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Volumn 21, Issue 10, 2011, Pages 1601-1615

Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells

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HISTONE H3;

EID: 80053559849     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.116095.110     Document Type: Article
Times cited : (188)

References (57)
  • 1
    • 67349169780 scopus 로고    scopus 로고
    • Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells
    • Araki Y, Wang Z, Zang C, Wood WH 3rd, Schones D, Cui K, Roh TY, Lhotsky B, Wersto RP, Peng W, et al. 2009. Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells. Immunity 30: 912-925.
    • (2009) Immunity , vol.30 , pp. 912-925
    • Araki, Y.1    Wang, Z.2    Zang, C.3    Wood III, W.H.4    Schones, D.5    Cui, K.6    Roh, T.Y.7    Lhotsky, B.8    Wersto, R.P.9    Peng, W.10
  • 2
    • 77955205559 scopus 로고    scopus 로고
    • Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus
    • doi: 10.1186/1755-8794-3-33
    • Bell CG, Teschendorff AE, Rakyan VK, Maxwell AP, Beck S, Savage DA. 2010. Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus. BMC Med Genomics 3: 33. doi: 10.1186/1755-8794-3-33.
    • (2010) BMC Med Genomics , vol.3 , pp. 33
    • Bell, C.G.1    Teschendorff, A.E.2    Rakyan, V.K.3    Maxwell, A.P.4    Beck, S.5    Savage, D.A.6
  • 3
    • 77953421054 scopus 로고    scopus 로고
    • Transcriptional activation of endothelial cells by TGFb coincides with acute microvascular plasticity following focal spinal cord ischaemia/ reperfusion injury
    • doi: 10.1042/AN20090008
    • Benton RL, Maddie MA, Dincman TA, Hagg T, Whittemore SR. 2009. Transcriptional activation of endothelial cells by TGFb coincides with acute microvascular plasticity following focal spinal cord ischaemia/ reperfusion injury. ASN Neuro 1: e00015. doi: 10.1042/AN20090008.
    • (2009) ASN Neuro , vol.1
    • Benton, R.L.1    Maddie, M.A.2    Dincman, T.A.3    Hagg, T.4    Whittemore, S.R.5
  • 5
    • 27744577751 scopus 로고    scopus 로고
    • BiQ Analyzer: Visualization and quality control for DNA methylation data from bisulfite sequencing
    • DOI 10.1093/bioinformatics/bti652
    • Bock C, Reither S, Mikeska T, Paulsen M, Walter J, Lengauer T. 2005. BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics 21: 4067-4068. (Pubitemid 41631851)
    • (2005) Bioinformatics , vol.21 , Issue.21 , pp. 4067-4068
    • Bock, C.1    Reither, S.2    Mikeska, T.3    Paulsen, M.4    Walter, J.5    Lengauer, T.6
  • 6
    • 65549170303 scopus 로고    scopus 로고
    • Hyperglycemia induces a dynamic cooperativity of histone methylase and demethylase enzymes associated with gene-activating epigenetic marks that coexist on the lysine tail
    • Brasacchio D, Okabe J, Tikellis C, Balcerczyk A, George P, Baker EK, Calkin AC, Brownlee M, Cooper ME, El-Osta A. 2009. Hyperglycemia induces a dynamic cooperativity of histone methylase and demethylase enzymes associated with gene-activating epigenetic marks that coexist on the lysine tail. Diabetes 58: 1229-1236.
    • (2009) Diabetes , vol.58 , pp. 1229-1236
    • Brasacchio, D.1    Okabe, J.2    Tikellis, C.3    Balcerczyk, A.4    George, P.5    Baker, E.K.6    Calkin, A.C.7    Brownlee, M.8    Cooper, M.E.9    El-Osta, A.10
  • 8
    • 0035856980 scopus 로고    scopus 로고
    • Biochemistry and molecular cell biology of diabetic complications
    • DOI 10.1038/414813a
    • Brownlee M. 2001. Biochemistry and molecular cell biology of diabetic complications. Nature 414: 813-820. (Pubitemid 34000785)
    • (2001) Nature , vol.414 , Issue.6865 , pp. 813-820
    • Brownlee, M.1
  • 9
    • 53749094476 scopus 로고    scopus 로고
    • UKPDS and the legacy effect
    • Chalmers J, Cooper ME. 2008. UKPDS and the legacy effect. N Engl J Med 359: 1618-1620.
