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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 ; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson’s disease Kangli Wang,1 Weikun Xia,1 Yingli Gu,1 Songpeng Zu,1 Qian Yang,2 Maria Luisa Amaral,1 Yaozhi Wang,1 Allen Wang,2 Xiang-Dong Fu,3 William C. Mobley,4 and Bing Ren1...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...are usually lost over short evolutionary timescales, but they can be retained through three primary mechanisms: conservation of wild-type function, in which duplicates alter gene dosage or provide redundancy; subfunctionalization, in which ancestral function is partitioned across copies...
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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
...transposition. Following post-GEM cleanup, libraries were preamplified by PCR, after which the sample was split into three parts: one part generated the snRNA-seq library, one part generated the snATAC-seq library, and the rest was kept at −20°C. SnATAC and snRNA libraries were indexed for multiplexing...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...and then quantified by quantitative polymerase chain reaction (PCR). Hi-C sequencing was performed by a Illumina HiSeq 2500 platform, using the paired-end of 150 bp reads.To assist gene prediction and dosage compensation analysis, 24 RNA-seq libraries were generated from brain, hindleg, and gonads with four...
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Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
- Étienne Fafard-Couture,
- Pierre-Étienne Jacques,
- and Michelle S. Scott
Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
...RNAs (Supplemental Fig. S12), underlining the crucial role of motif conservation in snoRNP formation. Overall, these results suggest that box sequence conservation (especially the C, H, and ACA motifs), snoRNA stability (global structure and at the terminal stem level), and host gene expression level...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...in genetic diversity and gene regulation, and are associated with various neurological and developmental disorders. They can also arise in sequencing reads generated by certain technologies, such as those used for sequencing circular molecules. A key challenge in analyzing tandem repeats is reconstructing...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...al. 2021b) and have biological significance. Additionally, primes could serve practical purposes, such as PCR primers, highly specific platforms in CRISPR construct designs, genomic barcodes, and sample labeling. Previous studies examined a limited number of s and derived 60,370 15 bp nucleic prime...
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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
...using the NEB Ultra II directional RNA library prep kit with sample purification beads (NEB E7765), with 10–14 PCR cycles (determined empirically to achieve the minimum number of cycles per library). Libraries were then sequenced on an Illumina HiSeq 2000 in single-end mode, except for the 12 h time...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...processed as for CNV (trimmed for adapter sequences, aligned with Burrows-Wheeler Aligner 0.7.18, and PCR duplicates removed). Mapped, filtered, and deduplicated reads were counted into genomic windows of distinct size (from 5- to 100-kb) using the intersect function from BEDTools 2.31.1 (Quinlan and Hall...
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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
...analysis reveals candidate TFs acting via endoderm HCNE CRMs. (A,B) High-confidence de novo motifs enriched in HCNEs overlapping both human PFG H3K27ac peaks and sox17E > sox17M DARs at 28 and/or 48 hpf for the human (A) and zebrafish (B) HCNE sequences. Pvalues and closest match vertebrate TFs assigned...

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