The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)
Open accessAbstract
A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear chromatin is a powerful and well-established method of identifying many different types of regulatory elements, but in the past it has been limited to analysis of single loci. We have recently described a protocol to generate a genome-wide library of DNase HS sites. Here, we report high-throughput analysis, using massively parallel signature sequencing (MPSS), of 230,000 tags from a DNase library generated from quiescent human CD4+ T cells. Of the tags that uniquely map to the genome, we identified 14,190 clusters of sequences that group within close proximity to each other. By using a real-time PCR strategy, we determined that the majority of these clusters represent valid DNase HS sites. Approximately 80% of these DNase HS sites uniquely map within one or more annotated regions of the genome believed to contain regulatory elements, including regions 2 kb upstream of genes, CpG islands, and highly conserved sequences. Most DNase HS sites identified in CD4+ T cells are also HS in CD8+ T cells, B cells, hepatocytes, human umbilical vein endothelial cells (HUVECs), and HeLa cells. However, ∼10% of the DNase HS sites are lymphocyte specific, indicating that this procedure can identify gene regulatory elements that control cell type specificity. This strategy, which can be applied to any cell line or tissue, will enable a better understanding of how chromatin structure dictates cell function and fate.
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Primer3 on the WWW for General Users and for Biologist Programmers
Rozen, S., & Skaletsky, H. (2003) · Bioinformatics Methods and Protocols · doi:10.1385/1-59259-192-2:365 · Cited by 15,013
Summaries of Affymetrix GeneChip probe level data
Irizarry, R. A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gng015 · Cited by 4,887
Barnett, V., Lewis, T., & Abeles, F. (1979) · Physics Today · doi:10.1063/1.2995737 · Cited by 2,824
The ENCODE (ENCyclopedia Of DNA Elements) Project
(2004) · Science · doi:10.1126/science.1105136 · Cited by 2,390
The UCSC Genome Browser Database
Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg129 · Cited by 1,887
A vision for the future of genomics research
Collins, F. S., Green, E. D., Guttmacher, A. E., Guyer, M. S., & on behalf of the US National Human Genome Research Institute (2003) · Nature · doi:10.1038/nature01626 · Cited by 1,752
Self-citationAtkinson, A., Barnett, V., & Lewis, T. (1995) · Journal of the Royal Statistical Society. Series A (Statistics in Society) · doi:10.2307/2983451 · Cited by 1,682
Large-scale analysis of the human and mouse transcriptomes
Su, A. I., Cooke, M. P., Ching, K. A., Hakak, Y., Walker, J. R., Wiltshire, T., Orth, A. P., Vega, R. G., Sapinoso, L. M., Moqrich, A., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.012025199 · Cited by 1,466
Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays.
Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D. H., Johnson, D., Luo, S., McCurdy, S., Foy, M., Ewan, M., et al. (2000) · Nature Biotechnology · doi:10.1038/76469 · Cited by 1,360
Self-citationNUCLEASE HYPERSENSITIVE SITES IN CHROMATIN
Gross, D. S., & Garrard, W. T. (1988) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.57.070188.001111 · Cited by 1,233
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Wang, Z., Zang, C., Rosenfeld, J. A., Schones, D. E., Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Peng, W., Zhang, M. Q., et al. (2008) · Nature Genetics · doi:10.1038/ng.154 · Cited by 2,331
High-Resolution Mapping and Characterization of Open Chromatin across the Genome
Boyle, A. P., Davis, S., Shulha, H. P., Meltzer, P., Margulies, E. H., Weng, Z., Furey, T. S., & Crawford, G. E. (2008) · Cell · doi:10.1016/j.cell.2007.12.014 · Cited by 1,415
Self-citationBenchmark and integration of resources for the estimation of human transcription factor activities
Garcia-Alonso, L., Holland, C. H., Ibrahim, M. M., Turei, D., & Saez-Rodriguez, J. (2019) · Genome Research · doi:10.1101/gr.240663.118 · Cited by 1,122
Metadata
- Authors
- Crawford, G. E., Holt, I. E., Whittle, J., Webb, B. D., Tai, D., Davis, S., Margulies, E. H., Chen, Y., Bernat, J. A., Ginsburg, D., Zhou, D., Luo, S., Vasicek, T. J., Daly, M. J., Wolfsberg, T. G., & Collins, F. S.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2005-12-12
- Volume
- 16
- Issue
- 1
- Pages
- 123-131
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2121607820
- Cited by
- 486
- References
- 21
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Crawford, G. E., Holt, I. E., Whittle, J., Webb, B. D., Tai, D., Davis, S., Margulies, E. H., Chen, Y., Bernat, J. A., Ginsburg, D., Zhou, D., Luo, S., Vasicek, T. J., Daly, M. J., Wolfsberg, T. G., & Collins, F. S. (2006). Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Research. https://doi.org/10.1101/gr.4074106
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