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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
...and testis of the Madagascar ground gecko was purified using ISOGEN (Nippon Gene 311-02501) and a direct-zol RNA miniprep kit (Zymo Research R2050). The cDNA was synthesized from total RNA using Verso cDNA synthesis kit (Thermo Fisher Scientific AB1453A). PCR was performed with 30 cycles of amplification (10...
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Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
- Tomáš Brůna,
- Alexandre Lomsadze,
- and Mark Borodovsky
Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
...-Hovhannisyan et al. 2008). The accuracy of gene predictions made by GeneMark-ES in compact fungal and protist s has been high and is still difficult to improve even by adding currently available extrinsic evidence. Since the advent of high-throughput sequencing, the rapid accumulation of RNA and protein...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
..., regulate the expression of both a protein-coding gene (Snrpn-Snurf [a bicistronic transcript] and Plagl1, respectively) and a lncRNA (Snhg14 and Hymai, respectively) (Table 1; Fig. 1). Most of these promoters display tissue-specific activity that appears to rely on the dynamics of the repressive H3K27me3...
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Method: BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
- Lars Gabriel,
- Tomáš Brůna,
- Katharina J. Hoff,
- Matthis Ebel,
- Alexandre Lomsadze,
- Mark Borodovsky,
- and Mario Stanke
Genome Res. May 2024 34: 769-777; Published in Advance June 12, 2024, doi:10.1101/gr.278090.123
...alone, for example, AUGUSTUS (Stanke et al. 2006) and GeneMark-ES (Lomsadze et al. 2005). However, the ab initio models are prone to errors when used alone. Therefore, more precise gene predictions are made when predictions based on statistical models are corrected by extrinsic evidence (Stanke et al...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...Nanopore long-read data. We collected the raw long reads that are aligned to the centromere (listed in their Supplemental Fig. S4). Each of the long reads may contain more than one repeating region. Because our current method does not support detecting multiple repeating regions in a single input sequence...
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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 by spurious transcripts. This pool of Pol IV–suppressed sRNAs is partly dependent on RDR6 and DDM1, as the double mutants of these genes in the nrpd1 background showed a reduction in their abundance. Such spuriously transcribed loci showed a reduction in H3K27me3 occupancy (Fig. 3F...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...region indicated with dashed rectangles in the upper plot. MHC-I, MHC-II and APG are marked and labeled individually, with the width of rectangles corresponding to gene lengths. Maximum relative expression: the maximum fraction of total MHC-I expression (FPKM) attributable to a sequence across all RNA...
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Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...for the detection of many novel variants, especially in the previously unresolved regions. They also found that their novel reference reduces the number of false-positive calls mainly in protein-coding genes, and they highlight the increased sensitivity for detection of rare variants and singletons (Aganezov et al...
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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
...-suppressor genes that alter splicing and are inherited with cancer in their host families. Long-read genomic and cDNA sequencing, carried out in tandem, are effective in detecting this class of variation. With long-read genomic sequencing, most introns can be sequenced in single reads, thereby disentangling highly...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...chromosome integrity, piRNA clusters encoding host defenses against selfish elements, and virtually the entire Y Chromosome. These regions, formed by highly similar tandem arrays, pose significant challenges for experimental and computational studies, impeding sequence-level descriptions essential...
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