Searching journal content for articles similar to Markson et al. 19 (10): 1905.

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  1. Resource: A systems view on DNA damage response kinetics in Tetrahymena
    • Emily Nischwitz,
    • Vivien Schoonenberg,
    • Rachel Mullner,
    • Albert Fradera-Sola,
    • Susanne Zimbelmann,
    • Joshua J Smith,
    • and Falk Butter
    Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
    ...24 0 to 8 hours) integrates over 250 paired transcriptome and proteome measurements. We 25 observe upregulation of known DNA repair proteins as well as a global dynamic response of 26 not yet characterized transcripts and proteins. Using artificial neural networks, we classify 27 different expression...
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  2. LETTER: Control of Yeast Filamentous-Form Growth by Modules in an Integrated Molecular Network
    • Susanne Prinz,
    • Iliana Avila-Campillo,
    • Christine Aldridge,
    • Ajitha Srinivasan,
    • Krassen Dimitrov,
    • Andrew F. Siegel,
    • and Timothy Galitski
    Genome Res. March 2004 14: 380-390; doi:10.1101/gr.2020604
    ...a CUE domain that might be involved in binding ubiquitin-conjugating enzymes ( Shih et al. 2003 ). Moreover, two more genes encoding subunits of the 19S regulatory particle, RPN7 and RPN8 , are significantly induced in filamentous-form cells (Suppl. Table 1). Both proteins interact with Rpn12 ( Glickman...
  3. Research: Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins
    • Rosario Avolio,
    • Ilenia Agliarulo,
    • Daniela Criscuolo,
    • Daniela Sarnataro,
    • Margherita Auriemma,
    • Sabrina De Lella,
    • Sara Pennacchio,
    • Giovanni Calice,
    • Martin Y. Ng,
    • Carlotta Giorgi,
    • Paolo Pinton,
    • Barry S. Cooperman,
    • Matteo Landriscina,
    • Franca Esposito,
    • and Danilo Swann Matassa
    Genome Res. August 2023 33: 1242-1257; Published in Advance July 24, 2023, doi:10.1101/gr.277755.123
    ...is loosely associated to the endoplasmic reticulum membrane, facing the cytosol (Amoroso et al. 2012), and is bound to ribosomes and translation factors (Matassa et al. 2013). TRAP1 attenuates the rate of protein synthesis, thus allowing protein quality control and reducing cotranslational ubiquitination...
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  4. Research: Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states
    • Emily J. Collins,
    • Mariana P. Cervantes-Silva,
    • George A. Timmons,
    • James R. O'Siorain,
    • Annie M. Curtis,
    • and Jennifer M. Hurley
    Genome Res. February 2021 31: 171-185; Published in Advance January 12, 2021, doi:10.1101/gr.263814.120
    ...(Supplemental Fig. S4A). We modeled and calculated the average level of rhythmic proteins involved in protein ubiquitination/degradation over the day. We found that the average peak of protein degrading enzymes was in the late phase (Fig. 3D; Supplemental Fig. S4D). This suggests that ubiquitin...
  5. Research: Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
    • Kamal Ajit,
    • Adele Alagia,
    • Kaspar Burger,
    • and Monika Gullerova
    Genome Res. February 2024 34: 201-216; Published in Advance March 11, 2024, doi:10.1101/gr.278644.123
    ...2 leads to loss of transcriptional repression. Our results reveal a novel function of Y1P-dependent PROMPTs in mediating PRC2 recruitment to chromatin and RNA Pol II promoter pausing in response to DNA damage.RNA polymerase II (RNA Pol II) is an essential enzyme that catalyzes the transcription...
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  6. Research: SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
    • Fu-Yuan Zhu,
    • Xin Chen,
    • Yu-Chen Song,
    • Lydia Pui Ying Lam,
    • Yuki Tobimatsu,
    • Bei Gao,
    • Mo-Xian Chen,
    • and Fu-Liang Cao
    Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122
    ...–qPCR experiments. PtUBIC (ubiquitin-conjugating) and PtACT6 (Actin6) were used as internal reference genes (Supplemental Fig. S11). All the primers, including the isoform-specific primers used for the RT–qPCR experiments, are listed in Supplemental Table S4.Measurement of the Pb(II) content in poplarTransgenic Pt...
  7. LETTER: The Comparative Proteomics of Ubiquitination in Mouse
    • Colin A.M. Semple,
    • RIKEN GER Group,
    • and GSL Members
    Genome Res. June 2003 13: 1389-1394; doi:10.1101/gr.980303
    ...in eukaryotic cells, influencing many fundamental cellular processes. Defects in ubiquitination and the processes it mediates are involved in many human disease states. The ubiquitination of a substrate involves four classes of enzymes:a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2...
  8. Resource: Global analysis of protein homomerization in Saccharomyces cerevisiae
    • Yeonsoo Kim,
    • Jong Pil Jung,
    • Chan-Gi Pack,
    • and Won-Ki Huh
    Genome Res. January 2019 29: 135-145; Published in Advance December 19, 2018, doi:10.1101/gr.231860.117
    ...efficient ways for cells to regulate the function, concentration, and structure of proteins. It can help to minimize the size while providing the advantages of modular complex formation, and it has been reported that more than one-third of human enzymes function as homomers (Marianayagam et al. 2004...
  9. Research: Physiological intron retaining transcripts in the cytoplasm abound during human motor neurogenesis
    • Marija Petrić Howe,
    • Hamish Crerar,
    • Jacob Neeves,
    • Jasmine Harley,
    • Giulia E. Tyzack,
    • Pierre Klein,
    • Andres Ramos,
    • Rickie Patani,
    • and Raphaëlle Luisier
    Genome Res. October 2022 32: 1808-1825; Published in Advance September 30, 2022, doi:10.1101/gr.276898.122
    ...the five regions of interest for the {C4, C5, C6} groups as opposed to the other groups, where UPF1 is strictly enriched in R1 and R5 regions (Supplemental Fig. S2E). Different combinations of RBPs have been shown to coordinately regulate functionally coherent “networks” of exons and introns (Ule...
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  10. Method: TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance
    • Muhammad Yasir,
    • A. Keith Turner,
    • Sarah Bastkowski,
    • David Baker,
    • Andrew J. Page,
    • Andrea Telatin,
    • Minh-Duy Phan,
    • Leigh Monahan,
    • George M. Savva,
    • Aaron Darling,
    • Mark A. Webber,
    • and Ian G. Charles
    Genome Res. February 2020 30: 239-249; Published in Advance February 12, 2020, doi:10.1101/gr.254391.119
    ...that inhibit enzymes in this pathway have progressed to different stages of clinical development as novel antibiotics, but triclosan is the only one in widespread domestic use. Triclosan specifically inhibits the enzyme FabI; an enoyl-acyl carrier protein (ACP) reductase conserved across bacteria; hence...
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