CoChat
Sign Up
Cited by 43

The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.

OCT4 and SOX2 Work as Transcriptional Activators in Reprogramming Human Fibroblasts

Narayan, Santosh, Bryant, Gene, Shah, Shivangi, Berrozpe, Georgina, Ptashne, Mark·2017·Cell Reports
DOI 10.1016/j.celrep.2017.07.071PMC PMC5648000
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.celrep.2017.07.071

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • In mouse embryonic fibroblasts (MEFs), OCT4 binds somatic enhancers during reprogramming and may initiate their inactivation, whereas in human fetal fibroblasts, OCT4 and SOX2 bind putative enhancers and remain bound in iPS cells.

    “Specifically, in mouse embryonic fibroblasts (MEFs), OCT4 binds somatic enhancers during reprogramming and may initiate their inactivation, whereas in human fetal fibroblasts, OCT4 and SOX2 bind putative enhancers and remain bound in iPS cells.”

    From Mechanisms, pathways and strategies for rejuvenation through epigenetic reprogramming (2023) · cites this paper as [82]

    The Discussion (OCT4 and SOX2 work as activators during reprogramming; page unavailable) reports that Chronis et al. suggested OCT4 may initiate inactivation of pre-existing fibroblast enhancers, but does not identify those cells as MEFs. The Results (Putative enhancers at sites of bound transcription factors; page unavailable) confirm that OCT4 and SOX2 bind putative enhancers in day-5 human cells and iPS cells. The Discussion (Transcription factor repositioning; page unavailable) says most binding sites differ between those stages, so the claim is supported only if ‘remain bound’ means binding enhancers in iPS cells, not remaining at the same sites. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • Distinct mechanisms observed among combinations of OCT4 and SOX2 (without KLF4) versus OSK may explain the controversy regarding whether OSK mainly function as pioneer factors or bind readily open chromatin in early reprogramming, or both.

    “The distinct mechanisms observed among combinations of OCT4 and SOX2 (without KLF4) versus OSK may explain the controversy regarding whether OSK mainly function as the pioneer factors or bind readily open chromatin in early reprogramming, or both 80,82,83,85 .”

    From Mechanisms, pathways and strategies for rejuvenation through epigenetic reprogramming (2023) · cites this paper as [82]

    The Results section (‘Putative enhancers at sites of bound transcription factors’; page unavailable) reports that OCT4 and SOX2 often bound sites where new putative enhancers formed, whereas KLF4-bound enhancers were almost all pre-existing. This supports a distinction between the factors in early reprogramming, but the paper does not compare an OCT4–SOX2 combination without KLF4 against OSK or establish that such a comparison explains the pioneer-factor controversy. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

  • OSK factors interact with the genome and each other differently in mice than in human cells.

    “OSK factors interact with the genome and each other differently in mice than in human cells [80][81][82] , complicating the design and interpretation of studies.”

    From Mechanisms, pathways and strategies for rejuvenation through epigenetic reprogramming (2023) · cites this paper as [82]

    The Results (‘Changing locations of DNA bound factors’; page not available) describe OCT4 and SOX2 binding to DNA and co-binding in human cells. The paper does not compare those interactions—or KLF4’s—with mouse cells, so it does not support the claimed mouse–human difference. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 42

