Now showing items 1-20 of 59

    • Abelson Phosphorylation of CLASP2 Modulates its Association With Microtubules and Actin 

      Engel, Ulrike; Zhan, Yougen; Long, Jennifer B; Boyle, Scott N; Ballif, Bryan A; Dorey, Karel; Gygi, Steven P; Koleske, Anthony J; VanVactor, David (Blackwell Publishing Ltd, 2014)
      The Abelson (Abl) non-receptor tyrosine kinase regulates the cytoskeleton during multiple stages of neural development, from neurulation, to the articulation of axons and dendrites, to synapse formation and maintenance. ...
    • Activation of Multiple Proto-oncogenic Tyrosine Kinases in Breast Cancer via Loss of the PTPN12 Phosphatase 

      Sun, Tingting; Aceto, Nicola; Meerbrey, Kristen L.; Kessler, Jessica D.; Zhou, Chunshui; Migliaccio, Ilenia; Nguyen, Don X.; Pavlova, Natalya N.; Botero, Maria; Huang, Jian; Bernardi, Ronald J.; Schmitt, Earlene; Hu, Guang; Li, Mamie Z.; Dephoure, Noah; Rao, Mitchell; Creighton, Chad J.; Hilsenbeck, Susan G.; Shaw, Chad A.; Muzny, Donna; Gibbs, Richard A.; Wheeler, David A.; Osborne, C. Kent; Schiff, Rachel; Bentires-Alj, Mohamed; Westbrook, Thomas F.; Elledge, Stephen; Gygi, Steven (Elsevier BV, 2011-03)
      Among breast cancers, triple-negative breast cancer (TNBC) is the most poorly understood and is refractory to current targeted therapies. Using a genetic screen, we identify the PTPN12 tyrosine phosphatase as a tumor ...
    • Adapting Quantitative Protein and Phosphorylation Analyses to a Proteome-Wide Scale 

      Grady, Joshua Terrence Wilson (2013-09-30)
      Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) has become the preferred method for large-scale peptide and phosphopeptide identification and quantification. The dominance of LC-MS/MS is the result of ...
    • Adiporedoxin, an upstream regulator of ER oxidative folding and protein secretion in adipocytes 

      Jedrychowski, Mark P.; Liu, Libin; Laflamme, Collette J.; Karastergiou, Kalypso; Meshulam, Tova; Ding, Shi-Ying; Wu, Yuanyuan; Lee, Mi-Jeong; Gygi, Steven P.; Fried, Susan K.; Pilch, Paul F. (Elsevier, 2015)
      Objective: Adipocytes are robust protein secretors, most notably of adipokines, hormone-like polypeptides, which act in an endocrine and paracrine fashion to affect numerous physiological processes such as energy balance ...
    • C. elegans SIRT6/7 Homolog SIR-2.4 Promotes DAF-16 Relocalization and Function during Stress 

      Chiang, Wei-Chung; Tishkoff, Daniel X.; Yang, Bo; Grady, Joshua Terrence Wilson; Yu, Xiaokun; Mazer, Travis; Eckersdorff, Mark; Gygi, Steven P.; Lombard, David B.; Hsu, Ao-Lin (Public Library of Science, 2012)
      FoxO transcription factors and sirtuin family deacetylases regulate diverse biological processes, including stress responses and longevity. Here we show that the Caenorhabditis elegans sirtuin SIR-2.4—homolog of mammalian ...
    • Combining Amine Metabolomics and Quantitative Proteomics of Cancer Cells Using Derivatization with Isobaric Tags 

      Murphy, J. Patrick; Everley, Robert A.; Coloff, Jonathan L.; Gygi, Steven P. (American Chemical Society, 2014)
      Quantitative metabolomics and proteomics technologies are powerful approaches to explore cellular metabolic regulation. Unfortunately, combining the two technologies typically requires different LC-MS setups for sensitive ...
    • Combining Genetic Perturbations and Proteomics to Examine Kinase-Phosphatase Networks in Drosophila Embryos 

