Search Results - "Porter, Douglas F"

Methods to study RNA–protein interactions by Ramanathan, Muthukumar, Porter, Douglas F., Khavari, Paul A.

“…Noncoding RNA sequences, including long noncoding RNAs, small nucleolar RNAs, and untranslated mRNA regions, accomplish many of their diverse functions through…”
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easyCLIP analysis of RNA-protein interactions incorporating absolute quantification by Porter, Douglas F., Miao, Weili, Yang, Xue, Goda, Grant A., Ji, Andrew L., Donohue, Laura K. H., Aleman, Maria M., Dominguez, Daniel, Khavari, Paul A.

“…Quantitative criteria to identify proteins as RNA-binding proteins (RBPs) are presently lacking, as are criteria to define RBP target RNAs. Here, we develop an…”
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The PUF binding landscape in metazoan germ cells by Prasad, Aman, Porter, Douglas F, Kroll-Conner, Peggy L, Mohanty, Ipsita, Ryan, Anne R, Crittenden, Sarah L, Wickens, Marvin, Kimble, Judith

“…PUF (Pumilio/FBF) proteins are RNA-binding proteins and conserved stem cell regulators. The Caenorhabditis elegans PUF proteins FBF-1 and FBF-2 (collectively…”
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Target selection by natural and redesigned PUF proteins by Porter, Douglas F., Koh, Yvonne Y., VanVeller, Brett, Raines, Ronald T., Wickens, Marvin

“…Pumilio/fem-3 mRNA binding factor (PUF) proteins bind RNA with sequence specificity and modularity, and have become exemplary scaffolds in the reengineering of…”
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An RNA-Binding Multimer Specifies Nematode Sperm Fate by Aoki, Scott T., Porter, Douglas F., Prasad, Aman, Wickens, Marvin, Bingman, Craig A., Kimble, Judith

“…FOG-3 is a master regulator of sperm fate in Caenorhabditis elegans and homologous to Tob/BTG proteins, which in mammals are monomeric adaptors that recruit…”
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Toward Identifying Subnetworks from FBF Binding Landscapes in Caenorhabditis Spermatogenic or Oogenic Germlines by Porter, Douglas F, Prasad, Aman, Carrick, Brian H, Kroll-Connor, Peggy, Wickens, Marvin, Kimble, Judith

“…Metazoan PUF (Pumilio and FBF) RNA-binding proteins regulate various biological processes, but a common theme across phylogeny is stem cell regulation. In ,…”
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Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site by Valley, Cary T, Porter, Douglas F, Qiu, Chen, Campbell, Zachary T, Hall, Traci M. Tanaka, Wickens, Marvin

“…mRNA control hinges on the specificity and affinity of proteins for their RNA binding sites. Regulatory proteins must bind their own sites and reject even…”
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Targeted Proteomic Approaches for Proteome-Wide Characterizations of the AMP-Binding Capacities of Kinases by Miao, Weili, Yin, Jiekai, Porter, Douglas F., Jiang, Xiaogang, Khavari, Paul A., Wang, Yinsheng

“…Kinases play important roles in cell signaling, and adenosine monophosphate (AMP) is known to modulate cellular energy homeostasis through AMP-activated…”
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Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase by Preston, Melanie A., Porter, Douglas F., Chen, Fan, Buter, Natascha, Lapointe, Christopher P., Keles, Sunduz, Kimble, Judith, Wickens, Marvin

“…Ribonucleotidyl transferases (rNTases) add untemplated ribonucleotides to diverse RNAs. We have developed TRAID-seq, a screening strategy in Saccharomyces…”
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Records of RNA locations in living yeast revealed through covalent marks by Medina-Munoz, Hugo C., Lapointe, Christopher P., Porter, Douglas F., Wickens, Marvin

“…RNA movements and localization pervade biology, from embryonic development to disease. To identify RNAs at specific locations, we developed a strategy in which…”
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Cell-type-specific interacting proteins collaborate to regulate the timing of Cyclin B protein expression in male meiotic prophase by Baker, Catherine C, Gallicchio, Lorenzo, Matias, Neuza R, Porter, Douglas F, Parsanian, Lucineh, Taing, Emily, Tam, Cheuk, Fuller, Margaret T

“…During meiosis, germ cell and stage-specific components impose additional layers of regulation on the core cell cycle machinery to set up an extended G2 period…”
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Author Correction: Methods to study RNA–protein interactions by Ramanathan, Muthukumar, Porter, Douglas F., Khavari, Paul A.

