Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate
Tài liệu tham khảo
Amouroux, 2016, De novo DNA methylation drives 5hmC accumulation in mouse zygotes, Nat. Cell Biol., 18, 225, 10.1038/ncb3296
Apostolou, 2013, Chromatin dynamics during cellular reprogramming, Nature, 502, 462, 10.1038/nature12749
Bar-Nur, 2014, Small molecules facilitate rapid and synchronous iPSC generation, Nat. Methods, 11, 1170, 10.1038/nmeth.3142
Bird, 2002, DNA methylation patterns and epigenetic memory, Genes Dev., 16, 6, 10.1101/gad.947102
Boiani, 2002, Oct4 distribution and level in mouse clones: consequences for pluripotency, Genes Dev., 16, 1209, 10.1101/gad.966002
Booth, 2012, Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution, Science, 336, 934, 10.1126/science.1220671
Buenrostro, 2013, Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position, Nat. Methods, 10, 1213, 10.1038/nmeth.2688
Bussmann, 2009, A robust and highly efficient immune cell reprogramming system, Cell Stem Cell, 5, 554, 10.1016/j.stem.2009.10.004
Carey, 2010, Single-gene transgenic mouse strains for reprogramming adult somatic cells, Nat. Methods, 7, 56, 10.1038/nmeth.1410
Chen, 2008, Integration of external signaling pathways with the core transcriptional network in embryonic stem cells, Cell, 133, 1106, 10.1016/j.cell.2008.04.043
Chen, 2013, H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs, Nat. Genet., 45, 34, 10.1038/ng.2491
Chronis, 2017, Cooperative binding of transcription factors orchestrates reprogramming, Cell, 168, 442, 10.1016/j.cell.2016.12.016
Collins, 1987, A stromal cell line from myeloid long-term bone marrow cultures can support myelopoiesis and B lymphopoiesis, J. Immunol., 138, 1082, 10.4049/jimmunol.138.4.1082
2012, An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57, 10.1038/nature11247
Costa, 2013, NANOG-dependent function of TET1 and TET2 in establishment of pluripotency, Nature, 495, 370, 10.1038/nature11925
Croft, 2011, Reactome: a database of reactions, pathways and biological processes, Nucleic Acids Res., 39, D691, 10.1093/nar/gkq1018
de la Rica, 2013, PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation, Genome Biol., 14, R99, 10.1186/gb-2013-14-9-r99
Di Stefano, 2014, C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells, Nature, 506, 235, 10.1038/nature12885
Di Stefano, 2016, C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4, Nat. Cell Biol., 18, 371, 10.1038/ncb3326
Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635
Doege, 2012, Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2, Nature, 488, 652, 10.1038/nature11333
Domcke, 2015, Competition between DNA methylation and transcription factors determines binding of NRF1, Nature, 528, 575, 10.1038/nature16462
dos Santos, 2014, MBD3/NuRD facilitates induction of pluripotency in a context-dependent manner, Cell Stem Cell, 15, 102, 10.1016/j.stem.2014.04.019
Gibson, 2009, Enzymatic assembly of DNA molecules up to several hundred kilobases, Nat. Methods, 6, 343, 10.1038/nmeth.1318
Habibi, 2013, Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells, Cell Stem Cell, 13, 360, 10.1016/j.stem.2013.06.002
Hackett, 2014, Regulatory principles of pluripotency: from the ground state up, Cell Stem Cell, 15, 416, 10.1016/j.stem.2014.09.015
Han, 2016, A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations, Mol. Cell, 63, 711, 10.1016/j.molcel.2016.06.028
Hasemann, 2014, C/EBPα is required for long-term self-renewal and lineage priming of hematopoietic stem cells and for the maintenance of epigenetic configurations in multipotent progenitors, PLoS Genet., 10, e1004079, 10.1371/journal.pgen.1004079
Hu, 2014, Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming, Cell Stem Cell, 14, 512, 10.1016/j.stem.2014.01.001
Huber, 2015, Orchestrating high-throughput genomic analysis with Bioconductor, Nat. Methods, 12, 115, 10.1038/nmeth.3252
Kallin, 2012, Tet2 facilitates the derepression of myeloid target genes during CEBPα-induced transdifferentiation of pre-B cells, Mol. Cell, 48, 266, 10.1016/j.molcel.2012.08.007
Ko, 2010, Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2, Nature, 468, 839, 10.1038/nature09586
Kumar, 2007, Mfuzz: a software package for soft clustering of microarray data, Bioinformation, 2, 5, 10.6026/97320630002005
Lee, 2014, An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator, Nat. Commun., 5, 5619, 10.1038/ncomms6619
Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, 10.1186/s13059-014-0550-8
Marco-Sola, 2012, The GEM mapper: fast, accurate and versatile alignment by filtration, Nat. Methods, 9, 1185, 10.1038/nmeth.2221
Martello, 2013, Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor, EMBO J., 32, 2561, 10.1038/emboj.2013.177
Medina-Rivera, 2011, Theoretical and empirical quality assessment of transcription factor-binding motifs, Nucleic Acids Res., 39, 808, 10.1093/nar/gkq710
Medina-Rivera, 2015, RSAT 2015: Regulatory Sequence Analysis Tools, Nucleic Acids Res., 43, W50, 10.1093/nar/gkv362
Merkel, 2017, GEMBS: high through-put processing pipeline for DNA methylation data from Whole Genome Bisulfite Sequencing (WGBS), Bioinformatics
Milagre, 2017, Gender differences in global but not targeted demethylation in iPSC reprogramming, Cell Rep., 18, 1079, 10.1016/j.celrep.2017.01.008
Neph, 2012, BEDOPS: High-performance genomic feature operations, Bioinformatics, 28, 1919, 10.1093/bioinformatics/bts277
Pastor, 2013, TETonic shift: Biological roles of TET proteins in DNA demethylation and transcription, Nat. Rev. Mol. Cell Biol., 14, 341, 10.1038/nrm3589
Polo, 2012, A molecular roadmap of reprogramming somatic cells into iPS cells, Cell, 151, 1617, 10.1016/j.cell.2012.11.039
Rais, 2013, Deterministic direct reprogramming of somatic cells to pluripotency, Nature, 502, 65, 10.1038/nature12587
Ramírez, 2016, deepTools2: a next generation web server for deep-sequencing data analysis, Nucleic Acids Res., 44, 10.1093/nar/gkw257
Sardina, 2010, p22phox-dependent NADPH oxidase activity is required for megakaryocytic differentiation, Cell Death Differ., 17, 1842, 10.1038/cdd.2010.67
Schmidl, 2015, ChIPmentation: Fast, robust, low-input ChIP-seq for histones and transcription factors, Nat. Methods, 12, 963, 10.1038/nmeth.3542
Smith, 2013, DNA methylation: roles in mammalian development, Nat. Rev. Genet., 14, 204, 10.1038/nrg3354
Soufi, 2015, Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming, Cell, 161, 555, 10.1016/j.cell.2015.03.017
Stadhouders, 2018, Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming, Nat. Genet., 50, 238, 10.1038/s41588-017-0030-7
Stadtfeld, 2010, A reprogrammable mouse strain from gene-targeted embryonic stem cells, Nat. Methods, 7, 53, 10.1038/nmeth.1409
Takahashi, 2006, Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell, 126, 663, 10.1016/j.cell.2006.07.024
Thomas-Chollier, 2011, Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs, Nat. Protoc., 6, 1860, 10.1038/nprot.2011.409
van Oevelen, 2015, C/EBPα activates pre-existing and de novo macrophage enhancers during induced pre-B cell transdifferentiation and myelopoiesis, Stem Cell Reports, 5, 232, 10.1016/j.stemcr.2015.06.007
Vidal, 2014, Combinatorial modulation of signaling pathways reveals cell-type-specific requirements for highly efficient and synchronous iPSC reprogramming, Stem Cell Reports, 3, 574, 10.1016/j.stemcr.2014.08.003
Wang, 2015, WT1 recruits TET2 to regulate its target gene expression and suppress leukemia cell proliferation, Mol. Cell, 57, 662, 10.1016/j.molcel.2014.12.023
Wu, 2017, TET-mediated active DNA demethylation: mechanism, function and beyond, Nat. Rev. Genet., 18, 517, 10.1038/nrg.2017.33
Wu, 2014, Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing, Nat. Biotechnol., 32, 1231, 10.1038/nbt.3073
Xiong, 2016, Cooperative action between SALL4A and TET proteins in stepwise oxidation of 5-methylcytosine, Mol. Cell, 64, 913, 10.1016/j.molcel.2016.10.013
Yildirim, 2011, Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells, Cell, 147, 1498, 10.1016/j.cell.2011.11.054
Yin, 2017, Impact of cytosine methylation on DNA binding specificities of human transcription factors, Science, 10.1126/science.aaj2239
Ying, 2008, The ground state of embryonic stem cell self-renewal, Nature, 453, 519, 10.1038/nature06968
Yu, 2012, Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome, Cell, 149, 1368, 10.1016/j.cell.2012.04.027
Zhang, 1997, Absence of granulocyte colony-stimulating factor signaling and neutrophil development in CCAAT enhancer binding protein alpha-deficient mice, Proc. Natl. Acad. Sci. USA, 94, 569, 10.1073/pnas.94.2.569
Zhang, 2015, Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6, Nature, 525, 389, 10.1038/nature15252
Zhang, 2008, Model-based analysis of ChIP-Seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137