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Klf4 Organizes Long-Range Chromosomal Interactions with the Oct4 Locus in Reprogramming and Pluripotency

Wei, Zong, Gao, Fan, Kim, Sewoon, Yang, Hongzhen, Lyu, Jungmook, An, Woojin, Wang, Kai, Lu, Wange·2013·Cell Stem Cell
DOI 10.1016/j.stem.2013.05.010
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  • OCT4-SOX2 binding increases KLF4 binding by several folds, mostly in chromatin regions that are closed in human fibroblasts.

    “Co-immunoprecipitation and chromatin immunoprecipitation followed by sequencing studies reveal that OCT4-SOX2 binding increases KLF4 binding by several folds, mostly in chromatin regions that are closed in human fibroblasts 41,53,54 .”

    From Mechanisms, pathways and strategies for rejuvenation through epigenetic reprogramming (2023) · cites this paper as [54]

    The Results report that Oct4, Sox2, and Klf4 bind the Oct4 distal enhancer and that Klf4 occupancy is higher in SSEA1+ than SSEA1− cells. Neither those passages nor searches for increased Klf4 binding and closed chromatin in human fibroblasts establish that OCT4-SOX2 binding increases KLF4 binding several-fold, or where such an increase occurs. (LLM, conf=0.72)

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Research works printed but not linked: 57

