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Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome
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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 [53]
The Results section, “Oct4, Sox2, and Klf4 bind as pioneer factors to closed chromatin” (page unavailable), reports that most initial binding events occur in closed chromatin in human fibroblasts. But the reported several-fold increase is c-Myc enhancing Klf4 occupancy, not OCT4-SOX2 increasing KLF4 binding. The paper does not establish the claimed direction of that effect. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThe modulatory activities of OSK and MYC on each other are bidirectional.
“supporting the notion that the modulatory activities of OSK and MYC on each other are bidirectional.”
From Mechanisms, pathways and strategies for rejuvenation through epigenetic reprogramming (2023) · cites this paper as [53]
MYC binding increases by 40-fold with OSK.
“and MYC binding increases by 40-fold with OSK, supporting the notion that the modulatory activities of OSK and MYC on each other are bidirectional.”
From Mechanisms, pathways and strategies for rejuvenation through epigenetic reprogramming (2023) · cites this paper as [53]
The presence of MYC increases OSK binding by twofold.
“The presence of MYC increases OSK binding by twofold 53 , and MYC binding increases by 40-fold with OSK, supporting the notion that the modulatory activities of OSK and MYC on each other are bidirectional.”
From Mechanisms, pathways and strategies for rejuvenation through epigenetic reprogramming (2023) · cites this paper as [53]
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Takahashi, K., & Yamanaka, S. (2006) · Cell · doi:10.1016/j.cell.2006.07.024 · Cited by 26,673
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
Human DNA methylomes at base resolution show widespread epigenomic differences
Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature · doi:10.1038/nature08514 · Cited by 4,673
GREAT improves functional interpretation of cis-regulatory regions
McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M., & Bejerano, G. (2010) · Nature Biotechnology · doi:10.1038/nbt.1630 · Cited by 4,502
Pioneer transcription factors: establishing competence for gene expression
Zaret, K. S., & Carroll, J. S. (2011) · Genes & Development · doi:10.1101/gad.176826.111 · Cited by 1,589
Self-citationSuppression of induced pluripotent stem cell generation by the p53–p21 pathway
Hong, H., Takahashi, K., Ichisaka, T., Aoi, T., Kanagawa, O., Nakagawa, M., Okita, K., & Yamanaka, S. (2009) · Nature · doi:10.1038/nature08235 · Cited by 1,301
Linking the p53 tumour suppressor pathway to somatic cell reprogramming
Kawamura, T., Suzuki, J., Wang, Y. V., Menendez, S., Morera, L. B., Raya, A., Wahl, G. M., & Belmonte, J. C. I. (2009) · Nature · doi:10.1038/nature08311 · Cited by 1,115
A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity
Marión, R. M., Strati, K., Li, H., Murga, M., Blanco, R., Ortega, S., Fernandez-Capetillo, O., Serrano, M., & Blasco, M. A. (2009) · Nature · doi:10.1038/nature08287 · Cited by 1,028
Feeder-independent culture of human embryonic stem cells
Ludwig, T. E., Bergendahl, V., Levenstein, M. E., Yu, J., Probasco, M. D., & Thomson, J. A. (2006) · Nature Methods · doi:10.1038/nmeth902 · Cited by 681 · cited 1×
“For ChIP of the OSKM factors in ES/iPS cells, the chromatin was obtained from hFib-iPS cells at passage 15 and human H1-ES cells (Thomson et al., 1998) at passage 35 that were expanded under feeder-free conditions for three passages (Ludwig et al., 2006).”