  1. Adewumi, 2007, Characterization of human embryonic stem cell lines by the International Stem Cell Initiative, Nat. Biotechnol., 25, 803, 10.1038/nbt1318 · DOI
  2. Barski, 2007, High-resolution profiling of histone methylations in the human genome, Cell, 129, 823, 10.1016/j.cell.2007.05.009 · DOI · Paper page
  3. Berrozpe, 2006, A distant upstream locus control region is critical for expression of the Kit receptor gene in mast cells, Mol. Cell. Biol., 26, 5850, 10.1128/MCB.01854-05 · DOI
  4. Berrozpe, 2013, Regulation of a mammalian gene bearing a CpG island promoter and a distal enhancer, Cell Rep., 4, 445, 10.1016/j.celrep.2013.07.001 · DOI
  5. Birney, 2007, Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature, 447, 799, 10.1038/nature05874 · DOI · Paper page
  6. Boyer, 2005, Core transcriptional regulatory circuitry in human embryonic stem cells, Cell, 122, 947, 10.1016/j.cell.2005.08.020 · DOI · Paper page
  7. Cacchiarelli, 2015, Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency, Cell, 162, 412, 10.1016/j.cell.2015.06.016 · DOI
  8. Calo, 2013, Modification of enhancer chromatin: what, how, and why?, Mol. Cell, 49, 825, 10.1016/j.molcel.2013.01.038 · DOI · Paper page
  9. Chew, 2005, Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells, Mol. Cell. Biol., 25, 6031, 10.1128/MCB.25.14.6031-6046.2005 · DOI
  10. Do, 2009, Regulatory circuits underlying pluripotency and reprogramming, Trends Pharmacol. Sci., 30, 296, 10.1016/j.tips.2009.03.003 · DOI
  11. Golipour, 2012, A late transition in somatic cell reprogramming requires regulators distinct from the pluripotency network, Cell Stem Cell, 11, 769, 10.1016/j.stem.2012.11.008 · DOI
  12. Hammachi, 2012, Transcriptional activation by Oct4 is sufficient for the maintenance and induction of pluripotency, Cell Rep., 1, 99, 10.1016/j.celrep.2011.12.002 · DOI
  13. Heintzman, 2007, Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome, Nat. Genet., 39, 311, 10.1038/ng1966 · DOI · Paper page
  14. Hirai, 2011, Radical acceleration of nuclear reprogramming by chromatin remodeling with the transactivation domain of MyoD, Stem Cells, 29, 1349, 10.1002/stem.684 · DOI
  15. Inoue, 2017, A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity, Genome Res., 27, 38, 10.1101/gr.212092.116 · DOI · Paper page
  16. Jaenisch, 2008, Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming, Cell, 132, 567, 10.1016/j.cell.2008.01.015 · DOI
  17. Kim, 2008, An extended transcriptional network for pluripotency of embryonic stem cells, Cell, 132, 1049, 10.1016/j.cell.2008.02.039 · DOI
  18. Loh, 2006, The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells, Nat. Genet., 38, 431, 10.1038/ng1760 · DOI
  19. Martello, 2014, The nature of embryonic stem cells, Annu. Rev. Cell Dev. Biol., 30, 647, 10.1146/annurev-cellbio-100913-013116 · DOI
  20. Müller, 1990, Transcriptional enhancers can act in trans, Trends Genet., 6, 300, 10.1016/0168-9525(90)90236-Y · DOI
  21. 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
  22. Park, 2008, Reprogramming of human somatic cells to pluripotency with defined factors, Nature, 451, 141, 10.1038/nature06534 · DOI · Paper page
  23. Paull, 2015, Automated, high-throughput derivation, characterization and differentiation of induced pluripotent stem cells, Nat. Methods, 12, 885, 10.1038/nmeth.3507 · DOI · Paper page
  24. Perry, 2011, Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo, Proc. Natl. Acad. Sci. USA, 108, 13570, 10.1073/pnas.1109873108 · DOI · Paper page
  25. Rodda, 2005, Transcriptional regulation of nanog by OCT4 and SOX2, J. Biol. Chem., 280, 24731, 10.1074/jbc.M502573200 · DOI
  26. Rohani, 2014, The aging signature: a hallmark of induced pluripotent stem cells?, Aging Cell, 13, 2, 10.1111/acel.12182 · DOI
  27. Sadowski, 1988, GAL4-VP16 is an unusually potent transcriptional activator, Nature, 335, 563, 10.1038/335563a0 · DOI
  28. Shlyueva, 2014, Transcriptional enhancers: from properties to genome-wide predictions, Nat. Rev. Genet., 15, 272, 10.1038/nrg3682 · DOI · Paper page
  29. Sridharan, 2009, Role of the murine reprogramming factors in the induction of pluripotency, Cell, 136, 364, 10.1016/j.cell.2009.01.001 · DOI
  30. Stergachis, 2013, Developmental fate and cellular maturity encoded in human regulatory DNA landscapes, Cell, 154, 888, 10.1016/j.cell.2013.07.020 · DOI
  31. Studer, 2015, Programming and Reprogramming Cellular Age in the Era of Induced Pluripotency, Cell Stem Cell, 16, 591, 10.1016/j.stem.2015.05.004 · DOI
  32. 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
  33. 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
  34. Theunissen, 2014, Molecular control of induced pluripotency, Cell Stem Cell, 14, 720, 10.1016/j.stem.2014.05.002 · DOI
  35. Triezenberg, 1988, Evidence of DNA: protein interactions that mediate HSV-1 immediate early gene activation by VP16, Genes Dev., 2, 730, 10.1101/gad.2.6.730 · DOI
  36. Wang, 2011, Reprogramming of mouse and human somatic cells by high-performance engineered factors, EMBO Rep., 12, 373, 10.1038/embor.2011.11 · DOI
  37. 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
  38. Worringer, 2014, The let-7/LIN-41 pathway regulates reprogramming to human induced pluripotent stem cells by controlling expression of prodifferentiation genes, Cell Stem Cell, 14, 40, 10.1016/j.stem.2013.11.001 · DOI
  39. Yu, 2007, Induced pluripotent stem cell lines derived from human somatic cells, Science, 318, 1917, 10.1126/science.1151526 · DOI · Paper page
  40. Yuan, 1995, Developmental-specific activity of the FGF-4 enhancer requires the synergistic action of Sox2 and Oct-3, Genes Dev., 9, 2635, 10.1101/gad.9.21.2635 · DOI
  41. Zhou, 2011, Charting histone modifications and the functional organization of mammalian genomes, Nat. Rev. Genet., 12, 7, 10.1038/nrg2905 · DOI · Paper page
  42. Zunder, 2015, A continuous molecular roadmap to iPSC reprogramming through progression analysis of single-cell mass cytometry, Cell Stem Cell, 16, 323, 10.1016/j.stem.2015.01.015 · DOI

Cited by

Sorted by citations

Metadata

Authors
Narayan, S., Bryant, G., Shah, S., Berrozpe, G., & Ptashne, M.
Venue
Cell Reports
Publisher
Elsevier BV
Published
2017-08
Volume
20
Issue
7
Pages
1585-1596
ISSN
2211-1247
DOI
10.1016/j.celrep.2017.07.071
PMC
PMC5648000
Cited by
43
References
6
Language
en
Licence
Funders
  • NYSTEM (C029153, N09G-217, N11G-262)
  • MSKCC Support Grant/Core Grant (P30 CA008748)

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 ›

Are you an author, or do you see a problem with this page? Request a review