The DOI matches its Crossref record; 61 of the 61 references it cites were found in a registry or an index.
Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells
Open accessAbstract
Differentiation of human embryonic stem cells (hESCs) provides a unique opportunity to study the regulatory mechanisms that facilitate cellular transitions in a human context. To that end, we performed comprehensive transcriptional and epigenetic profiling of populations derived through directed differentiation of hESCs representing each of the three embryonic germ layers. Integration of whole-genome bisulfite sequencing, chromatin immunoprecipitation sequencing, and RNA sequencing reveals unique events associated with specification toward each lineage. Lineage-specific dynamic alterations in DNA methylation and H3K4me1 are evident at putative distal regulatory elements that are frequently bound by pluripotency factors in the undifferentiated hESCs. In addition, we identified germ-layer-specific H3K27me3 enrichment at sites exhibiting high DNA methylation in the undifferentiated state. A better understanding of these initial specification events will facilitate identification of deficiencies in current approaches, leading to more faithful differentiation strategies as well as providing insights into the rewiring of human regulatory programs during cellular transitions.
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.
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?
The cited source says what the claim attributes to it.
In the citing paper
“Therefore, methylation of CpG sites is an essential component of cell type-specific gene regulation, a fundamental mark of cell identity [12, 16, 41]”
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
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
Self-citationTrapnell, C., Roberts, A., Goff, L. A., Pertea, G. M., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 12,145
Self-citationTopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682
Self-citationNumerical Recipes, The Art of Scientific Computing
Press, W. H., Flannery, B. P., Teukolsky, S. A., Vetterling, W. T., & Gould, H. (1987) · American Journal of Physics · doi:10.1119/1.14981 · Cited by 10,032
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049
Numerical Recipes: The Art of Scientific Computing
Ziegel, E. R., Press, W. H., Flannery, B. P., Teukolsky, S. A., & Vetterling, W. T. (1987) · Technometrics · doi:10.2307/1269484 · Cited by 6,704
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
Histone H3K27ac separates active from poised enhancers and predicts developmental state
Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016071107 · Cited by 4,302
FIMO: scanning for occurrences of a given motif
Grant, C. E., Bailey, T. L., & Noble, W. S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr064 · Cited by 4,247
Flagged first, then by citations
Research works printed but not linked: 1
- Press, 2007
Cited by
Sorted by citations
Items 401–436 of 436
Analysis of spatiotemporal specificity of small RNAs regulating hPSC differentiation and beyondPreprint
Li, L., Li, J. F., Cao, D., Papadopoulos, V., & Chan, W. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/784819
Mattioli, K., Oliveros, W., Gerhardinger, C., Andergassen, D., Maass, P., Rinn, J., & Melé, M. (2019) · bioRxiv · doi:10.1101/847491
Self-citationInvestigating prenatal stress in a stem cell model of human neuronal development
Papst, L. (2019) · Elektronische Hochschulschriften der LMU München (Ludwig-Maximilians-Universität München) · doi:10.5282/edoc.25120
Epigenetic Regulation of Open Chromatin in Pluripotent Stem Cells
Kobayashi, H., Lowe, M., & Kikyo, N. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-800802-7.00001-0
Markouli, C., de Deckersberg, E. C., Dziedzicka, D., Regin, M., Franck, S., Keller, A., Gheldof, A., Geens, M., Sermon, K., & Spits, C. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.04.133496
Kim, S., Seo, S., Stein-O’Brien, G., Jaishankar, A., Ogawa, K., Micali, N., Luria, V. A., Karger, A., Wang, Y., Hyde, T. M., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.17.435870
Coulombe, B. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.727609300.793581674
Deschamps, J., & Neijts, R. (2014) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.718215518.793489889
Tiwari, V. K., & Mariappan, A. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.737245346.793573115
Epigenetic Regulation of Stem Cells
Mozzetta, C. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-821618-7.00258-3
Chen, S., Yan, X., Zhou, G., & Zhu, C. H. (2022) · Wiley eBooks · doi:10.1002/9781119000822.hfcm011.pub2
Matsui, S., Granitto, M., Buckley, M., Shiley, J. R., Zacharias, W. J., Mayhew, C. N., Lim, H., & Iwafuchi, M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.29.522251
Unlocking cross-modal interplay of single-cell and spatial joint profiling with CellMATEPreprint
Wang, Q., Zhang, B., Gong, L., Guo, Y., Li, E., & Yang, J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.06.610031
Ye, Z., Jiang, Y., Yang, H., Huang, Y., Wang, S., Han, S., & Ma, L. (2025) · Health engineering. · doi:10.26599/he.2025.9460007
