User:Odom:Schmidt: Difference between revisions
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< | *Ip, J.Y., <b> <u>Schmidt D.</u></b>, Pan, Q., Ramani, A.K., Fraser, A.G., Odom, D.T., and Blencowe, B. (2010). Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Research. | ||
*Hurtado, A., Holmes, K.A., Ross-Innes, C.S., <b> <u>Schmidt D.</u></b>, and Carroll, J.S. (2010). FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nature Genetics. | |||
*<b> <u>Schmidt D.</u></b>, Wilson, M.D., Ballester, B., Schwalie, P.C., Brown, G.D., Marshall, A., Kutter, C., Watt, S., Martinez-Jimenez, C.P., Mackay, S., et al. (2010b). Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328, 1036-1040. | |||
*<b> <u>Schmidt D.</u></b>, Schwalie, P.C., Ross-Innes, C.S., Hurtado, A., Brown, G.D., Carroll, J.S., Flicek, P., and Odom, D.T. (2010a). A CTCF-independent role for cohesin in tissue-specific transcription. Genome Research 20, 578-588. | |||
*Ross-Innes, C.S., Stark, R., Holmes, K.A., <b> <u>Schmidt D.</u></b>, Spyrou, C., Russell, R., Massie, C.E., Vowler, S.L., Eldridge, M., and Carroll, J.S. (2010). Cooperative interaction between retinoic acid receptor-alpha and estrogen receptor in breast cancer. Genes & Development 24, 171-182. | |||
*<b> <u>Schmidt D.</u></b>, Wilson, M.D., Spyrou, C., Brown, G.D., Hadfield, J., and Odom, D.T. (2009). ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48, 240-248. | |||
*Wilson, M.D., Barbosa-Morais, N.L., <b> <u>Schmidt D.</u></b>, Conboy, C.M., Vanes, L., Tybulewicz, V.L.J., Fisher, E.M.C., Tavaré, S., and Odom, D.T. (2008). Species-specific transcription in mice carrying human chromosome 21. Science 322, 434-438. | |||
*<b> <u>Schmidt D.</u></b>, Stark, R., Wilson, M.D., Brown, G.D., and Odom, D.T. (2008). Genome-scale validation of deep-sequencing libraries. PLoS ONE 3, e3713. | |||
*Sultan, M., Schulz, M.H., Richard, H., Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D.,<b> <u>Schmidt D.</u></b> et al. (2008). A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321, 956-960. | |||
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Revision as of 09:38, 20 December 2010
Odom laboratory
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Dominic Schmidt |
Qualifications and Personal History
Education
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Research
Research InterestsTranscription factors (TFs) direct gene expression by binding to DNA regulatory regions. To explore the evolution of gene regulation, we experimentally determined the genome-wide occupancy of two TFs, CEBPA and HNF4A, in livers of five vertebrates. Although each TF displays highly conserved DNA binding preferences, most binding is species-specific, and aligned binding events present in all five species are rare. Regions near genes with expression levels dependent on a TF are often bound by the TF in multiple species, yet show no enhanced DNA sequence constraint. Binding divergence between species can be largely explained by sequence changes to the bound motifs. Among the binding events lost in one lineage, only half are recovered by another binding event within 10 kilobases. Our results reveal large interspecies differences in transcriptional regulation and provide insight into their evolution: We recently showed that cohesin co-binds across the genome with transcription factors independently of CTCF, plays a functional role in estrogen-regulated transcription, and may help mediate tissue-specific transcriptional responses via long-range chromosomal interactions:
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Publications
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Miscellaneous
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