Searching journal content for articles similar to Petti and Church 15 (9): 1298.

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  1. Research: Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
    • Andre J. Faure,
    • Dominic Schmidt,
    • Stephen Watt,
    • Petra C. Schwalie,
    • Michael D. Wilson,
    • Huiling Xu,
    • Robert G. Ramsay,
    • Duncan T. Odom,
    • and Paul Flicek
    Genome Res. November 2012 22: 2163-2175; Published in Advance July 10, 2012, doi:10.1101/gr.136507.111
    ...Cohesin regulates tissue-specific expression by stabilizing highly occupied cis -regulatory modules Andre J. Faure 1 , 7 , Dominic Schmidt 2 , 3 , 7 , Stephen Watt 2 , 3 , Petra C. Schwalie 1 , Michael D. Wilson 2 , 3 , 8...
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  2. Research: Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation
    • Hélène Neyret-Kahn,
    • Moussa Benhamed,
    • Tao Ye,
    • Stéphanie Le Gras,
    • Jack-Christophe Cossec,
    • Pierre Lapaquette,
    • Oliver Bischof,
    • Maia Ouspenskaia,
    • Mary Dasso,
    • Jacob Seeler,
    • Irwin Davidson,
    • and Anne Dejean
    Genome Res. October 2013 23: 1563-1579; Published in Advance July 26, 2013, doi:10.1101/gr.154872.113
    ...Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation Hélène Neyret-Kahn 1 , 2 , 3 , Moussa Benhamed 1 , 2 , 3 , 6 , Tao Ye 4 , Stéphanie Le Gras 4 , Jack...
  3. 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
    ...of the clusters to modules is supported by significant coordinated expression change among cluster co-member genes, and the quantitative identification of collective functions controlling cell properties. The modular abstraction of the filamentation network enables the association of filamentous-form cell...
  4. Article: A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome
    • Bryan J. Venters and
    • B. Franklin Pugh
    Genome Res. March 2009 19: 360-371; Published in Advance January 5, 2009, doi:10.1101/gr.084970.108
    ...representative components of the gene regulatory machinery in Saccharomyces cerevisiae to an experimental resolution of <40 bp. Sequence-specific gene regulators, chromatin regulators, mediator, and RNA polymerase (Pol) II were found primarily near the downstream border from the “−1” nucleosome, which abuts...
  5. Method: System-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organization and function of RNA–protein complexes
    • Cornelia Kilchert,
    • Tea Kecman,
    • Emily Priest,
    • Svenja Hester,
    • Ebru Aydin,
    • Krzysztof Kus,
    • Oliver Rossbach,
    • Alfredo Castello,
    • Shabaz Mohammed,
    • and Lidia Vasiljeva
    Genome Res. July 2020 30: 1012-1026; Published in Advance June 18, 2020, doi:10.1101/gr.257006.119
    ...). For reference, standard gene names for enriched RPs are given in Supplemental Fig. S2B. (B) Structure of the Saccharomyces cerevisiae 80S ribosome [PDB:5MC6] (Schmidt et al. 2016). RPs with S. pombe orthologs that were highly significantly enriched on poly(A)+ RNA are designated in blue. For reference, the m...
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  6. Research: DDX54 regulates transcriptome dynamics during DNA damage response
    • Miha Milek,
    • Koshi Imami,
    • Neelanjan Mukherjee,
    • Francesca De Bortoli,
    • Ulrike Zinnall,
    • Orsalia Hazapis,
    • Christian Trahan,
    • Marlene Oeffinger,
    • Florian Heyd,
    • Uwe Ohler,
    • Matthias Selbach,
    • and Markus Landthaler
    Genome Res. August 2017 27: 1344-1359; Published in Advance June 8, 2017, doi:10.1101/gr.218438.116
    ...by a well-characterized network of DNA surveillance pathways. The contribution of post-transcriptional gene regulatory networks to the DNAdamage response (DDR) has not been extensively studied. Here, we systematically identified RNA-binding proteins differentially interacting with polyadenylated transcripts...
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  7. Research: Chromatin signatures of the Drosophila replication program
    • Matthew L. Eaton,
    • Joseph A. Prinz,
    • Heather K. MacAlpine,
    • George Tretyakov,
    • Peter V. Kharchenko,
    • and David M. MacAlpine
    Genome Res. February 2011 21: 164-174; Published in Advance December 22, 2010, doi:10.1101/gr.116038.110
    ...DNA replication initiates from thousands of start sites throughout the Drosophila genome and must be coordinated with other ongoing nuclear processes such as transcription to ensure genetic and epigenetic inheritance. Considerable progress has been made toward understanding how chromatin...
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  8. Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
    • Xingmin Han,
    • Chenghui Xu,
    • Yiyi Ren,
    • Meiling Guo,
    • Jiayue Yan,
    • Xuan Wang,
    • Chao Liu,
    • Qin Gu,
    • Xing-Xing Shen,
    • Zhonghua Ma,
    • and Yun Chen
    Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
    ...additional functions of Set2. Loss of SET2 in Saccharomyces cerevisiae leads to increased histone exchange and H3K56ac accumulation within gene bodies, facilitating aberrant transcriptional activation (Venkatesh et al. 2012). Set2-mediated H3K36 methylation is critical for proper pre-mRNA splicing, and its...
  9. 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
    ...phosphorylates Y1 in the CTD of RNA Pol II. Up-regulation of ABL1 was also reported as a consequence of activation of upstream DDR regulators such as DNA-dependent protein kinase (DNA-PK) and ATM. Another study (Yurko et al. 2017) showed overall increased levels of Y1P following IR in Saccharomyces cerevisiae...
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  10. Research: Sir3 mediates long-range chromosome interactions in budding yeast
    • Myriam Ruault,
    • Vittore F. Scolari,
    • Luciana Lazar-Stefanita,
    • Antoine Hocher,
    • Isabelle Loïodice,
    • Romain Koszul,
    • and Angela Taddei
    Genome Res. March 2021 31: 411-425; Published in Advance February 12, 2021, doi:10.1101/gr.267872.120
    ...of Saccharomyces cerevisiae cluster within 3 to 5 foci mainly found at the nuclear periphery, where the silencing information regulators Sir2, Sir3, and Sir4, forming the SIR complex, concentrate (Gotta et al. 1996). These clusters represent a well-documented example of a repressive nuclear subcompartment (Kueng...
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