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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...proteins in Fusarium graminearum, a globally significant fungal pathogen, reveals diverse roles in growth, development, and virulence. In-depth analyses of two H3K36-specific methyltransferases, Set2 and Ash1, uncover their distinct regulatory functions. Set2-mediated H3K36me3 is enriched in gene bodies...
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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
...to assess drug-based rescue of additional GAT1 variants in the future.It is important to note that not all functions of a protein of interest can be revealed by a single assay. For example, functional assessment of 18 different known pathogenic variants in KDM6B linked to neurodevelopmental diseases...
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Research: Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
- James L. Shepherdson,
- David M. Granas,
- Jie Li,
- Zara Shariff,
- Stephen P. Plassmeyer,
- Alex S. Holehouse,
- Michael A. White,
- and Barak A. Cohen
Genome Res. October 2024 34: 1540-1552; Published in Advance September 25, 2024, doi:10.1101/gr.279415.124
...in the intrinsically disordered transcriptional effector domain are particularly relevant in light of recent developments of machine learning-based computational variant effect predictors trained on protein sequence homology and structural data. The AlphaMissense, ESM1b, and EVE models predict variant pathogenicity...
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Research: Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response
- Ariadna Picart-Picolo,
- Stefan Grob,
- Nathalie Picault,
- Michal Franek,
- Christel Llauro,
- Thierry Halter,
- Tom R. Maier,
- Edouard Jobet,
- Julie Descombin,
- Panpan Zhang,
- Vijayapalani Paramasivan,
- Thomas J. Baum,
- Lionel Navarro,
- Martina Dvořáčková,
- Marie Mirouze,
- and Frédéric Pontvianne
Genome Res. November 2020 30: 1583-1592; Published in Advance October 8, 2020, doi:10.1101/gr.261586.120
...(Supplemental Fig. S17). Among them, ASYMETRIC LEAVES 1 (AS1), present in TDDO3, has an evolutionarily conserved role in plant–pathogen interactions (Yang et al. 2008). AS1 indeed acts as a positive regulator of extracellular defenses against bacterial pathogens in a salicylic acid-independent manner (Nurmberg...
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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
...ISWI1 complex proteins facilitate developmental editing in Paramecium Aditi Singh1,5, Lilia Häußermann1,5, Christiane Emmerich1, Emily Nischwitz2, Brandon K.B. Seah1, Falk Butter2,3, Mariusz Nowacki4 and Estienne C. Swart1 1Max Planck Institute for Biology, 72076 Tübingen, Germany; 2Institute...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...in the identification of all known mC readers as well as a variety of new candidate DNA methylation-binding proteins. We then focused on the characterization of their -wide binding pattern in vivo, and of high-order mutant plants lacking these proteins to interrogate the direct role of DNA methylation in Arabidopsis...
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Research: A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia
- Sivaranjani Namasivayam,
- Rodrigo P. Baptista,
- Wenyuan Xiao,
- Erica M. Hall,
- Joseph S. Doggett,
- Karin Troell,
- and Jessica C. Kissinger
Genome Res. May 2021 31: 852-865; Published in Advance April 27, 2021, doi:10.1101/gr.266403.120
..., lanes 2–4; Hikosaka et al. 2013).View larger version: In this window In a new window Figure 1. Sequence evidence of fragmented mtDNA and full-length protein-encoding genes. (A, D–F) Each row of colored blocks represents individual, annotated T. gondii (A) mtDNA-specific PCR amplicons; (D) EST reads; (E...
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Perspective: Challenges and considerations for reproducibility of STARR-seq assays
- Maitreya Das,
- Ayaan Hossain,
- Deepro Banerjee,
- Craig Alan Praul,
- and Santhosh Girirajan
Genome Res. April 2023 33: 479-495; Published in Advance May 2, 2023, doi:10.1101/gr.277204.122
...consistency and wider adoption for understanding function and regulation. STARR-seq, a popular assay for directly quantifying the activities of thousands of enhancer sequences simultaneously, has seen limited standardization across studies. The assay is long, with more than 250 steps, and frequent...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...and centromere architecture. (A) A diagram of kinetochore structure highlighting known plant proteins, including CENH3 (Talbert et al. 2002), CENP-C (Dawe et al. 1999), MIS12 (Ravi et al. 2011), KNL2 (Lermontova et al. 2013), NDC80 (Du and Dawe 2007), SPC24 (Shin et al. 2018), MAD2 (Yu et al. 1999), AUR3 (Komaki...
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Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
- Kavitha Uthanumallian,
- Andrea Del Cortona,
- Susana M. Coelho,
- Olivier De Clerck,
- Sebastian Duchene,
- and Heroen Verbruggen
Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
...Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage Kavitha Uthanumallian1, Andrea Del Cortona2, Susana M. Coelho3, Olivier De Clerck2, Sebastian Duchene4,5 and Heroen Verbruggen1,6 1Melbourne Integrative Genomics, School of Bio...
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