      Sopko, Richelle; Foos, Marianna; Vinayagam, Arunachalam; Zhai, Bo; Binari, Richard; Hu, Yanhui; Randklev, Sakara; Perkins, Lizabeth A.; Gygi, Steven; Perrimon, Norbert (Elsevier BV, 2014-10-13)
      Connecting phosphorylation events to kinases and phosphatases is key to understanding the molecular organization and signaling dynamics of networks. We have generated a validated set of transgenic RNA-interference reagents ...
    • A Conserved CCCH-type Zinc Finger Protein Regulates mRNA Nuclear Adenylation and Export 

      Hurt, Jessica A.; Obar, Robert Alan; Zhai, Bo; Farny, Natalie G.; Gygi, Steven P.; Silver, Pamela A. (The Rockefeller University Press, 2009)
      Coupling of messenger RNA (mRNA) nuclear export with prior processing steps aids in the fidelity and efficiency of mRNA transport to the cytoplasm. In this study, we show that the processes of export and polyadenylation ...
    • Cooperative Interaction between Phosphorylation Sites on PERIOD Maintains Circadian Period in Drosophila 

      Garbe, David S.; Fang, Yanshan; Zheng, Xiangzhong; Sowcik, Mallory; Anjum, Rana; Gygi, Steven P.; Sehgal, Amita (Public Library of Science, 2013)
      Circadian rhythms in Drosophila rely on cyclic regulation of the period (per) and timeless (tim) clock genes. The molecular cycle requires rhythmic phosphorylation of PER and TIM proteins, which is mediated by several ...
    • Dual DNA and Protein Tagging of Open Chromatin Unveils Dynamics of Epigenomic Landscapes in Leukemia 

      Lee, Jonathan D.; Paulo, Joao; Posey, Ryan R.; Mugoni, Vera; Kong, Nikki; Cheloni, Giulia; Lee, Yu-Ru; Slack, Frank; Tenen, Daniel; Clohessy, John; Gygi, Steven; Pandolfi, Pier Paolo (Springer Science and Business Media LLC, 2021-03-01)
      The architecture of chromatin specifies eukaryotic cell identity by controlling transcription factor access to sites of gene regulation. Here we describe a dual transposase/peroxidase approach, integrative DNA And Protein ...
    • During Muscle Atrophy, Thick, but not Thin, Filament Components are Degraded by MuRF1-Dependent Ubiquitylation 

      Cohen, Shenhav Orit; Brault, Jeffrey J.; Gygi, Steven P.; Glass, David Jonathan; Valenzuela, David M.; Gartner, Carlos; Latres, Esther; Goldberg, Alfred L. (Rockefeller University Press, 2009)
      Loss of myofibrillar proteins is a hallmark of atrophying muscle. Expression of muscle RING-finger 1 (MuRF1), a ubiquitin ligase, is markedly induced during atrophy, and MuRF1 deletion attenuates muscle wasting. We generated ...
    • eIF1A augments Ago2-mediated Dicer-independent miRNA biogenesis and RNA interference 

      Yi, Tingfang; Arthanari, Haribabu; Akabayov, Barak; Song, Huaidong; Papadopoulos, Evangelos; Qi, Hank H.; Jedrychowski, Mark; Güttler, Thomas; Guo, Cuicui; Luna, Rafael E.; Gygi, Steven P.; Huang, Stephen A.; Wagner, Gerhard (2015)
      MicroRNA (miRNA) biogenesis and miRNA-guided RNA interference (RNAi) are essential for gene expression in eukaryotes. Here we report that translation initiation factor eIF1A directly interacts with Ago2 and promotes Ago2 ...
    • An Erk/Cdk5 axis controls the diabetogenic actions of PPARγ 

      Banks, Alexander S.; McAllister, Fiona E.; Camporez, João Paulo G.; Zushin, Peter-James H.; Jurczak, Michael J.; Laznik-Bogoslavski, Dina; Shulman, Gerald I.; Gygi, Steven P.; Spiegelman, Bruce M. (2014)
      Obesity-linked insulin resistance is a major precursor to the development of type 2 diabetes. Previous work has shown that phosphorylation of PPARγ at serine 273 by Cdk5 stimulates diabetogenic gene expression in adipose ...
    • Evaluating Multiplexed Quantitative Phosphopeptide Analysis on a Hybrid Quadrupole Mass Filter/Linear Ion Trap/Orbitrap Mass Spectrometer 

