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643 results on '"Bulyk, Martha L"'

4. A stem cell epigenome is associated with primary nonresponse to CD19 CAR T cells in pediatric acute lymphoblastic leukemia

Author

Masih, Katherine E., Gardner, Rebecca A., Chou, Hsien-Chao, Abdelmaksoud, Abdalla, Song, Young K., Mariani, Luca, Gangalapudi, Vineela, Gryder, Berkley E., Wilson, Ashley L., Adebola, Serifat O., Stanton, Benjamin Z., Wang, Chaoyu, Milewski, David, Kim, Yong Yean, Tian, Meijie, Cheuk, Adam Tai-Chi, Wen, Xinyu, Zhang, Yue, Altan-Bonnet, Grégoire, Kelly, Michael C., Wei, Jun S., Bulyk, Martha L., Jensen, Michael C., Orentas, Rimas J., and Khan, Javed

Published
2023
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10. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

Author

Lambourne, Luke, primary, Mattioli, Kaia, additional, Santoso, Clarissa, additional, Sheynkman, Gloria, additional, Inukai, Sachi, additional, Kaundal, Babita, additional, Berenson, Anna, additional, Spirohn-Fitzgerald, Kerstin, additional, Bhattacharjee, Anukana, additional, Rothman, Elisabeth, additional, Shrestha, Shaleen, additional, Laval, Florent, additional, Yang, Zhipeng, additional, Bisht, Deepa, additional, Sewell, Jared A., additional, Li, Guangyuan, additional, Prasad, Anisa, additional, Phanor, Sabrina, additional, Lane, Ryan, additional, Campbell, Devlin M., additional, Hunt, Toby, additional, Balcha, Dawit, additional, Gebbia, Marinella, additional, Twizere, Jean-Claude, additional, Hao, Tong, additional, Frankish, Adam, additional, Riback, Josh A., additional, Salomonis, Nathan, additional, Calderwood, Michael A., additional, Hill, David E., additional, Sahni, Nidhi, additional, Vidal, Marc, additional, Bulyk, Martha L., additional, and Fuxman Bass, Juan I., additional

Published
2024
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13. Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits

Author

Choudhuri, Avik, Trompouki, Eirini, Abraham, Brian J., Colli, Leandro M., Kock, Kian Hong, Mallard, William, Yang, Min-Lee, Vinjamur, Divya S., Ghamari, Alireza, Sporrij, Audrey, Hoi, Karen, Hummel, Barbara, Boatman, Sonja, Chan, Victoria, Tseng, Sierra, Nandakumar, Satish K., Yang, Song, Lichtig, Asher, Superdock, Michael, Grimes, Seraj N., Bowman, Teresa V., Zhou, Yi, Takahashi, Shinichiro, Joehanes, Roby, Cantor, Alan B., Bauer, Daniel E., Ganesh, Santhi K., Rinn, John, Albert, Paul S., Bulyk, Martha L., Chanock, Stephen J., Young, Richard A., and Zon, Leonard I.

Published
2020
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17. 5′RNA-Seq identifies Fhl1 as a genetic modifier in cardiomyopathy

Author

Christodoulou, Danos C, Wakimoto, Hiroko, Onoue, Kenji, Eminaga, Seda, Gorham, Joshua M, DePalma, Steve R, Herman, Daniel S, Teekakirikul, Polakit, Conner, David A, McKean, David M, Domenighetti, Andrea A, Aboukhalil, Anton, Chang, Stephen, Srivastava, Gyan, McDonough, Barbara, De Jager, Philip L, Chen, Ju, Bulyk, Martha L, Muehlschlegel, Jochen D, Seidman, Christine E, and Seidman, JG

Subjects
Heart Disease, Genetics, Human Genome, Cardiovascular, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, 5' Flanking Region, Animals, Cardiomyopathy, Dilated, Cells, Cultured, Codon, Initiator, Female, Humans, Intracellular Signaling Peptides and Proteins, LIM Domain Proteins, Male, Mice, Mice, 129 Strain, Muscle Proteins, Mutation, Missense, Myocardium, Myocytes, Cardiac, Myosin Heavy Chains, Sequence Analysis, RNA, Transcriptome, Medical and Health Sciences, Immunology
Abstract

