Searching journal content for articles similar to Kliesmete et al. 34 (10): 1528.

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  1. Research: Independent evolution of transcript abundance and gene regulatory dynamics
    • Gat Krieger,
    • Offir Lupo,
    • Avraham A. Levy,
    • and Naama Barkai
    Genome Res. July 2020 30: 1000-1011; Published in Advance July 22, 2020, doi:10.1101/gr.261537.120
    ...between these two axes of divergence is fundamental for understanding the mechanisms of evolution. We reasoned that analysis of regulatory evolution, on a genomic scale, requires an extended comparative data set that surveys a large number of expression profiles obtained under a wide range of conditions...
  2. Research: Tempo and mode of regulatory evolution in Drosophila
    • Joseph D. Coolon,
    • C. Joel McManus,
    • Kraig R. Stevenson,
    • Brenton R. Graveley,
    • and Patricia J. Wittkopp
    Genome Res. May 2014 24: 797-808; Published in Advance February 24, 2014, doi:10.1101/gr.163014.113
    ...-acting mutations that compensate for cis-regulatory divergence of one gene are expected to have deleterious pleiotropic effects on expression of other genes (Wray et al. 2003; Carroll 2008; Stern and Orgogozo 2008). Goncalves et al. (2012) favored a similar explanation for the extensive compensatory cis- and trans-regulatory...
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  3. Research: Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids
    • Carina F. Mugal,
    • Mi Wang,
    • Niclas Backström,
    • David Wheatcroft,
    • Murielle Ålund,
    • Marie Sémon,
    • S. Eryn McFarlane,
    • Ludovic Dutoit,
    • Anna Qvarnström,
    • and Hans Ellegren
    Genome Res. December 2020 30: 1727-1739; Published in Advance November 3, 2020, doi:10.1101/gr.254508.119
    ...-specific nature of cis-regulatory evolution bypassing constraints associated with pleiotropic effects of genes.Following the seminal work of King and Wilson (1975) postulating that evolution occurs at two levels, the relative importance of changes in protein sequences and changes in gene expression has been...
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  4. Research: Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf
    • Charles Y. Feigin,
    • Axel H. Newton,
    • and Andrew J. Pask
    Genome Res. October 2019 29: 1648-1658; Published in Advance September 18, 2019, doi:10.1101/gr.244251.118
    ...in both species were common near genes with roles in brain development. Our findings support the hypothesis that, relative to protein-coding genes, positive selection on cis-regulatory elements is likely to be an essential driver of adaptive convergent evolution and may underpin thylacine–wolf phenotypic...
  5. Research: Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity
    • Hunter B. Fraser,
    • Sasha Levy,
    • Arun Chavan,
    • Hiral B. Shah,
    • J. Christian Perez,
    • Yiqi Zhou,
    • Mark L. Siegal,
    • and Himanshu Sinha
    Genome Res. October 2012 22: 1930-1939; Published in Advance May 29, 2012, doi:10.1101/gr.134080.111
    ...mitigated by compensatory mutations at other loci. These results suggest that cis -regulatory adaptation can occur at the level of physically interacting modules and that one such polygenic adaptation led to increased virulence during the evolution of a pathogenic yeast. Footnotes ↵ 7...
  6. Research: The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression
    • Colin D. Meiklejohn,
    • Joseph D. Coolon,
    • Daniel L. Hartl,
    • and Patricia J. Wittkopp
    Genome Res. January 2014 24: 84-95; Published in Advance September 16, 2013, doi:10.1101/gr.156414.113
    .... Such transgressive segregation is consistent with compensatory evolution within species and regulatory incompatibilities among species (Ranz et al. 2003; Ranz et al. 2004; Landry et al. 2005), some of which may contribute to the loss of fitness in hybrids (Michalak and Noor 2003; Michalak and Noor 2004; Good et al...
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  7. Research: Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4 grass
    • John T. Lovell,
    • Scott Schwartz,
    • David B. Lowry,
    • Eugene V. Shakirov,
    • Jason E. Bonnette,
    • Xiaoyu Weng,
    • Mei Wang,
    • Jenifer Johnson,
    • Avinash Sreedasyam,
    • Christopher Plott,
    • Jerry Jenkins,
    • Jeremy Schmutz,
    • and Thomas E. Juenger
    Genome Res. April 2016 26: 510-518; Published in Advance March 7, 2016, doi:10.1101/gr.198135.115
    .... 2014). Several studies have suggested that gene expression regulatory elements may be particularly likely to be involved in adaptive evolution (Wray et al. 2003; Wittkopp and Kalay 2011; Fraser 2013). This conclusion is supported by the observation that expression regulation can be tissue...
  8. Research: Genome-wide detection of novel regulatory RNAs in E. coli
    • Rahul Raghavan,
    • Eduardo A. Groisman,
    • and Howard Ochman
    Genome Res. September 2011 21: 1487-1497; Published in Advance June 10, 2011, doi:10.1101/gr.119370.110
    ...undergone compensatory mutations to preserve RNA secondary structures in related organisms is also a good strategy to predict the presence of new sRNAs (Table 3; Supplemental Table S7; Rivas et al. 2001), but this strategy also produces numerous false positives due to the presence of cis-regulatory elements...
  9. Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
    • Sarah M. Leichter,
    • Kami Ahmad,
    • and Steven Henikoff
    Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
    ...that aging not only weakens pre-existing Polycomb domains but also establishes new repressive marks in differentiated intestinal cells, reshaping the chromatin landscape in a cell type–specific manner.Changes in repression at regulatory elements with ageA major advantage of sciCUT&Tag is the ability...
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  10. Research: The mode of expression divergence in Drosophila fat body is infection-specific
    • Bryan A. Ramirez-Corona,
    • Stephanie Fruth,
    • Oluchi Ofoegbu,
    • and Zeba Wunderlich
    Genome Res. June 2021 31: 1024-1034; Published in Advance April 15, 2021, doi:10.1101/gr.269597.120
    ...). These expression differences can arise through sequence changes in cis-regulatory elements, such as enhancers, or in the coding regions of trans-acting factors, such as transcription factors. These two types of changes differ in their impact. Changes in cis are local, typically affecting the expression of one gene...
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