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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
...similarity between the two hybrid alleles (Fig. 7D). Furthermore, although only ∼1% of genes showed species-hybrid difference >0.2, 50% of cis-varying genes showed such an effect. This observation is different from our observation of cis-trans variations in expression levels (Supplemental Fig. S1D) in which...
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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
...in opposition would be evidence for compensatory evolution and widespread stabilizing selection to maintain expression level. Genes categorized as cis × trans, compensatory, and a subset of cis + trans (where variants act in opposition) show evidence of cis and trans changes acting in opposite directions (Fig...
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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
...were found to be sterile. It is therefore unlikely that incompatibilities between cis-trans regulatory changes explain the observed sterility. Instead, we found evidence that cis-regulatory changes play a significant role in the evolution of gene expression in testis, which illustrates the tissue...
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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
...- and/or trans-regulatory changes, were much more variable among studies. Finally, novel patterns, such as the relationship between dominance and cis/trans-regulatory changes (Lemos et al. 2008; McManus et al. 2010) and the frequency of compensatory cis- and trans-regulatory variants (Tirosh et al. 2009...
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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
...-regulation than cis trans cis Misexpressed Not Misexpressed Not Males All genes 394 271 37 35 $ 1.5-fold 38 9 9 8 $ twofold 15 5 4 3 Females All genes 362 128 24 22 $ 1.5-fold 55 9 3 7 $ twofold 23 2 1 3 Rows in boldface indicate that the proportion of misexpressed genes is significantly different (Fisher’s exact...
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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
...recovery conditions. In doing so, we characterize the effects of cis-, trans-, and drought-responsive gene expression regulation that may underlie physiological divergence between the upland and lowland ecotypes of P. hallii. Results and Discussion Climatic context of the experimental drought The two...
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Research: Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals
- Emily S. Wong,
- David Thybert,
- Bianca M. Schmitt,
- Klara Stefflova,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. February 2015 25: 167-178; Published in Advance November 13, 2014, doi:10.1101/gr.177840.114
...mouse species. For each transcription factor, TF-dependent genes and the TF binding sites most likely to influence mRNA expression were identified by comparing mRNA expression levels between wild-type and TF knockout mice. Independent evolution was observed genome-wide between the rate of change in TF...
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Research: Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast
- C. Joel McManus,
- Gemma E. May,
- Pieter Spealman,
- and Alan Shteyman
Genome Res. March 2014 24: 422-430; Published in Advance December 6, 2013, doi:10.1101/gr.164996.113
...that interspecies differences in translation contribute substantially to the evolution of gene expression. Compensatory differences in transcript abundance and translation efficiency may increase the robustness of gene regulation. Footnotes ↵ 1 Corresponding author E-mail mcmanus...
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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
...and F1 hybrids and no trans signal are cis-only. Genes showing differential expression in the parents and not the F1 hybrids are trans-only. Some genes show evidence of both cis and trans effects and are either compensatory (if the changes on expression are in opposite directions) or cis+trans (if...
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Research: Cis-acting variation is common across regulatory layers but is often buffered during embryonic development
- Swann Floc'hlay,
- Emily S. Wong,
- Bingqing Zhao,
- Rebecca R. Viales,
- Morgane Thomas-Chollier,
- Denis Thieffry,
- David A. Garfield,
- and Eileen E.M. Furlong
Genome Res. February 2021 31: 211-224; Published in Advance December 11, 2020, doi:10.1101/gr.266338.120
...(Landry et al. 2005; Tirosh et al. 2009; Goncalves et al. 2012; Wong et al. 2017) using a maximum likelihood framework that classified genes and features as cis, trans, cistrans, or conserved (Wong et al. 2017).Among noncoding chromatin features, cis-acting effects are more common than trans (59% vs. 41...
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