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RNA, Messenger

  • 1.
    Zhang D, Li S, King C, Wingreen N, Gitai Z, Li Z. Global and gene-specific translational regulation in Escherichia coli across different conditions. PLoS Comput Biol. 2022;18(10):e1010641. PMCID: PMC9624429
    Reference Link
  • 1.
    Li H, Gavis E. Drosophila FMRP controls miR-276-mediated regulation of nejire mRNA for space-filling dendrite development. G3 (Bethesda). 2022;12(11). PMCID: PMC9635640
    Reference Link
  • 1.
    Arguello E, Li A, Sun X, Eggert T, Mairhofer E, Kleiner R. Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases. Nat Commun. 2022;13(1):4176. PMCID: PMC9296451
    Reference Link
  • 1.
    Li H, Gavis E. The Drosophila fragile X mental retardation protein modulates the neuronal cytoskeleton to limit dendritic arborization. Development. 2022;149(10). PMID: 35502752
    Reference Link
  • 1.
    Valentino M, Ortega B, Ulrich B, Doyle D, Farnum E, Joiner D, Gavis E, Niepielko M. Computational modeling offers new insight into Drosophila germ granule development. Biophys J. 2022;121(8):1465–1482. PMCID: PMC9072583
    Reference Link
  • 1.
    Miangolarra M, Li S, Joanny J-F, Wingreen N, Castellana M. Steric interactions and out-of-equilibrium processes control the internal organization of bacteria. Proc Natl Acad Sci U S A. 2021;118(43). PMCID: PMC8639350
    Reference Link
  • 1.
    Gilmutdinov R, Kozlov E, Yakovlev K, Olenina L, Kotov A, Barr J, Zhukova M, Schedl P, Shidlovskii Y. The 3’UTR of the Drosophila CPEB translation factor gene orb2 plays a crucial role in spermatogenesis. Development. 2021;148(17). PMCID: PMC8513165
    Reference Link
  • 1.
    Cho S, Lee G, Pickering B, Jang C, Park J, He L, Mathur L, Kim S-S, Jung S, Tang H-W, Monette S, Rabinowitz J, Perrimon N, Jaffrey S, Blenis J. mTORC1 promotes cell growth via mA-dependent mRNA degradation. Mol Cell. 2021;81(10):2064–2075.e8. PMCID: PMC8356906
    Reference Link
  • 1.
    Eickhoff M, Fei C, Huang X, Bassler B. LuxT controls specific quorum-sensing-regulated behaviors in Vibrionaceae spp. via repression of qrr1, encoding a small regulatory RNA. PLoS Genet. 2021;17(4):e1009336. PMCID: PMC8043402
    Reference Link
  • 1.
    Kan L, Ott S, Joseph B, Park E, Dai W, Kleiner R, Claridge-Chang A, Lai E. A neural mA/Ythdf pathway is required for learning and memory in Drosophila. Nat Commun. 2021;12(1):1458. PMCID: PMC7935873
    Reference Link
  • 1.
    Diegmiller R, Zhang L, Gameiro M, Barr J, Alsous J, Schedl P, Shvartsman S, Mischaikow K. Mapping parameter spaces of biological switches. PLoS Comput Biol. 2021;17(2):e1008711. PMCID: PMC7895388
    Reference Link
  • 1.
    Seo K, Kleiner R. Mechanisms of epitranscriptomic gene regulation. Biopolymers. 2021;112(1):e23403. PMCID: PMC7855325
    Reference Link
  • 1.
    Cao W, Kabelitz S, Gupta M, Yeung E, Lin S, Rammelt C, Ihling C, Pekovic F, Low T, Siddiqui N, Cheng M, Angers S, Smibert C, Wühr M, Wahle E, Lipshitz H. Precise Temporal Regulation of Post-transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition. Cell Rep. 2020;31(12):107783. PMCID: PMC7372737
    Reference Link
  • 1.
    Trcek T, Douglas T, Grosch M, Yin Y, Eagle W, Gavis E, Shroff H, Rothenberg E, Lehmann R. Sequence-Independent Self-Assembly of Germ Granule mRNAs into Homotypic Clusters. Mol Cell. 2020;78(5):941–950.e12. PMCID: PMC7325742
    Reference Link
  • 1.
    Eichler C, Hakes A, Hull B, Gavis E. Compartmentalized degradation in the germ plasm safeguards germline development. Elife. 2020;9. PMCID: PMC6986870
    Reference Link
  • 1.
    Arey R, Kaletsky R, Murphy C. Nervous system-wide profiling of presynaptic mRNAs reveals regulators of associative memory. Sci Rep. 2019;9(1):20314. PMCID: PMC6937282
    Reference Link
  • 1.
    Seo K, Kleiner R. YTHDF2 Recognition of N-Methyladenosine (mA)-Modified RNA Is Associated with Transcript Destabilization. ACS Chem Biol. 2020;15(1):132–139. PMCID: PMC7025767
    Reference Link
  • 1.
