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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...27me3). Constitutive heterochromatin is enriched in features like H3K9 di- and trimethylation (H3K9me2/3) and the H3K9me2/3-binding protein CBX1 (also known as HP1B). It is likewise depleted in histone acetylation and generally localizes to the nuclear periphery or chromocenters (Allshire and Madhani...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
....The radiation of cactophilic Drosophila species across different hosts is an evolutionary outcome that gave rise to specific adaptations (Rane et al. 2019). They can be summarized into three steps: localization, acceptance, and host usage (Markow 2019). In the localization step, odorant-binding proteins (OBPs...
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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC origin and evolution, we use a population genomic approach to compare piC activity and sequence composition across eight geographically distant strains of D. melanogaster...
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Research: Relationship between histone modifications and transcription factor binding is protein family specific
- Beibei Xin and
- Remo Rohs
Genome Res. March 2018 28: 321-333; Published in Advance January 11, 2018, doi:10.1101/gr.220079.116
...fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies...
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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
..., Schizosaccharomyces pombe, Drosophila menlanogaster, Homo sapiens). A window of 300 kb is shown for each chromosome in a browser. (B) Summary of genomic features of the same organisms named in A. For details on collected data, see Methods. (C) Detection of histone modifications in vegetative Paramecium nuclei...
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Research: Broad chromosomal domains of histone modification patterns in C. elegans
- Tao Liu,
- Andreas Rechtsteiner,
- Thea A. Egelhofer,
- Anne Vielle,
- Isabel Latorre,
- Ming-Sin Cheung,
- Sevinc Ercan,
- Kohta Ikegami,
- Morten Jensen,
- Paulina Kolasinska-Zwierz,
- Heidi Rosenbaum,
- Hyunjin Shin,
- Scott Taing,
- Teruaki Takasaki,
- A. Leonardo Iniguez,
- Arshad Desai,
- Abby F. Dernburg,
- Hiroshi Kimura,
- Jason D. Lieb,
- Julie Ahringer,
- Susan Strome,
- and X. Shirley Liu
Genome Res. February 2011 21: 227-236; Published in Advance December 22, 2010, doi:10.1101/gr.115519.110
...chromosomes may not be maintained by unique boundary elements. H3K9 methylation in Drosophila and mammals has been shown to be important for the stability of repetitive sequences (Peng and Karpen 2008). The enrichment of H3K9methylation on the repeat-rich arm regions of C. elegans suggests a similar role...
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Research: Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin
- Kirsty Jamieson,
- Elizabeth T. Wiles,
- Kevin J. McNaught,
- Simone Sidoli,
- Neena Leggett,
- Yanchun Shao,
- Benjamin A. Garcia,
- and Eric U. Selker
Genome Res. January 2016 26: 97-107; Published in Advance November 4, 2015, doi:10.1101/gr.194555.115
...relationships between marks of constitutive and facultative heterochromatin. Specifically, we used the filamentous fungus Neurospora crassa, which unlike many other simple model eukaryotes (e.g., budding and fission yeasts,Drosophila and Caenorhabditis elegans) has both DNA methylation and H3K27me (Aramayo...
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Research: Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2
- Jacob M. Garrigues,
- Simone Sidoli,
- Benjamin A. Garcia,
- and Susan Strome
Genome Res. January 2015 25: 76-88; Published in Advance December 2, 2014, doi:10.1101/gr.180489.114
...of heterochromatin protein 1 (HP1), a highly conserved, small nonhistone protein first identified in Drosophila (James and Elgin 1986). Heterochromatin is typically concentrated at pericentric and subtelomeric regions. How heterochromatin is distributed in an organismwithnumerous centromeres distributed along...
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Resource: Gene expression networks in the Drosophila Genetic Reference Panel
- Logan J. Everett,
- Wen Huang,
- Shanshan Zhou,
- Mary Anna Carbone,
- Richard F. Lyman,
- Gunjan H. Arya,
- Matthew S. Geisz,
- Junwu Ma,
- Fabio Morgante,
- Genevieve St. Armour,
- Lavanya Turlapati,
- Robert R.H. Anholt,
- and Trudy F.C. Mackay
Genome Res. March 2020 30: 485-496; Published in Advance March 6, 2020, doi:10.1101/gr.257592.119
...and for which molecular endophenotypes and complex traits are assessed on the same genotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete sequences and for which phenotypes of many quantitative traits have been evaluated. We mapped expression...
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Research: Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals
- Antoine Molaro,
- Janet M. Young,
- and Harmit S. Malik
Genome Res. April 2018 28: 460-473; Published in Advance March 16, 2018, doi:10.1101/gr.229799.117
...@fhcrc.orgAbstractEukaryotic s must accomplish both compact packaging for stability and inheritance, as well as accessibility for gene expression. They do so using post-translational modifications of four ancient canonical histone proteins (H2A, H2B, H3, and H4) and by deploying histone variants with specialized chromatin...

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