Searching journal content for articles similar to Venters and Pugh 19 (3): 360.

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  1. Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
    • Kevin Moyung,
    • Yulong Li,
    • Heather K. MacAlpine,
    • Alexander J. Hartemink,
    • and David M. MacAlpine
    Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
    ...-wide landscape of chromatin occupancy for 201 transcriptional regulator mutants. (A) Functional classification of the 201 mutants in our MNase-seq data set. Labels are derived from the Saccharomyces Genome Database. (B) Schematic illustrating chromatin occupancy profiling of 201 yeast mutants via MNase...
  2. Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
    • Thomas D. Lewin,
    • Isabel Jiah-Yih Liao,
    • Mu-En Chen,
    • John D.D. Bishop,
    • Peter W.H. Holland,
    • and Yi-Jyun Luo
    Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
    ...; Lin et al. 2024), suggesting that there are substantial functional constraints to organization. Conservation of ALGs seems to be the norm at the phylum level, but several lineages at lower taxonomic levels have experienced genomic scrambling, including the breaking up or mixing of genes from different...
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  3. Resource: Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae
    • Zhaolian Lu and
    • Zhenguo Lin
    Genome Res. July 2019 29: 1198-1210; Published in Advance May 10, 2019, doi:10.1101/gr.245456.118
    ...in response to various environmental stimuli in a classic model organism Saccharomyces cerevisiae has not been systematically investigated. In this study, we generated quantitative maps of transcription start sites (TSSs) at a single-nucleotide resolution for S. cerevisiae grown in nine different conditions...
  4. Research: Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase
    • Boning Chen,
    • Heather K. MacAlpine,
    • Alexander J. Hartemink,
    • and David M. MacAlpine
    Genome Res. December 2023 33: 2108-2118; Published in Advance December 11, 2023, doi:10.1101/gr.278273.123
    ....In eukaryotic cells, genomic DNA is packaged into chromatin, a highly organized DNA–protein complex that encodes the epigenetic information essential for regulating DNA-mediated processes, including gene transcription (Jiang and Pugh 2009), DNA replication (Kurat et al. 2017), and DNA repair (Chen and Tyler...
  5. Research: Canonical nucleosome organization at promoters forms during genome activation
    • Yong Zhang,
    • Nadine L. Vastenhouw,
    • Jianxing Feng,
    • Kai Fu,
    • Chenfei Wang,
    • Ying Ge,
    • Andrea Pauli,
    • Paul van Hummelen,
    • Alexander F. Schier,
    • and X. Shirley Liu
    Genome Res. February 2014 24: 260-266; Published in Advance November 27, 2013, doi:10.1101/gr.157750.113
    ...transcription Nucleosome organization in promoters is proposed to facilitate recognition by the transcriptional machinery (Hughes et al. 2012; Yen et al. 2012). Since canonical nucleosome organization at the promoters consists of nucleosome-depleted regions and arrays of positioned nucleosomes, we investigated...
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  6. Resource: A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
    • Desislava P. Staneva,
    • Roberta Carloni,
    • Tatsiana Auchynnikava,
    • Pin Tong,
    • Juri Rappsilber,
    • A. Arockia Jeyaprakash,
    • Keith R. Matthews,
    • and Robin C. Allshire
    Genome Res. November 2021 31: 2138-2154; Published in Advance August 18, 2021, doi:10.1101/gr.275368.121
    ...details of the composition and organization of the chromatin regulatory machinery in T. brucei and establishes a route to explore divergence from eukaryotic norms in an evolutionarily ancient but experimentally accessible eukaryote.Nucleosomes are composed of eight highly conserved core histone subunits...
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  7. Method: Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
    • Deepani W. Poramba-Liyanage,
    • Tessy Korthout,
    • Christine E. Cucinotta,
    • Ila van Kruijsbergen,
    • Tibor van Welsem,
    • Dris El Atmioui,
    • Huib Ovaa,
    • Toshio Tsukiyama,
    • and Fred van Leeuwen
    Genome Res. April 2020 30: 635-646; Published in Advance March 18, 2020, doi:10.1101/gr.256255.119
    ..., eviction of the core transcriptional machinery was accompanied by the appearance of quiescent cell–specific repressors and rewiring of the interactions of protein-folding factors and metabolic enzymes. These results show that Epi-Decoder provides a powerful strategy for capturing the temporal binding...
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  8. 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
    ...regulatory sequences, and it induces cleavage of the nascent transcript followed by polyadenylation of the 3′ end (Wahle and Rüegsegger 1999; Zhao et al. 1999; Proudfoot 2011; Kumar et al. 2019; Thore and Fribourg 2019). Studies of the isolated protein complex revealed an organization into functionally...
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  9. Method: SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA
    • Nevena Cvetesic,
    • Harry G. Leitch,
    • Malgorzata Borkowska,
    • Ferenc Müller,
    • Piero Carninci,
    • Petra Hajkova,
    • and Boris Lenhard
    Genome Res. December 2018 28: 1943-1956; Published in Advance November 7, 2018, doi:10.1101/gr.235937.118
    ...machinery and general transcription factors bind to direct initiation by RNAPII (Smale and Kadonaga 2003). Information on exact TSS positions in the improves identification of core promoter sequences and led to the discovery of new core promoter and active enhancer sequences (Andersson et al. 2014...
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  10. Research: A novel role for the Pol I transcription factor UBTF in maintaining genome stability through the regulation of highly transcribed Pol II genes
    • Elaine Sanij,
    • Jeannine Diesch,
    • Analia Lesmana,
    • Gretchen Poortinga,
    • Nadine Hein,
    • Grace Lidgerwood,
    • Donald P. Cameron,
    • Jason Ellul,
    • Gregory J. Goodall,
    • Lee H. Wong,
    • Amardeep S. Dhillon,
    • Nourdine Hamdane,
    • Lawrence I. Rothblum,
    • Richard B. Pearson,
    • Izhak Haviv,
    • Tom Moss,
    • and Ross D. Hannan
    Genome Res. February 2015 25: 201-212; Published in Advance December 1, 2014, doi:10.1101/gr.176115.114
    ...A novel role for the Pol I transcription factor UBTF in maintaining genome stability through the regulation of highly transcribed Pol II genes Elaine Sanij 1 , 2 , 3 , Jeannine Diesch 1 , 2 , Analia Lesmana 1 , 2 , Gretchen Poortinga...
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