    • (2008) N Engl J Med , vol.359 , pp. 1618-1620
    • Chalmers, J.1    Cooper, M.E.2
  • 10
    • 78650694320 scopus 로고    scopus 로고
    • Epigenetics: Mechanisms and implications for diabetic complications
    • Cooper ME, El-Osta A. 2010. Epigenetics: mechanisms and implications for diabetic complications. Circ Res 107: 1403-1413.
    • (2010) Circ Res , vol.107 , pp. 1403-1413
    • Cooper, M.E.1    El-Osta, A.2
  • 11
    • 0037172724 scopus 로고    scopus 로고
    • A prediction-based resampling method for estimating the number of clusters in a dataset
    • RESEARCH0036. doi: 10.1186/gb-2002-3-7-research0036
    • Dudoit S, Fridlyand J. 2002. A prediction-based resampling method for estimating the number of clusters in a dataset. Genome Biol 3: RESEARCH0036. doi: 10.1186/gb-2002-3-7-research0036.
    • (2002) Genome Biol , vol.3
    • Dudoit, S.1    Fridlyand, J.2
  • 12
    • 77749270389 scopus 로고    scopus 로고
    • Cytosine methylation dysregulation in neonates following intrauterine growth restriction
    • doi: 10.1371/journal.pone.0008887
    • Einstein F, Thompson RF, Bhagat TD, Fazzari MJ, Verma A, Barzilai N, Greally JM. 2010. Cytosine methylation dysregulation in neonates following intrauterine growth restriction. PLoS ONE 5: e8887. doi: 10.1371/journal.pone. 0008887.
    • (2010) PLoS ONE , vol.5
    • Einstein, F.1    Thompson, R.F.2    Bhagat, T.D.3    Fazzari, M.J.4    Verma, A.5    Barzilai, N.6    Greally, J.M.7
  • 13
    • 0033678508 scopus 로고    scopus 로고
    • DNA methylation and histone deacetylation in the control of gene expression: Basic biochemistry to human development and disease
    • El-Osta A, Wolffe AP. 2000. DNA methylation and histone deacetylation in the control of gene expression: basic biochemistry to human development and disease. Gene Expr 9: 63-75.
    • (2000) Gene Expr , vol.9 , pp. 63-75
    • El-Osta, A.1    Wolffe, A.P.2
  • 14
    • 53349101264 scopus 로고    scopus 로고
    • Transient high glucose causes persistent epigenetic changes and altered gene expression during subsequent normoglycemia
    • El-Osta A, Brasacchio D, Yao D, Pocai A, Jones PL, Roeder RG, Cooper ME, Brownlee M. 2008. Transient high glucose causes persistent epigenetic changes and altered gene expression during subsequent normoglycemia. J Exp Med 205: 2409-2417.
    • (2008) J Exp Med , vol.205 , pp. 2409-2417
    • El-Osta, A.1    Brasacchio, D.2    Yao, D.3    Pocai, A.4    Jones, P.L.5    Roeder, R.G.6    Cooper, M.E.7    Brownlee, M.8
  • 15
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
    • (2007) Nature , vol.447 , pp. 799-816
  • 16
    • 78049427089 scopus 로고    scopus 로고
    • Introduction to epigenomics and epigenome wide analysis
    • Fazzari MJ, Greally JM. 2010. Introduction to epigenomics and epigenome wide analysis. Methods Mol Biol 620: 243-265.
    • (2010) Methods Mol Biol , vol.620 , pp. 243-265
    • Fazzari, M.J.1    Greally, J.M.2
  • 17
    • 33745700202 scopus 로고    scopus 로고
    • Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia
    • Gebhard C, Schwarzfischer L, Pham TH, Schilling E, Klug M, Andreesen R, Rehli M. 2006. Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia. Cancer Res 66: 6118-6128.
    • (2006) Cancer Res , vol.66 , pp. 6118-6128
    • Gebhard, C.1    Schwarzfischer, L.2    Pham, T.H.3    Schilling, E.4    Klug, M.5    Andreesen, R.6    Rehli, M.7
  • 26
    • 79952404725 scopus 로고    scopus 로고
    • The poisson margin test for normalization-free significance analysis of NGS data
    • Kowalczyk A, Bedo J, Conway T, Beresford-Smith B. 2011. The poisson margin test for normalization-free significance analysis of NGS data. J Comput Biol 18: 391-400.