The transcriptome is subject to multiple changes during pathogenesis, including the use of alternate 5' start-sites that can affect transcription levels and output. Current RNA sequencing techniques can assess mRNA levels, but do not robustly detect changes in 5' start-site use. Here, we developed a transcriptome sequencing strategy that detects genome-wide changes in start-site usage (5'RNA-Seq) and applied this methodology to identify regulatory events that occur in hypertrophic cardiomyopathy (HCM). Compared with transcripts from WT mice, 92 genes had altered start-site usage in a mouse model of HCM, including four-and-a-half LIM domains protein 1 (Fhl1). HCM-induced altered transcriptional regulation of Fhl1 resulted in robust myocyte expression of a distinct protein isoform, a response that was conserved in humans with genetic or acquired cardiomyopathies. Genetic ablation of Fhl1 in HCM mice was deleterious, which suggests that Fhl1 transcriptional changes provide salutary effects on stressed myocytes in this disease. Because Fhl1 is a chromosome X-encoded gene, stress-induced changes in its transcription may contribute to gender differences in the clinical severity of HCM. Our findings indicate that 5'RNA-Seq has the potential to identify genome-wide changes in 5' start-site usage that are associated with pathogenic phenotypes.

Published
2014

21. Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding

Author

Siggers, Trevor, Chang, Abraham B, Teixeira, Ana, Wong, Daniel, Williams, Kevin J, Ahmed, Bilal, Ragoussis, Jiannis, Udalova, Irina A, Smale, Stephen T, and Bulyk, Martha L

Subjects
Biochemistry and Cell Biology, Biological Sciences, Biotechnology, Genetics, Animals, Base Sequence, Binding Sites, Cluster Analysis, DNA, Databases, Genetic, Gene Expression Regulation, Humans, Macrophages, Mice, NF-kappa B, Protein Array Analysis, Protein Binding, Protein Multimerization, Immunology, Biochemistry and cell biology
Abstract

The unique DNA-binding properties of distinct NF-κB dimers influence the selective regulation of NF-κB target genes. To more thoroughly investigate these dimer-specific differences, we combined protein-binding microarrays and surface plasmon resonance to evaluate DNA sites recognized by eight different NF-κB dimers. We observed three distinct binding-specificity classes and clarified mechanisms by which dimers might regulate distinct sets of genes. We identified many new nontraditional NF-κB binding site (κB site) sequences and highlight the plasticity of NF-κB dimers in recognizing κB sites with a single consensus half-site. This study provides a database that can be used in efforts to identify NF-κB target sites and uncover gene regulatory circuitry.

Published
2012

22. Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding.

Author

Siggers, Trevor, Chang, Abraham B, Teixeira, Ana, Wong, Daniel, Williams, Kevin J, Ahmed, Bilal, Ragoussis, Jiannis, Udalova, Irina A, Smale, Stephen T, and Bulyk, Martha L

Subjects
Macrophages, Animals, Humans, Mice, NF-kappa B, DNA, Protein Array Analysis, Cluster Analysis, Gene Expression Regulation, Binding Sites, Base Sequence, Protein Binding, Databases, Genetic, Protein Multimerization, Databases, Genetic, Immunology
Abstract

The unique DNA-binding properties of distinct NF-κB dimers influence the selective regulation of NF-κB target genes. To more thoroughly investigate these dimer-specific differences, we combined protein-binding microarrays and surface plasmon resonance to evaluate DNA sites recognized by eight different NF-κB dimers. We observed three distinct binding-specificity classes and clarified mechanisms by which dimers might regulate distinct sets of genes. We identified many new nontraditional NF-κB binding site (κB site) sequences and highlight the plasticity of NF-κB dimers in recognizing κB sites with a single consensus half-site. This study provides a database that can be used in efforts to identify NF-κB target sites and uncover gene regulatory circuitry.

