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Your search keyword '"Cherbas, Lucy"' showing total 4 results
Start Over Author "Cherbas, Lucy" Topic histones
4 results on '"Cherbas, Lucy"'

1. Methylation at lysine 4 of histone H3 in ecdysone-dependent development of Drosophila.

Author

Sedkov Y, Cho E, Petruk S, Cherbas L, Smith ST, Jones RS, Cherbas P, Canaani E, Jaynes JB, and Mazo A

Subjects
Animals, Chromatin Assembly and Disassembly drug effects, Drosophila genetics, Drosophila metabolism, Drosophila Proteins genetics, Eye embryology, Eye metabolism, Female, Gene Expression Regulation, Developmental drug effects, Hedgehog Proteins, Histone-Lysine N-Methyltransferase genetics, Male, Methylation drug effects, Promoter Regions, Genetic genetics, Protein Binding, Receptors, Steroid metabolism, Drosophila drug effects, Drosophila embryology, Drosophila Proteins metabolism, Ecdysone pharmacology, Histone-Lysine N-Methyltransferase metabolism, Histones metabolism, Lysine metabolism
Abstract

Steroid hormones fulfil important functions in animal development. In Drosophila, ecdysone triggers moulting and metamorphosis through its effects on gene expression. Ecdysone works by binding to a nuclear receptor, EcR, which heterodimerizes with the retinoid X receptor homologue Ultraspiracle. Both partners are required for binding to ligand or DNA. Like most DNA-binding transcription factors, nuclear receptors activate or repress gene expression by recruiting co-regulators, some of which function as chromatin-modifying complexes. For example, p160 class coactivators associate with histone acetyltransferases and arginine histone methyltransferases. The Trithorax-related gene of Drosophila encodes the SET domain protein TRR. Here we report that TRR is a histone methyltransferases capable of trimethylating lysine 4 of histone H3 (H3-K4). trr acts upstream of hedgehog (hh) in progression of the morphogenetic furrow, and is required for retinal differentiation. Mutations in trr interact in eye development with EcR, and EcR and TRR can be co-immunoprecipitated on ecdysone treatment. TRR, EcR and trimethylated H3-K4 are detected at the ecdysone-inducible promoters of hh and BR-C in cultured cells, and H3-K4 trimethylation at these promoters is decreased in embryos lacking a functional copy of trr. We propose that TRR functions as a coactivator of EcR by altering the chromatin structure at ecdysone-responsive promoters.

Published
2003
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2. Comparative analysis of the transcriptome across distant species.

Author

Gerstein, Mark B, Rozowsky, Joel, Yan, Koon-Kiu, Wang, Daifeng, Cheng, Chao, Brown, James B, Davis, Carrie A, Hillier, LaDeana, Sisu, Cristina, Li, Jingyi Jessica, Pei, Baikang, Harmanci, Arif O, Duff, Michael O, Djebali, Sarah, Alexander, Roger P, Alver, Burak H, Auerbach, Raymond, Bell, Kimberly, Bickel, Peter J, Boeck, Max E, Boley, Nathan P, Booth, Benjamin W, Cherbas, Lucy, Cherbas, Peter, Di, Chao, Dobin, Alex, Drenkow, Jorg, Ewing, Brent, Fang, Gang, Fastuca, Megan, Feingold, Elise A, Frankish, Adam, Gao, Guanjun, Good, Peter J, Guigó, Roderic, Hammonds, Ann, Harrow, Jen, Hoskins, Roger A, Howald, Cédric, Hu, Long, Huang, Haiyan, Hubbard, Tim JP, Huynh, Chau, Jha, Sonali, Kasper, Dionna, Kato, Masaomi, Kaufman, Thomas C, Kitchen, Robert R, Ladewig, Erik, Lagarde, Julien, Lai, Eric, Leng, Jing, Lu, Zhi, MacCoss, Michael, May, Gemma, McWhirter, Rebecca, Merrihew, Gennifer, Miller, David M, Mortazavi, Ali, Murad, Rabi, Oliver, Brian, Olson, Sara, Park, Peter J, Pazin, Michael J, Perrimon, Norbert, Pervouchine, Dmitri, Reinke, Valerie, Reymond, Alexandre, Robinson, Garrett, Samsonova, Anastasia, Saunders, Gary I, Schlesinger, Felix, Sethi, Anurag, Slack, Frank J, Spencer, William C, Stoiber, Marcus H, Strasbourger, Pnina, Tanzer, Andrea, Thompson, Owen A, Wan, Kenneth H, Wang, Guilin, Wang, Huaien, Watkins, Kathie L, Wen, Jiayu, Wen, Kejia, Xue, Chenghai, Yang, Li, Yip, Kevin, Zaleski, Chris, Zhang, Yan, Zheng, Henry, Brenner, Steven E, Graveley, Brenton R, Celniker, Susan E, Gingeras, Thomas R, and Waterston, Robert

