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Research: Broad domains of histone marks in the highly compact Paramecium macronuclear genome
- Franziska Drews,
- Abdulrahman Salhab,
- Sivarajan Karunanithi,
- Miriam Cheaib,
- Martin Jung,
- Marcel H. Schulz,
- and Martin Simon
Genome Res. April 2022 32: 710-725; Published in Advance March 9, 2022, doi:10.1101/gr.276126.121
...Broad domains of histone marks in the highly compact Paramecium macronuclear Franziska Drews1,2, Abdulrahman Salhab3,7, Sivarajan Karunanithi4,5,7,8, Miriam Cheaib2, Martin Jung6, Marcel H. Schulz4,5 and Martin Simon1,2 1Molecular Cell Biology and Microbiology, Faculty for Mathematics and Natural...
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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
...editing efficiency, we amplified genomic DNA from puromycin-selected, doubly transfected C1 cells using primers targeting regions surrounding sites recognized by sgRNAs in RE1, -2, or -3 (Supplemental Fig. S49A). PCR products were analyzed by gel electrophoresis, purified, and sequenced (Supplemental Fig...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...indicates IRS distributions of individual KDs; below diagonal, correlation graphs of pairwise comparisons; above diagonal, corresponding Pearson correlation coefficients; red lines, ordinary least-square (OLS) regression; orange lines, LOWESS; and gray lines, orthogonal distance regression (ODR).PCRs...
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Research: Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing
- Wouter Steyaert,
- Lydia Sagath,
- German Demidov,
- Vicente A. Yépez,
- Anna Esteve-Codina,
- Julien Gagneur,
- Kornelia Ellwanger,
- Ronny Derks,
- Marjan Weiss,
- Amber den Ouden,
- Simone van den Heuvel,
- Hilde Swinkels,
- Nick Zomer,
- Marloes Steehouwer,
- Luke O'Gorman,
- Galuh Astuti,
- Kornelia Neveling,
- Rebecca Schüle,
- Jishu Xu,
- Matthis Synofzik,
- Danique Beijer,
- Holger Hengel,
- Ludger Schöls,
- Kristl G. Claeys,
- Jonathan Baets,
- Liedewei Van de Vondel,
- Alessandra Ferlini,
- Rita Selvatici,
- Heba Morsy,
- Marwa Saeed Abd Elmaksoud,
- Volker Straub,
- Juliane Müller,
- Veronica Pini,
- Luke Perry,
- Anna Sarkozy,
- Irina Zaharieva,
- Francesco Muntoni,
- Enrico Bugiardini,
- Kiran Polavarapu,
- Rita Horvath,
- Evan Reid,
- Hanns Lochmüller,
- Marco Spinazzi,
- Marco Savarese,
- Solve-RD DITF-ITHACA, Solve-RD DITF-Euro-NMD, Solve-RD DITF-RND, Solve-RD DITF-EpiCARE,
- Leslie Matalonga,
- Steven Laurie,
- Han G. Brunner,
- Holm Graessner,
- Sergi Beltran,
- Stephan Ossowski,
- Lisenka E.L.M. Vissers,
- Christian Gilissen,
- Alexander Hoischen,
- and on behalf of the Solve-RD consortium
Genome Res. April 2025 35: 755-768; Published in Advance March 26, 2025, doi:10.1101/gr.279414.124
.... The deletion breakpoints were confirmed by Sanger sequencing, and its absence in the siblings was confirmed by PCR and gel electrophoresis (Fig. 6G).PSMA3 is expressed in tissues throughout the body, including skeletal muscle and nerve tissues. As a proteasome subunit, the role of PSMA3 is to contribute...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...of a sentence. Scrambling has been used to describe the patterns of synteny loss in genomic comparisons of distantly related species, such as fugu and humans, whose organization has significantly diverged over hundreds of millions of years (Aparicio et al. 2002). However, fundamental questions remain...
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Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
- Susan M. Hiatt,
- James M.J. Lawlor,
- Lori H. Handley,
- Donald R. Latner,
- Zachary T. Bonnstetter,
- Candice R. Finnila,
- Michelle L. Thompson,
- Lori Beth Boston,
- Melissa Williams,
- Ivan Rodriguez Nunez,
- Jerry Jenkins,
- Whitley V. Kelley,
- E. Martina Bebin,
- Michael A. Lopez,
- Anna C.E. Hurst,
- Bruce R. Korf,
- Jeremy Schmutz,
- Jane Grimwood,
- and Gregory M. Cooper
Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
..., using a standard protocol that generally included PCR amplification (86/96). Genomes were sequenced at an approximate mean depth of 30×, with at least 80% of base positions reaching 20× coverage. Exomes were sequenced to a mean depth of 71×. For short-read reanalysis, srES and srGS reads were aligned...
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Research: H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity
- Kei Fukuda,
- Chikako Shimura,
- and Yoichi Shinkai
Genome Res. October 2025 35: 2199-2210; Published in Advance August 5, 2025, doi:10.1101/gr.280732.125
...buffer (20 mM Tris [pH 8.0], 10 mM EDTA, 400 mM NaCl). Input and ChIP samples were de-crosslinked by RNase A, SDS, and Proteinase K treatment, and purified with a QIAquick PCR purification Kit (Qiagen).Preparation of ChIP-seq libraryThe ChIP DNA was fragmented by Picoruptor (Diagenode) for 10 cycles...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...to assembly than either iso-1 or A4, like large and homogeneous duplications. This also hinted that the histone unit copy number was significantly higher than the typical expectation of ∼110. To validate our findings, we sequenced PCR-free Illumina libraries derived from the three strains (the same ones...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...and Staurotypus revealed strong interactions between proximal loci within chromosomes (in cis) with the expected exponential decay in interaction signal as the distance between genomic regions increased (Fig. 3A). And we note that the diagonal thickness, which reflects the level of chromatin compaction along each...
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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
...architecture, with stretches of heterochromatic DNA dominated by long retrotransposon insertions interspersed with compact, gene-rich regions. The absence of an enrichment of SSPs within TE-rich regions suggest a partially different genomic organization compared with the frequent TE...

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