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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
...and knockouts, investigating functions of human genes in their native context is impractical. Despite this limitation, accumulating omic data and in vitro studies of human genes have suggested the potential roles of evolutionarily young genes in basic cellular processes and complex phenotypic innovations...
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Research: The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible
- Yue Hao,
- Makenzie E. Mabry,
- Patrick P. Edger,
- Michael Freeling,
- Chunfang Zheng,
- Lingling Jin,
- Robert VanBuren,
- Marivi Colle,
- Hong An,
- R. Shawn Abrahams,
- Jacob D. Washburn,
- Xinshuai Qi,
- Kerrie Barry,
- Christopher Daum,
- Shengqiang Shu,
- Jeremy Schmutz,
- David Sankoff,
- Michael S. Barker,
- Eric Lyons,
- J. Chris Pires,
- and Gavin C. Conant
Genome Res. May 2021 31: 799-810; Published in Advance April 16, 2021, doi:10.1101/gr.270033.120
...The contributions from the progenitor s of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible Yue Hao1, Makenzie E. Mabry2, Patrick P. Edger3,4, Michael Freeling5, Chunfang Zheng6, Lingling Jin7, Robert VanBuren3,8, Marivi Colle3, Hong An2, R. Shawn Abrahams2...
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Research: Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence
- Wouter Meuleman,
- Daan Peric-Hupkes,
- Jop Kind,
- Jean-Bernard Beaudry,
- Ludo Pagie,
- Manolis Kellis,
- Marcel Reinders,
- Lodewyk Wessels,
- and Bas van Steensel
Genome Res. February 2013 23: 270-280; Published in Advance November 2, 2012, doi:10.1101/gr.141028.112
...in mouse or human. Meuleman et al. 272 Genome Research www..org intronic regions because coding sequences are subject to a variety of selective pressures that could confound this analysis. Surprisingly, the results show that both intergenic and intronic sequences in cLADs are generally less well conserved...
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LETTER: Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire
- Ali Mortazavi,
- Evonne Chen Leeper Thompson,
- Sarah T. Garcia,
- Richard M. Myers,
- and Barbara Wold
Genome Res. October 2006 16: 1208-1221; Published in Advance September 8, 2006, doi:10.1101/gr.4997306
...site predictions and enumerate the target gene cohort. We show that it is possible to begin with a single biologically defined, evolutionarily conserved NRSF/ REST site, then use conservation among mouse, human, and dog s to develop a refined model for NRSF sites. The resulting model is compared...
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Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
- Étienne Fafard-Couture,
- Pierre-Étienne Jacques,
- and Michelle S. Scott
Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
...(Bradnam and Korf 2008; Zhang and Edwards 2012). A significant difference is also found between expressed and nonexpressed intronic snoRNAs according to their intron rank computed from the 3′ end of the gene, highlighting that expressed snoRNAs are preferentially encoded farther away from the 3′ end than...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...propagation, RdDM extent, silencing components, and targets are different from other angiosperms, preferentially focused on potentially intact TEs. It also provides evidence for heterochromatin maintenance independently of DNA methylation in flowering plants. These discoveries highlight the diversity...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...from 3221 assemblies, we show that the copy number of retroelements correlates with that of ZNFs across at least 750 million years of metazoan evolution. Using computational predictions, we show that ZNFs preferentially bind TEs in diverse animal species. We further investigate the largest ZNF...
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Research: Proteome-wide structural analysis quantifies structural conservation across distant species
- Shijie Zhang,
- Teng Zhang,
- and Yuan Fu
Genome Res. November 2023 33: 1975-1993; Published in Advance November 22, 2023, doi:10.1101/gr.277771.123
...is not evolutionarily important. Therefore, tertiary structures of proteins are often more conserved than their amino acid sequences.An example to illustrate this point was shown in Figure 2, A and B, in which structural and sequence comparisons of H. sapiens glutathione S-transferase mu 4 and E. coli glutathione S...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...These authors contributed equally to this work. Corresponding authors: wang_yu@nwafu.edu.cn, gaoyuanpeng1990@163.comAbstractUltraconserved elements (UCEs) are the most conserved regions among the s of evolutionarily distant species and are thought to play critical biological functions. However, some UCEs...
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Method: Global mapping of RNA homodimers in living cells
- Marta M. Gabryelska,
- Andrew P. Badrock,
- Jian You Lau,
- Raymond T. O'Keefe,
- Yanick J. Crow,
- and Grzegorz Kudla
Genome Res. May 2022 32: 956-967; Published in Advance March 24, 2022, doi:10.1101/gr.275900.121
...dimerization in vitro and disrupt zebrafish development in vivo, suggesting an evolutionarily conserved role of this domain. Analysis of virus-infected cells reveals homodimerization of SARS-CoV-2 and Zika s, mediated by specific palindromic sequences located within protein-coding regions of N gene in SARS...
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