    • (2011) J Comput Biol , vol.18 , pp. 391-400
    • Kowalczyk, A.1    Bedo, J.2    Conway, T.3    Beresford-Smith, B.4
  • 28
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows- Wheeler transform
    • Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25: 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 29
    • 73249133400 scopus 로고    scopus 로고
    • Epigenetics: A molecular link between environmental factors and type 2 diabetes
    • Ling C, Groop L. 2009. Epigenetics: a molecular link between environmental factors and type 2 diabetes. Diabetes 58: 2718-2725.
    • (2009) Diabetes , vol.58 , pp. 2718-2725
    • Ling, C.1    Groop, L.2
  • 30
    • 77956513142 scopus 로고    scopus 로고
    • is-rSNP: A novel technique for in silico regulatory SNP detection
    • Macintyre G, Bailey J, Haviv I, Kowalczyk A. 2010. is-rSNP: a novel technique for in silico regulatory SNP detection. Bioinformatics 26: i524-i530.
    • (2010) Bioinformatics , vol.26
    • Macintyre, G.1    Bailey, J.2    Haviv, I.3    Kowalczyk, A.4
  • 32
    • 2342423022 scopus 로고    scopus 로고
    • In Vivo Chromatin Remodeling Events Leading to Inflammatory Gene Transcription under Diabetic Conditions
    • DOI 10.1074/jbc.M311786200
    • Miao F, Gonzalo IG, Lanting L, Natarajan R. 2004. In vivo chromatin remodeling events leading to inflammatory gene transcription under diabetic conditions. J Biol Chem 279: 18091-18097. (Pubitemid 38560579)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.17 , pp. 18091-18097
    • Miao, F.1    Gonzalo, I.G.2    Lanting, L.3    Natarajan, R.4
  • 33
    • 34250303104 scopus 로고    scopus 로고
    • Genome-wide analysis of histone lysine methylation variations caused by diabetic conditions in human monocytes
    • DOI 10.1074/jbc.M609446200
    • Miao F, Wu X, Zhang L, Yuan YC, Riggs AD, Natarajan R. 2007. Genome wide analysis of histone lysine methylation variations caused by diabetic conditions in human monocytes. J Biol Chem 282: 13854-13863. (Pubitemid 47100501)
    • (2007) Journal of Biological Chemistry , vol.282 , Issue.18 , pp. 13854-13863
    • Miao, F.1    Wu, X.2    Zhang, L.3    Yuan, Y.-C.4    Riggs, A.D.5    Natarajan, R.6
  • 34
    • 58149345088 scopus 로고    scopus 로고
    • Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: An epigenetic study in diabetes
    • Miao F, Smith DD, Zhang L, Min A, Feng W, Natarajan R. 2008. Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes. Diabetes 57: 3189-3198.
    • (2008) Diabetes , vol.57 , pp. 3189-3198
    • Miao, F.1    Smith, D.D.2    Zhang, L.3    Min, A.4    Feng, W.5    Natarajan, R.6
  • 35
    • 78651251739 scopus 로고    scopus 로고
    • Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias
    • Nair SS, CoolenMW, Stirzaker C, Song JZ, Statham AL, StrbenacD, Robinson MD, Clark SJ. 2011. Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics 6: 34-44.
    • (2011) Epigenetics , vol.6 , pp. 34-44
    • Nair, S.S.1    Coolen, M.W.2    Stirzaker, C.3    Song, J.Z.4    Statham, A.L.5    Strbenac, D.6    Robinson, M.D.7    Clark, S.J.8
  • 36
    • 0032574977 scopus 로고    scopus 로고
    • Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex
    • DOI 10.1038/30764
    • Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A. 1998. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393: 386-389. (Pubitemid 28269714)
    • (1998) Nature , vol.393 , Issue.6683 , pp. 386-389
    • Nan, X.1    Ng, H.-H.2    Johnson, C.A.3    Laherty, C.D.4    Turner, B.M.5    Eisenman, R.N.6    Bird, A.7
  • 38
    • 67749084303 scopus 로고    scopus 로고
    • Modern-day clinical course of type 1 diabetes mellitus after 30 years' duration: The diabetes control and complications trial/ epidemiology of diabetes interventions and complications and Pittsburgh epidemiology of diabetes complications experience (1983-2005)
    • Nathan DM, Zinman B, Cleary PA, Backlund JY, Genuth S, Miller R, Orchard TJ. 2009. Modern-day clinical course of type 1 diabetes mellitus after 30 years' duration: the diabetes control and complications trial/ epidemiology of diabetes interventions and complications and Pittsburgh epidemiology of diabetes complications experience (1983-2005). Arch Intern Med 169: 1307-1316.
