929):930–935
   PubMed Web of Science ®Google Scholar
• Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A. The behavior of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One. 2010;5(1):e8888. doi: 10.1371/journal.pone.0008888
   PubMed Web of Science ®Google Scholar
• Gao F, Xia Y, Wang J, et al. Integrated detection of both 5-mC and 5-hmC by high-throughput tag sequencing technology highlights methylation reprogramming of bivalent genes during cellular differentiation. Epigenetics. 2013;8(4) [Epub ahead of print]
   Google Scholar
• Ito S, D'Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y. Role of TET proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature. 2010;466(7310):1129–1133
   PubMed Web of Science ®Google Scholar
• Tsumagari K, Baribault C, Terragni J, et al. Early denovo DNA methylation and prolonged demethylation in the muscle lineage. Epigenetics. 2013;8(3):317–332
   PubMed Web of Science ®Google Scholar
• Yamaguchi S, Hong K, Liu R, et al. Dynamics of 5-methylcytosine and 5-hydroxymethylcytosine during germ cell reprogramming. Cell Res. 2013;23(3):329–339
   PubMed Web of Science ®Google Scholar
• Jin SG, Kadam S, Pfeifer GP. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res. 2010;38(11):e125. doi: 10.1093/nar/gkq223
   PubMed Web of Science ®Google Scholar
• Wu SC, Zhang Y. Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol. 2010;11(9):607–620
   PubMed Web of Science ®Google Scholar
• Williams K, Christensen J, Helin K. DNA methylation: TET proteins-guardians of CpG islands? EMBO Rep. 2011;13(1):28–35
   PubMed Web of Science ®Google Scholar
• Song CX, Yi C, He C. Mapping recently identified nucleotide variants in the genome and transcriptome. Nat Biotechnol. 2012;30(11):1107–1116
   PubMed Web of Science ®Google Scholar
• Stroud H, Feng S, Morey Kinney S, Pradhan S, Jacobsen SE. 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol. 2011;12(6):R54. doi: 10.1186/gb-2011-12-6-r54
   PubMed Web of Science ®Google Scholar
• Xu Y, Wu F, Tan L, et al. Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol Cell. 2011;42(4):451–464
   PubMed Web of Science ®Google Scholar
• Gao Y, Chen J, Li K, et al. Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA methylation and hydroxymethylation in reprogramming. Cell Stem Cell. 2013;12(4):453–469
   PubMed Web of Science ®Google Scholar
• Thomson JP, Lempiäinen H, Hackett JA, et al. Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome. Genome Biol. 2012;13(10):R93. doi: 10.1186/gb-2012-13-10-r93
   Google Scholar
• Jackson SA, Sridharan R. The nexus of Tet1 and the pluripotency network. Cell Stem Cell. 2013;12(4):387–388
   PubMed Web of Science ®Google Scholar
• Honda T, Ogata S, Mineo E, et al. A novel strategy for hemolytic uremic syndrome: successful treatment with thrombomodulin α. Pediatrics. 2013;131(3):e928–e933
   PubMed Web of Science ®Google Scholar
• Zawada AM, Rogacev KS, Hummel B, et al. SuperTAG methylation-specific digital karyotyping reveals uremia-induced epigenetic dysregulation of atherosclerosis-related genes. Circ Cardiovasc Genet. 2012;5(6):611–620
   Google Scholar
• Zoja C, Locatelli M, Pagani C, et al. Lack of the lectin-like domain of thrombomodulin worsens Shiga toxin-associated hemolytic uremic syndrome in mice. J Immunol. 2012;189(7):3661–3668
   PubMed Web of Science ®Google Scholar
• Schaefer F, Yoon SA, Nouri P, et al. Growth hormone-mediated janus associated kinase-signal transducers and activators of transcription signaling in the growth hormone-resistant potassium-deficient rat. J Am Soc Nephrol. 2004;15(9):2299–2306
   PubMed Web of Science ®Google Scholar
• Rabkin R, Sun DF, Chen Y, Tan J, Schaefer F. Growth hormone resistance in uremia, a role for impaired JAK/STAT signaling. Pediatr Nephrol. 2005;20(3):313–318
   PubMed Web of Science ®Google Scholar
• Shimizu H, Yisireyili M, Nishijima F, Niwa T. Stat3 contributes to indoxyl sulfate-induced inflammatory and fibrotic gene expression and cellular senescence. Am J Nephrol. 2012;36(2):184–189
   PubMed Web of Science ®Google Scholar