Modulating RNA condensates to control cell fate
Love, K. S., & Galloway, K. E. (2025) · Nature Biotechnology · doi:10.1038/s41587-025-02936-x
Dnmt3a2 expression during embryonic development is required for phenotypic stability
Liu, M., Urrutia, G., Shereda, R., Hostetter, G. H., Thomas, S. L., Liang, G., & Jones, P. A. (2025) · Communications Biology · doi:10.1038/s42003-025-09311-1 · Cited by 2
Yang, Q., Zhu, X., Liu, Y., He, Z., Xu, H., Zheng, H., Huang, Z., Wang, D., Lin, X., Guo, P., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25303145
Yang, Q., Zhu, X., Liu, Y., He, Z., Xu, H., Zheng, H., Huang, Z., Wang, D., Lin, X., Guo, P., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25303091
Zhou, B., Stueve, T. R., Mihalakakos, E. A., Miao, L., MULLEN, D. G., Wang, Y., Liu, Y., Luo, J., Tran, E., Siegmund, K. D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.17283993
Chen, B., Gan, C., Chen, S., Guo, D., Liang, G., Fang, X., Zhu, H., Deng, Z., Tang, Q., Xiao, Y., et al. (2026) · Plants · doi:10.3390/plants15050783
Role of PRC2 complexes in the regulation of cell differentiation during Arabidopsis root development
Morao, A. K. (2017) · theses.fr (ABES) · doi:10.70675/ceeb1d23z53a2z4d5fza34bzb49a202f3e5e
Laaref, A. M. (2017) · theses.fr (ABES) · doi:10.70675/c2cfd784z5dd2z47cez9ddcz4ee6e8af424e
GNAS et empreinte parentale : Caractérisation des GNAS-miRNAs et d’une nouvelle DMR
Hanna, P. (2018) · theses.fr (ABES) · doi:10.70675/f26357c5za41ez4af0zae5cz15644b8246db
Aditya, C. (2021) · theses.fr (ABES) · doi:10.70675/f72a0de8z9c92z4acfzb0c0z1849be9dcdcb
Critical and different roles of DNA methylation in male germ cell development
Dura, M. (2021) · theses.fr (ABES) · doi:10.70675/a86104ccz3d42z4526za2bczff2519550eda
Sicilia, A., Scialò, E., Catara, V., Dimaria, G., Malfa, S. L., & Piero, A. R. L. (2026) · Acta Horticulturae · doi:10.17660/actahortic.2026.1454.32
Epigenomic regulation of neural crest differentiation in human-induced pluripotent stem cells
Mukae, K., Shindo, M., Shi, T., Onuki, R., Yamashita, S., Hattori, N., Ushijima, T., Ohira, M., & Kamijo, T. (2026) · iScience · doi:10.1016/j.isci.2026.115993
Physics-Based Modeling of Sparse Single-Cell Hi-C Uncovers Structural and Epigenetic Variability
Vercellone, F., Kundu, S., Esposito, A., Chiariello, A. M., Conte, M., Abraham, A., Fontana, A., Pierno, F. D., Guha, S., Carluccio, C. D., et al. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27114803
Telomerase RNA regulates the epigenome primed for human lineage commitmentPreprint
Li, J., Su, P., Gao, M., Liu, C., Li, N., Feng, G., Yu, Y., Chen, Z. Q., Yin, G., Ye, X., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.03.736284
Yuan, Z., Zhang, W.-X., Su, X., Li, Z.-H., Zhang, J., Miao, L.-L., Wei, H., Wang, Z.-H., Chu, Y.-G., & Ding, C. (2026) · Forestry Research · doi:10.48130/forres-0026-0025
Zhang, J., Gao, S., & Kong, Q. (2026) · Trends Open · doi:10.1016/j.treopn.2026.08.011
An exploration of the mouse epigenome at metaphase and interphase during embryonic differentiation
Bowker, R. M. (2015) · University of Birmingham Institutional Research Archive (University of Birmingham)
ChIP-BS-Sequencing in Cancer Epigenomics
Natarajan, K., & Gao, F. (2015) · Springer eBooks · doi:10.1007/978-3-319-15811-2_12
Paternal Effects on Metabolism in Mammals: A Dissertation
Shea, J. M. (2015) · eScholarship@UMassChan · doi:10.13028/m27s3c
Metadata
- Authors
- Gifford, C. A., Ziller, M. J., Gu, H., Trapnell, C., Donaghey, J., Tsankov, A., Shalek, A. K., Kelley, D. R., Shishkin, A. A., Issner, R., Zhang, X., Coyne, M., Fostel, J. L., Holmes, L., Meldrim, J., Guttman, M., Epstein, C., Park, H., Kohlbacher, O., Rinn, J., Gnirke, A., Lander, E. S., Bernstein, B. E., & Meissner, A.
- Affiliations
- Broad Institute (US)
- Harvard University (US)
- Quantitative Biology Center (DE)
- Corresponding author
- Meissner, Alexander
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2013-05
- Volume
- 153
- Issue
- 5
- Pages
- 1149-1163
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3709577
- OpenAlex
- W2129924706
- Cited by
- 435
- References
- 61
- Citations by year
- 2026: 11 · 2025: 10 · 2024: 22 · 2023: 17 · 2022: 22 · 2021: 38 · 2020: 28 · 2019: 36 · 2018: 31 · 2017: 40 · 2016: 48 · 2015: 61 · 2014: 51 · 2013: 18
- FWCI
- 26.60
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Funders
- National Institute of General Medical Sciences (P01GM099117)
- National Institute of Diabetes and Digestive and Kidney Diseases (F32DK095537)
- National Institute of Environmental Health Sciences (U01ES017155)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- human embryonic stem cells, directed differentiation, germ layer specification, DNA methylation, H3K4me1, H3K27me3, distal regulatory elements, pluripotency factors, chromatin regulation, epigenetic regulation, transcriptional regulation
- MeSH terms
- Acetylation, Cell Differentiation, Chromatin, Enhancer Elements, Genetic, Histones, Humans, Methylation, Transcription, Genetic, DNA Methylation, Epigenesis, Genetic, Embryonic Stem Cells
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
