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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
...for genomic bin features, revealing strong consistency with RNA-based cell annotations (Supplemental Fig. S8A). We validated chromatin accessibility at marker genes for cell subclasses (Fig. 3A). Next, we performed peak calling on each subclass to identify reproducible peaks following a previous established...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...into distinct functional domains. TAD cliques are enriched in B compartments and can gain or lose TADs during differentiation, generally in correlation with gene repression or activation, respectively (Paulsen et al. 2019). Additionally, the nuclear envelope imposes positional constraints on chromatin...
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Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
- Lianne B Cohen,
- Tamara Hadzic,
- Caitlin Sauer,
- Julia R Gibbs,
- and Zeba Wunderlich
Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
...marcescens (HKSM), a gram-negative bacterium. In whole 84 organisms, 20E has been shown to regulate development as well as immunity, and treatment of 85 S2* cells with 20E induces expression of PGRP-LC, a critical receptor in the Imd pathway (Rus 86 et al. 2013). By analyzing the enhancers revealed by STARR...
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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
...@warwick.ac.ukAbstractAlthough vertebrate species are superficially diverse, they share key commonalities in terms of overall morphology, as well as organ configuration and function. Maintenance of these traits during evolution is partially explained by the conservation of critical genes governing...
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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
...strategies, including small-molecule treatments and marker-based 32 selection, are constrained by cytotoxicity, genomic scarring, and inconsistent 33 performance. Here, we present ESS-HDR (essential gene–supported scarless HDR), a 34 robust, drug- and marker-free platform that selectively enriches HDR...
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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...a negative correlation for GC content, gene density, and Ks with chromosome length, as well as a positive correlation of gene length (Supplemental Table 3; see Methods). This chromosome length-dependent pattern was not supported in human, sea lamprey, and teleost fishes, but was supported for multiple...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...and Schultze 1984; Grande 2010; Wright et al. 2012; Braasch et al. 2016; Brownstein and Lyson 2022). Using the new chromosome-scale assemblies, we reveal that every level of genomic organization in gars is experiencing evolutionary stasis. Gar s are so conserved that they more closely resemble those...
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Method: Examining the dynamics of three-dimensional genome organization with multitask matrix factorization
- Da-Inn Lee and
- Sushmita Roy
Genome Res. May 2025 35: 1179-1193; Published in Advance March 20, 2025, doi:10.1101/gr.279930.124
...Untangling the relationship between 3D organization and gene expression remains a key question in regulatory genomics. Although a direct mechanistic link between transcription and 3D organization has been observed (Heinz et al. 2018; van Steensel and Furlong 2019) during cell state transitions (Chen et al. 2024; Pollex et al...
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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
...hypoxia exposure, whereas other topics reflect processes found in one or several cell types.Most cell types exhibited a modest positive correlation between the transcriptional responses to hypoxia and hyperoxia (Fig. 2A; Supplemental Fig. S2B,E), and many gene families related to general response...
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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
....05.003 ↵Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR. 2013. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res 23: 169–180. doi:10.1101/gr.139618.112 ↵Bell AC, West AG, Felsenfeld G. 1999. The protein CTCF...

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