The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution
Open accessAbstract
The scarcity of accessible sites that are dynamic or cell type-specific in plants may be due in part to tissue heterogeneity in bulk studies. To assess the effects of tissue heterogeneity, we apply single-cell ATAC-seq to Arabidopsis thaliana roots and identify thousands of differentially accessible sites, sufficient to resolve all major cell types of the root. We find that the entirety of a cell’s regulatory landscape and its transcriptome independently capture cell type identity. We leverage this shared information on cell identity to integrate accessibility and transcriptome data to characterize developmental progression, endoreduplication and cell division. We further use the combined data to characterize cell type-specific motif enrichments of transcription factor families and link the expression of family members to changing accessibility at specific loci, resolving direct and indirect effects that shape expression. Our approach provides an analytical framework to infer the gene regulatory networks that execute plant development.
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Cites
Integrating single-cell transcriptomic data across different conditions, technologies, and species
Butler, A., Hoffman, P., Smibert, P., Papalexi, E., & Satija, R. (2018) · Nature Biotechnology · doi:10.1038/nbt.4096 · Cited by 13,174
Raudvere, U., Kolberg, L., Kuzmin, I., Arak, T., Adler, P., Peterson, H., & Vilo, J. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz369 · Cited by 5,045
The single-cell transcriptional landscape of mammalian organogenesis
Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D. M., Hill, A. J., Zhang, F., Mundlos, S., Christiansen, L., Steemers, F. J., et al. (2019) · Nature · doi:10.1038/s41586-019-0969-x · Cited by 4,490
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
Transcription factors: from enhancer binding to developmental control
Spitz, F., & Furlong, E. E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3207 · Cited by 2,227
Single-cell transcriptional diversity is a hallmark of developmental potential
Gulati, G. S., Sikandar, S. S., Wesche, D. J., Manjunath, A., Bharadwaj, A., Berger, M. J., Ilagan, F., Kuo, A. H., Hsieh, R. W., Cai, S., et al. (2020) · Science · doi:10.1126/science.aax0249 · Cited by 1,571
Cao, J., Packer, J. S., Ramani, V., Cusanovich, D. A., Huynh, C., Daza, R., Qiu, X., Lee, C., Furlan, S. N., Steemers, F. J., et al. (2017) · doi:10.1101/104844 · Cited by 1,402
Joint profiling of chromatin accessibility and gene expression in thousands of single cells
Cao, J., Cusanovich, D. A., Ramani, V., Aghamirzaie, D., Pliner, H. A., Hill, A. J., Daza, R. M., McFaline-Figueroa, J. L., Packer, J. S., Christiansen, L., et al. (2018) · Science · doi:10.1126/science.aau0730 · Cited by 938
Thyroid hormone regulates distinct paths to maturation in pigment cell lineages
Saunders, L. M., Mishra, A. K., Aman, A. J., Lewis, V. M., Toomey, M. B., Packer, J. S., Qiu, X., McFaline-Figueroa, J. L., Corbo, J. C., Trapnell, C., et al. (2019) · eLife · doi:10.7554/elife.45181 · Cited by 170
Cited by
Shahan, R., Hsu, C.-W., Nolan, T. M., Cole, B. J., Taylor, I. W., Greenstreet, L., Zhang, S., Afanassiev, A., Vlot, A. H. C., Schiebinger, G., et al. (2022) · Developmental Cell · doi:10.1016/j.devcel.2022.01.008 · Cited by 363
Metadata
- Authors
- Dorrity, M. W., Alexandre, C. M., Hamm, M. O., Vigil, A.-L., Fields, S., Queitsch, C., & Cuperus, J. T.
- Venue
- Nature Communications
- Published
- 2021-06-07
- Volume
- 12
- Issue
- 1
- Pages
- 3334-3334
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W3166204775
- Cited by
- 184
- References
- 9
- FWCI
- 7.92
- Type
- journal article
- Language
- en
- Open access
- gold
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- Dorrity, M. W., Alexandre, C. M., Hamm, M. O., Vigil, A.-L., Fields, S., Queitsch, C., & Cuperus, J. T. (2021). The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution. Nature Communications. https://doi.org/10.1038/s41467-021-23675-y
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