    • (2009) Arch Intern Med , vol.169 , pp. 1307-1316
    • Nathan, D.M.1    Zinman, B.2    Cleary, P.A.3    Backlund, J.Y.4    Genuth, S.5    Miller, R.6    Orchard, T.J.7
  • 39
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: Advantages and challenges of a maturing technology
    • Park PJ. 2009. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680.
    • (2009) Nat Rev Genet , vol.10 , pp. 669-680
    • Park, P.J.1
  • 40
    • 0030667807 scopus 로고    scopus 로고
    • Activation of nuclear factor-kB in cultured endothelial cells by increased glucose concentration: Prevention by calphostin C
    • Pieper GM, Riaz ul H. 1997. Activation of nuclear factor-kB in cultured endothelial cells by increased glucose concentration: prevention by calphostin C. J Cardiovasc Pharmacol 30: 528-532.
    • (1997) J Cardiovasc Pharmacol , vol.30 , pp. 528-532
    • Pieper, G.M.1    Riaz Ul, H.2
  • 41
    • 34447298871 scopus 로고    scopus 로고
    • Short-term high glucose exposure induces monocyte-endothelial cells adhesion and transmigration by increasing VCAM-1 and MCP-1 expression in human aortic endothelial cells
    • DOI 10.1016/j.atherosclerosis.2006.09.016, PII S0021915006005831
    • Piga R, Naito Y, Kokura S, Handa O, Yoshikawa T. 2007. Short-term high glucose exposure induces monocyte-endothelial cells adhesion and transmigration by increasing VCAM-1 and MCP-1 expression in human aortic endothelial cells. Atherosclerosis 193: 328-334. (Pubitemid 47058120)
    • (2007) Atherosclerosis , vol.193 , Issue.2 , pp. 328-334
    • Piga, R.1    Naito, Y.2    Kokura, S.3    Handa, O.4    Yoshikawa, T.5
  • 42
    • 0025067393 scopus 로고
    • Overexpression of fibronectin induced by diabetes or high glucose: Phenomenon with a memory
    • Roy S, Sala R, Cagliero E, Lorenzi M. 1990. Overexpression of fibronectin induced by diabetes or high glucose: phenomenon with a memory. Proc Natl Acad Sci 87: 404-408.
    • (1990) Proc Natl Acad Sci , vol.87 , pp. 404-408
    • Roy, S.1    Sala, R.2    Cagliero, E.3    Lorenzi, M.4
  • 43
    • 39449088572 scopus 로고    scopus 로고
    • Genome-wide approaches to studying chromatin modifications
    • DOI 10.1038/nrg2270, PII NRG2270
    • Schones DE, Zhao K. 2008. Genome wide approaches to studying chromatin modifications. Nat Rev Genet 9: 179-191. (Pubitemid 351271798)
    • (2008) Nature Reviews Genetics , vol.9 , Issue.3 , pp. 179-191
    • Schones, D.E.1    Zhao, K.2
  • 46
    • 0034610814 scopus 로고    scopus 로고
    • The language of covalent histone modifications
    • DOI 10.1038/47412
    • Strahl BD, Allis CD. 2000. The language of covalent histone modifications. Nature 403: 41-45. (Pubitemid 30038513)
    • (2000) Nature , vol.403 , Issue.6765 , pp. 41-45
    • Strahl, B.D.1    Allis, C.D.2
  • 47
    • 77950527721 scopus 로고    scopus 로고
    • Optimized design and data analysis of tag-based cytosine methylation assays
    • doi: 10.1186/gb-2010-11-4-r36
    • Suzuki M, Jing Q, Lia D, Pascual M, McLellan A, Greally JM. 2010. Optimized design and data analysis of tag-based cytosine methylation assays. Genome Biol 11: R36. doi: 10.1186/gb-2010-11-4-r36.
    • (2010) Genome Biol , vol.11
    • Suzuki, M.1    Jing, Q.2    Lia, D.3    Pascual, M.4    McLellan, A.5    Greally, J.M.6
  • 48
    • 77952061606 scopus 로고    scopus 로고
    • Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of rats
    • Thompson RF, Fazzari MJ, Niu H, Barzilai N, Simmons RA, Greally JM. 2010. Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of rats. J Biol Chem 285: 15111-15118.
