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Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
- Yidi Deng,
- Jiadong Mao,
- Jarny Choi,
- and Kim-Anh Le Cao
Genome Res. March 5, 2026 gr.281171.125; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...(TFs) to specific DNA sequences 36 to either activate or repress target gene expression. This regulation directs crucial cellular processes 37 such as differentiation, proliferation, and responses to environmental stimuli. The emergence of 38 high-throughput sequencing, particularly in transcriptomics...
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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
...multiple PQN-85 binding sitesNIPBL protein is important for cohesin recruitment to DNA (Ciosk et al. 2000). Thus, we next analyzed the distribution and function of the C. elegans ortholog of NIPBL, encoded by pqn-85/scc-2 (Lightfoot et al. 2011). The strength of the fountains positively correlated...
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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
...). Although informative, they are not quantitative, incapable of determining direct enhancer activity, and cannot uncouple epigenomic from genomic mechanisms. On the other hand, reporter assays overcome some of these limitations by measuring enhancer activity on nonchromatinized DNA templates, isolating...
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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
...-seq) experiments. Within Con SEs, we identify 20 candidate critical enhancers with meat and carcass-associated DNA variations that affect enhancer activity, and infer their upstream transcription factors and downstream target genes. As a proof of concept, we experimentally validate the role of one such enhancer...
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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. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...reveal a highly significant association between endoderm HCNEs and genes encoding DNA-binding and gene regulatory proteins, including HMG domain-containing and chromatin binding factors. Notably, however, the endodermHCNEs appear to show a greater enrichment of such genes compared with all HCNEs...
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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. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...investigation into aging mechanisms. While traditional aging studies often compare just two age 76 groups, a more nuanced approach incorporating multiple age points can detect molecular 77 changes that may occur at different stages of aging, enhancing our understanding of aging 78 processes. Mice, for example...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...method. (Right) Comparative genomic features between interspecific and intraspecific strains, including sizes (A), gene numbers (B), repeat content as a percentage of the (C), proportions of repeat types among total repeats (D), gene length distributions (E), and coding DNA sequence (CDS) length...
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Research: Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma
- Raquel Ordoñez,
- Marta Kulis,
- Nuria Russiñol,
- Vicente Chapaprieta,
- Arantxa Carrasco-Leon,
- Beatriz García-Torre,
- Stella Charalampopoulou,
- Guillem Clot,
- Renée Beekman,
- Cem Meydan,
- Martí Duran-Ferrer,
- Núria Verdaguer-Dot,
- Roser Vilarrasa-Blasi,
- Paula Soler-Vila,
- Leire Garate,
- Estíbaliz Miranda,
- Edurne San José-Enériz,
- Juan R. Rodriguez-Madoz,
- Teresa Ezponda,
- Rebeca Martínez-Turrilas,
- Amaia Vilas-Zornoza,
- David Lara-Astiaso,
- Daphné Dupéré-Richer,
- Joost H.A. Martens,
- Halima El-Omri,
- Ruba Y. Taha,
- Maria J. Calasanz,
- Bruno Paiva,
- Jesus San Miguel,
- Paul Flicek,
- Ivo Gut,
- Ari Melnick,
- Constantine S. Mitsiades,
- Jonathan D. Licht,
- Elias Campo,
- Hendrik G. Stunnenberg,
- Xabier Agirre,
- Felipe Prosper,
- and Jose I. Martin-Subero
Genome Res. September 2020 30: 1217-1227; Published in Advance August 20, 2020, doi:10.1101/gr.265520.120
..., Segura V, Bergmann A, Esteve A, Merkel A, Raineri E, et al. 2015. Whole-epi analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers. Genome Res 25: 478–487. doi:10.1101/gr.180240.114 ↵Agnarelli A, Chevassut T, Mancini EJ. 2018. IRF4 in multiple myeloma—biology, disease...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
....DiscussionEnDeep4mC achieves state-of-the-art prediction performance and provides novel insights into the evolutionary dynamics of DNA 4mC modification. A key insight is its enhanced intraclass transferability for prokaryotes, as evidenced in cross-species predictions. These observations are consistent...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...region of Chromosome 2L (early-mid), the fourth chromosome (early), and the rDNA locus (early) (Fig. 5B). Although replication timing for the X Chromosome was found to be early-mid and the Y Chromosome to be late-mid in both GSC-like and CySC-like cells (Supplemental Table S5), the Z-scores revealed more...
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