The DOI matches its Crossref record; 60 of the 60 references it cites were found in a registry or an index.
Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis
Open accessAbstract
Differentiation of mouse embryonic stem cells (mESCs) is accompanied by changes in replication timing. To explore the relationship between replication timing and cell fate transitions, we constructed genome-wide replication-timing profiles of 22 independent mouse cell lines representing 10 stages of early mouse development, and transcription profiles for seven of these stages. Replication profiles were cell-type specific, with 45% of the genome exhibiting significant changes at some point during development that were generally coordinated with changes in transcription. Comparison of early and late epiblast cell culture models revealed a set of early-to-late replication switches completed at a stage equivalent to the post-implantation epiblast, prior to germ layer specification and down-regulation of key pluripotency transcription factors [POU5F1 (also known as OCT4)/NANOG/SOX2] and coinciding with the emergence of compact chromatin near the nuclear periphery. These changes were maintained in all subsequent lineages (lineage-independent) and involved a group of irreversibly down-regulated genes, at least some of which were repositioned closer to the nuclear periphery. Importantly, many genomic regions of partially reprogrammed induced pluripotent stem cells (piPSCs) failed to re-establish ESC-specific replication-timing and transcription programs. These regions were enriched for lineage-independent early-to-late changes, which in female cells included the inactive X chromosome. Together, these results constitute a comprehensive “fate map” of replication-timing changes during early mouse development. Moreover, they support a model in which a distinct set of replication domains undergoes a form of “autosomal Lyonization” in the epiblast that is difficult to reprogram and coincides with an epigenetic commitment to differentiation prior to germ layer specification.
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Cites
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
Open source clustering software
de Hoon, M. J. L., Imoto, S., Nolan, J., & Miyano, S. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth078 · Cited by 3,043
Java Treeview—extensible visualization of microarray data
Saldanha, A. J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth349 · Cited by 2,991
Weber, M., Hellmann, I., Stadler, M. B., Ramos, L., Pääbo, S., Rebhan, M., & Schübeler, D. (2007) · Nature Genetics · doi:10.1038/ng1990 · Cited by 2,221
New cell lines from mouse epiblast share defining features with human embryonic stem cells
Tesar, P. J., Chenoweth, J. G., Brook, F. A., Davies, T. J., Evans, E. P., Mack, D. L., Gardner, R. L., & McKay, R. D. G. (2007) · Nature · doi:10.1038/nature05972 · Cited by 2,152
Derivation of pluripotent epiblast stem cells from mammalian embryos
Brons, I. G. M., Smithers, L. E., Trotter, M. W. B., Rugg-Gunn, P., Sun, B., Chuva de Sousa Lopes, S. M., Howlett, S. K., Clarkson, A., Ahrlund-Richter, L., Pedersen, R. A., et al. (2007) · Nature · doi:10.1038/nature05950 · Cited by 2,007
Maherali, N., Sridharan, R., Xie, W., Utikal, J., Eminli, S., Arnold, K., Stadtfeld, M., Yachechko, R., Tchieu, J., Jaenisch, R., et al. (2007) · Cell stem cell · doi:10.1016/j.stem.2007.05.014 · Cited by 1,725
Self-citationNanog safeguards pluripotency and mediates germline development
Chambers, I., Silva, J., Colby, D., Nichols, J., Nijmeijer, B., Robertson, M., Vrana, J., Jones, K., Grotewold, L., & Smith, A. (2007) · Nature · doi:10.1038/nature06403 · Cited by 1,500
Beyond the Sequence: Cellular Organization of Genome Function
Misteli, T. (2007) · Cell · doi:10.1016/j.cell.2007.01.028 · Cited by 1,148
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Guo, G., Yang, J., Nichols, J., Hall, J. S., Eyres, I., Mansfield, W., & Smith, A. (2009) · Development · doi:10.1242/dev.030957 · Cited by 765
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A comparative encyclopedia of DNA elements in the mouse genome
Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., et al. (2014) · Nature · doi:10.1038/nature13992 · Cited by 1,781
Self-citationMultiscale 3D Genome Rewiring during Mouse Neural Development
Bonev, B., Mendelson Cohen, N., Szabo, Q., Fritsch, L., Papadopoulos, G. L., Lubling, Y., Xu, X., Lv, X., Hugnot, J.-P., Tanay, A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.043 · Cited by 1,338
Ryba, T., Hiratani, I., Lu, J., Itoh, M., Kulik, M., Zhang, J., Schulz, T. C., Robins, A. J., Dalton, S., & Gilbert, D. M. (2010) · Genome Research · doi:10.1101/gr.099655.109 · Cited by 621
Self-citationDNA replication origin activation in space and time
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Metadata
- Authors
- Hiratani, I., Ryba, T., Itoh, M., Rathjen, J., Kulik, M., Papp, B., Fussner, E., Bazett-Jones, D. P., Plath, K., Dalton, S., Rathjen, P. D., & Gilbert, D. M.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2009-12-01
- Volume
- 20
- Issue
- 2
- Pages
- 155-169
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2157251845
- Cited by
- 323
- References
- 60
- Type
- posted content
- Language
- en
- Open access
- bronze
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