Search Results - "McKay, Daniel J."

A Common Set of DNA Regulatory Elements Shapes Drosophila Appendages by McKay, Daniel J., Lieb, Jason D.

“…Animals have body parts made of similar cell types located at different axial positions, such as limbs. The identity and distinct morphology of each structure…”
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Memes: A motif analysis environment in R using tools from the MEME Suite by Nystrom, Spencer L, McKay, Daniel J

“…Identification of biopolymer motifs represents a key step in the analysis of biological sequences. The MEME Suite is a widely used toolkit for comprehensive…”
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Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cells by Ma, Yiqin, McKay, Daniel J, Buttitta, Laura

“…During terminal differentiation, most cells exit the cell cycle and enter into a prolonged or permanent G0 in which they are refractory to mitogenic signals…”
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Expression of E93 provides an instructive cue to control dynamic enhancer activity and chromatin accessibility during development by Nystrom, Spencer L, Niederhuber, Matthew J, McKay, Daniel J

“…How temporal cues combine with spatial inputs to control gene expression during development is poorly understood. Here, we test the hypothesis that the…”
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Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo by Schulz, Katharine N, Bondra, Eliana R, Moshe, Arbel, Villalta, Jacqueline E, Lieb, Jason D, Kaplan, Tommy, McKay, Daniel J, Harrison, Melissa M

“…The transition from a specified germ cell to a population of pluripotent cells occurs rapidly following fertilization. During this developmental transition,…”
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Interrogating the Function of Metazoan Histones using Engineered Gene Clusters by McKay, Daniel J., Klusza, Stephen, Penke, Taylor J.R., Meers, Michael P., Curry, Kaitlin P., McDaniel, Stephen L., Malek, Pamela Y., Cooper, Stephen W., Tatomer, Deirdre C., Lieb, Jason D., Strahl, Brian D., Duronio, Robert J., Matera, A. Gregory

“…Histones and their posttranslational modifications influence the regulation of many DNA-dependent processes. Although an essential role for histone-modifying…”
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Hormone-dependent control of developmental timing through regulation of chromatin accessibility by Uyehara, Christopher M, Nystrom, Spencer L, Niederhuber, Matthew J, Leatham-Jensen, Mary, Ma, Yiqin, Buttitta, Laura A, McKay, Daniel J

“…Specification of tissue identity during development requires precise coordination of gene expression in both space and time. Spatially, master regulatory…”
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Supramolecular assembly of the beta-catenin destruction complex and the effect of Wnt signaling on its localization, molecular size, and activity in vivo by Schaefer, Kristina N, Bonello, Teresa T, Zhang, Shiping, Williams, Clara E, Roberts, David M, McKay, Daniel J, Peifer, Mark

“…Wnt signaling provides a paradigm for cell-cell signals that regulate embryonic development and stem cell homeostasis and are inappropriately activated in…”
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Concentrating pre-mRNA processing factors in the histone locus body facilitates efficient histone mRNA biogenesis by Tatomer, Deirdre C, Terzo, Esteban, Curry, Kaitlin P, Salzler, Harmony, Sabath, Ivan, Zapotoczny, Grzegorz, McKay, Daniel J, Dominski, Zbigniew, Marzluff, William F, Duronio, Robert J

“…The histone locus body (HLB) assembles at replication-dependent histone genes and concentrates factors required for histone messenger RNA (mRNA) biosynthesis…”
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Direct interrogation of the role of H3K9 in metazoan heterochromatin function by Penke, Taylor J R, McKay, Daniel J, Strahl, Brian D, Matera, A Gregory, Duronio, Robert J

“…A defining feature of heterochromatin is methylation of Lys9 of histone H3 (H3K9me), a binding site for heterochromatin protein 1 (HP1). Although H3K9…”
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Lysine 27 of replication-independent histone H3.3 is required for Polycomb target gene silencing but not for gene activation by Leatham-Jensen, Mary, Uyehara, Christopher M, Strahl, Brian D, Matera, A Gregory, Duronio, Robert J, McKay, Daniel J

