-
1
-
-
66149146320
-
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1
-
Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930-935 (2009).
-
(2009)
Science
, vol.324
, pp. 930-935
-
-
Tahiliani, M.1
-
2
-
-
66749152204
-
Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids
-
Iyer, L. M., Tahiliani, M., Rao, A.&Aravind, L. Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle 8, 1698-1710 (2009).
-
(2009)
Cell Cycle
, vol.8
, pp. 1698-1710
-
-
Iyer, L.M.1
Tahiliani, M.2
Rao, A.3
Aravind, L.4
-
3
-
-
78650175023
-
Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2
-
Ko, M. et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 468, 839-843 (2010).
-
(2010)
Nature
, vol.468
, pp. 839-843
-
-
Ko, M.1
-
4
-
-
80052461558
-
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
-
Ito, S. et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300-1303 (2011).
-
(2011)
Science
, vol.333
, pp. 1300-1303
-
-
Ito, S.1
-
5
-
-
80052495940
-
Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA
-
He, Y. F. et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333, 1303-1307 (2011).
-
(2011)
Science
, vol.333
, pp. 1303-1307
-
-
He, Y.F.1
-
6
-
-
79955119592
-
Dependence of substrate binding and catalysis onpH, ionic strength, and temperature for thymine DNA glycosylase: Insights into recognition and processing of G.T mispairs
-
Maiti, A.&Drohat, A. C. Dependence of substrate binding and catalysis onpH, ionic strength, and temperature for thymine DNA glycosylase: Insights into recognition and processing of G.T mispairs. DNA Repair 10, 545-553 (2011).
-
(2011)
DNA Repair
, vol.10
, pp. 545-553
-
-
Maiti, A.1
Drohat, A.C.2
-
7
-
-
0034749352
-
Inhibition of the Wnt signaling pathway by Idax, a novel Dvl-binding protein
-
Hino, S. et al. Inhibition of the Wnt signaling pathway by Idax, a novel Dvl-binding protein. Mol. Cell. Biol. 21, 330-342 (2001).
-
(2001)
Mol. Cell. Biol
, vol.21
, pp. 330-342
-
-
Hino, S.1
-
8
-
-
58249097231
-
Decreased expression of CXXC4 promotes a malignant phenotype in renal cell carcinomaby activatingWnt signaling
-
Kojima, T. et al. Decreased expression of CXXC4 promotes a malignant phenotype in renal cell carcinomaby activatingWnt signaling.Oncogene28, 297-305 (2009).
-
(2009)
Oncogene
, vol.28
, pp. 297-305
-
-
Kojima, T.1
-
9
-
-
77954736347
-
Differentiation of tubular and villous adenomas based onWnt pathway-related gene expression profiles
-
Nguyen, A. V., Albers, C. G. & Holcombe, R. F. Differentiation of tubular and villous adenomas based onWnt pathway-related gene expression profiles. Int. J.Mol.Med. 26, 121-125 (2010).
-
(2010)
Int. J.Mol.Med
, vol.26
, pp. 121-125
-
-
Nguyen, A.V.1
Albers, C.G.2
Holcombe, R.F.3
-
10
-
-
79955072337
-
Natural history of eukaryoticDNA methylation systems
-
Iyer, L. M., Abhiman, S.& Aravind, L. Natural history of eukaryoticDNA methylation systems. Prog. Mol. Biol. Transl. Sci. 101, 25-104 (2011).
-
(2011)
Prog. Mol. Biol. Transl. Sci
, vol.101
, pp. 25-104
-
-
Iyer, L.M.1
Abhiman, S.2
Aravind, L.3
-
11
-
-
0035976968
-
Identification and characterization of the DNA binding domain ofCpG-binding protein
-
Lee, J. H., Voo, K. S. & Skalnik, D. G. Identification and characterization of the DNA binding domain ofCpG-binding protein. J. Biol. Chem. 276, 44669-44676 (2001).
-
(2001)
J. Biol. Chem
, vol.276
, pp. 44669-44676
-
-
Lee, J.H.1
Voo, K.S.2
Skalnik, D.G.3
-
12
-
-
77449101855
-
Structure of the MLL CXXC domain-DNA complex and its functional role in MLL-AF9 leukemia
-
Cierpicki, T. et al. Structure of the MLL CXXC domain-DNA complex and its functional role in MLL-AF9 leukemia. Nature Struct. Mol. Biol. 17, 62-68 (2010).
