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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...and strongly with sXIST in male glia show functional enrichment in axon assembly and cilia signaling, with many of them sharing putative miRNA binding sites with sXIST, whereas the negatively correlated genes are enriched for processes important for neuromuscular junctions. This suggests possible functions...
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Editorial: Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases
- Ana Conesa,
- Alexander Hoischen,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: xi-xiv; doi:10.1101/gr.280665.125
...of Genome Research and had access to all papers before publication. F.J.S. obtained research support from Illumina, PacBio, and ONT. For some research studies by A.H., reagent costs were in part shared between Radboudumc and Bionano or Radboudumc and PacBio. A.C. obtained in-kind support from PacBio. A...
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Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
...≤ 0.01) (Bhattacharyya et al. 2019). Overlap of peak-to-peak loops revealed 7275 loops specific to Wnt-OFF and 6434 specific to Wnt-ON (hereafter referred to as Wnt-ON/OFF-only loops), whereas 2023 loops are shared between both conditions and represent 21.7% of Wnt-OFF and 23.9% of Wnt-ON loops (Fig...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...John Beaulaurier1,3,†, Lynn Ly1,3, J. Andrew Duty2, Carly Tyer1, Christian Stevens2, Chuan-Tien Hung2, Akash Sookdeo1, Alex W. Drong1, Shreyas Kowdle2, Axel Guzman-Solis2, Domenico Tortorella2, Daniel J. Turner1, Sissel Juul1, Scott Hickey1 and Benhur Lee2 1Oxford Nanopore Technologies, Inc., New...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...containing IGHV3-23 and compared them to each other (Fig. 6B). The five centromeric segments had identical V gene sequence, corresponding to the IGHV3-23*03 allele. The two telomeric copies also shared identical nucleotide sequence corresponding to the IGHV3-23*01 allele. Notably, this donor had two...
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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
...(Supplemental table S5). Groups are 146 connected through shared genes that reached peaks of expression during 147 gastrulation and segmentation stages, as well as by a small set of genes with 148 high expression at early and late stages along the “string” of the bow-shaped 149 graph (Figure 3A; Supplemental...
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Research: Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y
- Shruthi Rengarajan,
- Jason Derks,
- Daniel W. Bellott,
- Nikolai Slavov,
- and David C. Page
Genome Res. January 2025 35: 20-30; Published in Advance January 10, 2025, doi:10.1101/gr.279707.124
...elevated and DDX3Y transcript levels significantly reduced in fibroblasts with multiple Chr X. R-values and statistical significance were calculated using Pearson's correlation.We asked whether this inverse relationship is shared across all X–Y gene pairs or is a unique feature of DDX3X and DDX3Y. For each...
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Method: An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride
- Inswasti Cahyani,
- John Tyson,
- Nadine Holmes,
- Josh Quick,
- Chris Moore,
- Nick Loman,
- and Matthew Loose
Genome Res. May 2025 35: 1154-1166; Published in Advance March 24, 2025, doi:10.1101/gr.279943.124
...Nemo protocol will be generally applicable to tissue samples, could be readily multiplexed, and is likely compatible with automation. Finally, open-source development and sharing of protocols is crucial to enable the widest access to cost-effective high-throughput UL sequencing and troubleshooting. We...
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Research: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
...in sperm are dominated by cell-free chromatin contamination. (A) ATAC-seq browser tracks for sperm subject to the indicated conditions. (B) Heatmaps for the four indicated libraries, sorted into three categories: peaks specific to the untreated data set (I; n = 13,605), shared peaks (II; n = 2148...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
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