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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...Corresponding authors: twang@wustl.edu, gzhao@wustl.eduAbstractFollowing amputation, zebrafish regenerate their injured caudal fin through lineage-restricted reprogramming. Although previous studies have charted various genetic and epigenetic dimensions of this process, the intricate gene regulatory programs...
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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
...polyadenylation (APA) plays a crucial role in gene regulation and phenotypic diversity. Whereas extensive studies have explored the global APA landscape using bulk RNA-seq data, in-depth analyses of APA events at the single-cell level remain limited—particularly in farm animals. In this study, we construct...
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Research: Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development
- Hiroto S. Fukushima,
- Hiroyuki Takeda,
- and Ryohei Nakamura
Genome Res. April 2023 33: 572-586; Published in Advance April 28, 2023, doi:10.1101/gr.277577.122
...accessibility after ZGA; (ii) H3K9me3 is globally erased but specifically retained at telomeric regions, which is required for maintenance of genomic stability during the cleavage stage. These results expand the understanding of diversity and conservation of reprogramming in vertebrates, and unveil previously...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...they are less common nearby or within genes than DNA transposons, because their promoters and other cis-regulatory elements have greater potential to interfere with gene expression. Similarly, we found that SINEs, which are usually transcribed by RNA pol III and therefore less likely to interfere with pol II...
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Resource: The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
- Stefan Schoenfelder,
- Mayra Furlan-Magaril,
- Borbala Mifsud,
- Filipe Tavares-Cadete,
- Robert Sugar,
- Biola-Maria Javierre,
- Takashi Nagano,
- Yulia Katsman,
- Moorthy Sakthidevi,
- Steven W. Wingett,
- Emilia Dimitrova,
- Andrew Dimond,
- Lucas B. Edelman,
- Sarah Elderkin,
- Kristina Tabbada,
- Elodie Darbo,
- Simon Andrews,
- Bram Herman,
- Andy Higgs,
- Emily LeProust,
- Cameron S. Osborne,
- Jennifer A. Mitchell,
- Nicholas M. Luscombe,
- and Peter Fraser
Genome Res. April 2015 25: 582-597; Published in Advance March 9, 2015, doi:10.1101/gr.185272.114
...with repressive histone marks, demonstrating the regulatory potential of the distal elements identified. Furthermore, we find that coregulated genes cluster nonrandomly in spatial interaction networks correlated with their biological function and expression level. Interestingly, we find the strongest gene...
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Research: Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
- Charles E. Vejnar,
- Mario Abdel Messih,
- Carter M. Takacs,
- Valeria Yartseva,
- Panos Oikonomou,
- Romain Christiano,
- Marlon Stoeckius,
- Stephanie Lau,
- Miler T. Lee,
- Jean-Denis Beaudoin,
- Damir Musaev,
- Hiba Darwich-Codore,
- Tobias C. Walther,
- Saeed Tavazoie,
- Daniel Cifuentes,
- and Antonio J. Giraldez
Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
...RNA contains adjacent stabilizing U-rich motifs and destabilizing miR-430 target sites. Combining these elements on the same mRNAs may provide differential temporal or spatial regulation, creating specific patterns of gene expression. We propose that these transcripts are first stabilized by maternally...
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Research: Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes
- Yuvia A. Pérez-Rico,
- Valentina Boeva,
- Allison C. Mallory,
- Angelo Bitetti,
- Sara Majello,
- Emmanuel Barillot,
- and Alena Shkumatava
Genome Res. February 2017 27: 259-268; Published in Advance December 13, 2016, doi:10.1101/gr.203679.115
...vertebrates, permitting future gene regulatory studies in several tissues. [Supplemental material is available for this article.] The identification of transcriptional regulators is central for understanding tissue-specific expression programs. Enhancers are cisregulatory elements able to recruit...
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Research: ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm
- Marta Bozek,
- Roberto Cortini,
- Andrea Ennio Storti,
- Ulrich Unnerstall,
- Ulrike Gaul,
- and Nicolas Gompel
Genome Res. May 2019 29: 771-783; Published in Advance April 8, 2019, doi:10.1101/gr.242362.118
...to each enhancer, which in turn promotes transcription of a target gene in a specific spatial pattern. However, the interplay between an enhancer regulatory activity and its accessibility as determined by local chromatin organization is not well understood. We profiled chromatin accessibility with ATAC...
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Research: Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice
- Michael C. Saul,
- Christopher H. Seward,
- Joseph M. Troy,
- Huimin Zhang,
- Laura G. Sloofman,
- Xiaochen Lu,
- Patricia A. Weisner,
- Derek Caetano-Anolles,
- Hao Sun,
- Sihai Dave Zhao,
- Sriram Chandrasekaran,
- Saurabh Sinha,
- and Lisa Stubbs
Genome Res. June 2017 27: 959-972; Published in Advance March 29, 2017, doi:10.1101/gr.214221.116
...point (for details, see Supplemental Table S11). Saul et al. 966 Genome Research www..org shifts in chromatin accessibility over time and across the brain, particularly affecting regulatory elements that are far distal from the TSS of nearest genes, are correlated with these events. TRN reconstruction...
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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
...18 across consecutive stages. By integrating multi-histone ChIP-seq with ATAC-19 seq, we built a -wide chromatin state model, defining promoter and 20 enhancer activity across stages. Diverse transcription factor binding motifs were 21 detected within regulatory elements showing differential...
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