The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Vitamin C Promotes Widespread Yet Specific DNA Demethylation of the Epigenome in Human Embryonic Stem Cells
Abstract
Vitamin C (ascorbate) is a widely used medium supplement in embryonic stem cell culture. Here, we show that ascorbate causes widespread, consistent, and remarkably specific DNA demethylation of 1,847 genes in human embryonic stem cells (hESCs), including important stem cell genes, with a clear bias toward demethylation at CpG island boundaries. We show that a subset of these DNA demethylated genes displays concomitant gene expression changes and that the position of the demethylated CpGs relative to the transcription start site is correlated to such changes. We further show that the ascorbate-demethylated gene set not only overlaps with gene sets that have bivalent marks, but also with the gene sets that are demethylated during differentiation of hESCs and during reprogramming of fibroblasts to induced pluritotent stem cells (iPSCs). Our data thus identify a novel link between ascorbate-mediated signaling and specific epigenetic changes in hESCs that might impact on pluripotency and reprogramming pathways.
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.
Integrity signals
Registry
Cites
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.
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
Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829
DAVID: Database for Annotation, Visualization, and Integrated Discovery
Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-5-p3 · Cited by 9,327
Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1
Tahiliani, M., Koh, K. P., Shen, Y., Pastor, W. A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L. M., Liu, D. R., Aravind, L., et al. (2009) · Science · doi:10.1126/science.1170116 · Cited by 5,836
Cited by
Chemically defined conditions for human iPSC derivation and culture
Chen, G., Gulbranson, D. R., Hou, Z., Bolin, J. M., Ruotti, V., Probasco, M. D., Smuga-Otto, K., Howden, S. E., Diol, N. R., Propson, N. E., et al. (2011) · Nature Methods · doi:10.1038/nmeth.1593 · Cited by 1,447
Ascorbic acid: Chemistry, biology and the treatment of cancer
Du, J., Cullen, J. J., & Buettner, G. R. (2012) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2012.06.003 · Cited by 1,070
Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells
Blaschke, K., Ebata, K. T., Karimi, M. M., Zepeda-Martínez, J. A., Goyal, P., Mahapatra, S., Tam, A., Laird, D. J., Hirst, M., Rao, A., et al. (2013) · Nature · doi:10.1038/nature12362 · Cited by 865
Restoration of TET2 Function Blocks Aberrant Self-Renewal and Leukemia Progression
Cimmino, L., Dolgalev, I., Wang, Y., Yoshimi, A., Martin, G. H., Wang, J., Ng, V., Xia, B., Witkowski, M. T., Mitchell-Flack, M., et al. (2017) · Cell · doi:10.1016/j.cell.2017.07.032 · Cited by 707
Yin, R., Mao, S.-Q., Zhao, B., Chong, Z., Yang, Y., Zhao, C., Zhang, D., Huang, H., Gao, J., Li, Z., et al. (2013) · Journal of the American Chemical Society · doi:10.1021/ja4028346 · Cited by 609
Interplay between Metabolism and Epigenetics: A Nuclear Adaptation to Environmental Changes
Etchegaray, J.-P., & Mostoslavsky, R. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.029 · Cited by 518
Wang, T., Chen, K., Zeng, X., Yang, J., Wu, Y., Shi, X., Qin, B., Zeng, L., Esteban, M. A., Pan, G., et al. (2011) · Cell Stem Cell · doi:10.1016/j.stem.2011.10.005 · Cited by 458
Minor, E. A., Court, B. L., Young, J. I., & Wang, G. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.c113.464800 · Cited by 413
Role of Vitamin C in the Function of the Vascular Endothelium
May, J. M., & Harrison, F. E. (2013) · Antioxidants & Redox Signaling · doi:10.1089/ars.2013.5205 · Cited by 358
Regulation of the epigenome by vitamin C
Young, J. I., Züchner, S., & Wang, G. (2015) · Annual Review of Nutrition · doi:10.1146/annurev-nutr-071714-034228 · Cited by 319
Stadtfeld, M., Apostolou, E., Ferrari, F., Choi, J., Walsh, R. M., Chen, T., Ooi, S. S. K., Kim, S. Y., Bestor, T. H., Shioda, T., et al. (2012) · Nature Genetics · doi:10.1038/ng.1110 · Cited by 238
Vitamin C increases viral mimicry induced by 5-aza-2′-deoxycytidine
Liu, M., Ohtani, H., Zhou, W., Ørskov, A. D., Charlet, J., Zhang, Y. W., Shen, H., Baylin, S. B., Liang, G., Grønbæk, K., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1612262113 · Cited by 225
Vitamin C in stem cell reprogramming and cancer
Cimmino, L., Neel, B. G., & Aifantis, I. (2018) · Trends in Cell Biology · doi:10.1016/j.tcb.2018.04.001 · Cited by 197
Metabolic Inputs into the Epigenome
Sharma, U., & Rando, O. J. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.02.003 · Cited by 167
Breathing-in epigenetic change with vitamin C
Monfort, A., & Wutz, A. (2013) · The EMBO Reports · doi:10.1038/embor.2013.29 · Cited by 140
Influence of Vitamin C on Lymphocytes: An Overview
Van Gorkom, G., Klein Wolterink, R., Van Elssen, C., Wieten, L., Germeraad, W., & Bos, G. (2018) · Antioxidants · doi:10.3390/antiox7030041 · Cited by 139
Reprogramming the epigenome with vitamin C
Lee Chong, T., Ahearn, E. L., & Cimmino, L. (2019) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2019.00128 · Cited by 120
Variability of human pluripotent stem cell lines
Ortmann, D., & Vallier, L. (2017) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2017.07.004 · Cited by 117
Myths, Artifacts, and Fatal Flaws: Identifying Limitations and Opportunities in Vitamin C Research
Michels, A., & Frei, B. (2013) · Nutrients · doi:10.3390/nu5125161 · Cited by 111
Vitamin C – A new player in regulation of the cancer epigenome
Gillberg, L., Ørskov, A. D., Liu, M., Harsløf, L. B. S., Jones, P. A., & Grønbæk, K. (2018) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2017.11.001 · Cited by 100
Dey, C., Raina, K., Haridhasapavalan, K. K., Thool, M., Sundaravadivelu, P. K., Adhikari, P., Gogoi, R., & Thummer, R. P. (2021) · Recent Advances in iPSC Technology · doi:10.1016/b978-0-12-822231-7.00011-4 · Cited by 23
Metadata
- Authors
- Chung, T.-L., Brena, R. M., Kolle, G., Grimmond, S. M., Berman, B. P., Laird, P. W., Pera, M. F., & Wolvetang, E. J.
- Venue
- Stem Cells
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-10-01
- Volume
- 28
- Issue
- 10
- Pages
- 1848-1855
- ISSN
- 1066-5099 (ISSN-L)
- 1549-4918
- OpenAlex
- W1991698857
- Cited by
- 182
- References
- 3
- FWCI
- 3.54
- Type
- journal article
- Language
- en
- Open access
- closed
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
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
