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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...analysis and identified genes positively correlated with different PLAAT4 isoforms (Fig. 6A). Our results revealed that genes specifically correlated with canonical PLAAT4 were enriched in virus defense functions (Supplemental Fig. S12A), whereas those correlated with LTR7-PLAAT4 isoform 1 were enriched...
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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
...remarkable versatility in their ability to create new transcripts or genes 66 through exonization, while also modulating gene expression through strategic placement of 67 enhancers or promoters near genes (Guillaume et al. 2018; Sophie and Gaël 2020). Current 68 studies reveals important functional aspects...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...1 Title 1 Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals 2 conserved gene alterations linked to Parkinson’s disease 3 Running title: Substantia nigra aging linked to Parkinson 4 Kangli Wang1, Weikun Xia1, Yingli Gu1, Songpeng Zu1, Qian Yang2, Maria Luisa Amaral1...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...and horizontal gene transfer in microorganisms may result in different strains of the same species, which further increases the biological diversity and complexity of microbial communities. Diversity of microbial communities at the level of strains is a key factor in microbiome-related research, as it does...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...Repli-seq and RNA-seq methods (Fig. 3). Standard Repli-seq was performed on HepG2 nuclei as previously described (RiveraMulia et al. 2022). For standard RNA-seq, RNA was isolated from 0.5 million cells, and libraries were prepared for stranded mRNA sequencing. These standard analyses confirmed the close...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...organogenesis and define a compendium of highly conserved CRMs that should be prioritized for analysis of neuro-pancreatic gene transcriptional control and of anterior embryonic patterning. [Supplemental material is available for this article.] Although vertebrates exhibit remarkable phenotypic diversity...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...of growth (P < 5 × 10−9, GO:BP, g:Profiler) (Supplemental Table 9).Postduplication FIEs are distributed in a wider variety of genes, with less than half occurring in known cancer genesFewer FIEs were identified postduplication compared with preduplication (LUAD, 18.5%; LUSC, 30.8% of total FIEs), and less...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...al. 2016; Yu et al. 2016; Guo et al. 2023). Here, we present an example in the bZIP53 transcription factor gene, comparing Ribo-seq/RNA-seq profiles with PARE-seq data (Nagarajan et al. 2019) to evaluate potential mRNA decay associated with ribosome stalling (Fig. 5B). PARE-seq detects the 5...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...coding gene expression with qPCR-validated targets. Our findings demonstrate that quantifying mRNA fragments from sRNA-seq experiments provides a reliable approach to investigate microRNA–mRNA interactions when total RNA-seq is unavailable.The analysis of gene expression is a cornerstone of functional...
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Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
- Shelley Reich,
- Tobias Loschko,
- Julie Jung,
- Samantha Nestel,
- Ralf J. Sommer,
- and Michael S. Werner
Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
...across development from 0 h post egg-synchronization (embryos) to 72 h (young adults) (Fig. 1C). We extracted and sequenced mRNA to a minimum depth of 3 million reads and with a minimum quality score of 30, ultimately resulting in more than 3.5 billion high-quality reads that we anticipate...
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