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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
...A -wide survey reveals a diverse array of enhancers coordinates the Drosophila 1 innate immune response 2 3 Lianne B. Cohen1, 2, Tamara Hadzic2, 3, Caitlin Sauer1, 2, Julia R. Gibbs1, 2, Zeba Wunderlich1, 2, 3, 4 4* 5 1. Department of Biology, Boston University, Boston, MA 02215, USA 6 2...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...more peaks in introns than worms. The distribution of peaks in C. elegans is slightly farther upstream of the TSS than in Drosophila, perhaps reflecting the fact that for many C. elegans gene models the annotated TSS is the site of trans-splicing, with the start of transcription occurring further...
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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...diversity. Our findings and case studies unveil systemic exon inclusion roles in regulating diversity in coding region. Correspondingly, annotation of protein-coding genes and associated transcripts from C. elegans, D. melanogaster, D. rerio, M. musculus, and H. sapiens are publicly accessible...
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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: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...and that (few) surviving transcripts gain stable and broader expressions, presumably via fast epigenetic control (Schmitz et al. 2020). Zhao et al. (2014) identified 106 de novo genes specifically expressed in the testis of laboratory strains of Drosophila melanogaster. Furthermore, Moyers and Zhang (2016...
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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
...significance (GUS) that are difficult to interpret, even with the integration of the latest bioinformatic tools. In this Perspective, we review how studies using the fruit fly Drosophila melanogaster have facilitated rare disease diagnosis by uncovering the clinical relevance of GUS and classifying rare...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...; Van Oss and Carvunis 2019; Betrán and Long 2022; Zhang et al. 2022). New genes can be integrated into essential bioprocesses, such as transcriptional regulation, RNA synthesis, and DNA repair (Ciccarelli et al. 2005; Ding et al. 2021). In Drosophila species, lineage-specific genes may control the key...
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Research: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
- Divya Selvaraju,
- Filip Wierzbicki,
- and Robert Kofler
Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
...at the transcriptional and the post-transcriptional level (Brennecke et al. 2007; Gunawardane et al. 2007; Sienski et al. 2012; Le Thomas et al. 2013). Most piRNAs are derived from discrete genomic source loci, termed piRNA clusters (Brennecke et al. 2007). In Drosophila melanogaster about 142 clusters were found, which...
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Research: Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains
- Marta Coronado-Zamora and
- Josefa González
Genome Res. September 2023 33: 1541-1553; Published in Advance October 4, 2023, doi:10.1101/gr.277565.122
...chimeric transcripts are by providing alternative promoters and protein domains. In human and mouse, 2.8% and 5.2% of the total transcript start sites occur within retrotransposons, respectively (Faulkner et al. 2009). In Drosophila melanogaster, >40% of all genes are expressed from two or more promoters...
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Resource: The Release 6 reference sequence of the Drosophila melanogaster genome
- Roger A. Hoskins,
- Joseph W. Carlson,
- Kenneth H. Wan,
- Soo Park,
- Ivonne Mendez,
- Samuel E. Galle,
- Benjamin W. Booth,
- Barret D. Pfeiffer,
- Reed A. George,
- Robert Svirskas,
- Martin Krzywinski,
- Jacqueline Schein,
- Maria Carmela Accardo,
- Elisabetta Damia,
- Giovanni Messina,
- María Méndez-Lago,
- Beatriz de Pablos,
- Olga V. Demakova,
- Evgeniya N. Andreyeva,
- Lidiya V. Boldyreva,
- Marco Marra,
- A. Bernardo Carvalho,
- Patrizio Dimitri,
- Alfredo Villasante,
- Igor F. Zhimulev,
- Gerald M. Rubin,
- Gary H. Karpen,
- and Susan E. Celniker
Genome Res. March 2015 25: 445-458; Published in Advance January 14, 2015, doi:10.1101/gr.185579.114
...Resource The Release 6 reference sequence of the Drosophila melanogaster Roger A. Hoskins,1 Joseph W. Carlson,1,10 Kenneth H. Wan,1 Soo Park,1 Ivonne Mendez,1 Samuel E. Galle,1 Benjamin W. Booth,1 Barret D. Pfeiffer,2 Reed A. George,2 Robert Svirskas,2 Martin Krzywinski,3 Jacqueline Schein,3 Maria...
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