    Barr J, Gilmutdinov R, Wang L, Shidlovskii Y ii, Schedl P. The CPEB Protein Orb Specifies Oocyte Fate by a 3’UTR-Dependent Autoregulatory Loop. Genetics. 2019;213(4):1431–1446. PMCID: PMC6893371
    Reference Link
  • 1.
    Rath S, Prangley E, Donovan J, Demarest K, Wingreen N, Meir Y, Korennykh A. Concerted 2-5A-Mediated mRNA Decay and Transcription Reprogram Protein Synthesis in the dsRNA Response. Mol Cell. 2019;75(6):1218–1228.e6. PMCID: PMC6754276
    Reference Link
  • 1.
    Rodriguez A, Ducker G, Billingham L, Martinez C, Mainolfi N, Suri V, Friedman A, Manfredi M, Weinberg S, Rabinowitz J, Chandel N. Serine Metabolism Supports Macrophage IL-1β Production. Cell Metab. 2019;29(4):1003–1011.e4. PMCID: PMC6447453
    Reference Link
  • 1.
    Barr J, Charania S, Gilmutdinov R, Yakovlev K, Shidlovskii Y ii, Schedl P. The CPEB translational regulator, Orb, functions together with Par proteins to polarize the Drosophila oocyte. PLoS Genet. 2019;15(3):e1008012. PMCID: PMC6433291
    Reference Link
  • 1.
    Zhuo W, Liu Y, Li S, Guo D, Sun Q, Jin J, Rao X, Li M, Sun M, Jiang M, Xu Y, Teng L, Jin Y, Si J, Liu W, Kang Y, Zhou T. Long Noncoding RNA GMAN, Up-regulated in Gastric Cancer Tissues, Is Associated With Metastasis in Patients and Promotes Translation of Ephrin A1 by Competitively Binding GMAN-AS. Gastroenterology. 2019;156(3):676–691.e11. PMID: 30445010
    Reference Link
  • 1.
    Eagle W, Yeboah-Kordieh D, Niepielko M, Gavis E. Distinct -acting elements mediate targeting and clustering of polar granule mRNAs. Development. 2018;145(22). PMCID: PMC6262787
    Reference Link
  • 1.
    Gilbertson S, Federspiel J, Hartenian E, Cristea I, Glaunsinger B. Changes in mRNA abundance drive shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription. Elife. 2018;7. PMCID: PMC6203436
    Reference Link
  • 1.
    Kachaev Z, Lebedeva L, Kozlov E, Toropygin I, Schedl P, Shidlovskii Y. Paip2 is localized to active promoters and loaded onto nascent mRNA in Drosophila. Cell Cycle. 2018;17(14):1708–1720. PMCID: PMC6133343
    Reference Link
  • 1.
    Fröhlich K, Förstner K, Gitai Z. Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus. Nucleic Acids Res. 2018;46(20):10969–10982. PMCID: PMC6237742
    Reference Link
  • 1.
    Painter H, Chung N, Sebastian A, Albert I, Storey J, Llinás M. Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development. Nat Commun. 2018;9(1):2656. PMCID: PMC6037754
    Reference Link
  • 1.
    Niepielko M, Eagle W, Gavis E. Stochastic Seeding Coupled with mRNA Self-Recruitment Generates Heterogeneous Drosophila Germ Granules. Curr Biol. 2018;28(12):1872–1881.e3. PMCID: PMC6008217
    Reference Link
  • 1.
    Little S, Gregor T. Single mRNA Molecule Detection in Drosophila. Methods Mol Biol. 2018;1649:127–142. PMCID: PMC5772605
    Reference Link
  • 1.
    Garcia H, Gregor T. Live Imaging of mRNA Synthesis in Drosophila. Methods Mol Biol. 2018;1649:349–357. PMCID: PMC5909709
    Reference Link
  • 1.
    Wilson M, Ravindran P, Lim W, Toettcher J. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell. 2017;67(5):757–769.e5. PMCID: PMC5591080
    Reference Link
  • 1.
    Geronimo C, Zakian V. Getting it done at the ends: Pif1 family DNA helicases and telomeres. DNA Repair (Amst). 2016;44:151–158. PMCID: PMC5441554
    Reference Link
  • 1.
    Son H, Seo M, Ham S, Hwang W, Lee D, An S, Artan M, Seo K, Kaletsky R, Arey R, Ryu Y, Ha C, Kim Y, Murphy C, Roh T-Y, Nam H, Lee S-J. RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans. Nat Commun. 2017;8:14749. PMCID: PMC5347137
    Reference Link
  • 1.
    Ziehr B, Lenarcic E, Vincent H, Cecil C, Garcia B, Shenk T, Moorman N. Human cytomegalovirus TRS1 protein associates with the 7-methylguanosine mRNA cap and facilitates translation. Proteomics. 2015;15(12):1983–94. PMCID: PMC4492309
    Reference Link
  • 1.
