Cited by 171

The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.

Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming

Taberlay, Phillippa C., Kelly, Theresa K., Liu, Chun-Chi, You, Jueng Soo, De Carvalho, Daniel D., Miranda, Tina B., Zhou, Xianghong J., Liang, Gangning, Jones, Peter A.·2011·Cell

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.cell.2011.10.040

Cites

11 of 11 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?

  • OCT4 directly binds enhancers of Polycomb group-repressed genes to induce conversion of their associated promoters from monovalent to bivalent domains.

    “Second, OCT4 directly binds enhancers of Polycomb group-repressed genes, which modify histones and silence target genes, to induce conversion of their associated promoters from monovalent to bivalent domains 40,41 .”

    From Mechanisms, pathways and strategies for rejuvenation through epigenetic reprogramming (2023) · cites this paper as [40]

    The Results section reports OCT4 occupancy at the MYOD1 enhancer before the MYOD1 promoter acquired a bivalent signature. But the Discussion says OCT4 may establish bivalency directly or may act through indirect global changes; the experiment does not establish a direct causal mechanism across Polycomb-repressed genes generally. (LLM, conf=0.88)

    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: 40

  1. Asakura, 1995, The regulation of MyoD gene expression: conserved elements mediate expression in embryonic axial muscle, Dev. Biol., 171, 386, 10.1006/dbio.1995.1290 · DOI
  2. Atchison, 1988, Complementation between two cell lines lacking kappa enhancer activity: implications for the developmental control of immunoglobulin transcription, EMBO J., 7, 4213, 10.1002/j.1460-2075.1988.tb03318.x · DOI
  3. Azuara, 2006, Chromatin signatures of pluripotent cell lines, Nat. Cell Biol., 8, 532, 10.1038/ncb1403 · DOI
  4. Boukamp, 1992, Progressive stages of “transdifferentiation” from epidermal to mesenchymal phenotype induced by MyoD1 transfection, 5-aza-2′-deoxycytidine treatment, and selection for reduced cell attachment in the human keratinocyte line HaCaT, J. Cell Biol., 116, 1257, 10.1083/jcb.116.5.1257 · DOI
  5. Carnac, 1992, 3,5,3′-Triiodothyronine positively regulates both MyoD1 gene transcription and terminal differentiation in C2 myoblasts, Mol. Endocrinol., 6, 1185
  6. Creyghton, 2008, H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment, Cell, 135, 649, 10.1016/j.cell.2008.09.056 · DOI
  7. Creyghton, 2010, Histone H3K27ac separates active from poised enhancers and predicts developmental state, Proc. Natl. Acad. Sci. USA, 107, 21931, 10.1073/pnas.1016071107 · DOI · Paper page
  8. Daley, 2011, Reprogramming: What's Unknown?, Cell, 145, 811, 10.1016/j.cell.2011.05.035 · DOI
  9. Dekker, 2006, The three ‘C’ s of chromosome conformation capture: controls, controls, controls, Nat. Methods, 3, 17, 10.1038/nmeth823 · DOI
  10. Faerman, 1995, The distal human myoD enhancer sequences direct unique muscle-specific patterns of lacZ expression during mouse development, Dev. Biol., 171, 27, 10.1006/dbio.1995.1257 · DOI
  11. Gal-Yam, 2008, Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line, Proc. Natl. Acad. Sci. USA, 105, 12979, 10.1073/pnas.0806437105 · DOI
  12. Goldhamer, 1995, Embryonic activation of the myoD gene is regulated by a highly conserved distal control element, Development, 121, 637, 10.1242/dev.121.3.637 · DOI
  13. Hinshelwood, 2009, Aberrant de novo methylation of the p16INK4A CpG island is initiated post gene silencing in association with chromatin remodelling and mimics nucleosome positioning, Hum. Mol. Genet., 18, 3098, 10.1093/hmg/ddp251 · DOI
  14. Hollenberg, 1993, Use of a conditional MyoD transcription factor in studies of MyoD trans-activation and muscle determination, Proc. Natl. Acad. Sci. USA, 90, 8028, 10.1073/pnas.90.17.8028 · DOI
  15. Jin, 2009, H3.3/H2A.Z double variant-containing nucleosomes mark ‘nucleosome-free regions’ of active promoters and other regulatory regions, Nat. Genet., 41, 941, 10.1038/ng.409 · DOI
