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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
...(Qiagen MinElute PCR kit), and the DNA was purified using the Qiagen MinElute PCR kit according to the manufacturer's protocol. The purified DNA, eluted in 10 µL, was either stored at −20°C or used directly for library preparation. ATAC-seq libraries were generated using 10 µL transposed DNA, custom made...
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Method: MCHelper automatically curates transposable element libraries across eukaryotic species
- Simon Orozco-Arias,
- Pío Sierra,
- Richard Durbin,
- and Josefa González
Genome Res. December 2024 34: 2256-2268; Published in Advance December 9, 2024, doi:10.1101/gr.278821.123
...the elements that contain one or more retrotransposon-like domains in the first case or DNA-like domains in the latter case, but it was not possible to assign a deeper classification. EDTA is not included in this figure because the software does not report any “unknown/unclassified” elements.We also used...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...rare in eukaryotes(Beaulaurier et al. 2019). Similar to 6mA and 5mC, 4mC plays critical roles in many biological processes, including DNA repair and replication. It operates as a core component in the antiphage immune system of bacteria, mainly reflected in the participation of 4mC in the bacterial...
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Method: Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases
- Ming Yan,
- Thea O. Andersen,
- Phillip B. Pope,
- and Zhongtang Yu
Genome Res. February 2025 35: 368-378; Published in Advance December 27, 2024, doi:10.1101/gr.279825.124
...) with original DNA sequences as inputs, as illustrated by a recent study (Hou et al. 2024). We tested Tiara and EukRep for their ability to identify gut eukaryotic sequences using a data set from 52 SAGs of rumen protozoa (see Methods) (Li et al. 2022). Tiara and EukRep correctly classify only 30,081 and 44...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...shows the generally late replication timing of this chromosome. The fraction of the Y Chromosome that is earlier replicating in each cell type is presented above each bar. (I) Compared with female Kc cells, all male cells have a greater total genomic size of earlier replicating DNA on the X Chromosome...
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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
...for gene prediction in assembled transcripts and (2) the genomic level one used for gene prediction in genomic DNA. The training of the transcript level GHMM did follow the path described for GeneMarkS-T (Tang et al. 2015). However, the training process of the genomic GHMM was organized differently...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...). Combining the dCPD-seq data for the two aligned strands confirmed that dCPD enrichment in cells relative to the naked DNA control was generally elevated at backbone-out positions and suppressed at backbone-in positions (Fig. 8B).View larger version: In this window In a new window Figure 8. Structural...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...expression (P-value = 4.4 × 10−40), RNA-induced silencing complex (RISC) (P-value = 9.2 × 10−38), DNA-binding transcription factor activity (P-value = 1.6 × 10−13), and structural component of ribosome (P-value = 1.9 × 10−10) (Supplemental Fig. S16).View larger version: In this window In a new window Figure...
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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
...involved in gene sets relating to DNA storage (histones), DNA replication, RNA transcription, and protein translation (ribosome), as well as the distribution of structural similarities for genes relating to fatty acid metabolism and sugar metabolism (Fig. 7B–F). Lokiarchaeum sp. GC14_75 and C...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
..., but solo-LTRs themselves are not fully functional or active anymore. The DNA transposon Cirt2 and the LTR-retrotransposon Tca2 are expressed in C. albicans (Matthews et al. 1997; Potocki et al. 2019). However, it is not clear whether TE expression is sufficient to generate new insertions, or if new TE...

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