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Research: APOBEC3A drives deaminase mutagenesis in human gastric epithelium
- Yohan An,
- Ji-Hyun Lee,
- Joonoh Lim,
- Jeonghwan Youk,
- Seongyeol Park,
- Ji-Hyung Park,
- Kijong Yi,
- Taewoo Kim,
- Chang Hyun Nam,
- Won Hee Lee,
- Soo A Oh,
- Yoo Jin Bae,
- Thomas M. Klompstra,
- Haeun Lee,
- Jinju Han,
- Junehwak Lee,
- Jung Woo Park,
- Jie-Hyun Kim,
- Hyunki Kim,
- Hugo Snippert,
- Bon-Kyoung Koo,
- and Young Seok Ju
Genome Res. October 2025 35: 2158-2172; Published in Advance August 26, 2025, doi:10.1101/gr.280338.124
...Technology, #07922) (see Supplemental Methods; Supplemental Table S11).Preparation of vectors for transfectionTwo vectors were purchased: (1) CMV-rtTA-HygR vector (Addgene, #102423) and (2) CRISPR-Cas9 vectors containing gRNA sequence for TP53 (Addgene, #121917). To generate the pPB-CMVmin-APOBEC (A3A or A3B...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...to evaluate significant differences. (G,H) Gene Ontology (GO) enrichment analysis of biological processes for C. nigoni–specific dispensable genes (H) and C. briggsae–specific dispensable genes (G). The most significantly enriched category for C. nigoni–specific dispensable genes, namely, innate immune...
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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically...
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Research: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
- Thiago L. Knittel,
- Brooke E. Montgomery,
- Alex J. Tate,
- Ennis W. Deihl,
- Anastasia S. Nawrocki,
- Frederic J. Hoerndli,
- and Taiowa A. Montgomery
Genome Res. December 2024 34: 2203-2216; Published in Advance December 2, 2024, doi:10.1101/gr.279083.124
...fertility, likely due to loss of siRNA activity (Okamura et al. 2004; Xu et al. 2004; Deshpande et al. 2005; Wen et al. 2015). Similar subtle phenotypes could emerge for rde-1 mutants through more detailed analyses. We identified several genes with possible roles in innate immunity downregulated in rde-1...
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Research: Global loss of cellular m⁶A RNA methylation following infection with different SARS-CoV-2 variants
- Roshan Vaid,
- Akram Mendez,
- Ketan Thombare,
- Rebeca Burgos-Panadero,
- Rémy Robinot,
- Barbara F. Fonseca,
- Nikhil R. Gandasi,
- Johan Ringlander,
- Mohammad Hassan Baig,
- Jae-June Dong,
- Jae Yong Cho,
- Björn Reinius,
- Lisa A. Chakrabarti,
- Kristina Nystrom,
- and Tanmoy Mondal
Genome Res. March 2023 33: 299-313; Published in Advance March 1, 2023, doi:10.1101/gr.276407.121
...of motile cilia after SARS-CoV-2 infection (Robinot et al. 2021). The genes with lost m6A involved in covalent chromatin modification and up-regulated during infection, such as KDM6A (Supplemental Data S2), were recently identified as proviral genes in a CRISPR screen (Wei et al. 2021b). Thus, our data...
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Research: Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)
- Sünje J. Pamp,
- Eoghan D. Harrington,
- Stephen R. Quake,
- David A. Relman,
- and Paul C. Blainey
Genome Res. June 2012 22: 1107-1119; Published in Advance March 20, 2012, doi:10.1101/gr.131482.111
...identity to the other SFB-mouse s. Among the chromosomal features that exhibit highest variability among the SFB-mouse s are the CRISPR-arrays, some phage-related genes, and hypothetical proteins, including Cluster.1 and Cluster.3 SFB-specific proteins (Fig. 3; Supplemental Material; see above). Discussion...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...by the common ancestor. Our genomic analysis provides a robust list of potential candidate genes in which Helitrons might play a regulatory role. This is an interesting hypothesis that can be determined through cutting-edge technologies such as CRISPR methods to delete insertions with site-specific resolution...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...and the cells’ innate immune response (Russell et al. 2019). The value of long reads for both DNA and RNA sequencing was demonstrated by a study of the human adaptive immune system's response to MMR vaccination. ONT sequencing was used to characterize both the transcriptome of single B cells and relevant loci...
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Research: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory
- Varsha Poondi Krishnan,
- Barbara Morone,
- Shir Toubiana,
- Monika Krzak,
- Salvatore Fioriniello,
- Floriana Della Ragione,
- Maria Strazzullo,
- Claudia Angelini,
- Sara Selig,
- and Maria R. Matarazzo
Genome Res. February 2023 33: 169-183; Published in Advance February 24, 2023, doi:10.1101/gr.276986.122
...patient peripheral blood and lymphoblastoid cell lines. These regions include large CpG island domains, as well as promoters and enhancers of several lineage-specific genes, in particular immune-related, suggesting that they are premarked during early development. CRISPR-corrected ICF1 iPSCs reveal...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...is thus likely transferred to the protein level for at least a subset of genes.First, from DNA to RNA levels, -wide correspondence between genomic proximity and coexpression in colorectal cancer was detected. Such an observation triggers us to speculate that the long-range interactions of the genomic...

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