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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
...expectations for when differential gene expression should matter. Here, we collated existing data into a gene-regulatory network (GRN) and performed developmental transcriptomics across different environmental conditions, genetic backgrounds, and mutants to assess the regulatory logic of mouth-form plasticity...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
...,036 potential causal variants (posterior inclusion probability [PIP] > 0.9) for 1186, 3592, 1685, and 2996 eGenes in the liver, ovary, shell gland, and spleen, respectively (Supplemental Table S6). These results provide a high-confidence set of candidate regulatory variants that can serve as reliable targets...
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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. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...outcomes, there must also be consistent regulation of such genes by cis-regulatory modules (CRMs). CRMs consist of clusters of transcription factor binding sites (TFBSs) that regulate the expression of target genes through collective or competitive binding of operative transcription factors (TFs). However...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...–specific TFs in regulating key genes associated with AD progression, linking transcriptional changes to genetic risk loci and highlighting potential mechanisms underlying disease pathology.View larger version: In this window In a new window Figure 5. Cell type–specific TF regulatory network. (A) TF regulatory...
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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
...sitesA eukaryotic gene typically consists of regulatory elements such as distal enhancers, which can act over long distances; a proximal promoter containing key TF binding sites; a core promoter surrounding the transcription start site (TSS) where the preinitiation complex assembles, followed...
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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...). Consistent with expectation, hypoxic treatment, specifically, also induced a well-recognized core regulatory program across all cell types, including the upregulation of hypoxia-inducible factor (HIF) target genes (Cummins and Taylor 2005; Semenza 2012; Chang et al. 2015). Consistent with this, the hypoxia...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
..., and interpretable exploration of causal GRNs with prior knowledge and multi-omics data.Gene regulatory networks (GRNs), which encapsulate the complex interactions among transcription factors (TFs), target genes, and various regulatory elements, constitute the core machinery of gene regulation (Levine and Davidson...
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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. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...transcriptional programs. Gene expression is regulated by cis-regulatory elements (CREs) in a spatiotemporal manner through precise gene regulatory networks (Lee and Young 2013; Levine et al. 2014; Long et al. 2016). Understanding these regulatory mechanisms beyond transcription may reveal critical aspects of how...
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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...were normalized by the mean of the pre-exercise samples. (C) Network plot reveals the cell-type-specific target genes (blue) of PPARD (orange) identified by the integrated regulatory circuit analysis. Selected GO terms enriched in the target genes are annotated below. (D,E) Log2 fold-change (log2FC...
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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
...correction applied).TE-chimeric transcript–derived peptides are validated as putative neoantigensTo overcome the resistance associated with LTR7-PLAAT4 and target lethal cancers driven by aberrant epigenetic activation of TEs, we turned to recent investigations that revealed the capacity of TEs in harboring...
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