Published
2011

28. Survey of variation in human transcription factors reveals prevalent DNA binding changes

Author

Barrera, Luis A., Vedenko, Anastasia, Kurland, Jesse V., Rogers, Julia M., Gisselbrecht, Stephen S., Rossin, Elizabeth J., Woodard, Jaie, Mariani, Luca, Kock, Kian Hong, Inukai, Sachi, Siggers, Trevor, Shokri, Leila, Gordân, Raluca, Sahni, Nidhi, Cotsapas, Chris, Hao, Tong, Yi, Song, Kellis, Manolis, Daly, Mark J., Vidal, Marc, Hill, David E., and Bulyk, Martha L.

Published
2016

29. Data from EP300 Selectively Controls the Enhancer Landscape of MYCN-Amplified Neuroblastoma

Author

Durbin, Adam D., primary, Wang, Tingjian, primary, Wimalasena, Virangika K., primary, Zimmerman, Mark W., primary, Li, Deyao, primary, Dharia, Neekesh V., primary, Mariani, Luca, primary, Shendy, Noha A.M., primary, Nance, Stephanie, primary, Patel, Anand G., primary, Shao, Ying, primary, Mundada, Maya, primary, Maxham, Lily, primary, Park, Paul M.C., primary, Sigua, Logan H., primary, Morita, Ken, primary, Conway, Amy Saur, primary, Robichaud, Amanda L., primary, Perez-Atayde, Antonio R., primary, Bikowitz, Melissa J., primary, Quinn, Taylor R., primary, Wiest, Olaf, primary, Easton, John, primary, Schönbrunn, Ernst, primary, Bulyk, Martha L., primary, Abraham, Brian J., primary, Stegmaier, Kimberly, primary, Look, A. Thomas, primary, and Qi, Jun, primary

Published
2023
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30. Supplementary Data from EP300 Selectively Controls the Enhancer Landscape of MYCN-Amplified Neuroblastoma

Author

Durbin, Adam D., primary, Wang, Tingjian, primary, Wimalasena, Virangika K., primary, Zimmerman, Mark W., primary, Li, Deyao, primary, Dharia, Neekesh V., primary, Mariani, Luca, primary, Shendy, Noha A.M., primary, Nance, Stephanie, primary, Patel, Anand G., primary, Shao, Ying, primary, Mundada, Maya, primary, Maxham, Lily, primary, Park, Paul M.C., primary, Sigua, Logan H., primary, Morita, Ken, primary, Conway, Amy Saur, primary, Robichaud, Amanda L., primary, Perez-Atayde, Antonio R., primary, Bikowitz, Melissa J., primary, Quinn, Taylor R., primary, Wiest, Olaf, primary, Easton, John, primary, Schönbrunn, Ernst, primary, Bulyk, Martha L., primary, Abraham, Brian J., primary, Stegmaier, Kimberly, primary, Look, A. Thomas, primary, and Qi, Jun, primary

Published
2023
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42. The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain

Author

Weber, Lisa Marie, primary, Jia, Yulin, additional, Stielow, Bastian, additional, Gisselbrecht, Stephen S, additional, Cao, Yinghua, additional, Ren, Yanpeng, additional, Rohner, Iris, additional, King, Jessica, additional, Rothman, Elisabeth, additional, Fischer, Sabrina, additional, Simon, Clara, additional, Forné, Ignasi, additional, Nist, Andrea, additional, Stiewe, Thorsten, additional, Bulyk, Martha L, additional, Wang, Zhanxin, additional, and Liefke, Robert, additional

Published
2022
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43. The NF-κB Genomic Landscape in Lymphoblastoid B Cells

Author

Zhao, Bo, Barrera, Luis A., Ersing, Ina, Willox, Bradford, Schmidt, Stefanie C.S., Greenfeld, Hannah, Zhou, Hufeng, Mollo, Sarah B., Shi, Tommy T., Takasaki, Kaoru, Jiang, Sizun, Cahir-McFarland, Ellen, Kellis, Manolis, Bulyk, Martha L., Kieff, Elliott, and Gewurz, Benjamin E.

Published
2014
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