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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
...Pan analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility Dongying Xie1,2,3, Pohao Ye1,3, Yiming Ma1 and Zhongying Zhao1 1Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China; 2Institute for Research...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...sections, displays variants that segregate within families. The first section shows the family (the family ID/study column), the variant (the location/variant column), the segregation pattern (the pedigree column), and the variant's predicted effect on the protein-coding genes (the worst effect...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...a coevolutionary relationship between the two (Thomas and Schneider 2011). This was bolstered by subsequent ChIP-seq experiments in humans and mice mapping the -wide binding of hundreds of KZNFs, which revealed that most target specific TE families (Imbeault et al. 2017; Wolf et al. 2020). Furthermore, KZNF...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...impacts and evolutionary patterns over time remain elusive in humans owing to the technical and ethical complexities of functional studies. Integrating gene age dating with Mendelian disease phenotyping, we reveal a gradual rise in disease gene proportion as gene age increases. Logistic regression...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...), the chromatin TRN recapitulates most, if not all, of the significant interactions (overlapping nodes are indicated in orange) (Fig. 7B). In fact, the chromatin TRN of bas1Δ also revealed two targets (GCV2 and HIS5) belonging to the glycine and histidine pathways that were not present in the gene expression TRN...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...exon, altering only the 3′ UTR sequence while leaving the protein-coding sequence unchanged. Because the 3′ UTR contains many essential regulatory elements—such as microRNA and RNA-binding protein (RBP) binding sites—variation in 3′ UTR length can modulate target mRNA function, stability...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...of integration breakpoints revealed that introns and intergenic regions were the most frequently targeted genomic loci (Supplemental Fig. S8A,B), suggesting that HBV may cis-regulate neighboring gene expression. We therefore examined changes in the expression levels of genes within ±500 kb of integration sites...
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Research: ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development
- Charlie Y. Shi,
- Lara E. Elcavage,
- Raghu R. Chivukula,
- Joanna Stefano,
- Benjamin Kleaveland,
- and David P. Bartel
Genome Res. September 2023 33: 1482-1496; Published in Advance August 2, 2023, doi:10.1101/gr.278073.123
...author: dbartel@wi.mit.eduAbstractMicroRNAs (miRNAs) pair to sites in mRNAs to direct the degradation of these RNA transcripts. Conversely, certain RNA transcripts can direct the degradation of particular miRNAs. This target-directed miRNA degradation (TDMD) requires the ZSWIM8 E3 ubiquitin ligase. Here...
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Research: Cotargeting among microRNAs in the brain
- Jennifer M. Cherone,
- Vjola Jorgji,
- and Christopher B. Burge
Genome Res. November 2019 29: 1791-1804; Published in Advance October 24, 2019, doi:10.1101/gr.249201.119
...results uncover an unexpected pattern in which combinations of miRNAs collaborate to robustly repress cotargets, and suggest important developmental roles for cotargeting.MicroRNAs (miRNAs) are 21- to 23-nt noncoding RNAs that specify the repression of target mRNAs by the RNA-induced silencing complex...
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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...(K27me3 LADs) in purple, Cluster 1 (K9me3 LADs) in blue, Cluster 2 (K9me2 LADs) in gold.Chromatin profiles across LADs in each cluster revealed stark differences in both the overall abundance of histone PTMs and their pattern over the LAD (Fig. 3C,D). As expected, H3K9ac and H3K27ac are highly...
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