Subjects
Chromatin, Animals, Humans, Drosophila melanogaster, Caenorhabditis elegans, Histones, RNA, Untranslated, Cluster Analysis, Gene Expression Profiling, Sequence Analysis, RNA, Gene Expression Regulation, Developmental, Larva, Pupa, Models, Genetic, Promoter Regions, Genetic, Molecular Sequence Annotation, Transcriptome, Genetics, Human Genome, Generic health relevance, General Science & Technology
Abstract

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

Published
2014

3. Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Author

The modeENCODE Consortium, Roy, Sushmita, Ernst, Jason, Kharchenko, Peter V., Kheradpour, Pouya, Negre, Nicolas, Eaton, Matthew L., Landolin, Jane M., Bristow, Christopher A., Ma, Lijia, Lin, Michael F., Washietl, Stefan, Arshinoff, Bradley I., Ay, Ferhat, Meyer, Patrick E., Robine, Nicolas, Washington, Nicole L., Di Stefano, Luisa, Berezikov, Eugene, Brown, Christopher D., Candeias, Rogerio, Carlson, Joseph W., Carr, Adrian, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel, Tolstorukov, Michael Y., Will, Sebastian, Alekseyenko, Artyom A., Artieri, Carlo, Booth, Benjamin W., Brooks, Angela N., Dai, Qi, Davis, Carrie A., Duff, Michael O., Feng, Xin, Gorchakov, Andrey A., Gu, Tingting, Henikoff, Jorja G., Kapranov, Philipp, Li, Renhua, MacAlpine, Heather K., Malone, John, Minoda, Aki, Nordman, Jared, Okamura, Katsutomo, Perry, Marc, Powell, Sara K., Riddle, Nicole C., Sakai, Akiko, Samsonova, Anastasia, Sandler, Jeremy E., Schwartz, Yuri B., Sher, Noa, Spokony, Rebecca, Sturgill, David, van Baren, Marijke, Wan, Kenneth H., Yang, Li, Yu, Charles, Feingold, Elise, Good, Peter, Guyer, Mark, Lowdon, Rebecca, Ahmad, Kami, Andrews, Justen, Berger, Bonnie, Brenner, Steven E., Brent, Michael R., Cherbas, Lucy, Elgin, Sarah C. R., Gingeras, Thomas R., Grossman, Robert, Hoskins, Roger A., Kaufman, Thomas C., Kent, William, Kuroda, Mitzi I., Orr-Weaver, Terry, Perrimon, Norbert, Pirrotta, Vincenzo, Posakony, James W., Ren, Bing, Russell, Steven, Cherbas, Peter, Graveley, Brenton R., Lewis, Suzanna, Micklem, Gos, Oliver, Brian, Park, Peter J., Celniker, Susan E., Henikoff, Steven, Karpen, Gary H., Lai, Eric C., MacAlpine, David M., Stein, Lincoln D., White, Kevin P., and Kellis, Manolis

