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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...confirmed (TEC)” and “immunoglobulin (IG) variable chain or T cell receptor (TR) genes” biotypes were removed. In addition, complex loci where alternative promoter or recombined segments are annotated with different gene names but cannot be considered as independent genes were also removed (Jung et al. 2006...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...to decipher tissue-specific codes of gene regulation for individual and groups of TFs using available single-cell gene expression data in both species. Studying key conserved factors in worm and fly greatly will enhance analysis, interpretation, and the broader relevance of data gathered in ENCODE and other...
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Method: A transcriptome-based single-cell biological age model and resource for tissue-specific aging measures
- Shulin Mao,
- Jiayu Su,
- Longteng Wang,
- Xiaochen Bo,
- Cheng Li,
- and Hebing Chen
Genome Res. August 2023 33: 1381-1394; Published in Advance July 31, 2023, doi:10.1101/gr.277491.122
...age-DEGs implies that there likely remain many more aging genes yet to be confirmed by experiments (Fig. 2F,G). Many of them, indeed, could represent tissue-specific aging programs driven by stress factors and cell–cell interactions in the local environment (Zhang et al. 2021). Furthermore, not all...
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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
...component of mole-rat adaptations. Last, we investigated the contribution of repetitive elements to lineage-specific gene regulation in the mole-rat clade.ResultsComparative epigenomics of liver and heart regulatory activities in mole-ratsTo investigate the contribution of enhancer evolution to tissue-specific...
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Research: The human genome contains over a million autonomous exons
- Nicholas Stepankiw,
- Ally W.H. Yang,
- and Timothy R. Hughes
Genome Res. November 2023 33: 1865-1878; Published in Advance November 9, 2023, doi:10.1101/gr.277792.123
...to internal exons from protein-coding genes, despite these exons representing less than 1% of the .The cutoff of 100 reads retains the majority of GENCODE mRNA (61%) (and lncRNA [53%]) internal exons in the trapped exons. Thus, even though only a single cell line was used, the assay clearly shows...
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Research: Enhancers with tissue-specific activity are enriched in intronic regions
- Beatrice Borsari,
- Pablo Villegas-Mirón,
- Sílvia Pérez-Lluch,
- Isabel Turpin,
- Hafid Laayouni,
- Alba Segarra-Casas,
- Jaume Bertranpetit,
- Roderic Guigó,
- and Sandra Acosta
Genome Res. August 2021 31: 1325-1336; Published in Advance July 21, 2021, doi:10.1101/gr.270371.120
..., respectively. Conversely, genes harboring common ELSs reported terms related to ordinary cell functions and membrane composition (Supplemental Table 5). Although this suggests an implication of intronic ELSs in tissue-specific functions, likely through tissue-specific gene regulation mechanisms...
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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
...of regulation by DNA methylation, depending on factors such as cell type, developmental stage, and environmental conditions (Gardiner-Garden and Frommer 1987; Jaenisch and Bird 2003; Illingworth and Bird 2009; Loyfer et al. 2023). CG-rich sequences are predominantly found in the 5′-flanking regions of genes...
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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
....Visualization is emphasized in cell biology research to generate hypotheses and results. However, in omics studies, the visualization of sequencing data within genes of interest remains underutilized owing to a lack of appropriate tools. Recent advancements in plotting tools in the R programming language (R Core Team 2025...
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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
...isoform expression levels and dynamic APA changes in each tissue and cell type. We identified a total of 40,748 PASs across 12,111 genes. Of these, 26.9% of genes had a single PAS, whereas 73.1% exhibited multiple PASs (Fig. 1B). Classification based on genomic annotation revealed that 63.1% of PASs were...
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Method: Co-expression networks reveal the tissue-specific regulation of transcription and splicing
- Ashis Saha,
- Yungil Kim,
- Ariel D.H. Gewirtz,
- Brian Jo,
- Chuan Gao,
- Ian C. McDowell,
- The GTEx Consortium,
- Barbara E. Engelhardt,
- and Alexis Battle
Genome Res. November 2017 27: 1843-1858; Published in Advance October 11, 2017, doi:10.1101/gr.216721.116
...evidence that splicing is more similar in tissues with shared cell type compositions (Qian et al. 2005; Ong and Corces 2011; The GTEx Consortium 2017). Table 1. Top 20 cross-tissue TE-IR hubs Rank Hub gene #Tissues Evidence (and references) 1 TMEM160 16 2 RBM14 15 Nuclear receptor coactivator...
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