The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules
Open accessPublished version of a preprint
Abstract
ABSTRACT The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis -regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the Assay for Transposase-Accessible Chromatin (ATAC-seq) in four plant species ( Arabidopsis thaliana , Medicago truncatula , Solanum lycopersicum , and Oryza sativa ) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-gene networks are generally conserved. Comparative ATAC-seq profiling of Arabidopsis root hair and non-hair cell types revealed extensive similarity as well as many cell type-specific differences. Analyzing TF binding sites in differentially accessible regions identified a MYB-driven regulatory module unique to the hair cell, which appears to control both cell fate regulators and abiotic stress responses. Our analyses revealed common regulatory principles among species and shed light on the mechanisms producing cell type-specific transcriptomes during development.
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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
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422
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
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
Histone modifications at human enhancers reflect global cell-type-specific gene expression
Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533
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
Enhancer function: new insights into the regulation of tissue-specific gene expression
Ong, C.-T., & Corces, V. G. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2957 · Cited by 929
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
Mumbach, M. R., Satpathy, A. T., Boyle, E. A., Dai, C., Gowen, B. G., Cho, S. W., Nguyen, M. L., Rubin, A. J., Granja, J. M., Kazane, K. R., et al. (2017) · Nature Genetics · doi:10.1038/ng.3963 · Cited by 490
Cited by
The prevalence, evolution and chromatin signatures of plant regulatory elements
Lu, Z., Marand, A. P., Ricci, W. A., Ethridge, C. L., Zhang, X., & Schmitz, R. J. (2019) · Nature Plants · doi:10.1038/s41477-019-0548-z · Cited by 384
Chromatin accessibility profiling methods
Minnoye, L., Marinov, G. K., Krausgruber, T., Pan, L., Marand, A. P., Secchia, S., Greenleaf, W. J., Furlong, E. E. M., Zhao, K., Schmitz, R. J., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00008-9 · Cited by 206
Multi-omics revolution to promote plant breeding efficiency
Mahmood, U., Li, X., Fan, Y., Chang, W., Niu, Y., Li, J., Qu, C., & Lu, K. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.1062952 · Cited by 145
How Stress Facilitates Phenotypic Innovation Through Epigenetic Diversity
Srikant, T., & Drost, H.-G. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2020.606800 · Cited by 67
Metadata
- Authors
- Maher, K. A., Bajic, M., Kajala, K., Reynoso, M., Pauluzzi, G., West, D. A., Zumstein, K., Woodhouse, M., Bubb, K., Dorrity, M. W., Queitsch, C., Bailey-Serres, J., Sinha, N., Brady, S. M., & Deal, R. B.
- Venue
- The Plant Cell
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-12-11
- Volume
- 30
- Issue
- 1
- Pages
- 15-36
- ISSN
- 1040-4651 (ISSN-L)
- 1532-298X
- OpenAlex
- W2737673717
- Cited by
- 286
- References
- 9
- FWCI
- 18.01
- Type
- journal article
- Language
- en
- Open access
- green
- Funders
- National Science Foundation (IOS-123843)
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- Maher, K. A., Bajic, M., Kajala, K., Reynoso, M., Pauluzzi, G., West, D. A., Zumstein, K., Woodhouse, M., Bubb, K., Dorrity, M. W., Queitsch, C., Bailey-Serres, J., Sinha, N., Brady, S. M., & Deal, R. B. (2018). Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules. The Plant Cell. https://doi.org/10.1105/tpc.17.00581
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