Published
2010

4. Identification of functional elements and regulatory circuits by Drosophila modENCODE

Author

Roy, Sushmita, Ernst, Jason, Kharchenko, Peter V., Kheradpour, Pouya, Negre, Nicolas, Eaton, Matthew L., Landolin, Jane M., Bristow, Christopher A., Ma, Lijia, Lin, Michael F., Washietl, Stefan, Arshinoff, Bradley I., Ay, Ferhat, Meyer, Patrick E., Robine, Nicolas, Washington, Nicole L., Di Stefano, Luisa, Berezikov, Eugene, Brown, Christopher D., Candeias, Rogerio, Carlson, Joseph W., Carr, Adrian, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel, Tolstorukov, Michael Y., Will, Sebastian, Alekseyenko, Artyom A., Artieri, Carlo, Booth, Benjamin W., Brooks, Angela N., Dai, Qi, Davis, Carrie A., Duff, Michael O., Feng, Xin, Gorchakov, Andrey A., Gu, Tingting, Henikoff, Jorja G., Kapranov, Philipp, Li, Renhua, MacAlpine, Heather K., Malone, John, Minoda, Aki, Nordman, Jared, Okamura, Katsutomo, Perry, Marc, Powell, Sara K., Riddle, Nicole C., Sakai, Akiko, Samsonova, Anastasia A., Sandler, Jeremy E., Schwartz, Yuri B., Sher, Noa, Spokony, Rebecca, Sturgill, David, van Baren, Marijke, Wan, Kenneth H., Yang, Li, Yu, Charles, Feingold, Elise, Good, Peter, Guyer, Mark, Lowdon, Rebecca, Ahmad, Kami, Andrews, Justen, Berger, Bonnie, Brenner, Steven E., Brent, Michael R., Cherbas, Lucy, Elgin, Sarah C.R., Gingeras, Thomas R., Grossman, Robert, Hoskins, Roger A., Kaufman, Thomas C., Kent, William, Kuroda, Mitzi I., Orr-Weaver, Terry, Perrimon, Norbert, Pirrotta, Vincenzo, Posakony, James W., Ren, Bing, Russell, Steven, Cherbas, Peter, Graveley, Brenton R., Lewis, Suzanna, Micklem, Gos, Oliver, Brian, Park, Peter J., Celniker, Susan E., Henikoff, Steven, Karpen, Gary H., Lai, Eric C., MacAlpine, David M., Stein, Lincoln D., White, Kevin P., Kellis, Manolis, Booth, Benjamin, Comstock, Charles L.G., Dobin, Alex, Drenkow, Jorg, Dudoit, Sandrine, Dumais, Jacqueline, Fagegaltier, Delphine, Ghosh, Srinka, Hansen, Kasper D., Jha, Sonali, Langton, Laura, Lin, Wei, Miller, David, Tenney, Aaron E., Wang, Huaien, Willingham, Aarron T., Zaleski, Chris, Zhang, Dayu, Acevedo, David, Bishop, Eric P., Gadel, Sarah E., Jung, Youngsook L., Kennedy, Cameron D., Lee, Ok Kyung, Linder-Basso, Daniela, Marchetti, Sarah E., Shanower, Gregory, Nègre, Nicolas, Grossman, Robert L., Auburn, Richard, Bellen, Hugo J., Chen, Jia, Domanus, Marc H., Hanley, David, Heinz, Elizabeth, Li, Zirong, Meyer, Folker, Miller, Steven W., Morrison, Carolyn A., Scheftner, Douglas A., Senderowicz, Lionel, Shah, Parantu K., Suchy, Sarah, Tian, Feng, Venken, Koen J.T., White, Robert, Wilkening, Jared, Zieba, Jennifer, Nordman, Jared T., Orr-Weaver, Terry L., DeNapoli, Leyna C., Ding, Queying, Eng, Thomas, Kashevsky, Helena, Li, Sharon, Prinz, Joseph A., Hannon, Gregory J., Hirst, Martin, Marra, Marco, Rooks, Michelle, Zhao, Yongjun, Bryson, Terri D., Perry, Marc D., Kent, William J., Lewis, Suzanna E., Barber, Galt, Chateigner, Aurelien, Clawson, Hiram, Contrino, Sergio, Guillier, Francois, Hinrichs, Angie S., Kephart, Ellen T., Lloyd, Paul, Lyne, Rachel, McKay, Sheldon, Moore, Richard A., Mungall, Chris, Rutherford, Kim M., Ruzanov, Peter, Smith, Richard, Stinson, E. O., Zha, Zheng, Artieri, Carlo G., Malone, John H., Jiang, Lichun, Mattiuzzo, Nicolas, Feingold, Elise A., Good, Peter J., Guyer, Mark S., Lowdon, Rebecca F., Stem Cell Aging Leukemia and Lymphoma (SALL), and Restoring Organ Function by Means of Regenerative Medicine (REGENERATE)

Subjects
Transcription, Genetic, Genome, Insect, Gene regulatory network, Genomics, Genes, Insect, Computational biology, Biology, Genome, Article, Epigenesis, Genetic, Histones, Nucleosome, Animals, Drosophila Proteins, Gene Regulatory Networks, Promoter Regions, Genetic, Gene, Genetics, Multidisciplinary, Binding Sites, REDfly, Computational Biology, Molecular Sequence Annotation, Chromatin, Nucleosomes, Drosophila melanogaster, Gene Expression Regulation, RNA, Small Untranslated, Drosophila Protein, Transcription Factors
Abstract

From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation is still needed to characterize how the genome is used to help to produce a functional organism (see the Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for the Caenorhabditis elegans genome, and The modENCODE Consortium (p. 1787 ) summarize for the Drosophila melanogaster genome, full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites, and high-resolution maps of chromatin organization. Both studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized. Overall, the studies provide insights into the organization, structure, and function of the two genomes and provide basic information needed to guide and correlate both focused and genome-wide studies.

Published
2010

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