Searching journal content for articles similar to Pereira-Leal and Teichmann 15 (4): 552.

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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
...-rat adaptations in metabolic and functional pathways and suggest candidate genetic loci that may underlie mole-rat innovations. Second, we evaluated ancestral and species-specific regulatory changes in the study phylogeny and report several candidate pathways experiencing stepwise remodeling during the evolution...
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Research: Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish
- Amaury Herpin,
- Manfred Schartl,
- Alexandra Depincé,
- Yann Guiguen,
- Julien Bobe,
- Aurélie Hua-Van,
- Edward S. Hayman,
- Anna Octavera,
- Goro Yoshizaki,
- Krista M. Nichols,
- Giles W. Goetz,
- and J. Adam Luckenbach
Genome Res. August 2021 31: 1366-1380; Published in Advance June 28, 2021, doi:10.1101/gr.274266.120
...Data S1 for raw data.Male-specific transcriptional regulation of gsdfY by Dmrt1 and Wt1(-KTS)We then sought to determine if the function of the Y- and X- specific inserts in modulating gsdfY and gsdfX transcriptional regulation might be mediated by Dmrt1 and Wt1(-KTS). For this purpose, cotransfections...
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Research: The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes
- Drew R. Schield,
- Daren C. Card,
- Nicole R. Hales,
- Blair W. Perry,
- Giulia M. Pasquesi,
- Heath Blackmon,
- Richard H. Adams,
- Andrew B. Corbin,
- Cara F. Smith,
- Balan Ramesh,
- Jeffery P. Demuth,
- Esther Betrán,
- Marc Tollis,
- Jesse M. Meik,
- Stephen P. Mackessy,
- and Todd A. Castoe
Genome Res. April 2019 29: 590-601; Published in Advance March 21, 2019, doi:10.1101/gr.240952.118
...multiple tandem duplication events in multiple gene families. By overlaying chromatin structure information and gene expression data, we find evidence for venom gene-specific chromatin contact domains and identify how chromatin structure guides precise expression of multiple venom gene families. Further...
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Research: Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate
- Gilad Fuchs,
- Dror Hollander,
- Yoav Voichek,
- Gil Ast,
- and Moshe Oren
Genome Res. October 2014 24: 1572-1583; Published in Advance July 21, 2014, doi:10.1101/gr.176487.114
...(Chandrasekharan et al. 2009), regulation of H2A-H2B dimer displacement (Pavri et al. 2006), and modulation of the recruitment of specific factors to chromatin (Shema-Yaacoby et al. 2013). H2Bub1 ubiquitylation has been particularly linked with transcription regulation (for review, see Sen and Bhaumik 2013...
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PERSPECTIVE: Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
- Michael Freeling and
- Brian C. Thomas
Genome Res. July 2006 16: 805-814; doi:10.1101/gr.3681406
...that novel functional specificities have happened in the evolution of yeast by duplication of functional modules ( Pereira-Leal and Teichmann 2005 ); this work is particularly relevant to this discussion because they attempt to differentiate between simultaneous and stepwise evolution of a duplicated module...
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Research: Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
- Alexis Battle,
- Sara Mostafavi,
- Xiaowei Zhu,
- James B. Potash,
- Myrna M. Weissman,
- Courtney McCormick,
- Christian D. Haudenschild,
- Kenneth B. Beckman,
- Jianxin Shi,
- Rui Mei,
- Alexander E. Urban,
- Stephen B. Montgomery,
- Douglas F. Levinson,
- and Daphne Koller
Genome Res. January 2014 24: 14-24; Published in Advance October 3, 2013, doi:10.1101/gr.155192.113
...of known splicing QTLs by nearly an order of magnitude. By evaluating distal, -wide regulatory impact of each genetic variant, we highlight a pattern of modularity, or coregulation of many genes by a smaller number of individual genetic variants, and intra-chromosomal modules specifically influenced...
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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
...contributed equally to this work. Abstract The acquisition of new genes, via horizontal transfer or gene duplication/diversification, has been the dominant mechanism thus far implicated in the evolution of microbial pathogenicity. In contrast, the role of many other modes of evolution...
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Research: Delineation of key regulatory elements identifies points of vulnerability in the mitogen-activated signaling network
- Noor Jailkhani,
- Srikanth Ravichandran,
- Shubhada R. Hegde,
- Zaved Siddiqui,
- Shekhar C. Mande,
- and Kanury V.S. Rao
Genome Res. December 2011 21: 2067-2081; Published in Advance August 24, 2011, doi:10.1101/gr.116145.110
...’’ characterization of the hits obtained in the siRNA screen, based on the phase-specific effects obtained. The genes described here are the human orthologs of the murine counterparts (see text). The flowchart in panel C provides a stepwise summary of the in silico methodologies used for eventual identification...
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Letter: Repertoire and evolution of miRNA genes in four divergent nematode species
- Elzo de Wit,
- Sam E.V. Linsen,
- Edwin Cuppen,
- and Eugene Berezikov
Genome Res. November 2009 19: 2064-2074; Published in Advance September 15, 2009, doi:10.1101/gr.093781.109
...of this species. Species-specific miRNAs have most likely emerged in the specific lineages rather than lost in all other lineages, which allows estimation of miRNA gene fixation rate. Given the estimated 80–110 Myr divergence time between C. elegans and C. briggsae (Hillier et al. 2007) and Table 2. mi...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...traits (Claussnitzer et al. 2020).Evolutionarily new genes—such as de novo genes, chimeric genes, and gene duplicates—integrate into the human throughout microevolutionary processes (Brosius 1991; Kaessmann et al. 2002; Conrad and Antonarakis 2007; Baertsch et al. 2008; Wu et al. 2011; Long et al. 2013...
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