A High-Efficiency System for the Generation and Study of Human Induced Pluripotent Stem Cells
Maherali, N., Ahfeldt, T., Rigamonti, A., Utikal, J., Cowan, C., & Hochedlinger, K. (2008) · Cell Stem Cell · doi:10.1016/j.stem.2008.08.003 · Cited by 563 · cited 1×
“Using microarray expression data sets of human fibroblasts and ES cells (Lowry et al., 2008; Maherali et al., 2008), we found that silent genes were extensively targeted by the O, S, K, and M factors at 48 hr, which is in contrast to that seen in ES cells (Chen et al., 2008; Sridharan et al.,…”
Flagged first, then by citations
Research works printed but not linked: 54
- Adams, 1995, Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative, Mol. Cell. Biol., 15, 1405, 10.1128/MCB.15.3.1405 · DOI
- 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
- Bailey, 1998, Combining evidence using p-values: application to sequence homology searches, Bioinformatics, 14, 48, 10.1093/bioinformatics/14.1.48 · DOI
- Boyer, 2005, Core transcriptional regulatory circuitry in human embryonic stem cells, Cell, 122, 947, 10.1016/j.cell.2005.08.020 · DOI · Paper page
- Brambrink, 2008, Sequential expression of pluripotency markers during direct reprogramming of mouse somatic cells, Cell Stem Cell, 2, 151, 10.1016/j.stem.2008.01.004 · DOI
- Bryne, 2008, JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update, Nucleic Acids Res., 36, D102
- Buganim, 2012, Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase, Cell, 150, 1209, 10.1016/j.cell.2012.08.023 · DOI · Paper page
- Chandra, 2012, Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation, Mol. Cell, 47, 203, 10.1016/j.molcel.2012.06.010 · DOI · Paper page
- 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
- Cirillo, 1998, Binding of the winged-helix transcription factor HNF3 to a linker histone site on the nucleosome, EMBO J., 17, 244, 10.1093/emboj/17.1.244 · DOI
- Cirillo, 2002, Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4, Mol. Cell, 9, 279, 10.1016/S1097-2765(02)00459-8 · DOI
- Clark, 1993, Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5, Nature, 364, 412, 10.1038/364412a0 · DOI
- Filion, 2010, Systematic protein location mapping reveals five principal chromatin types in Drosophila cells, Cell, 143, 212, 10.1016/j.cell.2010.09.009 · DOI
- Graf, 2009, Forcing cells to change lineages, Nature, 462, 587, 10.1038/nature08533 · DOI · Paper page
- Gualdi, 1996, Hepatic specification of the gut endoderm in vitro: cell signaling and transcriptional control, Genes Dev., 10, 1670, 10.1101/gad.10.13.1670 · DOI
- Guelen, 2008, Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions, Nature, 453, 948, 10.1038/nature06947 · DOI
- Hanna, 2009, Direct cell reprogramming is a stochastic process amenable to acceleration, Nature, 462, 595, 10.1038/nature08592 · DOI · Paper page
- Hockemeyer, 2008, A drug-inducible system for direct reprogramming of human somatic cells to pluripotency, Cell Stem Cell, 3, 346, 10.1016/j.stem.2008.08.014 · DOI
- Kim, 2008, An extended transcriptional network for pluripotency of embryonic stem cells, Cell, 132, 1049, 10.1016/j.cell.2008.02.039 · DOI
- Knoepfler, 2008, Why myc? An unexpected ingredient in the stem cell cocktail, Cell Stem Cell, 2, 18, 10.1016/j.stem.2007.12.004 · DOI
- 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
- Lerou, 2008, Derivation and maintenance of human embryonic stem cells from poor-quality in vitro fertilization embryos, Nat. Protoc., 3, 923, 10.1038/nprot.2008.60 · DOI
- Li, 2010, A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts, Cell Stem Cell, 7, 51, 10.1016/j.stem.2010.04.014 · DOI · Paper page
- Lister, 2011, Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells, Nature, 471, 68, 10.1038/nature09798 · DOI
- Lowry, 2008, Generation of human induced pluripotent stem cells from dermal fibroblasts, Proc. Natl. Acad. Sci. USA, 105, 2883, 10.1073/pnas.0711983105 · DOI · Paper page
- Machanick, 2011, MEME-ChIP: motif analysis of large DNA datasets, Bioinformatics, 27, 1696, 10.1093/bioinformatics/btr189 · DOI