“…Proper determination of cell fates depends on epigenetic information that is used to preserve memory of decisions made earlier in development…”
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Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum by Lai, Yi-Ting, Deem, Kevin D, Borràs-Castells, Ferran, Sambrani, Nagraj, Rudolf, Heike, Suryamohan, Kushal, El-Sherif, Ezzat, Halfon, Marc S, McKay, Daniel J, Tomoyasu, Yoshinori

“…Evolution of -regulatory elements (such as enhancers) plays an important role in the production of diverse morphology. However, a mechanistic understanding is…”
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Damage-responsive, maturity-silenced enhancers regulate multiple genes that direct regeneration in Drosophila by Harris, Robin E, Stinchfield, Michael J, Nystrom, Spencer L, McKay, Daniel J, Hariharan, Iswar K

“…Like tissues of many organisms, imaginal discs lose the ability to regenerate as they mature. This loss of regenerative capacity coincides with reduced…”
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Transcription factors mediate long-range enhancer-promoter interactions by Nolis, Ilias K, McKay, Daniel J, Mantouvalou, Eva, Lomvardas, Stavros, Merika, Menie, Thanos, Dimitris

“…We examined how remote enhancers establish physical communication with target promoters to activate gene transcription in response to environmental signals…”
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Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster by Meers, Michael P, Adelman, Karen, Duronio, Robert J, Strahl, Brian D, McKay, Daniel J, Matera, A Gregory

“…High-resolution transcription start site (TSS) mapping in D. melanogaster embryos and cell lines has revealed a rich and detailed landscape of both cis- and…”
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Structure-Based and Property-Driven Optimization of N‑Aryl Imidazoles toward Potent and Selective Oral RORγt Inhibitors by Hoegenauer, Klemens, Kallen, Joerg, Jiménez-Núñez, Eloísa, Strang, Ross, Ertl, Peter, Cooke, Nigel G, Hintermann, Samuel, Voegtle, Markus, Betschart, Claudia, McKay, Daniel J. J, Wagner, Juergen, Ottl, Johannes, Beerli, Christian, Billich, Andreas, Dawson, Janet, Kaupmann, Klemens, Streiff, Markus, Gobeau, Nathalie, Harlfinger, Stephanie, Stringer, Rowan, Guntermann, Christine

“…Retinoic acid receptor-related orphan receptor gamma-t (RORγt) is considered to be the master transcription factor for the development of Th17 cells that…”
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Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila by Armstrong, Robin L, Penke, Taylor J R, Strahl, Brian D, Matera, A Gregory, McKay, Daniel J, MacAlpine, David M, Duronio, Robert J

“…Chromatin structure has emerged as a key contributor to spatial and temporal control over the initiation of DNA replication. However, despite genome-wide…”
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Time-Averaged Distributions of Solute and Solvent Motions: Exploring Proton Wires of GFP and PfM2DH by Velez-Vega, Camilo, McKay, Daniel J. J, Aravamuthan, Vibhas, Pearlstein, Robert, Duca, José S

“…Proton translocation pathways of selected variants of the green fluorescent protein (GFP) and Pseudomonas fluorescens mannitol 2-dehydrogenase (PfM2DH) were…”
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Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen–Hydrogen Correlations by Velez-Vega, Camilo, McKay, Daniel J. J, Kurtzman, Tom, Aravamuthan, Vibhas, Pearlstein, Robert A, Duca, José S

“…A statistical-mechanical framework for estimation of solvation entropies and enthalpies is proposed, which is based on the analysis of water as a mixture of…”
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Developmental Regulation of Chromatin Conformation by Hox Proteins in Drosophila by Agelopoulos, Marios, McKay, Daniel J., Mann, Richard S.

“…We present a strategy to examine the chromatin conformation of individual loci in specific cell types during Drosophila embryogenesis. Regulatory DNA is tagged…”
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