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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
...Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster Harsh G. Shukla1,2, Mahul Chakraborty3 and J.J. Emerson1,4 1Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA; 2Graduate Program in Mathematical...
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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
...Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species Daniel Siqueira de Oliveira1,2,3, Anaïs Larue2, William Vilas Boas Nunes2, Francois Sabot4, Alejandra Bodelón5, María Pilar García Guerreiro5, Cristina Vieira2 and Claudia Marcia...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...and is susceptible to splice variant “blindness.” Human cancer is especially rich in variations, including coding region mutations of TF genes; these features can sometimes offer similar insights as knockdown/knockout experiments. The Eukaryotic Promoter Database has the SNP2TFBS subdatabase linking genetic variants...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...GPT was utilized to generate the R script for analyzing data generated using MEME Suite.RNA sequencingTotal RNA was extracted from iPSC-CMs using the Norgen total RNA purification plus kit and sequenced by Azenta with standard RNA sequencing and rRNA depletion. Adapter sequences were trimmed, and reads were...
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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
...for the eight strains with 129 TE families. Next, RepeatModeler2 was run on the seven DSPR s and reference iso-1 strain followed by removal of non-TE repeats like tRNA, satellites, rRNA, etc., as well as TE subfamilies using bash scripts (Flynn et al. 2020). Putative novel TE family consensus was identified...
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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
...a pipeline (Supplemental Fig. S1) that (1) removes adapter and rRNA sequences, (2) aligns and quantifies expressed TE sequences and microbial transcripts, (3) verifies the origin of each sample, and (4) quantifies known and novel D. melanogaster transcripts and corrects for potential alignment bias owing...
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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: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...repetitive DNA to evolve, such as sex-chromosome meiotic drive. Such conflicts have driven the proliferation of sex-linked gene families in mammals and Drosophila (Cocquet et al. 2012; Kruger et al. 2019; for review, see Jaenike 2001). These conflicts may also impose selection pressures that trigger...
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Research: Limited allele-specific gene expression in highly polyploid sugarcane
- Gabriel Rodrigues Alves Margarido,
- Fernando Henrique Correr,
- Agnelo Furtado,
- Frederik C. Botha,
- and Robert James Henry
Genome Res. February 2022 32: 297-308; Published in Advance December 23, 2021, doi:10.1101/gr.275904.121
...were calculated based on the relative frequency of the reference allele, and the default complete linkage method was used to find clusters.Assessment of allele-specific expressionBased on the clustering pattern and the amount of rRNA and PCR duplicates, four samples that were of comparatively lower...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...this process to the ecology or biology of C. japonica. Nevertheless, common knockout phenotypes of these genes are related to slow growth and larva viability. In general, we found ribosomal proteins under positive selection in the nematodes C. briggsae, C. drosophilae, C. inopinata, O. tipulae, P. pacificus, R...

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