1.
Guo JU, Su Y, Zhong C, Ming G-l, Song H: Emerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation
and beyond. cc 2011, 10(16):2662-2668.
2.
Ito K, Suda T: Metabolic requirements for the maintenance of self-renewing stem cells. Nat Rev Mol Cell Biol 2014, 15(4):243-256.
3.
Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM,
Liu DR, Aravind L et al: Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL
Partner TET1. Science 2009, 324(5929):930-935.
4.
Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, He C, Zhang Y: Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011, 333(6047):1300-1303.
5.
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.
6.
Cortazar D, Kunz C, Selfridge J, Lettieri T, Saito Y, MacDougall E, Wirz A, Schuermann
D, Jacobs AL, Siegrist F et al: Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability. Nature 2011, 470(7334):419-423.
7.
Cortellino S, Xu J, Sannai M, Moore R, Caretti E, Cigliano A, Le Coz M, Devarajan
K, Wessels A, Soprano D et al: Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base
excision repair. Cell 2011, 146(1):67-79.
8.
Muller U, Bauer C, Siegl M, Rottach A, Leonhardt H: TET-mediated oxidation of methylcytosine causes TDG or NEIL glycosylase dependent
gene reactivation. Nucleic Acids Res 2014, 42(13):8592-8604.
9.
Koh KP, Yabuuchi A, Rao S, Huang Y, Cunniff K, Nardone J, Laiho A, Tahiliani M, Sommer
CA, Mostoslavsky G et al: Tet1 and Tet2 Regulate 5-Hydroxymethylcytosine Production and Cell Lineage Specification
in Mouse Embryonic Stem Cells. Cell Stem Cell 2011, 8(2):200-213.
10.
Dawlaty MM, Ganz K, Powell BE, Hu Y-C, Markoulaki S, Cheng AW, Gao Q, Kim J, Choi
S-W, Page DC et al: Tet1 Is Dispensable for Maintaining Pluripotency and Its Loss Is Compatible with Embryonic
and Postnatal Development. Cell Stem Cell 2011, 9(2):166-175.
11.
Li Z, Cai X, Cai CL, Wang J, Zhang W, Petersen BE, Yang FC, Xu M: Deletion of Tet2 in mice leads to dysregulated hematopoietic stem cells and subsequent
development of myeloid malignancies. Blood 2011, 118(17):4509-4518.
12.
Dawlaty MM, Breiling A, Le T, Raddatz G, Barrasa MI, Cheng AW, Gao Q, Powell BE, Li
Z, Xu M et al: Combined Deficiency of Tet1 and Tet2 Causes Epigenetic Abnormalities but Is Compatible
with Postnatal Development. Developmental Cell 2013, 24(3):310-323.
13.
Dawlaty MM, Breiling A, Le T, Barrasa MI, Raddatz G, Gao Q, Powell BE, Cheng AW, Faull
KF, Lyko F et al: Loss of Tet Enzymes Compromises Proper Differentiation of Embryonic Stem Cells. Developmental Cell 2014, 29(1):102-111.
14.
Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R: One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated
Genome Engineering. Cell 2013, 153(4):910-918.
15.
Yang H, Wang H, Shivalila CS, Cheng AW, Shi L, Jaenisch R: One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated
Genome Engineering. Cell 2013, 154(6):1370-1379.
16.
Hu X, Zhang L, Mao S-Q, Li Z, Chen J, Zhang R-R, Wu H-P, Gao J, Guo F, Liu W et al: Tet and TDG Mediate DNA Demethylation Essential for Mesenchymal-to-Epithelial Transition
in Somatic Cell Reprogramming. Stem Cell 2014, 14(4):512-522.
17.
Hon GC, Song C-X, Du T, Jin F, Selvaraj S, Lee AY, Yen C-a, Ye Z, Mao S-Q, Wang B-A et al: 5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming
during Differentiation. Mol Cell 2014:1-12.
18.
