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Research: Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts
- Isabela T. Pereira,
- Izabela Mamede,
- Paulo P. Amaral,
- Gloria R. Franco,
- and John L. Rinn
Genome Res. October 2025 35: 2189-2198; Published in Advance August 26, 2025, doi:10.1101/gr.280431.125
...immunoprecipitation) data sets (The ENCODE Project Consortium 2012) to investigate if each retained intron would have an enrichment in protein binding at retained introns compared to the non-retained introns in the same gene (Supplemental Fig. S4). In total, we found 8617 events exclusive to GET introns, 9940 events...
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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
...disrupt endogenous gene regulation and 106 compromise genomic stability. Thus, selection cassettes are sometimes placed in 107 intronic regions to mitigate this limitation (Wang et al. 2022); however, these can 108 interfere with splicing and generate aberrant transcripts. Meanwhile, “safe harbor” loci...
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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
...by the coding region (exons and introns); and ending with a terminator and polyadenylation signals that ensure proper transcript processing and stability. Before we can determine proteins that directly regulate GOI expression, we must identify the regulatory DNA sequences relevant to the GOI such as its...
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Research: Systematic identification and characterization of exon–intron circRNAs
- Yinchun Zhong,
- Yan Yang,
- Xiaolin Wang,
- Bingbing Ren,
- Xueren Wang,
- Ge Shan,
- and Liang Chen
Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
...expressed PCGs (overall-control) or 2000 randomly selected PCGs (random-control) (Fig. 3C; Supplemental Fig. S6A).View larger version: In this window In a new window Figure 3. Parental genes of EIciRNAs are actively transcribed. (A) Boxplots displaying the distributions of percentages of CIRs and introns...
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Research: Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells
- Johannes Hiltunen,
- Laura Helminen,
- Niina Aaltonen,
- Kaisa-Mari Launonen,
- Hanna Laakso,
- Marjo Malinen,
- Einari A. Niskanen,
- Jorma J. Palvimo,
- and Ville Paakinaho
Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
...role in regulating DexDHT-associated metabolic and estrogen response pathways in PCa cells (Audet-Walsh et al. 2017). Analysis of GRO-seq and scRNA-seq data revealed that ESRRG is expressed at higher levels than ESR1 (Supplemental Fig. S7D, S7G). Notably, the ESRRG locus contains both intronic...
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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
...(causing loss of function), activating, latent (enabling another distinct driver mutation) (Nussinov and Tsai 2015), or, in rare cases, neofunctional, in which the protein function differs from the wild type and benefits the tumor. Many computational tools have been developed to predict cancer driver genes...
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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. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...influenced by cytoplasmic mRNA stability and export, as supported by analyses of intronic (nuclear) versus exonic reads in RNA-seq (Zaghlool et al. 2013; Gaidatzis et al. 2015; Bakken et al. 2018; Oh et al. 2022; Engström et al. 2025). In principle, our PARTAGE workflow can be adapted to whole...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...signature scoring in scRNA-seq data measures the activity of biological processes represented by predefined gene signatures. Such signatures are sets of genes associated with specific biological pathways, transcriptional states, or cell types and are used as a surrogate representation for a biological...
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Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
- Tsung-Kai Hung,
- Wan-Chi Liu,
- Sheng-Kai Lai,
- Hui-Wen Chuang,
- Yi-Che Lee,
- Hong-Ye Lin,
- Chia-Lang Hsu,
- Chien-Yu Chen,
- Ya-Chien Yang,
- Jacob Shujui Hsu,
- and Pei-Lung Chen
Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
...-M, the first row in Fig. 2D), these PacBio HiFi reads supported the existence of the KIR2DS4/3DL1 fusion gene. We also explored the potential evolutionary relationship between the KIR2DS4, KIR3DL1, and KIR2DS4/3DL1 fusion genes. Several regions within intron 7 of KIR2DS4 and KIR3DL1 exhibited high...
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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
...3 nt periodicity, a hallmark of translating ribosomes, within a gene-structure context, including introns and untranslated regions, enabling the study of novel open reading frames (ORFs), translation of different isoforms, and mechanisms of translational regulation. ggRibo can plot multiple Ribo...
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