Searching journal content for articles similar to de Boer et al. 24 (1): 154.

Displaying results 1-10 of 97
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  1. Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
    • Robert A. Policastro,
    • R. Taylor Raborn,
    • Volker P. Brendel,
    • and Gabriel E. Zentner
    Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
    .... Including depletion of uncapped RNA and reaction cleanups, a STRIPE-seq library can be constructed in about 5 h. We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for quantification of transcript levels and analysis of differential gene...
  2. Research: Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression
    • Sarah K. Sasse,
    • Margaret Gruca,
    • Mary A. Allen,
    • Vineela Kadiyala,
    • Tengyao Song,
    • Fabienne Gally,
    • Arnav Gupta,
    • Miles A. Pufall,
    • Robin D. Dowell,
    • and Anthony N. Gerber
    Genome Res. November 2019 29: 1753-1765; Published in Advance September 13, 2019, doi:10.1101/gr.248187.119
    ...that redistribution of limiting amounts of specific coregulators from one set of enhancers to another is a unifying explanation for rapid repression in association with transcriptional induction (Guertin et al. 2014; Schmidt et al. 2016), which has been observed in a variety of other signaling contexts (Hah et al...
  3. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...of Oncobiology and Epigenetics, University of Lodz, 90-237 Lodz, Poland ↵6 These authors contributed equally to this work. Corresponding authors: urszula.mcclurg@liverpool.ac.uk, mratajewski@cbm.pan.pl, lpulaski@uni.lodz.plAbstractTranscriptional regulation lies at the heart of cellular identity and function...
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  4. Research: Heritable variation of mRNA decay rates in yeast
    • Jennifer M. Andrie,
    • Jon Wakefield,
    • and Joshua M. Akey
    Genome Res. December 2014 24: 2000-2010; Published in Advance September 25, 2014, doi:10.1101/gr.175802.114
    ...(Storey 2002; Storey and Tibshirani 2003; Storey et al. 2004) and imposing a threshold on the magnitude of effect sizes needed to be called as significant (see Supplemental Methods and Results; Supplemental Fig. S2). We note that, in order to inhibit transcription, we subjected the yeast to mild heat...
  5. Method: A versatile type VI CRISPR-based approach for targeted m6A demethylation in mRNAs
    • Panagiotis G. Adamopoulos,
    • Konstantina Athanasopoulou,
    • and Andreas Scorilas
    Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
    ...: padamopoulos@biol.uoa.grAbstractEpitranscriptomics, a rapidly evolving field mainly driven by massive parallel sequencing technologies, explores post-transcriptional RNA modifications. N6-methyladenosine (m6A) has emerged as the most prominent and dynamically regulated modification in human mRNAs, being...
  6. Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
    • Jun Kim,
    • Haoyu Wang,
    • and Sevinç Ercan
    Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
    ...a pattern consistently observed in many organisms, in which distinct peaks of binding are detected at promoters and enhancers (Peters et al. 2008; Rittenhouse and Dowen 2024). We also observe that prominent fountains are formed at regions of high transcription. Earlier studies in yeast suggested that RNA...
  7. Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
    • Robin Kosch,
    • Katharina Limm,
    • Annette M. Staiger,
    • Nadine S. Kurz,
    • Nicole Seifert,
    • Bence Oláh,
    • Stefan Solbrig,
    • Viola Poeschel,
    • Gerhard Held,
    • Marita Ziepert,
    • Norbert Schmitz,
    • Emil Chteinberg,
    • Reiner Siebert,
    • Rainer Spang,
    • Helena U. Zacharias,
    • German Ott,
    • Peter J. Oefner,
    • and Michael Altenbuchinger
    Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
    ...) is used to model common latent factors across multiple omics layers (Argelaguet et al. 2018). Unified nonnegative matrix factorization (UNMF) focuses on decomposing nonnegative matrices into interpretable, lower-dimensional components that capture the underlying structure and patterns within individual...
  8. Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
    • Ursula Oggenfuss,
    • Robert T. Todd,
    • Natthapon Soisangwan,
    • Bailey Kemp,
    • Alison Guyer,
    • Annette Beach,
    • and Anna Selmecki
    Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
    ...in an isochromosome structure, called i(5L) (Selmecki et al. 2006; Butler et al. 2009; Hickman et al. 2013; Harrison et al. 2014; Ford et al. 2015; Ropars et al. 2018). i(5L) contains two genes involved in antifungal resistance, ERG11, encoding the azole drug target, and TAC1, encoding a transcriptional activator...
  9. ARTICLE: Retroviruses and yeast retrotransposons use overlapping sets of host genes
    • Becky Irwin,
    • Michael Aye,
    • Pierre Baldi,
    • Nadejda Beliakova-Bethell,
    • Henry Cheng,
    • Yimeng Dou,
    • Willy Liou,
    • and Suzanne Sandmeyer
    Genome Res. May 2005 15: 641-654; Published in Advance April 18, 2005, doi:10.1101/gr.3739005
    ...Retroviruses and yeast retrotransposons use overlapping sets of host genes Becky Irwin 1 , 4 , Michael Aye 1 , 3 , 4 , Pierre Baldi 1 , 2 , 3 , Nadejda Beliakova-Bethell 1 , Henry Cheng 1 , Yimeng Dou 2 , 3 , Willy...
    OPEN ACCESS ARTICLE
  10. Research: Evidence for compensatory evolution within pleiotropic regulatory elements
    • Zane Kliesmete,
    • Peter Orchard,
    • Victor Yan Kin Lee,
    • Johanna Geuder,
    • Simon M. Krauß,
    • Mari Ohnuki,
    • Jessica Jocher,
    • Beate Vieth,
    • Wolfgang Enard,
    • and Ines Hellmann
    Genome Res. October 2024 34: 1528-1539; Published in Advance September 10, 2024, doi:10.1101/gr.279001.124
    ...of higher conservation for higher degrees of pleiotropy persists when analyzing the transcription factor binding repertoire. In contrast, simple DNA sequence conservation of orthologous sites between species tends to be even lower for pleiotropic CREs than for species-specific CREs. Combining various lines...
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