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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...stem cells (CySCs), the Drosophila testis provides an excellent in vivo model for studying adult stem cells. However, the small number of stem cells and the cellular heterogeneity of this tissue have limited comprehensive genomic studies. In this study, we develop cell-type-specific genomic techniques...
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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
...on mutational processes shaping two functionally important tandem arrays in the Drosophila .ResultsGenome assembliesThe strains selected include the Drosophila community's reference strain (iso-1) (Adams et al. 2000) and two strains from the Drosophila Synthetic Population Resource (A3 and A4) (King et al. 2012...
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Method: Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe
- Arnaud Belcour,
- Jeanne Got,
- Méziane Aite,
- Ludovic Delage,
- Jonas Collén,
- Clémence Frioux,
- Catherine Leblanc,
- Simon M. Dittami,
- Samuel Blanquart,
- Gabriel V. Markov,
- and Anne Siegel
Genome Res. June 2023 33: 972-987; Published in Advance July 19, 2023, doi:10.1101/gr.277056.122
...).The fungal data set includes 74 fungal s which were selected according to the method of Wang et al. (2009) as representative of the fungal diversity, together with three outgroup s: Caenorhabditis elegans, Drosophila melanogaster, and Monosiga brevicollis. All proteomes and s were downloaded from...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...RNA-mRNA interaction that can best explain our mRNA-seq data in response to sponge perturbations. These software had been used to predict the post-transcriptional regulation of specific tsRNAs on putative target genes in human and Drosophila cells (Luo et al. 2018; Chen et al. 2022; Tu et al. 2023). We note...
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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
...by changing the epigenetic status of their surrounding regions. In Drosophila, repressive histone marks enriched at TEs spread beyond TE sequences, which is often associated with gene down-regulation (Lee and Karpen 2017). However, there is also evidence that TEs containing active chromatin marks can lead...
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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
...). Several predicted de novo genes in the Drosophila genus were shown to have become essential for male fertility (Gubala et al. 2017; Rivard et al. 2021). Overall, many of the predicted de novo genes in metazoa seem to be associated with either developmental processes of the neuronal system...
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Research: Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
- Yi Liao,
- Xinwen Zhang,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. March 2021 31: 397-410; Published in Advance February 9, 2021, doi:10.1101/gr.266130.120
...million years of divergence, showed that ∼30%–40% of their s retain conserved TADs. Comparative genomic analysis of 17 Drosophila species revealed that chromosomal rearrangement breakpoints are enriched at TAD boundaries but depleted within TADs. Additionally, genes within conserved TADs show lower...
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Research: Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome
- Christoph D. Treiber and
- Scott Waddell
Genome Res. November 2020 30: 1559-1569; Published in Advance September 24, 2020, doi:10.1101/gr.259200.119
...single-cell RNA-seq (scRNA-seq) to map transposon expression to individual cells in the Drosophila midbrain. Combining these data with high-coverage genomic DNA (gDNA) sequencing of the same inbred fly strain permitted neural transposon expression to be correlated with that of genes within which...
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Resource: The developmental proteome of Drosophila melanogaster
- Nuria Casas-Vila,
- Alina Bluhm,
- Sergi Sayols,
- Nadja Dinges,
- Mario Dejung,
- Tina Altenhein,
- Dennis Kappei,
- Benjamin Altenhein,
- Jean-Yves Roignant,
- and Falk Butter
Genome Res. July 2017 27: 1273-1285; Published in Advance April 5, 2017, doi:10.1101/gr.213694.116
...including embryo, larva, pupa, and adult, undergoing a complete phenotypic metamorphosis (Lawrence 1992). These transitions are based on tightly regulated gene expression at the transcriptional, epigenetic, and translational level. Currently, most developmental gene expression studies in Drosophila rely...
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Research: microRNA target prediction programs predict many false positives
- Natalia Pinzón,
- Blaise Li,
- Laura Martinez,
- Anna Sergeeva,
- Jessy Presumey,
- Florence Apparailly,
- and Hervé Seitz
Genome Res. February 2017 27: 234-245; Published in Advance November 15, 2016, doi:10.1101/gr.205146.116
...for miR-965 in Drosophila (Verma and Cohen 2015). All the other published in vivo assessments of the implication of targets in miRNA mutant phenotypes pointed to a single target each. Recent technological advances now allow a precise dissection of regulatory networks: Mutating miRNAs and targets...

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