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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
...examples of L1 co-option for vertebrate proteins have been reported. Here, we describe protein isoforms, in which the L1 retrotransposons are incorporated into host genes as protein-coding exons by alternative splicing. L1 ORF1 protein (ORF1p) is an RNA-binding protein that binds to L1 RNA and is required...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...Studies examining how evolutionary forces mold the genomic TE-landscape underscore the significant role of purifying selection in limiting TE accumulation within protein-coding gene sequences (Bartolomé et al. 2002; Rizzon et al. 2003), but also in noncoding regions (Hollister and Gaut 2009; Bergthorsson et al...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...) technologies continue to make whole- sequencing more complete, affordable, and accurate. LRS provides significant advantages over short-read sequencing approaches, including phased de novo assembly, access to previously excluded genomic regions, and discovery of more complex structural variants (SVs...
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Resource: Discordant calls across genotype discovery approaches elucidate variants with systematic errors
- Elizabeth G. Atkinson,
- Mykyta Artomov,
- Alexander A. Loboda,
- Heidi L. Rehm,
- Daniel G. MacArthur,
- Konrad J. Karczewski,
- Benjamin M. Neale,
- and Mark J. Daly
Genome Res. May 30, 2023 ; Published in Advance May 30, 2023, doi:10.1101/gr.277908.123
...genotype calls is of major importance, as such loci give misleading information regarding population allele frequencies (AFs) and could be incorrectly identified as being phenotypically meaningful in gene discovery. By leveraging the unprecedented size and depth of the Genome Aggregation Database (gnom...
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Method: High-confidence coding and noncoding transcriptome maps
- Bo-Hyun You,
- Sang-Ho Yoon,
- and Jin-Wu Nam
Genome Res. June 2017 27: 1050-1062; Published in Advance April 10, 2017, doi:10.1101/gr.214288.116
...) (Supplemental Fig. S14; Kong et al. 2007); and (2) PhyloCSF (Lin et al. 2011) (see the “Classification of lncRNAs” section in Supplemental Methods for more details). Novel lncRNAs totaling 2222 (from 1725 loci) (Supplemental Table S8) were identified as our human lncRNA catalog (Fig. 7A). Although the novel lnc...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
...) data from the tumor tissue, as well as from the blood of the patient to serve as the germline control. WGS provides the most comprehensive coverage to sequence both protein-coding and noncoding regions across the entire , whereas WES provides an efficient alternative to WGS by targeting only protein-coding...
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Research: The human genome contains over a million autonomous exons
- Nicholas Stepankiw,
- Ally W.H. Yang,
- and Timothy R. Hughes
Genome Res. November 2023 33: 1865-1878; Published in Advance November 9, 2023, doi:10.1101/gr.277792.123
...sites of both constitutive and alternative exons, but it does not directly report the identity of full exons. In addition, as a CNN with ∼700,000 parameters, it is inherently challenging to interpret. Moreover, exon-associated sequence features (e.g., those that would contribute to protein-coding...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
...one of the foremost endeavors of the genomic era. Led by -wide association studies (GWAS), there have been numerous discoveries of phenotype-associated genetic traits, in areas ranging from cancer (Liang et al. 2020) to drug metabolism (Motsinger-Reif et al. 2013). GWAS typically use single...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
...disentangled the underlying meiotic processes and provided insight into the 's trajectory under the particular type of reproduction (Booth et al. 2012; Card et al. 2021).We here set out to elucidate possible facultative selfing in the West African cichlid fish Benitochromis nigrodorsalis, which has been...
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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
...triggered production of suppressed sRNAs (Supplemental Fig. S26), which are conserved across monocots and dicots.Pol IV–suppressed sRNAs are loaded into AGO1 to induce PTGS at protein-coding lociGiven that these abundant atypical sRNAs are from gene coding regions and they did not change the DNA methylation...
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