-
(2010)
Nature Struct. Mol. Biol
, vol.17
, pp. 62-68
-
-
Cierpicki, T.1
-
13
-
-
33749369772
-
Solutionstructure of the nonmethyl-CpG-bindingCXXCdomain of the leukaemia-associated MLL histone methyltransferase
-
Allen, M. D. et al. Solutionstructure of the nonmethyl-CpG- bindingCXXCdomain of the leukaemia-associated MLL histone methyltransferase. EMBO J. 25, 4503-4512 (2006).
-
(2006)
EMBO J
, vol.25
, pp. 4503-4512
-
-
Allen, M.D.1
-
14
-
-
79952473660
-
The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain
-
Xu, C., Bian, C., Lam, R., Dong, A. & Min, J. The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain. Nature Commun. 2, 227 (2011).
-
(2011)
Nature Commun
, vol.2
, pp. 227
-
-
Xu, C.1
Bian, C.2
Lam, R.3
Dong, A.4
Min, J.5
-
15
-
-
79952053850
-
Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation
-
Song, J., Rechkoblit, O., Bestor, T. H. & Patel, D. J. Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science 331, 1036-1040 (2011).
-
(2011)
Science
, vol.331
, pp. 1036-1040
-
-
Song, J.1
Rechkoblit, O.2
Bestor, T.H.3
Patel, D.J.4
-
16
-
-
77950882645
-
CpG islands recruit a histone H3 lysine 36 demethylase
-
Blackledge, N. P. et al. CpG islands recruit a histone H3 lysine 36 demethylase. Mol. Cell 38, 179-190 (2010).
-
(2010)
Mol. Cell
, vol.38
, pp. 179-190
-
-
Blackledge, N.P.1
-
17
-
-
84870883633
-
Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development
-
Xu, Y. et al. Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development. Cell 151, 1200-1213 (2012).
-
(2012)
Cell
, vol.151
, pp. 1200-1213
-
-
Xu, Y.1
-
18
-
-
79551587102
-
Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells
-
Koh, K. P. et al. Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 8, 200-213 (2011).
-
(2011)
Cell Stem Cell
, vol.8
, pp. 200-213
-
-
Koh, K.P.1
-
19
-
-
80052284526
-
Ten-Eleven-Translocation 2 (TET2) negatively regulates homeostasis and differentiation of hematopoietic stem cells in mice
-
Ko, M. et al. Ten-Eleven-Translocation 2 (TET2) negatively regulates homeostasis and differentiation of hematopoietic stem cells in mice. Proc. Natl Acad. Sci. USA 108, 14566-14571 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 14566-14571
-
-
Ko, M.1
-
20
-
-
80053160998
-
RINF (CXXC5) is overexpressed in solid tumors and is an unfavorable prognostic factor in breast cancer
-
Knappskog, S. et al. RINF (CXXC5) is overexpressed in solid tumors and is an unfavorable prognostic factor in breast cancer. Ann. Oncol. 22, 2208-2215 (2011).
-
(2011)
Ann. Oncol
, vol.22
, pp. 2208-2215
-
-
Knappskog, S.1
-
21
-
-
77951986098
-
A novel Wilms tumor 1 (WT1) target gene negatively regulates the WNT signaling pathway
-
Kim, M. S. et al. A novel Wilms tumor 1 (WT1) target gene negatively regulates the WNT signaling pathway. J. Biol. Chem. 285, 14585-14593 (2010).
-
(2010)
J. Biol. Chem
, vol.285
, pp. 14585-14593
-
-
Kim, M.S.1
-
22
-
-
65349118891
-
Functional involvement of RINF, retinoid-inducible nuclear factor (CXXC5), in normal and tumoral human myelopoiesis
-
Pendino, F. et al. Functional involvement of RINF, retinoid-inducible nuclear factor (CXXC5), in normal and tumoral human myelopoiesis. Blood 113, 3172-3181 (2009).
-
(2009)
Blood
, vol.113
, pp. 3172-3181
-
-
Pendino, F.1
-
23
-
-
44349111132
-
Caspase activitymediates the differentiationofembryonic stemcells
-
Fujita, J. et al.Caspase activitymediates the differentiationofembryonic stemcells. Cell Stem Cell 2, 595-601 (2008).