- Maekawa, 2011, Direct reprogramming of somatic cells is promoted by maternal transcription factor Glis1, Nature, 474, 225, 10.1038/nature10106 · DOI
- Mah, 2011, Molecular insights into reprogramming-initiation events mediated by the OSKM gene regulatory network, PLoS ONE, 6, e24351, 10.1371/journal.pone.0024351 · DOI
- Mikkelsen, 2008, Dissecting direct reprogramming through integrative genomic analysis, Nature, 454, 49, 10.1038/nature07056 · DOI
- Myers, 2011, A user's guide to the encyclopedia of DNA elements (ENCODE), PLoS Biol., 9, e1001046, 10.1371/journal.pbio.1001046 · DOI
- Nair, 2003, X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors, Cell, 112, 193, 10.1016/S0092-8674(02)01284-9 · DOI · Paper page
- 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
- Onder, 2012, Chromatin-modifying enzymes as modulators of reprogramming, Nature, 483, 598, 10.1038/nature10953 · DOI
- Park, 2008, Generation of human-induced pluripotent stem cells, Nat. Protoc., 3, 1180, 10.1038/nprot.2008.92 · DOI
- Plath, 2011, Progress in understanding reprogramming to the induced pluripotent state, Nat. Rev. Genet., 12, 253, 10.1038/nrg2955 · DOI
- Reményi, 2003, Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers, Genes Dev., 17, 2048, 10.1101/gad.269303 · DOI
- Samavarchi-Tehrani, 2010, Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming, Cell Stem Cell, 7, 64, 10.1016/j.stem.2010.04.015 · DOI · Paper page
- Schuetz, 2011, The structure of the Klf4 DNA-binding domain links to self-renewal and macrophage differentiation, Cell. Mol. Life Sci., 68, 3121, 10.1007/s00018-010-0618-x · DOI · Paper page
- Smith, 2010, Dynamic single-cell imaging of direct reprogramming reveals an early specifying event, Nat. Biotechnol., 28, 521, 10.1038/nbt.1632 · DOI
- Sridharan, 2009, Role of the murine reprogramming factors in the induction of pluripotency, Cell, 136, 364, 10.1016/j.cell.2009.01.001 · DOI
- Taberlay, 2011, Polycomb-repressed genes have permissive enhancers that initiate reprogramming, Cell, 147, 1283, 10.1016/j.cell.2011.10.040 · DOI · Paper page
- Takahashi, 2007, Induction of pluripotent stem cells from adult human fibroblasts by defined factors, Cell, 131, 861, 10.1016/j.cell.2007.11.019 · DOI · Paper page
- Thomson, 1998, Embryonic stem cell lines derived from human blastocysts, Science, 282, 1145, 10.1126/science.282.5391.1145 · DOI
- Visel, 2007, VISTA Enhancer Browser—a database of tissue-specific human enhancers, Nucleic Acids Res., 35, D88, 10.1093/nar/gkl822 · DOI · Paper page
- Wen, 2009, Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells, Nat. Genet., 41, 246, 10.1038/ng.297 · DOI
- Wernig, 2008, c-Myc is dispensable for direct reprogramming of mouse fibroblasts, Cell Stem Cell, 2, 10, 10.1016/j.stem.2007.12.001 · DOI
- Xu, 2009, Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells, Genes Dev., 23, 2824, 10.1101/gad.1861209 · DOI
- Zhang, 2008, Model-based analysis of ChIP-Seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137 · DOI · Paper page
- Bernstein, B.E., Stamatoyannopoulos, J.A., Costello, J.F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M.A., Beaudet, A.L., Ecker, J.R., et al. (2010). The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol. 28, 1045–1048. · DOI · Paper page
- Cai, Z., Chattopadhyay, N., Liu, W.J., Chan, C., Pignol, J.P., and Reilly, R.M. (2011). Optimized digital counting colonies of clonogenic assays using ImageJ software and customized macros: comparison with manual counting. Int. J. Radiat. Biol. 87, 1135–1146. · DOI
- Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863–14868. · DOI · Paper page
- Hawkins, R.D., Hon, G.C., Lee, L.K., Ngo, Q., Lister, R., Pelizzola, M., Edsall, L.E., Kuan, S., Luu, Y., Klugman, S., et al. (2010). Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479–491. · DOI · Paper page
- Page, R.D. (1996). TreeView: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12, 357–358. · DOI
