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Research: Noncoding regions underpin avian bill shape diversification at macroevolutionary scales
- Leeban Yusuf,
- Matthew C. Heatley,
- Joseph P.G. Palmer,
- Henry J. Barton,
- Christopher R. Cooney,
- and Toni I. Gossmann
Genome Res. April 2020 30: 553-565; Published in Advance April 8, 2020, doi:10.1101/gr.255752.119
...spanning >97% of avian genera (Cooney et al. 2017). Using this approach, we were able to link genetic and morphological diversification on a macroevolutionary scale.ResultsPrevious work has identified several genes and genomic regions that are under selection as likely species-specific drivers of bird beak...
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Research: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells
- Agustín F. Fernández,
- Gustavo F. Bayón,
- Rocío G. Urdinguio,
- Estela G. Toraño,
- María G. García,
- Antonella Carella,
- Sandra Petrus-Reurer,
- Cecilia Ferrero,
- Pablo Martinez-Camblor,
- Isabel Cubillo,
- Javier García-Castro,
- Jesús Delgado-Calle,
- Flor M. Pérez-Campo,
- José A. Riancho,
- Clara Bueno,
- Pablo Menéndez,
- Anouk Mentink,
- Katia Mareschi,
- Fabian Claire,
- Corrado Fagnani,
- Emanuela Medda,
- Virgilia Toccaceli,
- Sonia Brescianini,
- Sebastián Moran,
- Manel Esteller,
- Alexandra Stolzing,
- Jan de Boer,
- Lorenza Nisticò,
- Maria A. Stazi,
- and Mario F. Fraga
Genome Res. January 2015 25: 27-40; Published in Advance September 30, 2014, doi:10.1101/gr.169011.113
....00, respectively) (Fig. 3D). Both divergent and convergent sequences were more abundant in intragenic regions (χ2 test; P < 0.001, OR = 1.38 and P < 0.001, OR = 1.16, respectively), with HV being more frequently found in intergenic regions (χ2 test; P < 0.001, OR = 1.50) and LV in promoter regions (χ2 test; P < 0...
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Research: Natural selection drives the accumulation of amino acid tandem repeats in human proteins
- Loris Mularoni,
- Alice Ledda,
- Macarena Toll-Riera,
- and M. Mar Albà
Genome Res. June 2010 20: 745-754; Published in Advance March 24, 2010, doi:10.1101/gr.101261.109
...of repeat evolution we have used sequences with the same DNA triplet composition as the coding sequences—and thus expected to be subject to the same mutational forces—but located in syntenic noncoding genomic regions. The results strongly indicate that selection has played a more important role than...
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LETTER: Low-Complexity Regions in Plasmodium falciparum Proteins
- Elisabetta Pizzi and
- Clara Frontali
Genome Res. February 1, 2001 11: 218-229; Published in Advance January 18, 2001, doi:10.1101/gr.152201
...regions that fail to crystalize into fixed structures. Based on a learning set of X-ray-invisible regions from 7 to &gt;45 amino acids long, Romero et al. (1997) developed a prediction algorithm to discriminate between structured and locally disordered regions. In selecting predictive features...
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Method: Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
- Borislav Hrisimirov Hristov,
- William Stafford Noble,
- and Alessandro Bertero
Genome Res. October 2024 34: 1610-1623; Published in Advance September 25, 2024, doi:10.1101/gr.278327.123
...with more IDRs form stronger interactions in trans. In all, trans-C allowed us to identify a large set of DBP enriched for IDR regions that are involved in strong TIDs proximal to nuclear speckles and that may thus be important in efficient transcriptional regulation of their target genes.Selected RNA...
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Research: High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes
- Penka Markova-Raina and
- Dmitri Petrov
Genome Res. June 2011 21: 863-874; Published in Advance March 10, 2011, doi:10.1101/gr.115949.110
...composition, specifically containing runs of repeating amino acids and elevated numbers of some amino acids. Because these patterns appeared consistent with those of protein disorder, we investigatedwhether sites inferred to be under selection were indeed preferentially located in intrinsically disordered...
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Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
..., representing an average of 2.6% of a given species’ pan. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across...
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Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
...a likely mechanism of splicing repression by the RNA-binding protein UNC-75/CELF via interactions with cis elements that overlap a 5′ splice site. Alternatively spliced exons also overlap more frequently with intrinsically disordered peptide regions than constitutive exons. Moreover, regulated exons...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...of the lack of purifying selection implies that, the deeper the phylogeny becomes, the less likely the noncoding regions that are homologous to a predicted de novo gene can be identified. More sensitive phylogenetic procedures that rigorously refine the first-trawl-results from phylostratigraphic analyses...
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Research: RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels
- Brigitta Szabo,
- Therese C. Mandl,
- Bernhard Woldrich,
- Gregor Diensthuber,
- David Martin,
- Michael F. Jantsch,
- and Konstantin Licht
Genome Res. February 2024 34: 231-242; Published in Advance March 12, 2024, doi:10.1101/gr.277686.123
.... 2014; Liddicoat et al. 2015). ADARB1 editing on the other hand targets several protein-coding transcripts in which both coding and noncoding regions can be affected (Pullirsch and Jantsch 2010; Tajaddod et al. 2016).A major target of ADARB1 is the glutamate receptor subunit 2 (Gria2). The lethal...
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