Searching journal content for articles similar to McManus et al. 20 (6): 816.

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  1. Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
    • Daniel Siqueira de Oliveira,
    • Anaïs Larue,
    • William Vilas Boas Nunes,
    • Francois Sabot,
    • Alejandra Bodelón,
    • María Pilar García Guerreiro,
    • Cristina Vieira,
    • and Claudia Marcia Aparecida Carareto
    Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
    ..., demonstrating an unprecedented putative cis-regulatory role of Helitrons in Drosophila. Differential expression analysis between species with different preferred hosts reveals divergence in gene expression in heads and larvae. Although TEs’ presence does not affect overall gene expression, we observe 6...
  2. Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
    • Junling Shi,
    • Jiaqi Xu,
    • Jun Ma,
    • and Feng He
    Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
    ...RNAs in early pupae exert regulatory activities on their putative target genes during normal development, we analyzed our mRNA-seq data of WT across different stages. Enriched GO groups of genes with an increased mRNA level include “mitochondrion organization” (GO:0007005), “cuticle development” (GO:0042335...
  3. 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
    ...the two primary signaling pathways in the Drosophila innate immune response. The mode of expression divergence strongly depends on the condition, with trans-acting effects dominating in response to Gram-negative infection and cis-acting effects dominating in Gram-positive and preinfection conditions...
  4. 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
    ...Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4 grass John T. Lovell 1 , Scott Schwartz 1 , David B. Lowry 2 , Eugene V. Shakirov 1 , 3 , Jason E. Bonnette 1 , Xiaoyu Weng...
  5. 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
    ...with predominantly cis- or trans-regulatory variation. We find that trans-varying alleles are dominantly inherited, and that cis-variations are often complemented by variations in trans. Based on these results, we suggest that gene expression diverges primarily through changes in expression levels, but does...
  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
    ...accumulate with divergence time. Here, we address these issues by comparing gene expression among strains and species of Drosophila with a range of divergence times and use F1 hybrids to examine inheritance patterns and disentangle cis- and trans-regulatory changes. We find that the fixation of compensatory...
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  7. 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
    ...as mutations in regulatory elements accumulate (Johnson and Porter 2000; Wittkopp and Kalay 2012). Because of this, regulation of gene expression may be of particular relevance to speciation where the interaction between divergent cis- and trans-regulatory elements is a candidate process for the formation...
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  8. Research: Evolution of splicing regulatory networks in Drosophila
    • C. Joel McManus,
    • Joseph D. Coolon,
    • Jodi Eipper-Mains,
    • Patricia J. Wittkopp,
    • and Brenton R. Graveley
    Genome Res. May 2014 24: 786-796; Published in Advance February 10, 2014, doi:10.1101/gr.161521.113
    ...and trans-acting regulatory changes. Intriguingly, exon skipping is the most dynamic class of alternative splicing throughout D. melanogaster development, suggesting that Figure 1. Comparing splicing regulation among Drosophila species. (A) Comparison of divergence times for strains and species used. (B...
  9. Research: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast
    • Gregory T. Booth,
    • Isabel X. Wang,
    • Vivian G. Cheung,
    • and John T. Lis
    Genome Res. June 2016 26: 799-811; Published in Advance May 12, 2016, doi:10.1101/gr.204578.116
    ...). The deletion of Spt4 was confirmed by absence of any reads from the locus (Supplemental Fig. S7A,B), and mRNA levels were found to be highly reproducible between biological replicates (Supplemental Fig. S9A–D).Using the gene-body region to quantify gene activity from PRO-seq or mRNA-seq data, we observed...
  10. Research: Conservation of an RNA regulatory map between Drosophila and mammals
    • Angela N. Brooks,
    • Li Yang,
    • Michael O. Duff,
    • Kasper D. Hansen,
    • Jung W. Park,
    • Sandrine Dudoit,
    • Steven E. Brenner,
    • and Brenton R. Graveley
    Genome Res. February 2011 21: 193-202; Published in Advance October 4, 2010, doi:10.1101/gr.108662.110
    ...Alternative splicing is generally controlled by proteins that bind directly to regulatory sequence elements and either activate or repress splicing of adjacent splice sites in a target pre-mRNA. Here, we have combined RNAi and mRNA-seq to identify exons that are regulated by Pasilla (PS), the Drosophila...
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