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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...Corresponding authors: kitao.z7deb13@gmail.com, so@tokai.ac.jpAbstractTransposons, occasionally domesticated as novel host protein-coding genes, are responsible for the lineage-specific functions in vertebrates. LINE-1 (L1) is one of the most active transposons in the vertebrate s. Despite its abundance, few...
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Research: Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
- Vivek Hari Sundar G,
- Chenna Swetha,
- Debjani Basu,
- Kannan Pachamuthu,
- Steffi Raju,
- Tania Chakraborty,
- Rebecca A. Mosher,
- and P.V. Shivaprasad
Genome Res. May 2023 33: 715-728; Published in Advance June 5, 2023, doi:10.1101/gr.277353.122
...is mediated using several factors including chromatin modifiers. However, factors that avoid the intrusion of silencing signals into protein-coding genes are poorly understood. Here we show that a plant specific paralog of RNA polymerase (Pol) II, named Pol IV, is involved in avoidance of facultative...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
..., with a special focus on de novo gene birth.View this table: In this window In a new window Table 1. Studies investigating the origin of ORFans in bacteriaORFans as artifactsOur discussion of bacterial ORFans focuses only on protein-coding annotated genes, noting that not all annotated genes are functional...
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Research: High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes
- Walter Muskovic,
- Eve Slavich,
- Ben Maslen,
- Dominik C. Kaczorowski,
- Joseph Cursons,
- Edmund Crampin,
- and Maria Kavallaris
Genome Res. August 2022 32: 1463-1473; Published in Advance June 27, 2022, doi:10.1101/gr.276818.122
.... To overcome this, de novo transcriptome assembly was performed (see Methods), identifying 2803 lncRNAs in addition to 3552 protein-coding genes activated in response to serum stimulation. Of the identified lncRNAs, 33.2% had no overlap with either GENCODE (Derrien et al. 2012) or FANTOM CAT (Hon et al. 2017...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...for the S. uvarum mitochondrion, with 100% query coverage and 99.89% identity.Genome annotationWe used the GALBA pipeline to predict and annotate the protein-coding genes for each sub/haplotype of S. bayanus CBS380 (Brůna et al. 2023). The pipeline is well suited to our use case, given its capability...
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Resource: Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition
- Guillaume Dumas,
- Simon Malesys,
- and Thomas Bourgeron
Genome Res. March 2021 31: 484-496; Published in Advance January 13, 2021, doi:10.1101/gr.262113.120
...author: guillaume.dumas@centraliens.netAbstractThe human brain differs from that of other primates, but the genetic basis of these differences remains unclear. We investigated the evolutionary pressures acting on almost all human protein-coding genes (N = 11,667; 1:1 orthologs in primates) based...
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Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- Jonathan M. Mudge,
- Irwin Jungreis,
- Toby Hunt,
- Jose Manuel Gonzalez,
- James C. Wright,
- Mike Kay,
- Claire Davidson,
- Stephen Fitzgerald,
- Ruth Seal,
- Susan Tweedie,
- Liang He,
- Robert M. Waterhouse,
- Yue Li,
- Elspeth Bruford,
- Jyoti S. Choudhary,
- Adam Frankish,
- and Manolis Kellis
Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
...Discovery of high-confidence human protein-coding genes and exons by whole- PhyloCSF helps elucidate 118 GWAS loci Jonathan M. Mudge1,9, Irwin Jungreis2,3,9, Toby Hunt1, Jose Manuel Gonzalez1, James C. Wright4, Mike Kay1, Claire Davidson1, Stephen Fitzgerald5, Ruth Seal1,6, Susan Tweedie1, Liang He...
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Method: An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
- Ulrich Omasits,
- Adithi R. Varadarajan,
- Michael Schmid,
- Sandra Goetze,
- Damianos Melidis,
- Marc Bourqui,
- Olga Nikolayeva,
- Maxime Québatte,
- Andrea Patrignani,
- Christoph Dehio,
- Juerg E. Frey,
- Mark D. Robinson,
- Bernd Wollscheid,
- and Christian H. Ahrens
Genome Res. December 2017 27: 2083-2095; Published in Advance November 15, 2017, doi:10.1101/gr.218255.116
...of completely sequenced s, the large majority of which (>90%) originate from prokaryotes (Reddy et al. 2015). The accurate annotation of all protein-coding genes (interchangeably used with CDSs from here on) is essential to exploit this genomic information at multiple levels: from small, focused experiments, up...
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Research: The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome
- Young-Lim Lee,
- Aniek C. Bouwman,
- Chad Harland,
- Mirte Bosse,
- Gabriel Costa Monteiro Moreira,
- Roel F. Veerkamp,
- Erik Mullaart,
- Nadine Cambisano,
- Martien A.M. Groenen,
- Latifa Karim,
- Wouter Coppieters,
- Michel Georges,
- and Carole Charlier
Genome Res. September 2023 33: 1455-1464; Published in Advance October 4, 2023, doi:10.1101/gr.277884.123
...Figs. S1–S24). This corresponds to one dnSV per 6.7 births, which is in line with recent estimates in human studies (vide supra) (Supplemental Fig. S25; Supplemental Table S1). Three of the 19 dnSVs encompassed protein-coding exons, including one that disrupted the centromere protein C (CENPC) gene...
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Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
- Mark E. Gill,
- Alexia Rohmer,
- Serap Erkek-Ozhan,
- Ching-Yeu Liang,
- Sunwoo Chun,
- Evgeniy A. Ozonov,
- and Antoine H.F.M. Peters
Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
...have arisen recently in evolutionary time and possess low coding potential. Nonetheless, we identify several novel protein-coding genes harboring open reading frames that encode proteins containing matches to conserved protein domains. Analysis of mass-spectrometry data from adult mouse testes confirms...
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