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Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes
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SUMMARY Cellular-state information between generations of developing cells may be propagated via regulatory regions. We report consistent patterns of gain and loss of DNase I-hypersensitive sites (DHSs) as cells progress from embryonic stem cells (ESCs) to terminal fates. DHS patterns alone convey rich information about cell fate and lineage relationships distinct from information conveyed by gene expression. Developing cells share a proportion of their DHS landscapes with ESCs; that proportion decreases continuously in each cell type as differentiation progresses, providing a quantitative benchmark of developmental maturity. Developmentally stable DHSs densely encode binding sites for transcription factors involved in autoregulatory feedback circuits. In contrast to normal cells, cancer cells extensively reactivate silenced ESC DHSs and those from developmental programs external to the cell lineage from which the malignancy derives. Our results point to changes in regulatory DNA landscapes as quantitative indicators of cell-fate transitions, lineage relationships, and dysfunction.
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Citations
Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
On computable numbers, with an application to the entscheidungsproblem
Turing, A. M. (1937) · Proceedings of the London Mathematical Society · doi:10.1112/plms/s2-42.1.230 · Cited by 8,283
DNA methylation patterns and epigenetic memory
Bird, A. (2002) · Genes & Development · doi:10.1101/gad.947102 · Cited by 7,124
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361
The accessible chromatin landscape of the human genome
Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012) · Nature · doi:10.1038/nature11232 · Cited by 2,679
Self-citationHuman cardiovascular progenitor cells develop from a KDR+ embryonic-stem-cell-derived population
Yang, L., Soonpaa, M. H., Adler, E. D., Roepke, T. K., Kattman, S. J., Kennedy, M., Henckaerts, E., Bonham, K., Abbott, G. W., Linden, R. M., et al. (2008) · Nature · doi:10.1038/nature06894 · Cited by 1,389
In vivo enhancer analysis of human conserved non-coding sequences
Pennacchio, L. A., Ahituv, N., Moses, A. M., Prabhakar, S., Nobrega, M. A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K. D., et al. (2006) · Nature · doi:10.1038/nature05295 · Cited by 1,165
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
Hesselberth, J. R., Chen, X., Zhang, Z., Sabo, P. J., Sandstrom, R., Reynolds, A. P., Thurman, R. E., Neph, S., Kuehn, M. S., Noble, W. S., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1313 · Cited by 559
Self-citationFoxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification
Samstein, R. M., Arvey, A., Josefowicz, S. Z., Peng, X., Reynolds, A., Sandstrom, R., Neph, S., Sabo, P., Kim, J. M., Liao, W., et al. (2012) · Cell · doi:10.1016/j.cell.2012.06.053 · Cited by 472
Self-citationCircuitry and Dynamics of Human Transcription Factor Regulatory Networks
Neph, S., Stergachis, A. B., Reynolds, A., Sandstrom, R., Borenstein, E., & Stamatoyannopoulos, J. A. (2012) · Cell · doi:10.1016/j.cell.2012.04.040 · Cited by 467
Self-citation
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Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment
Lavin, Y., Winter, D., Blecher-Gonen, R., David, E., Keren-Shaul, H., Merad, M., Jung, S., & Amit, I. (2014) · Cell · doi:10.1016/j.cell.2014.11.018 · Cited by 2,167
Epigenetic plasticity and the hallmarks of cancer
Flavahan, W. A., Gaskell, E., & Bernstein, B. E. (2017) · Science · doi:10.1126/science.aal2380 · Cited by 1,340
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
Cusanovich, D. A., Daza, R., Adey, A., Pliner, H. A., Christiansen, L., Gunderson, K. L., Steemers, F. J., Trapnell, C., & Shendure, J. (2015) · Science · doi:10.1126/science.aab1601 · Cited by 1,248