  1. Anokye-Danso, 2011, Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency, Cell Stem Cell, 8, 376, 10.1016/j.stem.2011.03.001 · DOI
  2. Apostolou, 2013, Genome-wide Chromatin Interactions of the Nanog Locus in Pluripotency, Differentiation, and Reprogramming, Cell Stem Cell, 12, 699, 10.1016/j.stem.2013.04.013 · DOI
  3. Brookes, 2012, Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs, Cell Stem Cell, 10, 157, 10.1016/j.stem.2011.12.017 · DOI
  4. Chakalova, 2010, Organization of transcription, Cold Spring Harb. Perspect. Biol., 2, a000729, 10.1101/cshperspect.a000729 · DOI
  5. 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 · DOI
  6. Cuylen, 2010, A new cohesive team to mediate DNA looping, Cell Stem Cell, 7, 424, 10.1016/j.stem.2010.09.006 · DOI
  7. Doege, 2012, Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2, Nature, 488, 652, 10.1038/nature11333 · DOI
  8. Drissen, 2004, The active spatial organization of the beta-globin locus requires the transcription factor EKLF, Genes Dev., 18, 2485, 10.1101/gad.317004 · DOI · Paper page
  9. Evans, 2007, Kruppel-like factor 4 is acetylated by p300 and regulates gene transcription via modulation of histone acetylation, J. Biol. Chem., 282, 33994, 10.1074/jbc.M701847200 · DOI
  10. Fullwood, 2009, An oestrogen-receptor-alpha-bound human chromatin interactome, Nature, 462, 58, 10.1038/nature08497 · DOI
  11. Gamper, 2012, Regulation of KLF4 turnover reveals an unexpected tissue-specific role of pVHL in tumorigenesis, Mol. Cell, 45, 233, 10.1016/j.molcel.2011.11.031 · DOI
  12. Gurdon, 2008, Nuclear reprogramming in cells, Science, 322, 1811, 10.1126/science.1160810 · DOI
  13. Hanna, 2010, Pluripotency and cellular reprogramming: facts, hypotheses, unresolved issues, Cell, 143, 508, 10.1016/j.cell.2010.10.008 · DOI
  14. Heng, 2010, The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent cells, Cell Stem Cell, 6, 167, 10.1016/j.stem.2009.12.009 · DOI
  15. Hiratani, 2010, Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis, Genome Res., 20, 155, 10.1101/gr.099796.109 · DOI
  16. Ichida, 2009, A small-molecule inhibitor of tgf-Beta signaling replaces sox2 in reprogramming by inducing nanog, Cell Stem Cell, 5, 491, 10.1016/j.stem.2009.09.012 · DOI · Paper page
  17. Jaenisch, 2008, Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming, Cell, 132, 567, 10.1016/j.cell.2008.01.015 · DOI
  18. Jiang, 2008, A core Klf circuitry regulates self-renewal of embryonic stem cells, Nat. Cell Biol., 10, 353, 10.1038/ncb1698 · DOI
  19. Kidder, 2012, HDAC1 regulates pluripotency and lineage specific transcriptional networks in embryonic and trophoblast stem cells, Nucleic Acids Res., 40, 2925, 10.1093/nar/gkr1151 · DOI
  20. Kim, 2009, Oct4-induced pluripotency in adult neural stem cells, Cell, 136, 411, 10.1016/j.cell.2009.01.023 · DOI
  21. Kind, 2013, Single-cell dynamics of genome-nuclear lamina interactions, Cell, 153, 178, 10.1016/j.cell.2013.02.028 · DOI
  22. Koche, 2011, Reprogramming factor expression initiates widespread targeted chromatin remodeling, Cell Stem Cell, 8, 96, 10.1016/j.stem.2010.12.001 · DOI · Paper page
  23. Levasseur, 2008, Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells, Genes Dev., 22, 575, 10.1101/gad.1606308 · DOI
  24. Lieberman-Aiden, 2009, Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, 326, 289, 10.1126/science.1181369 · DOI · Paper page
  25. Mansour, 2012, The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming, Nature, 488, 409, 10.1038/nature11272 · DOI
  26. Merika, 1995, Functional synergy and physical interactions of the erythroid transcription factor GATA-1 with the Krüppel family proteins Sp1 and EKLF, Mol. Cell. Biol., 15, 2437, 10.1128/MCB.15.5.2437 · DOI · Paper page
  27. Meshorer, 2006, Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells, Dev. Cell, 10, 105, 10.1016/j.devcel.2005.10.017 · DOI
  28. Mikkelsen, 2008, Dissecting direct reprogramming through integrative genomic analysis, Nature, 454, 49, 10.1038/nature07056 · DOI
  29. Nakagawa, 2008, Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts, Nat. Biotechnol., 26, 101, 10.1038/nbt1374 · DOI · Paper page
  30. Nitzsche, 2011, RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity, PLoS ONE, 6, e19470, 10.1371/journal.pone.0019470 · DOI
  31. Noordermeer, 2011, Variegated gene expression caused by cell-specific long-range DNA interactions, Nat. Cell Biol., 13, 944, 10.1038/ncb2278 · DOI
  32. Noordermeer, 2011, The dynamic architecture of Hox gene clusters, Science, 334, 222, 10.1126/science.1207194 · DOI
  33. Noti, 2005, The leukocyte integrin gene CD11d is repressed by gut-enriched Kruppel-like factor 4 in myeloid cells, J. Biol. Chem., 280, 3449, 10.1074/jbc.M412627200 · DOI
  34. Onder, 2012, Chromatin-modifying enzymes as modulators of reprogramming, Nature, 483, 598, 10.1038/nature10953 · DOI
  35. Orkin, 2011, Chromatin connections to pluripotency and cellular reprogramming, Cell, 145, 835, 10.1016/j.cell.2011.05.019 · DOI
  36. Palstra, 2008, Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription, PloS One, 3, e1661, 10.1371/journal.pone.0001661 · DOI
  37. Pan, 2002, Stem cell pluripotency and transcription factor Oct4, Cell Res., 12, 321, 10.1038/sj.cr.7290134 · DOI
  38. Phillips, 2009, CTCF: master weaver of the genome, Cell, 137, 1194, 10.1016/j.cell.2009.06.001 · DOI
  39. Plath, 2011, Progress in understanding reprogramming to the induced pluripotent state, Nat. Rev. Genet., 12, 253, 10.1038/nrg2955 · DOI
  40. Probst, 2011, Heterochromatin establishment in the context of genome-wide epigenetic reprogramming, Trends Genet., 27, 177, 10.1016/j.tig.2011.02.002 · DOI
  41. Remeseiro, 2013, Cohesin, a chromatin engagement ring, Curr. Opin. Cell Biol., 25, 63, 10.1016/j.ceb.2012.10.013 · DOI
  42. Ryba, 2010, Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types, Genome Res., 20, 761, 10.1101/gr.099655.109 · DOI
  43. Schoenfelder, 2010, Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells, Nat. Genet., 42, 53, 10.1038/ng.496 · DOI
  44. Simonis, 2006, Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C), Nat. Genet., 38, 1348, 10.1038/ng1896 · DOI · Paper page
  45. Splinter, 2011, The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA, Genes Dev., 25, 1371, 10.1101/gad.633311 · DOI
  46. Sridharan, 2009, Role of the murine reprogramming factors in the induction of pluripotency, Cell, 136, 364, 10.1016/j.cell.2009.01.001 · DOI
  47. 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 · DOI · Paper page
  48. Takebayashi, 2012, Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding, Proc. Natl. Acad. Sci. USA, 109, 12574, 10.1073/pnas.1207185109 · DOI
  49. Theunissen, 2011, Nanog overcomes reprogramming barriers and induces pluripotency in minimal conditions, Curr. Biol., 21, 65, 10.1016/j.cub.2010.11.074 · DOI
  50. Tiwari, 2008, PcG proteins, DNA methylation, and gene repression by chromatin looping, PLoS Biol., 6, 2911, 10.1371/journal.pbio.0060306 · DOI
  51. Vakoc, 2005, Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1, Mol. Cell, 17, 453, 10.1016/j.molcel.2004.12.028 · DOI · Paper page
  52. van de Werken, 2012, 4C technology: protocols and data analysis, Methods Enzymol., 513, 89, 10.1016/B978-0-12-391938-0.00004-5 · DOI
  53. Wei, 2009, Klf4 interacts directly with Oct4 and Sox2 to promote reprogramming, Stem Cells, 27, 2969, 10.1002/stem.231 · DOI
  54. Whyte, 2013, Master transcription factors and mediator establish super-enhancers at key cell identity genes, Cell, 153, 307, 10.1016/j.cell.2013.03.035 · DOI · Paper page
  55. Williams, 2010, Interchromosomal association and gene regulation in trans, Trends Genet., 26, 188, 10.1016/j.tig.2010.01.007 · DOI
  56. Zhang, 2010, Kruppel-like factor 4 (Klf4) prevents embryonic stem (ES) cell differentiation by regulating Nanog gene expression, J. Biol. Chem., 285, 9180, 10.1074/jbc.M109.077958 · DOI
  57. Zhao, 2006, Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions, Nat. Genet., 38, 1341, 10.1038/ng1891 · DOI

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Metadata

Authors
Wei, Z., Gao, F., Kim, S., Yang, H., Lyu, J., An, W., Wang, K., & Lu, W.
Venue
Cell Stem Cell
Publisher
Elsevier BV
Published
2013-07
Volume
13
Issue
1
Pages
36-47
ISSN
1934-5909
DOI
10.1016/j.stem.2013.05.010
Cited by
214
References
6
Language
en
Licence

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