Searching journal content for articles similar to Routhier et al. 31 (2): 317.

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  1. Method: A systematic genome-wide account of binding sites for the model transcription factor Gcn4
    • Christopher T. Coey and
    • David J. Clark
    Genome Res. February 2022 32: 367-377; Published in Advance December 16, 2021, doi:10.1101/gr.276080.121
    ...Corresponding author: clarkda@mail.nih.govAbstractSequence-specific DNA-binding transcription factors are central to gene regulation. They are often associated with consensus binding sites that predict far more genomic sites than are bound in vivo. One explanation is that most sites are blocked by nucleosomes...
  2. Resource: Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis
    • Rui Yokomori,
    • Kotaro Shimai,
    • Koki Nishitsuji,
    • Yutaka Suzuki,
    • Takehiro G. Kusakabe,
    • and Kenta Nakai
    Genome Res. January 2016 26: 140-150; Published in Advance December 14, 2015, doi:10.1101/gr.184648.114
    ...-type promoters inDrosophila aremore likely to be associated with nonpositionally fixed motifs such as a DNA replication-related element (DRE) (Ni et al. 2010). In human and Drosophila, it has been shown that broad-type promoters exhibitmore precise nucleosome positioning than sharp-type promoters (Nozaki et al...
  3. Research: Thermal stress accelerates Arabidopsis thaliana mutation rate
    • Eric J. Belfield,
    • Carly Brown,
    • Zhong Jie Ding,
    • Lottie Chapman,
    • Mengqian Luo,
    • Eleanor Hinde,
    • Sam W. van Es,
    • Sophie Johnson,
    • Youzheng Ning,
    • Shao Jian Zheng,
    • Aziz Mithani,
    • and Nicholas P. Harberd
    Genome Res. January 2021 31: 40-50; Published in Advance December 17, 2020, doi:10.1101/gr.259853.119
    ...) (Ossowski et al. 2010; Jiang et al. 2014) mutations are preferentially distributed between nucleosomal versus nonnucleosomal DNA, combining mutations located in nucleosome and edge-of-nucleosome regions into a single nucleosome-associated category. First, we overlaid the genomic positions of SNVs onto...
  4. Research: Numerical and spatial patterning of yeast meiotic DNA breaks by Tel1
    • Neeman Mohibullah and
    • Scott Keeney
    Genome Res. February 2017 27: 278-288; Published in Advance December 6, 2016, doi:10.1101/gr.213587.116
    .../threonine kinase ATM/Tel1 (ataxia telangiectasia mutated in mammals; telomere maintenance in S. cerevisiae). ATM controls cell-cycle checkpoints and promotes DNA repair in somatic cells and is essential for meiosis in mammals (Shiloh and Ziv 2013). Testes from Atm−/− mice display a large increase in DSB numbers...
  5. Research: Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome
    • Sara González,
    • Alicia García,
    • Enrique Vázquez,
    • Rebeca Serrano,
    • Mar Sánchez,
    • Luis Quintales,
    • and Francisco Antequera
    Genome Res. November 2016 26: 1532-1543; Published in Advance September 23, 2016, doi:10.1101/gr.207241.116
    ..., Spain Corresponding author: cpg@usal.es ↵ 3 These authors contributed equally to this work. Abstract In the yeast genome, a large proportion of nucleosomes occupy well-defined and stable positions. While the contribution of chromatin remodelers and DNA binding...
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  6. Research: Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging
    • Benjamin P. Barré,
    • Johan Hallin,
    • Jia-Xing Yue,
    • Karl Persson,
    • Ekaterina Mikhalev,
    • Agurtzane Irizar,
    • Sylvester Holt,
    • Dawn Thompson,
    • Mikael Molin,
    • Jonas Warringer,
    • and Gianni Liti
    Genome Res. May 2020 30: 697-710; Published in Advance April 10, 2020, doi:10.1101/gr.253351.119
    ...) was deleted in NA and WA haploids using homologous recombination with a URA3 cassette. Then, the HPF1 segments to be swapped were PCR-amplified from the desired alleles with Platinum SuperFi (Thermo Fisher Scientific) DNA polymerase and swapped into the orthologous position of the recipient strain using...
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  7. Research: Core promoter sequence in yeast is a major determinant of expression level
    • Shai Lubliner,
    • Ifat Regev,
    • Maya Lotan-Pompan,
    • Sarit Edelheit,
    • Adina Weinberger,
    • and Eran Segal
    Genome Res. July 2015 25: 1008-1017; Published in Advance May 12, 2015, doi:10.1101/gr.188193.114
    ...promoter is the region towhich Pol II and itsaccompanyinggeneral transcriptionfactorsarerecruited to theDNA, formthepre-initiationcomplex (PIC), andact to initiate transcription (Smale and Kadonaga 2003). In yeast, the PIC is recruited to a TATA element, either a consensus TATA box or a weaker one with 1...
  8. Method: Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants
    • Ilaria Mogno,
    • Jamie C. Kwasnieski,
    • and Barak A. Cohen
    Genome Res. November 2013 23: 1908-1915; Published in Advance August 6, 2013, doi:10.1101/gr.157891.113
    ...parameters proportional to DGs of the interactions between proteins and DNA and between proteins. We did not model nucleosome effects. We scanned our promoter sequences with the Nucleosome Positioning prediction software (Kaplan et al. 2008) and found very low correlation between predicted nucleosome...
  9. Method: A unified model for yeast transcript definition
    • Carl G. de Boer,
    • Harm van Bakel,
    • Kyle Tsui,
    • Joyce Li,
    • Quaid D. Morris,
    • Corey Nislow,
    • Jack F. Greenblatt,
    • and Timothy R. Hughes
    Genome Res. January 2014 24: 154-166; Published in Advance October 29, 2013, doi:10.1101/gr.164327.113
    ...the transcript structure predicted by the model to the transcription generated by the cell for synthetic DNA segments of random design. We show that the UM identifies transcription start sites more accurately than the initiation classifier alone, indicating that the relative arrangement of promoter...
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  10. Research: Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters
    • Danny Zeevi,
    • Shai Lubliner,
    • Maya Lotan-Pompan,
    • Eran Hodis,
    • Rita Vesterman,
    • Adina Weinberger,
    • and Eran Segal
    Genome Res. December 2014 24: 1991-1999; Published in Advance October 7, 2014, doi:10.1101/gr.179259.114
    ...al. 2011). Briefly, in order to introduce orthologous promoters into S. cerevisiae, we extracted genomic DNA from each species and amplified by PCR the desired promoters. Each promoter was linked (Linshiz et al. 2008) to aURA3 selectionmarker and integrated into the of a yeast master strain, upstream...
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