Satpathy, A. T., Granja, J. M., Yost, K. E., Qi, Y., Meschi, F., McDermott, G. P., Olsen, B. N., Mumbach, M. R., Pierce, S. E., Corces, M. R., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0206-z · Cited by 980
G-quadruplex structures mark human regulatory chromatin
Hänsel-Hertsch, R., Beraldi, D., Lensing, S. V., Marsico, G., Zyner, K., Parry, A., Di Antonio, M., Pike, J., Kimura, H., Narita, M., et al. (2016) · Nature Genetics · doi:10.1038/ng.3662 · Cited by 964
Palantir characterizes cell fate continuities in human hematopoiesis
Setty, M., Kiseliovas, V., Levine, J., Gayoso, A., Mazutis, L., & Pe’er, D. (2018) · doi:10.1101/385328 · Cited by 836
Characterization of cell fate probabilities in single-cell data with Palantir
Setty, M., Kiseliovas, V., Levine, J., Gayoso, A., Mazutis, L., & Pe’er, D. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0068-4 · Cited by 833
Defining cell types and states with single-cell genomics
Trapnell, C. (2015) · Genome Research · doi:10.1101/gr.190595.115 · Cited by 813
Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo
Ricci, M. A., Manzo, C., García-Parajo, M. F., Lakadamyali, M., & Cosma, M. P. (2015) · Cell · doi:10.1016/j.cell.2015.01.054 · Cited by 736
Core, L. J., Martins, A. L., Danko, C. G., Waters, C. T., Siepel, A., & Lis, J. T. (2014) · Nature Genetics · doi:10.1038/ng.3142 · Cited by 693
Rivera, C. M., & Ren, B. (2013) · Cell · doi:10.1016/j.cell.2013.09.011 · Cited by 550
Trevino, A. E., Müller, F., Andersen, J., Sundaram, L., Kathiria, A., Shcherbina, A., Farh, K., Chang, H. Y., Pașca, A. M., Kundaje, A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.07.039 · Cited by 478
Absence of a simple code: how transcription factors read the genome
Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.07.002 · Cited by 537
Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development
Nord, A. S., Blow, M. J., Attanasio, C., Akiyama, J. A., Holt, A., Hosseini, R., Phouanenavong, S., Plajzer-Frick, I., Shoukry, M., Afzal, V., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.033 · Cited by 375
Sequencing thousands of single-cell genomes with combinatorial indexing
Vitak, S. A., Torkenczy, K. A., Rosenkrantz, J. L., Fields, A. J., Christiansen, L., Wong, M. H., Carbone, L., Steemers, F. J., & Adey, A. (2017) · Nature Methods · doi:10.1038/nmeth.4154 · Cited by 294
Index and biological spectrum of human DNase I hypersensitive sites
Meuleman, W., Muratov, A., Rynes, E., Halow, J., Lee, K., Bates, D., Diegel, M., Dunn, D., Neri, F., Teodosiadis, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2559-3 · Cited by 331
Self-citationDisease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis
Ang, Y.-S., Rivas, R. N., Ribeiro, A. J. S., Srivas, R., Rivera, J., Stone, N. R., Pratt, K., Mohamed, T. M. A., Fu, J.-D., Spencer, C. I., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.033 · Cited by 294
YAP Partially Reprograms Chromatin Accessibility to Directly Induce Adult Cardiogenesis In Vivo
Monroe, T. O., Hill, M. C., Morikawa, Y., Leach, J. P., Heallen, T., Cao, S., Krijger, P. H. L., de Laat, W., Wehrens, X. H. T., Rodney, G. G., et al. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.01.017 · Cited by 289
Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells
Sabbagh, M. F., Heng, J. S., Luo, C., Castanon, R. G., Nery, J. R., Rattner, A., Goff, L. A., Ecker, J. R., & Nathans, J. (2018) · eLife · doi:10.7554/elife.36187 · Cited by 245
Single-molecule regulatory architectures captured by chromatin fiber sequencing
Stergachis, A. B., Debo, B. M., Haugen, E., Churchman, L. S., & Stamatoyannopoulos, J. A. (2020) · Science · doi:10.1126/science.aaz1646 · Cited by 257
Self-citationChromatin accessibility dynamics in a model of human forebrain development