Risso D, Ngai J, Speed TP, Dudoit S: Normalization of RNA-seq data using factor analis of control genes or samples. Nature Biotechnology 2014, 32(9):896-902.
19.
Muruganujan A, Ebert D, Mi H, Thomas PD, Huang X: PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment
analysis tools. Nucleic Acids Research 2018, 47(D1):D419-D426.
20.
Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PAC, Rappsilber J, Helin
K: TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011, 473(7347):343-348.
21.
Wu H, D’alessio AC, Ito S, Xia K, Wang Z, Cui K, Zhao K, Eve Sun Y, Zhang Y: Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 2011, 473(7347):389-393.
22.
Lu F, Liu Y, Jiang L, Yamaguchi S, Zhang Y: Role of Tet proteins in enhancer activity and telomere elongation. Genes Dev 2014, 28(19):2103-2119.
23.
Lengner CJ, Camargo FD, Hochedlinger K, Welstead GG, Zaidi S, Gokhale S, Scholer HR,
Tomilin A, Jaenisch R: Oct4 expression is not required for mouse somatic stem cell self-renewal. Cell Stem Cell 2007, 1(4):403-415.
24.
Balasubramanian D, Akhtar-Zaidi B, Song L, Bartels CF, Veigl M, Beard L, Myeroff L,
Guda K, Lutterbaugh J, Willis J et al: H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing
start sites. Genome medicine 2012, 4(5):47.
25.
Zhu F, Zhu Q, Ye D, Zhang Q, Yang Y, Guo X, Liu Z, Jiapaer Z, Wan X, Wang G et al: Sin3a-Tet1 interaction activates gene transcription and is required for embryonic
stem cell pluripotency. Nucleic Acids Res 2018, 46(12):6026-6040.
26.
Neri F, Incarnato D, Krepelova A, Rapelli S, Pagnani A, Zecchina R, Parlato C, Oliviero
S: Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive
complex 2 in mouse embryonic stem cells. Genome Biology 2013, 14(8):R91-32.
27.
Li Y, Zheng H, Wang Q, Zhou C, Wei L, Liu X, Zhang W, Zhang Y, Du Z, Wang X et al: Genome-wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA
methylation valleys. Genome Biology 2018, 19(1):18.
28.
Verma N, Pan H, x000E LCD, Shukla A, Li QV, Pelham-Webb B, Teijeiro V, lez FGxE, Krivtsov
A, Chang C-J et al: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic
stem cells. Nat Genet 2017:1-19.
29.
Costa Y, Ding J, Theunissen TW, Faiola F, Hore TA, Shliaha PV, Fidalgo M, Saunders
A, Lawrence M, Dietmann S et al: NANOG-dependent function of TET1 and TET2 in establishment of pluripotency. Nature 2013:1-5.
30.
Pulakanti K, Pinello L, Stelloh C, Blinka S, Allred J, Milanovich S, Kiblawi S, Peterson
J, Wang A, Yuan G-C et al: Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions. Epigenetics 2013, 8(12):1303-1320.
31.
Blinka S, Reimer MH, Jr., Pulakanti K, Rao S: Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated
Genes. Cell Rep 2016, 17(1):19-28.
32.
Stelloh C, Reimer MH, Pulakanti K, Blinka S, Peterson J, Pinello L, Jia S, Roumiantsev
S, Hessner MJ, Milanovich S et al: The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene
silencing. Epigenetics & chromatin 2016, 9:14.
33.
M M: Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetJournal 2011, 17(1).
34.
Krueger F, Andrews SR: Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 2011, 27(11):1571-1572.
35.
Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Meth 2012, 9(4):357-359.
36.
Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE:
methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation
profiles. Genome Biology 2012, 13(10):R87.
37.
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh
H, Glass CK: Simple combinations of lineage-determining transcription factors prime cis-regulatory
elements required for macrophage and B cell identities. Mol Cell 2010, 38(4):576-589.
38.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M,
Gingeras TR: STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29(1):15-21.
39.
Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biol 2010, 11(10):R106.