“…In the version of this paper originally published, three references were accidentally omitted: Schwartz, J. C. et al. Cell Rep . 5 , 918–925 (2013); Tundup, S…”
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Glucose binds and activates NSUN2 to promote translation and epidermal differentiation by Miao, Weili, Porter, Douglas F, Li, Ya, Meservey, Lindsey M, Yang, Yen-Yu, Ma, Chengjie, Ferguson, Ian D, Tien, Vivian B, Jack, Timothy M, Ducoli, Luca, Lopez-Pajares, Vanessa, Tao, Shiying, Savage, Paul B, Wang, Yinsheng, Khavari, Paul A

“…Elevations in intracellular glucose concentrations are essential for epithelial cell differentiation by mechanisms that are not fully understood. Glucose has…”
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Glucose dissociates DDX21 dimers to regulate mRNA splicing and tissue differentiation by Miao, Weili, Porter, Douglas F., Lopez-Pajares, Vanessa, Siprashvili, Zurab, Meyers, Robin M., Bai, Yunhao, Nguyen, Duy T., Ko, Lisa A., Zarnegar, Brian J., Ferguson, Ian D., Mills, Matthew M., Jilly-Rehak, Christie E., Wu, Cheng-Guo, Yang, Yen-Yu, Meyers, Jordan M., Hong, Audrey W., Reynolds, David L., Ramanathan, Muthukumar, Tao, Shiying, Jiang, Sizun, Flynn, Ryan A., Wang, Yinsheng, Nolan, Garry P., Khavari, Paul A.

“…Glucose is a universal bioenergy source; however, its role in controlling protein interactions is unappreciated, as are its actions during…”
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PROBER identifies proteins associated with programmable sequence-specific DNA in living cells by Mondal, Smarajit, Ramanathan, Muthukumar, Miao, Weili, Meyers, Robin M., Rao, Deepti, Lopez-Pajares, Vanessa, Siprashvili, Zurab, Reynolds, David L., Porter, Douglas F., Ferguson, Ian, Neela, Poornima, Zhao, Yang, Meservey, Lindsey M., Guo, Margaret, Yang, Yen-Yu, Li, Lin, Wang, Yinsheng, Khavari, Paul A.

“…DNA–protein interactions mediate physiologic gene regulation and may be altered by DNA variants linked to polygenic disease. To enhance the speed and…”
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Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity by Qiu, Chen, Dutcher, Robert C, Porter, Douglas F, Arava, Yoav, Wickens, Marvin, Hall, Traci M Tanaka

“…PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and…”
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Germline stem cells and their regulation in the nematode Caenorhabditis elegans by Kershner, Aaron, Crittenden, Sarah L, Friend, Kyle, Sorensen, Erika B, Porter, Douglas F, Kimble, Judith

“…C. elegans germline stem cells exist within a stem cell pool that is maintained by a single-celled mesenchymal niche and Notch signaling. Downstream of Notch…”
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Analyzing RNA-Protein Interactions by Cross-Link Rates and CLIP-seq Libraries by Porter, Douglas F, Garg, Raghav M, Meyers, Robin M, Miao, Weili, Ducoli, Luca, Zarnegar, Brian J, Khavari, Paul A

“…UV cross-linking-based methods are the most common tool to explore in vivo RNA-protein interactions. UV cross-linking enables the freezing of direct…”
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Mechanism-based crosslinking as a gauge for functional interaction of modular synthases by Worthington, Andrew S, Porter, Douglas F, Burkart, Michael D

“…Protein-protein interactions between domains within fatty acid and polyketide synthases are critical to catalysis, but their contributions remain incompletely…”
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An RNA-Binding Multimer Specifies Nematode Sperm Fate by Aoki, Scott T., Porter, Douglas F., Prasad, Aman, Wickens, Marvin, Bingman, Craig A., Kimble, Judith

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