- Urlinger, S., Baron, U., Thellmann, M., Hasan, M.T., Bujard, H., and Hillen, W. (2000). Exploring the sequence space for tetracycline-dependent transcriptional activators: novel mutations yield expanded range and sensitivity. Proc. Natl. Acad. Sci. USA 97, 7963–7968. · DOI · Paper page
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Gao, Y., Chen, J., Li, K., Wu, T., Huang, B., Liu, W., Kou, X., Zhang, Y., Huang, H., Jiang, Y., et al. (2013) · Cell Stem Cell · doi:10.1016/j.stem.2013.02.005 · Cited by 362
Cai, Y., Zhang, Y., Loh, Y. P., Tng, J. Q., Lim, M. C., Cao, Z., Raju, A., Lieberman Aiden, E., Li, S., Manikandan, L., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-20940-y · Cited by 321
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Sridharan, R., Gonzales-Cope, M., Chronis, C., Bonora, G., McKee, R., Huang, C., Patel, S., Lopez, D., Mishra, N., Pellegrini, M., et al. (2013) · Nature Cell Biology · doi:10.1038/ncb2768 · Cited by 220
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Takaku, M., Grimm, S. A., Shimbo, T., Perera, L., Menafra, R., Stunnenberg, H. G., Archer, T. K., Machida, S., Kurumizaka, H., & Wade, P. A. (2016) · Genome Biology · doi:10.1186/s13059-016-0897-0 · Cited by 151
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Stelzer, Y., Shivalila, C. S., Soldner, F., Markoulaki, S., & Jaenisch, R. (2015) · Cell · doi:10.1016/j.cell.2015.08.046 · Cited by 141
Boxer, L. D., Barajas, B., Tao, S., Zhang, J., & Khavari, P. A. (2014) · Genes & Development · doi:10.1101/gad.246579.114 · Cited by 147
Abernathy, D. G., Kim, W. K., McCoy, M. J., Lake, A. M., Ouwenga, R., Lee, S. W., Xing, X., Li, D., Lee, H. J., Heuckeroth, R. O., et al. (2017) · Cell Stem Cell · doi:10.1016/j.stem.2017.08.002 · Cited by 145
Poetsch, M. S., Strano, A., & Guan, K. (2022) · Stem Cells · doi:10.1093/stmcls/sxac020 · Cited by 144
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Beagan, J. A., Gilgenast, T. G., Kim, J., Plona, Z., Norton, H. K., Hu, G., Hsu, S. C., Shields, E. J., Lyu, X., Apostolou, E., et al. (2016) · Cell Stem Cell · doi:10.1016/j.stem.2016.04.004 · Cited by 134
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“This is a hallmark of pioneering activity in developmental gene regulation (98, 108), but in this case it exposes a particularly intricate post-transcriptional relationship between PU.”
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Guerreiro, I., & Kind, J. (2019) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2019.04.008 · Cited by 59
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Lee, Q. Y., Mall, M., Chanda, S., Zhou, B., Sharma, K. S., Schaukowitch, K., Adrian-Segarra, J. M., Grieder, S. D., Kareta, M. S., Wapinski, O. L., et al. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0490-3 · Cited by 50
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Rand, T. A., Sutou, K., Tanabe, K., Jeong, D., Nomura, M., Kitaoka, F., Tomoda, E., Narita, M., Nakamura, M., Nakamura, M., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.057 · Cited by 37
Grindheim, J. M., Nicetto, D., Donahue, G., & Zaret, K. S. (2019) · Gastroenterology · doi:10.1053/j.gastro.2019.01.041 · Cited by 35
Self-citationCellular reprogramming in vivo initiated by SOX4 pioneer factor activity
Katsuda, T., Sussman, J. H., Ito, K., Katznelson, A., Yuan, S., Takenaka, N., Li, J., Merrell, A. J., Cure, H., Li, Q., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-45939-z · Cited by 33
Self-citationEpigenetic preparation of future gene induction kinetics
Xiong, J., & Zhu, B. (2025) · Annual Review of Genetics · doi:10.1146/annurev-genet-012825-093148 · Cited by 12
Metadata
- Authors
- Soufi, A., Donahue, G., & Zaret, K. S.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-11
- Volume
- 151
- Issue
- 5
- Pages
- 994-1004
- ISSN
- 0092-8674
- PMC
- PMC3508134
- Cited by
- 933
- References
- 10
- Language
- en
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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