Searching journal content for articles similar to Kuo et al. 20 (12): 1672.

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  1. 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 the best predictors for protein sequence and expression conservation. In this study, we investigated its effect on the evolution of cis-regulatory elements (CREs). To this end, we carefully reanalyzed the Epigenomics Roadmap data for nine fetal tissues, assigning a measure of pleiotropic degree to nearly...
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  2. Method: Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules
    • Sushmita Roy,
    • Ilan Wapinski,
    • Jenna Pfiffner,
    • Courtney French,
    • Amanda Socha,
    • Jay Konieczka,
    • Naomi Habib,
    • Manolis Kellis,
    • Dawn Thompson,
    • and Aviv Regev
    Genome Res. June 2013 23: 1039-1050; Published in Advance May 2, 2013, doi:10.1101/gr.146233.112
    ...Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules Sushmita Roy 1 , 2 , 6 , 7 , Ilan Wapinski 1 , 3 , Jenna Pfiffner 1 , Courtney French 1 , Amanda Socha 1 , Jay...
  3. Research: The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus
    • Li Ren,
    • Wuhui Li,
    • Qinbo Qin,
    • He Dai,
    • Fengming Han,
    • Jun Xiao,
    • Xin Gao,
    • Jialin Cui,
    • Chang Wu,
    • Xiaojing Yan,
    • Guoliang Wang,
    • Guiming Liu,
    • Jia Liu,
    • Jiaming Li,
    • Zhong Wan,
    • Conghui Yang,
    • Chun Zhang,
    • Min Tao,
    • Jing Wang,
    • Kaikun Luo,
    • Shi Wang,
    • Fangzhou Hu,
    • Rurong Zhao,
    • Xuming Li,
    • Min Liu,
    • Hongkun Zheng,
    • Rong Zhou,
    • Yuqin Shu,
    • Yude Wang,
    • Qinfeng Liu,
    • Chenchen Tang,
    • Wei Duan,
    • and Shaojun Liu
    Genome Res. November 2019 29: 1805-1815; Published in Advance October 24, 2019, doi:10.1101/gr.249805.119
    ...of transcription factors (Wittkopp et al. 2004; Maheshwari and Barbash 2012). The co-evolution always occurred in the interaction of cis-regulatory sequences with trans-regulatory factors, causing divergence of gene expression and changes of biochemical processes after hybridization (McManus et al. 2010...
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  4. Research: Gene regulation and speciation in house mice
    • Katya L. Mack,
    • Polly Campbell,
    • and Michael W. Nachman
    Genome Res. April 2016 26: 451-461; Published in Advance February 1, 2016, doi:10.1101/gr.195743.115
    ...divergence betweenM. m. musculus andM. m. domesticus, largely attributable to cis-regulatory changes.When both cis and trans changes occurred, theywere observed in oppositionmuchmore often than expected under a neutralmodel, providing strong evidence of widespread compensatory evolution. We also found...
  5. 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
    ...(trans). While cis-acting elements typically cause expression variation in a single gene, transacting modifiers may affect expression of several or, in the case of global transcription factors, thousands of genes. Mutations at loci with wide-ranging pleiotropic effects are typically deleterious...
  6. 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...
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  7. Research: Regulatory divergence in Drosophila revealed by mRNA-seq
    • C. Joel McManus,
    • Joseph D. Coolon,
    • Michael O. Duff,
    • Jodi Eipper-Mains,
    • Brenton R. Graveley,
    • and Patricia J. Wittkopp
    Genome Res. June 2010 20: 816-825; Published in Advance March 30, 2010, doi:10.1101/gr.102491.109
    ...; ISSN 1088-9051/10; www..org et al. 2005), which found that selection in natural populations eliminatedmost trans-actingmutations that affected expression of many genes. Such a pattern of selection could cause cis-regulatory mutations to accumulate preferentially over time, and cis-regulatory divergence...
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  8. Resource: Genome-wide discovery of human splicing branchpoints
    • Tim R. Mercer,
    • Michael B. Clark,
    • Stacey B. Andersen,
    • Marion E. Brunck,
    • Wilfried Haerty,
    • Joanna Crawford,
    • Ryan J. Taft,
    • Lars K. Nielsen,
    • Marcel E. Dinger,
    • and John S. Mattick
    Genome Res. February 2015 25: 290-303; Published in Advance January 5, 2015, doi:10.1101/gr.182899.114
    ...regulatory splicing code. Lastly, although branchpoints are refractory to common mutational processes and genetic variation, mutations occurring at branchpoint nucleotides are enriched for disease associations. Footnotes [Supplemental material is available for this article.] Article...
  9. LETTER: Functional conservation of Rel binding sites in drosophilid genomes
    • Richard R. Copley,
    • Maxim Totrov,
    • Jane Linnell,
    • Simon Field,
    • Jiannis Ragoussis,
    • and Irina A. Udalova
    Genome Res. September 2007 17: 1327-1335; doi:10.1101/gr.6490707
    ...constructs driven by orthologous Dif-regulated promoters in divergent Drosophila species ( Gompel et al. 2005 ; Prud’homme et al. 2006 ). Ludwig et al. (2005) suggested that the coevolution of cis - and trans -acting elements may involve changes in expression patterns or levels rather than changes...
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