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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
...in tandem for ∼100–110 times (Lifton et al. 1978; Strausbaugh and Weinberg 1982). Each unit is ∼5 kb in length, and this tandem organization is present in distantly related Drosophila species, indicating old evolutionary origins (Kakita et al. 2003). In contrast, Stellate is a D. melanogaster...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...://dazzlerblog.wordpress.com/2014/05/15/on-perfect-assembly/). The success of LRS in many organisms attests to this being generally true.However, when the first LRS data set of Drosophila melanogaster was released (Kim et al. 2014), Carvalho and colleagues (2016) reported an unexpected failure: Several single-copy exons of the Y...
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Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
- Lianne B Cohen,
- Tamara Hadzic,
- Caitlin Sauer,
- Julia R Gibbs,
- and Zeba Wunderlich
Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
...infections. The fruit fly Drosophila melanogaster relies on its innate immune system to 42 defend against invading pathogens, without the aid of an adaptive immune system (Lemaitre 43 and Hoffmann 2007; Buchon et al. 2014). From the fat body, a liver-like organ, and hemocytes, 44 Drosophila blood cells...
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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
...al. 2020), suggesting compartment switching significantly impacts gene expression control (Ibrahim and Mundlos 2020; Sood and Misteli 2022).Breast cancer is the most common cancer in women. These cancers have been classified into five subtypes based on the expression of receptors for human epidermal...
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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: 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
...-derived sequences (Lipatov et al. 2005). A recent transcriptome-wide study identified 327 genes in Drosophila melanogaster that generate chimeric transcripts across different populations (Oliveira et al. 2023). Among all genes, 76 generate chimeric transcripts from TE insertions that were present in one strain...
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Research: ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells
- Elina Abaev-Schneiderman,
- Linh Nguyen,
- Raz Shalev,
- Tzofit Elbaz Biton,
- Anand Chopra,
- Giritharan Jagadeesan,
- Daniel Sevilla-Sanchez,
- Nili Tickotsky Moskovitz,
- Liron Levin,
- Michal Feldman,
- Capucine Van Rechem,
- and Dan Levy
Genome Res. April 2026 36: 684-694; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
...that were upregulated in the cells expressing the ACTB mutant are represented by Clusters 2 and 4. Conversely, target genes that were downregulated in the ACTB mutant compared to WT are represented by Clusters 1 and 3. qPCR validation for the down- and the upregulated genes in the ACTB mutant condition...
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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...chromatin than previously profiled Drosophila tissues (Supplemental Fig. S9A,B). Genome-wide analyses have shown that the majority of Pc binding sites in other Drosophila tissues are located outside of H3K27me3-marked domains (Orsi et al. 2014; Loubiere et al. 2016; Brown et al. 2018). Promoter-proximal Pc...
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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
...to mediate interactions with ISWI1 in diverse eukaryotes (Aravind and Iyer 2012), we assessed whether this signature is needed to form the ISWI1–ICOP complex. ICOPa and ICOPb have two GxDs (Fig. 3A). As aspartate was proposed to drive the interaction in the GxD signature (Aravind and Iyer 2012), ICOP mutants...
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Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- Peter O. Mulhair,
- Liam Crowley,
- Douglas H. Boyes,
- Amber Harper,
- Owen T. Lewis,
- Darwin Tree of Life Consortium,
- and Peter W.H. Holland
Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
...be inverted, and the zen gene may be duplicated (e.g., zen, zen2, and bcd in Drosophila melanogaster), but radical gene order changes are rare, documented only within individual species or close relatives (Negre et al. 2005). A difficulty in studying gene order is that intergenic distances may be large...
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