Research Terms
Lei, I., West, J., Yan, Z., Gao, X., Fang, P., Dennis, J. H., Gnatovskiy, L., Wang, W., Kingston, R. E., Wang, Z. 2015. BAF250a regulates nucleosome occupancy and histone modifications in priming embryonic stem cell differentiation. J Biol Chem. 2015 Jun 12. pii: jbc.M115.637389. PMID: 26070559.
Fincher, J. A., Tyson, G. S., Dennis, J. H. 2015. DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function. Int J Genomics. 2015:167578. doi: 10.1155/2015/167578. PMID: 25861617.
Pope, B. D., Ryba, T., Dileep, V., Yue, F., Wu, W., Denas, O., Vera, D. L., Wang, Y., Hansen, R. S., Canfield, T. K., Thurman, R. E., Cheng, Y., Gülsoy, G., Dennis, J. H., Snyder, M. P., Stamatoyannopoulos, J. A., Taylor, J., Hardison, R. C., Kahveci, T., Ren, B., Gilbert, D. M. 2014. Topologically associating domains are stable units of replication-timing regulation. Nature. Nov 20;515(7527):402-5. doi: 10.1038/nature13986. PMID: 25409831.
Vera, D. L., Madzima, T. F., Labonne, J. D., Alam, M. P., Hoffman, G. G., Girimurugan, S. B., Zhang, J., McGinnis, K. M., Dennis, J. H., Bass, H. W. 2014. Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize. Plant Cell. 2014 Oct;26(10):3883-93. doi: 10.1105/tpc.114.130609. PMID: 25361955.
Sexton, B. S., Avey, D., Druliner, B. R., Fincher, J. A., Vera, D. L., Grau, D. J., Borowsky, M. L., Gupta, S., Girimurugan, S. B., Chicken, E., Zhang, J., Noble, W. S., Zhu, F., Kingston, R. E., & Dennis, J. H. 2014. The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed. Genome Research, 24: 251-259.
Druliner, B. R., Fincher, J. A., Sexton, B. S., Vera, D. L., Roche, M., Lyle, S., & Dennis, J. H. 2013. Chromatin patterns associated with lung adenocarcinoma progression. Cell Cycle, 12(10), 1536-43.
Fincher, J. A., Vera, D. L., Hughes, D. D., McGinnis, K. M., Dennis, J. H., & Bass, H. W. 2013. Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales. Plant Physiology, 162(2), 1127-41.
Takebayashi, S., Dileep, V., Ryba, T., Dennis, J. H., & Gilbert, D. M. 2012. Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding.Proc Natl Acad Sci U S A, 109(31), 12574-9.
Fincher, J. A., and J. H. Dennis. 2011. DNA sequence contribution to nucleosome distribution. Pages 133-142 in J. Craig and N. Wong, eds., Epigenetics: A Reference Manual. Horizon Scientific Press, Norwich, U.K.
Spetman, B., S. Lueking, B. Roberts, and J. H. Dennis. 2011. Microarray mapping of nucleosome position. Pages in J. Craig and N. Wong, eds., Epigenetics: A Reference Manual. Horizon Scientific Press, Norwich, U.K.
Lubelsky, Y., T. Sasaki, M. A. Kuipers, I. Lucas, M. M. Le Beau, S. Carignon, M. Debatisse, J. A. Prinz, J. H. Dennis, and D. M. Gilbert. 2010. Pre-replication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone. Nucleic Acids Research 38:3141-3155. doi: 10.1093/nar/gkq1276.
Fincher, J. A., and J. H. Dennis. 2010. A computational exploration of gene regulation by nucleosome position.Proceedings of ACM International Conference on Bioinformatics and Computational Biology, 386-389. doi: 10.1145/1854776.1854836.
Zhang, Y., X. Liu, J. A. Fincher, and J. H. Dennis. 2010. DNA sequence feature selection for intrinsic nucleosome positioning signals using AdaBoost. Proceedings of ACM International Conference on Bioinformatics and Computational Biology, 469-471. doi: 10.1145/1854776.1854860.
Gupta, S., J. H. Dennis, R. E. Thurman, R. E. Kingston, J. A. Stamatoyannopoulos, and W. S. Noble. 2008. Predicting human nucleosome occupancy from primary sequence. PLoS Computational Biology 4(8):e1000134.
Dennis, J. H., H.-Y. Fan, S. Reynolds, G. Yuan, J. G. Meldrim, D. J. Richter, D. G. Peterson, O. J. Rando, W. S. Noble, and R. E. Kingston. 2007. Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Research 17:928-939.
Lee, S. A., D. Ndisang, C. Patel, J. H. Dennis, D. J. Faulkes, C. D'Arrigo, L. Samady, S. Farooqui-Kabir, R. J. Heads, D. S. Latchman, and V. S. Budhram-Mahadeo. 2005. Expression of the Brn-3b transcription factor correlates with expression of HSP-27 in breast cancer biopsies and is required for maximal activation of the HSP-27 promoter. Cancer Research 65:3072-3080.
ENCODE Project Consortium. 2004. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306:636-640.
Samady, L., J. H. Dennis, V. Budhram-Mahadeo, and D. S. Latchman. 2004. Activation of CDK4 gene expression in human breast cancer Cells by the Brn-3b POU family transcription factor. Cancer Biology and Therapy 3:317-323.
Dennis, J. H., V. Budhram-Mahadeo, and D. S. Latchman. 2002. Functional interaction between Brn-3a and Src-1 coactivates Brn-3a-mediated transactivation. Biochemical and Biophysical Research Communications 29:487-495.
Dennis, J. H., V. B. Mahadeo, and D. S. Latchman. 2001. The Brn-3b POU family transcription factor regulates the cellular growth, proliferation and anchorage dependence of MCF7 human breast cancer cells. Oncogene 20:4961-4971.
This invention brings significant improvement to our ability to query the chromatin structure of select important regions of the entire human genome. Utilizing a unique sequencing strategy, the invention offers a solution-based sequence capture method enabling the enrichment of the 2000 bp surrounding the transcription start site of 25,464 human open reading frames. This enrichment reduces the sequence space of the human genome from 3.4 Gb in total to 50 Mb of transcription start sites, a 98.5% reduction. Additionally, the enrichment is analogous to that achieved for well-documented exome sequencing experiments. This sequence capture approach will allow researchers to multiplex chromatin structure analyses in Illumina HiSeq2500 lanes, thereby opening this strategy for a wide range of diagnostic and prognostic indicators in human disease.
This invention brings significant improvement to our ability to query the chromatin structure of select important regions of the entire human genome. Utilizing a unique sequencing strategy, the invention offers a solution-based sequence capture method enabling the enrichment of the 2000 bp surrounding the transcription start site of 25,464 human open reading frames. This enrichment reduces the sequence space of the human genome from 3.4 Gb in total to 50 Mb of transcription start sites, a 98.5% reduction. Additionally, the enrichment is analogous to that achieved for well-documented exome sequencing experiments. This sequence capture approach will allow researchers to multiplex chromatin structure analyses in Illumina HiSeq2500 lanes, thereby opening this strategy for a wide range of diagnostic and prognostic indicators in human disease.
| Year: | 2014 |
| Link Address: | e0RZj7utrMg |
| Source: | youtube |
| Duration: | 00:01:36 |