  16. Kablar, 1997, MyoD and Myf-5 differentially regulate the development of limb versus trunk skeletal muscle, Development, 124, 4729, 10.1242/dev.124.23.4729 · DOI
  17. Kablar, 1999, Myogenic determination occurs independently in somites and limb buds, Dev. Biol., 206, 219, 10.1006/dbio.1998.9126 · DOI
  18. Kelly, 2010, H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes, Mol. Cell, 39, 901, 10.1016/j.molcel.2010.08.026 · DOI
  19. Koch, 2007, The landscape of histone modifications across 1% of the human genome in five human cell lines, Genome Res., 17, 691, 10.1101/gr.5704207 · DOI
  20. Lassar, 1986, Transfection of a DNA locus that mediates the conversion of 10T1/2 fibroblasts to myoblasts, Cell, 47, 649, 10.1016/0092-8674(86)90507-6 · DOI
  21. Lepikhov, 2004, Differential dynamics of histone H3 methylation at positions K4 and K9 in the mouse zygote, BMC Dev. Biol., 4, 12, 10.1186/1471-213X-4-12 · DOI
  22. Lin, 2007, Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island, Cancer Cell, 12, 432, 10.1016/j.ccr.2007.10.014 · DOI
  23. MacIsaac, 2010, A quantitative model of transcriptional regulation reveals the influence of binding location on expression, PLoS Comput. Biol., 6, e1000773, 10.1371/journal.pcbi.1000773 · DOI
  24. Maherali, 2007, Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution, Cell Stem Cell, 1, 55, 10.1016/j.stem.2007.05.014 · DOI · Paper page
  25. Miele, 2009, Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C), Methods Mol. Biol., 464, 105, 10.1007/978-1-60327-461-6_7 · DOI
  26. Pinset, 1988, Control of myogenesis in the mouse myogenic C2 cell line by medium composition and by insulin: characterization of permissive and inducible C2 myoblasts, Differentiation, 38, 28, 10.1111/j.1432-0436.1988.tb00588.x · DOI
  27. Raney, 2011, ENCODE whole-genome data in the UCSC genome browser (2011 update), Nucleic Acids Res., 39, D871, 10.1093/nar/gkq1017 · DOI
  28. Rideout, 2001, Nuclear cloning and epigenetic reprogramming of the genome, Science, 293, 1093, 10.1126/science.1063206 · DOI
  29. Schmidt, 2010, A CTCF-independent role for cohesin in tissue-specific transcription, Genome Res., 20, 578, 10.1101/gr.100479.109 · DOI
  30. Schmitges, 2011, Histone methylation by PRC2 is inhibited by active chromatin marks, Mol. Cell, 42, 330, 10.1016/j.molcel.2011.03.025 · DOI
  31. Schreiber, 1989, Rapid detection of octamer binding proteins with ‘mini-extracts’, prepared from a small number of cells, Nucleic Acids Res., 17, 6419, 10.1093/nar/17.15.6419 · DOI
  32. Stamatoyannopoulos, 2006, Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays, Nat. Methods, 3, 511, 10.1038/nmeth890 · DOI
  33. 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
  34. 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
  35. Tapscott, 1992, A novel myoblast enhancer element mediates MyoD transcription, Mol. Cell. Biol., 12, 4994
  36. Weintraub, 1989, Activation of muscle-specific genes in pigment, nerve, fat, liver, and fibroblast cell lines by forced expression of MyoD, Proc. Natl. Acad. Sci. USA, 86, 5434, 10.1073/pnas.86.14.5434 · DOI
  37. Wolff, 2010, Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer, PLoS Genet., 6, e1000917, 10.1371/journal.pgen.1000917 · DOI
  38. Xi, 2007, Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome, PLoS Genet., 3, e136, 10.1371/journal.pgen.0030136 · DOI
  39. You, 2011, OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes, Proc. Natl. Acad. Sci. USA, 108, 14497, 10.1073/pnas.1111309108 · DOI · Paper page
  40. Robinson, J.T., Thorvaldsdottir, H., Winckler, W., Guttman, M., Lander, E.S., Getz, G., and Mesirov, J.P. (2011). Integrative genomics viewer. Nat. Biotechnol. 29, 24–26. · DOI · Paper page

Cited by

Sorted by citations

Metadata

Authors
Taberlay, P. C., Kelly, T. K., Liu, C.-C., You, J. S., De Carvalho, D. D., Miranda, T. B., Zhou, X. J., Liang, G., & Jones, P. A.
Venue
Cell
Publisher
Elsevier BV
Published
2011-12
Volume
147
Issue
6
Pages
1283-1294
ISSN
0092-8674
Cited by
171
References
11
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 ›

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