Cited by 436Pluripotent Stem Cells ResearchEpigenetics and DNA MethylationGenomics and Chromatin Dynamics

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Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

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Gifford, Casey A., Ziller, Michael J., Gu, Hongcang, Trapnell, Cole, Donaghey, Julie, Tsankov, Alexander, Shalek, Alex K., Kelley, David R., Shishkin, Alexander A., Issner, Robbyn, Zhang, Xiaolan, Coyne, Michael, Fostel, Jennifer L., Holmes, Laurie, Meldrim, Jim, Guttman, Mitchell, Epstein, Charles, Park, Hongkun, Kohlbacher, Oliver, Rinn, John, Gnirke, Andreas, Lander, Eric S., Bernstein, Bradley E., Meissner, Alexander·2013·Cell

DOI 10.1016/j.cell.2013.04.037PMC PMC3709577

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Abstract

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.

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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
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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Trapnell, 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
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Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682
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Numerical 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

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Grandi, F. C., Rosser, J. M., Newkirk, S. J., Yin, J., Jiang, X., Xing, Z., Whitmore, L. S., Bashir, S., Ivics, Z., Izsvák, Z., et al. (2015) · Genome Research · doi:10.1101/gr.185132.114 · Cited by 53
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Bian, Q., & Cahan, P. (2016) · Trends in biotechnology · doi:10.1016/j.tibtech.2016.05.010 · Cited by 46
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Esposito, A., Bianco, S., Chiariello, A. M., Abraham, A., Fiorillo, L., Conte, M., Campanile, R., & Nicodemi, M. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110601 · Cited by 47
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Oger, F., Dubois‐Chevalier, J., Gheeraert, C., Avner, S., Durand, E., Froguel, P., Salbert, G., Staels, B., Lefèbvre, P., & Eeckhoute, J. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.526996 · Cited by 42
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Yu, W., Briones, V. R., Lister, R., MCINTOSH, C. E., Han, Y., Lee, E. Y., Ren, J., Terashima, M., Leighty, R. M., Ecker, J. R., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1320945111 · Cited by 41
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Dvir, S., Argoetti, A., Lesnik, C., Roytblat, M., Shriki, K., Amit, M., Hashimshony, T., & Mandel‐Gutfreund, Y. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109198 · Cited by 39
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Giles, K. A., Phan, L., Clark, S. J., & Taberlay, P. C. (2014) · Epigenomics · doi:10.2217/epi.14.37 · Cited by 40
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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: Gifford, Casey A.
Ziller, Michael J.
Gu, Hongcang
Trapnell, Cole
Tsankov, Alexander
Shalek, Alex K.
Kelley, David R.
Issner, Robbyn
Zhang, Xiaolan
Coyne, Michael
Guttman, Mitchell
Epstein, Charles
Park, Hongkun
Kohlbacher, Oliver
Rinn, John
Gnirke, Andreas
Lander, Eric S.
Bernstein, Bradley E.
Meissner, Alexander
Venue: Cell
Publisher: Elsevier BV
Published: 2013-05
Volume: 153
Issue: 5
Pages: 1149-1163
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/j.cell.2013.04.037
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: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 387 d)
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

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Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

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