      Erickson, Brian K.; Jedrychowski, Mark P.; McAlister, Graeme C.; Everley, Robert A.; Kunz, Ryan; Gygi, Steven P. (American Chemical Society, 2014)
      As a driver for many biological processes, phosphorylation remains an area of intense research interest. Advances in multiplexed quantitation utilizing isobaric tags (e.g., TMT and iTRAQ) have the potential to create a new ...
    • Evidence that a consensus element found in naturally intronless mRNAs promotes mRNA export 

      Lei, Haixin; Zhai, Bo; Yin, Shanye; Gygi, Steve; Reed, Robin (Oxford University Press, 2012)
      We previously showed that mRNAs synthesized from three genes that naturally lack introns contain a portion of their coding sequence, known as a cytoplasmic accumulation region (CAR), which is essential for stable accumulation ...
    • Extended ubiquitin species are protein-based DUB inhibitors 

      Krutauz, Daria; Reis, Noa; Nakasone, Mark A.; Siman, Peter; Zhang, Daoning; Kirkpatrick, Donald S.; Gygi, Steven P.; Brik, Ashraf; Fushman, David; Glickman, Michael H. (2015)
      A frame-shift mutation in the transcript of the ubiquitin-B gene leads to a C-terminally extended ubiquitin, UBB+1. UBB+1 has been considered to inhibit proteasomes, and as such to be the underlying cause for toxic protein ...
    • Hem-1 Complexes Are Essential for Rac Activation, Actin Polymerization, and Myosin Regulation during Neutrophil Chemotaxis 

      Weiner, Orion D; Rentel, Maike C; Ott, Alex; Bourne, Henry R; Schliwa, Manfred; Brown, Glenn E.; Jedrychowski, Mark P.; Yaffe, Michael Bruce; Gygi, Steven P.; Cantley, Lewis C.; Kirschner, Marc W. (Public Library of Science, 2006)
      Migrating cells need to make different actin assemblies at the cell's leading and trailing edges and to maintain physical separation of signals for these assemblies. This asymmetric control of activities represents one ...
    • The Hippo Signaling Pathway Interactome 

      Kwon, Young; Vinayagam, Arunachalam; Sun, Xiaoyun; Dephoure, Noah; Gygi, Steven; Hong, Pengyu; Perrimon, Norbert (American Association for the Advancement of Science (AAAS), 2013-11-08)
      The Hippo pathway controls metazoan organ growth by regulating cell proliferation and apoptosis. Many components have been identified, but our knowledge of the composition and structure of this pathway is still incomplete. ...
    • The histone demethylase LSD1/KDM1A promotes the DNA damage response 

      Mosammaparast, Nima; Kim, Haeyoung; Laurent, Benoit; Zhao, Yu; Lim, Hui Jun; Majid, Mona C.; Dango, Sebastian; Luo, Yuying; Hempel, Kristina; Sowa, Mathew E.; Gygi, Steven P.; Steen, Hanno; Harper, J. Wade; Yankner, Bruce; Shi, Yang (The Rockefeller University Press, 2013)
      Histone demethylation is known to regulate transcription, but its role in other processes is largely unknown. We report a role for the histone demethylase LSD1/KDM1A in the DNA damage response (DDR). We show that LSD1 is ...
    • Identification of a Unique TGF-β Dependent Molecular and Functional Signature in Microglia 

      Butovsky, Oleg; Jedrychowski, Mark P.; Moore, Craig S.; Cialic, Ron; Lanser, Amanda J.; Gabriely, Galina; Koeglsperger, Thomas; Dake, Ben; Wu, Pauline M.; Doykan, Camille E.; Fanek, Zain; Liu, LiPing; Chen, Zhuoxun; Rothstein, Jeffrey D.; Ransohoff, Richard M.; Gygi, Steven P.; Antel, Jack P.; Weiner, Howard L. (2014)
      Microglia are myeloid cells of the central nervous system (CNS) that participate both in normal CNS function and disease. We investigated the molecular signature of microglia and identified 239 genes and 8 microRNAs that ...