    • (2010) J Biol Chem , vol.285 , pp. 15111-15118
    • Thompson, R.F.1    Fazzari, M.J.2    Niu, H.3    Barzilai, N.4    Simmons, R.A.5    Greally, J.M.6
  • 50
    • 0032511583 scopus 로고    scopus 로고
    • Intensive blood-glucose control with sulphonylureas or insulin compared with conventional treatment and risk of complications in patients with type 2 diabetes (UKPDS 33)
    • UK Prospective Diabetes Study (UKPDS) Group
    • UK Prospective Diabetes Study (UKPDS) Group. 1998. Intensive blood-glucose control with sulphonylureas or insulin compared with conventional treatment and risk of complications in patients with type 2 diabetes (UKPDS 33). Lancet 352: 837-853.
    • (1998) Lancet , vol.352 , pp. 837-853
  • 51
    • 69249235740 scopus 로고    scopus 로고
    • Calorie restriction and the exercise of chromatin
    • Vaquero A, Reinberg D. 2009. Calorie restriction and the exercise of chromatin. Genes Dev 23: 1849-1869.
    • (2009) Genes Dev , vol.23 , pp. 1849-1869
    • Vaquero, A.1    Reinberg, D.2
  • 52
    • 48249127225 scopus 로고    scopus 로고
    • Epigenetic histone H3 lysine 9 methylation in metabolic memory and inflammatory phenotype of vascular smooth muscle cells in diabetes
    • Villeneuve LM, Reddy MA, Lanting LL, Wang M, Meng L, Natarajan R. 2008. Epigenetic histone H3 lysine 9 methylation in metabolic memory and inflammatory phenotype of vascular smooth muscle cells in diabetes. Proc Natl Acad Sci 105: 9047-9052.
    • (2008) Proc Natl Acad Sci , vol.105 , pp. 9047-9052
    • Villeneuve, L.M.1    Reddy, M.A.2    Lanting, L.L.3    Wang, M.4    Meng, L.5    Natarajan, R.6
  • 54
    • 69449102464 scopus 로고    scopus 로고
    • Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes
    • Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K. 2009. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138: 1019-1031.
    • (2009) Cell , vol.138 , pp. 1019-1031
    • Wang, Z.1    Zang, C.2    Cui, K.3    Schones, D.E.4    Barski, A.5    Peng, W.6    Zhao, K.7
  • 55
    • 0037093012 scopus 로고    scopus 로고
    • Effect of intensive therapy on the microvascular complications of type 1 diabetes mellitus
    • Writing Team for the Diabetes Control and Complications Trial/ Epidemiology of Diabetes Interventions and Complications Research Group
    • Writing Team for the Diabetes Control and Complications Trial/ Epidemiology of Diabetes Interventions and Complications Research Group. 2002. Effect of intensive therapy on the microvascular complications of type 1 diabetes mellitus. JAMA 287: 2563-2569.
    • (2002) JAMA , vol.287 , pp. 2563-2569
  • 56
    • 0033037930 scopus 로고    scopus 로고
    • Hyperglycemia-induced activation of nuclear transcription factor κB in vascular smooth muscle cells
    • Yerneni KK, Bai W, Khan BV, Medford RM, Natarajan R. 1999. Hyperglycemia-induced activation of nuclear transcription factor κB in vascular smooth muscle cells. Diabetes 48: 855-864. (Pubitemid 29153087)
    • (1999) Diabetes , vol.48 , Issue.4 , pp. 855-864
    • Yerneni, K.K.V.1    Bai, W.2    Khan, B.V.3    Medford, R.M.4    Natarajan, R.5
  • 57
    • 0035195520 scopus 로고    scopus 로고
    • Human endothelial cell response to gram-negative lipopolysaccharide assessed with cDNA microarrays
    • Zhao B, Bowden RA, Stavchansky SA, Bowman PD. 2001. Human endothelial cell response to gram-negative lipopolysaccharide assessed with cDNA microarrays. Am J Physiol Cell Physiol 281: C1587-C1595.
    • (2001) Am J Physiol Cell Physiol , vol.281
    • Zhao, B.1    Bowden, R.A.2    Stavchansky, S.A.3    Bowman, P.D.4


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