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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...properties of topologically associating domains (TADs) are overall maintained, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observe a restructuring of TAD–TAD interactions...
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Research: Semiconservative transmission of DNA N⁶-adenine methylation in a unicellular eukaryote
- Yalan Sheng,
- Yuanyuan Wang,
- Wentao Yang,
- Xue Qing Wang,
- Jiuwei Lu,
- Bo Pan,
- Bei Nan,
- Yongqiang Liu,
- Fei Ye,
- Chun Li,
- Jikui Song,
- Yali Dou,
- Shan Gao,
- and Yifan Liu
Genome Res. May 2024 34: 740-756; Published in Advance May 14, 2024, doi:10.1101/gr.277843.123
...; Bochtler and Fernandes 2021). 6mA studies in eukaryotes are complicated by varying abundance and divergent functions across species. In protists, green algae, and basal fungi, 6mA is abundant, enriched at the ApT dinucleotide, and associated with genes, all of which are consistent with its role...
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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
...fusion proteins will increase with future studies. First, the evolutionarily conservation of fusion proteins with other LINE ORFs, including ORF2 and primate L1 ORF0 (Denli et al. 2015), remains to be elucidated. Second, improved gene annotation in assemblies of nonmodel organisms will also facilitate...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...change in cow). Thus, both ancient and lineage-specific TE subfamilies have contributed to the NF-kB binding repertoire.RELA-bound TEs possess active enhancer features for target gene regulationTo explore the regulatory potential of the TE-derived RELA-bound regions, we assessed epigenomic proxies...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...in aging. This is not to suggest that a predominant down-regulation of genes occurs in physiological aging as we have seen here, as many studies have shown that different cell types and organisms do not show such a clear transcriptional effect but rather show an increased transcriptional variability (Bahar...
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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...karyotypes of individual species are organized. For example, in the chicken , early replicating regions tend to be found in small chromosomes, known as “microchromosomes” (see below). It is still unknown how such intragenomic heterogeneity is accommodated by variable karyotypes as well as how it arose during...
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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
...discussing. First, phylogenetic corrections in PGLMM assume a linear association between the covariate (measured as nucleotide divergence in core genes) and the response variable (gene abundances). Therefore, the model can accommodate cross-strain variation in evolutionary rates as long as such variation...
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Research: Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures
- Jiseon Lim,
- Wonjoo Kim,
- Jun Kim,
- and Junho Lee
Genome Res. November 2023 33: 1947-1957; Published in Advance November 2, 2023, doi:10.1101/gr.278124.123
...; Sobinoff and Pickett 2017). ALT, which refers to alternative mechanisms that substitute telomerase function for telomere maintenance at the chromosome ends (Bryan et al. 1995), is crucial in telomerase mutant eukaryotic cells, such as those in yeast, Caenorhabditis elegans, the mouse, and human, and can...
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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
...Highly efficient and scarless editing via essential gene-coupled 1 homology-directed repair 2 Running title: Efficient scarless editing via essential gene HDR 3 4 Joo Hye Yeo1,2,3, Hyongbum Henry Kim2,3,4,5,6,7,8,9, Sang Ho Oh10, Jinu Lee1,* 5 6 1College of Pharmacy, Yonsei Institute...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...sitesA eukaryotic gene typically consists of regulatory elements such as distal enhancers, which can act over long distances; a proximal promoter containing key TF binding sites; a core promoter surrounding the transcription start site (TSS) where the preinitiation complex assembles, followed...
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