    Trovisco V, Belaya K, Nashchekin D, Irion U, Sirinakis G, Butler R, Lee J, Gavis E, St Johnston D. mRNA localises to the oocyte anterior by random Dynein-mediated transport and anchoring. Elife. 2016;5. PMCID: PMC5125753
    Reference Link
  • 1.
    Chikina M, Gerald C, Li X, Ge Y, Pincas H, Nair V, Wong A, Krishnan A, Troyanskaya O, Raymond D, Saunders-Pullman R, Bressman S, Yue Z, Sealfon S. Low-variance RNAs identify Parkinson’s disease molecular signature in blood. Mov Disord. 2015;30(6):813–21. PMCID: PMC4439364
    Reference Link
  • 1.
    Crow M, Lum K, Sheng X, Song B, Cristea I. Diverse mechanisms evolved by DNA viruses to inhibit early host defenses. Crit Rev Biochem Mol Biol. 2016;51(6):452–481. PMCID: PMC5285405
    Reference Link
  • 1.
    Robinson J, Brynildsen M. An ensemble-guided approach identifies ClpP as a major regulator of transcript levels in nitric oxide-stressed Escherichia coli. Metab Eng. 2015;31:22–34. PMID: 26112956
    Reference Link
  • 1.
    Crocker A, Guan X-J, Murphy C, Murthy M. Cell-Type-Specific Transcriptome Analysis in the Drosophila Mushroom Body Reveals Memory-Related Changes in Gene Expression. Cell Rep. 2016;15(7):1580–1596. PMCID: PMC5047377
    Reference Link
  • 1.
    Misra M, Edmund H, Ennis D, Schlueter M, Marot J, Tambasco J, Barlow I, Sigurbjornsdottir S, Mathew R, Vallés A, Wojciech W, Roth S, Davis I, Leptin M, Gavis E. A Genome-Wide Screen for Dendritically Localized RNAs Identifies Genes Required for Dendrite Morphogenesis. G3 (Bethesda). 2016;6(8):2397–405. PMCID: PMC4978894
    Reference Link
  • 1.
    Castellana M, Li S, Wingreen N. Spatial organization of bacterial transcription and translation. Proc Natl Acad Sci U S A. 2016;113(33):9286–91. PMCID: PMC4995950
    Reference Link
  • 1.
    Kim H, Pang M-F, Varner V, Kojima L, Miller E, Radisky D, Nelson C. Localized Smooth Muscle Differentiation Is Essential for Epithelial Bifurcation during Branching Morphogenesis of the Mammalian Lung. Dev Cell. 2015;34(6):719–26. PMCID: PMC4589145
    Reference Link
  • 1.
    Zhang H, Elbaum-Garfinkle S, Langdon E, Taylor N, Occhipinti P, Bridges A, Brangwynne C, Gladfelter A. RNA Controls PolyQ Protein Phase Transitions. Mol Cell. 2015;60(2):220–30. PMCID: PMC5221516
    Reference Link
  • 1.
    Elbaum-Garfinkle S, Brangwynne C. Liquids, Fibers, and Gels: The Many Phases of Neurodegeneration. Dev Cell. 2015;35(5):531–532. PMID: 26651288
    Reference Link
  • 1.
    Tetruashvily M, Melson J, Park J, Peng X, Boulanger L. Expression and alternative splicing of classical and nonclassical MHCI genes in the hippocampus and neuromuscular junction. Mol Cell Neurosci. 2016;72:34–45. PMCID: PMC4821772
    Reference Link
  • 1.
    Little S, Sinsimer K, Lee J, Wieschaus E, Gavis E. Independent and coordinate trafficking of single Drosophila germ plasm mRNAs. Nat Cell Biol. 2015;17(5):558–68. PMCID: PMC4417036
    Reference Link
  • 1.
    Bothma J, Garcia H, Esposito E, Schlissel G, Gregor T, Levine M. Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos. Proc Natl Acad Sci U S A. 2014;111(29):10598–603. PMCID: PMC4115566
    Reference Link
  • 1.
    Barr J, Yakovlev K, Shidlovskii Y ii, Schedl P. Establishing and maintaining cell polarity with mRNA localization in Drosophila. Bioessays. 2016;38(3):244–53. PMCID: PMC4871591
    Reference Link
  • 1.
    Li W, Klovstad M, Schüpbach T. Repression of Gurken translation by a meiotic checkpoint in Drosophila oogenesis is suppressed by a reduction in the dose of eIF1A. Development. 2014;141(20):3910–21. PMCID: PMC4197705
    Reference Link
  • 1.
    Desai V, Hsia H, Schwarzbauer J. Reversible modulation of myofibroblast differentiation in adipose-derived mesenchymal stem cells. PLoS One. 2014;9(1):e86865. PMCID: PMC3900664
    Reference Link

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