Trevino, A. E., Sinnott-Armstrong, N., Andersen, J., Yoon, S.-J., Huber, N., Pritchard, J. K., Chang, H. Y., Greenleaf, W. J., & Pașca, S. P. (2020) · Science · doi:10.1126/science.aay1645 · Cited by 251
Barozzi, I., Simonatto, M., Bonifacio, S., Yang, L., Rohs, R., Ghisletti, S., & Natoli, G. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.04.006 · Cited by 209
Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer
Risom, T., Langer, E. M., Chapman, M. P., Rantala, J., Fields, A. J., Boniface, C., Alvarez, M. J., Kendsersky, N. D., Pelz, C. R., Johnson-Camacho, K., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05729-w · Cited by 174
Bao, X., Rubin, A. J., Qu, K., Zhang, J., Giresi, P. G., Chang, H. Y., & Khavari, P. A. (2015) · Genome Biology · doi:10.1186/s13059-015-0840-9 · Cited by 164
A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity
D’Alessio, A. C., Fan, Z. P., Wert, K. J., Baranov, P., Cohen, M. A., Saini, J. S., Cohick, E., Charniga, C., Dadon, D., Hannett, N. M., et al. (2015) · Stem Cell Reports · doi:10.1016/j.stemcr.2015.09.016 · Cited by 172
Genomic Perspectives of Transcriptional Regulation in Forebrain Development
Nord, A. S., Pattabiraman, K., Visel, A., & Rubenstein, J. L. R. (2015) · Neuron · doi:10.1016/j.neuron.2014.11.011 · Cited by 152
Andersson, R. (2015) · BioEssays · doi:10.1002/bies.201400162 · Cited by 127
NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence
Parry, A. J., Hoare, M., Bihary, D., Hänsel-Hertsch, R., Smith, S., Tomimatsu, K., Mannion, E., Smith, A., D’Santos, P., Russell, I. A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04283-9 · Cited by 102
Short-term gain, long-term pain: the senescence life cycle and cancer
Chan, A. S. L., & Narita, M. (2019) · Genes & Development · doi:10.1101/gad.320937.118 · Cited by 80
Human neuronal maturation comes of age: cellular mechanisms and species differences
Wallace, J. L., & Pollen, A. A. (2024) · Nature Reviews Neuroscience · doi:10.1038/s41583-023-00760-3 · Cited by 82
Using transgenic reporter assays to functionally characterize enhancers in animals
Kvon, E. Z. (2015) · Genomics · doi:10.1016/j.ygeno.2015.06.007 · Cited by 73
Genetic Networks Governing Heart Development
Waardenberg, A. J., Ramialison, M., Bouveret, R., & Harvey, R. P. (2014) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a013839 · Cited by 59
Yuan, X., Song, M., Devine, P., Bruneau, B. G., Scott, I. C., & Wilson, M. D. (2018) · Nature Communications · doi:10.1038/s41467-018-07451-z · Cited by 51
OCT4 and SOX2 Work as Transcriptional Activators in Reprogramming Human Fibroblasts
Narayan, S., Bryant, G., Shah, S., Berrozpe, G., & Ptashne, M. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.07.071 · Cited by 43
Biophysically Motivated Regulatory Network Inference: Progress and Prospects
Äijö, T., & Bonneau, R. (2016) · Human Heredity · doi:10.1159/000446614 · Cited by 30
Locus-specific induction of gene expression from heterochromatin loci during cellular senescence
Tomimatsu, K., Bihary, D., Olan, I., Parry, A. J., Schoenfelder, S., Chan, A. S. L., Slater, G. S. C., Ito, Y., Rugg-Gunn, P. J., Kirschner, K., et al. (2021) · Nature Aging · doi:10.1038/s43587-021-00147-y · Cited by 25
Yuan, W.-C., Earl, A. S., Ma, S., Alcedo, K., Russell, J. O., Duarte, F. M., Chu, Y.-T., Chang, P.-C., Chen, H.-Y., Chi, H.-H., et al. (2025) · Cell Stem Cell · doi:10.1016/j.stem.2025.04.010 · Cited by 7
Metadata
- Authors
- Stergachis, A. B., Neph, S., Reynolds, A., Humbert, R., Miller, B., Paige, S. L., Vernot, B., Cheng, J. B., Thurman, R. E., Sandstrom, R., Haugen, E., Heimfeld, S., Murry, C. E., Akey, J. M., & Stamatoyannopoulos, J. A.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2013-08
- Volume
- 154
- Issue
- 4
- Pages
- 888-903
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2024000011
- Cited by
- 338
- References
- 14
- FWCI
- 16.54
- Type
- journal article
- Language
- en
- Open access
- bronze
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