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Resource: Epigenomics of embryogenesis in turbot
- Oscar Aramburu,
- Belen G Pardo,
- Ada Jimenez-Gonzalez,
- Andrés Blanco-Hortas,
- Daniel Macqueen,
- Carmen Bouza,
- and Paulino Martinez
Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
...421 developmental transitions and lineage specification 422 To identify the main TFs associated with chromatin accessibility dynamics in 423 candidate CREs regulated during embryogenesis, TFBM enrichment was 424 conducted for all DARs associated with promoters and putative enhancers. 425 Significant...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...), consistent with the essential role of these TFs in five out of the six conditions in developmental processes. Imbalanced peaks are also slightly less conserved (Supplemental Fig. S3G).Overall, our results demonstrate that genetic variation has an extensive impact on TF occupancy during embryogenesis in vivo...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...of C. elegans cohesin is about 10-fold shorter, and the binding of NIPBL ortholog does not depend on cohesin. We propose that preferential loading and loop extrusion by cohesin is an evolutionarily conserved mechanism that regulates the 3D interactions of enhancers in animal s.In mammalian s, cohesin...
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Method: Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover
- An Wang,
- Stephanie Hicks,
- Donald Geman,
- and Laurent Younes
Genome Res. December 2025 35: 2744-2755; Published in Advance November 12, 2025, doi:10.1101/gr.280539.125
...and conditionsTo identify robust biological signals that characterize conserved cellular programs, we can naturally extend geneCover to enable marker gene selection across multiple samples and conditions. In this generalized formulation, we require every gene in the transcriptome G to be covered by at least one...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...contribution of the epi to selective enhancer activation by ESR1 remains to be fully elucidated. To address this, we employ a massively parallel reporter assay to profile 7576 individual ESR1 binding sites for hormone responsiveness. Only a minority of ESR1-occupied enhancers exhibit hormone-induced activity...
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Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...BP GO term enrichment of genes adjacent to CrxK88N-reduced ATAC-seq peaks.CrxK88N-increased accessibility CREs show progenitor cell regulatory signatures and are developmentally silenced during photoreceptor differentiationLast, we sought to understand the functional significance of CRXK88N...
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Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
- Song Zhang,
- Chao Wang,
- Shenghua Qin,
- Choulin Chen,
- Yongzhou Bao,
- Yuanyuan Zhang,
- Lingna Xu,
- Qingyou Liu,
- Yunxiang Zhao,
- Kui Li,
- Zhonglin Tang,
- and Yuwen Liu
Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
...to postnatal stages, and pinpointing critical trait-affecting enhancers remains largely unaddressed. In the present study, we aim to fill this gap by identifying potential critical enhancers and their gene regulatory networks during PSM development.Our approach involves analyzing developmental trajectories...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
....35) with Williams–Beuren syndrome DDT (WSD) or D-TOX E motif. The conserved GxD signature is highlighted with a red bar. (Q) Query (ICOPa), (ss_pred) secondary structure prediction, and (T) template. For a more detailed output format description, please consult https://toolkit.tuebingen.mpg.de/tools/hhpred. (B...
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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
...al. 2013; Werner et al. 2017), demonstrating a genetic basis, and possible selection, for mouth-form ratios in the wild.View larger version: In this window In a new window Figure 1. Developmental transcriptomics of mouth-form plasticity in Pristionchus pacificus. (A) The two mouth forms developed...
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Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
...the original reference data to 50% and evaluated the accuracy of both CAMUS and random sampling. The performance of CAMUS still significantly outperforms random selection (Supplemental Fig. S1D). This implies that reference data selection can enhance annotation accuracy and rare cell type identification...

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