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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
...electrophoresis. A total of three different replicates of double transfections with puromycin treatment conducted at different times was processed. Two milligrams of total RNA was used for generation of cDNA primed with oligo(dT) according to the manufacturer's instructions (AffinityScript cDNA synthesis kit...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...kb mitochondrial , for which we obtained a complete and circularized sequence, whereas contigs 19–29 contain only 45S rDNA arrays. We found an enrichment of TTAGGG telomere repeats, typical of many eukaryotes, including true truffles (Martin et al. 2010), toward both ends of all 17 majors nuclear...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...sequence tags (ESTs) and cDNAs, with fewer than 0.5 M cDNAs and ∼8.5 M ESTs ever captured. In an era of relative data sparsity, annotating every transcript detected was a plausible goal notwithstanding the immaturity of much of the software and computational tooling supporting the annotation effort...
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Research: Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing
- Jesper Eisfeldt,
- Edward J. Higginbotham,
- Felix Lenner,
- Jennifer Howe,
- Bridget A. Fernandez,
- Anna Lindstrand,
- Stephen W. Scherer,
- and Lars Feuk
Genome Res. November 2024 34: 1763-1773; Published in Advance October 29, 2024, doi:10.1101/gr.279263.124
...the detection of genomic DNA, TaqMan assays with a probe spanning an exon junction of the target transcript were selected, and specificity for cDNA was confirmed using noRT controls. Reactions were multiplexed with a TBP endogenous control assay which was chosen for its stable expression levels in LCLs (Lossos...
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Research: The human genome contains over a million autonomous exons
- Nicholas Stepankiw,
- Ally W.H. Yang,
- and Timothy R. Hughes
Genome Res. November 2023 33: 1865-1878; Published in Advance November 9, 2023, doi:10.1101/gr.277792.123
..., 72°C 60 sec [N times]; 72°C 120 sec). At this and subsequent PCR steps, we performed qPCR to determine the number of cycles to amplify the library. We used the Q5 HF protocol scaled to 60 µL with 1 µL of cDNA, dispensed as three replicates of 15 µL, 1× Evagreen dye, 0.5 mM primer. We selected...
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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
...of the transcription end site (TES) of up-regulated (DE Up), down-regulated (DE Down), and non-DE (divided into expressed and nonexpressed genes based on expression level in control cells) showing chromatin accessibility (ATAC) and H3K4me3, H3K27ac, H3K27me3, H3K9me3 H3K27ac, H3K9me3 ChIP-seq data. (J) Boxplots...
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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
...the manufacturer's instructions. Each paired-end cDNA library was sequenced with a read length of 150 bp using the Illumina HiSeq 2500 sequencing platform. All sequencing was performed by the Biomarker Technologies Company.Genome assemblyThe PacBio long (∼12 kb) and highly accurate (>99%) HiFi reads were assembled...
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Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...-specific expression of Leish Chr 31. Another peculiarity of Leish Chr 31 (and in all TASC) that could impact gene expression is the arrangement of the majority of genes on the same coding strand. SSRs are important genomic regions in trypanosomatids, because they define the ends of polycistronic units, playing roles...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...; Polysciences, Inc.) in accordance with the manufacturer's protocol. Cells were harvested 24 h after transfection, and total RNA was extracted using RNeasy Mini Kit (Qiagen). Two micrograms of total RNA was subjected to reverse transcription (RT) using random hexamer primers (PrimeScript 1st strand cDNA...
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Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
- Shudi Zhao,
- Yuedong Li,
- Guanping Chen,
- Xingyang Wang,
- Nan Chen,
- and Xiaofeng Wu
Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
...in the Supplemental Methods.Generation of in situ Hi-C libraries and analysis of sequencing dataThe Hi-C libraries were constructed as described in previous studies (Rao et al. 2014). The DNA in the nuclei was digested by the restriction enzyme MboI, and the cohesive ends were marked with biotin-14-dCTP. The marked...

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