-
(2008)
Cell Stem Cell
, vol.2
, pp. 595-601
-
-
Fujita, J.1
-
24
-
-
84861869979
-
Ubiquitin and proteasomes in transcription
-
Geng, F., Wenzel, S. & Tansey, W. P. Ubiquitin and proteasomes in transcription. Annu. Rev. Biochem. 81, 177-201 (2012).
-
(2012)
Annu. Rev. Biochem
, vol.81
, pp. 177-201
-
-
Geng, F.1
Wenzel, S.2
Tansey, W.P.3
-
25
-
-
84857891830
-
Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes
-
Nestor, C. E. et al. Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes. Genome Res. 22, 467-477 (2012).
-
(2012)
Genome Res
, vol.22
, pp. 467-477
-
-
Nestor, C.E.1
-
26
-
-
78650826181
-
Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates
-
Globisch, D. et al. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS ONE 5, e15367 (2010).
-
(2010)
PLoS ONE
, vol.5
-
-
Globisch, D.1
-
27
-
-
84856058152
-
Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers
-
Haffner, M. C. et al. Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers. Oncotarget 2, 627-637 (2011).
-
(2011)
Oncotarget
, vol.2
, pp. 627-637
-
-
Haffner, M.C.1
-
28
-
-
80053063127
-
Maintaining embryonic stem cell pluripotency with Wnt signaling
-
Sokol, S. Y. Maintaining embryonic stem cell pluripotency with Wnt signaling. Development 138, 4341-4350 (2011).
-
(2011)
Development
, vol.138
, pp. 4341-4350
-
-
Sokol, S.Y.1
-
29
-
-
84873411803
-
Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation
-
Yang, H. et al. Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation. Oncogene 32, 663-669 (2013).
-
(2013)
Oncogene
, vol.32
, pp. 663-669
-
-
Yang, H.1
-
30
-
-
84866419591
-
Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma
-
Lian, C. G. et al. Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell 150, 1135-1146 (2012).
-
(2012)
Cell
, vol.150
, pp. 1135-1146
-
-
Lian, C.G.1
-
31
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
-
32
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
-
(2008)
Genome Biol
, vol.9
-
-
Zhang, Y.1
-
33
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589 (2010).
-
(2010)
Mol. Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
-
34
-
-
0023216891
-
CpG islands in vertebrate genomes
-
Gardiner-Garden, M. et al. CpG islands in vertebrate genomes. J. Mol. Biol. 196, 261-282 (1987).
-
(1987)
J. Mol. Biol
, vol.196
, pp. 261-282
-
-
Gardiner-Garden, M.1
-
35
-
-
84859865967
-
The UCSC genome browser database: Extensions and updates 2011
-
Dreszer, T. R. et al. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res. 40, D918-D923 (2012).
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Dreszer, T.R.1
-
36
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.C.1
-
37
-
-
60849113411
-
The proteinmodel portal
-
Arnold, K. et al. The proteinmodel portal. J. Struct. Funct. Genomics 10, 1-8 (2009).
-
(2009)
J. Struct. Funct. Genomics
, vol.10
, pp. 1-8
-
-
Arnold, K.1
-
38
-
-
9144244232
-
MODBASE, a database of annotated comparative protein structure models and associated resources
-
Pieper, U. et al. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 32, D217-D222 (2004).
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Pieper, U.1
-
40
-
-
13244281317
-
Coot: Model-building tools for molecular graphics
-
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004).
-
(2004)
Acta Crystallogr. D
, vol.60
, pp. 2126-2132
-
-
Emsley, P.1
Cowtan, K.2
-
41
-
-
0000577528
-
-
Pacific Symposium on Biocomputing
-
Huang, C. C., Couch, G. S., Pettersen, E. F. & Ferrin, T. E. Chimera: an Extensible Molecular Modeling Application Constructed Using Standard Components Vol. 1, 724 (Pacific Symposium on Biocomputing, 1996).
-
(1996)
Chimera: An Extensible Molecular Modeling Application Constructed Using Standard Components
, vol.1
, pp. 724
-
-
Huang, C.C.1
Couch, G.S.2
Pettersen, E.F.3
Ferrin, T.E.4
|