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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
...enrichment despite lacking well-positioned nucleosomes (Fig. 3E). This noncanonical H3K27me3 enrichment resembles the pattern observed in female Drosophila GSCs, in which H3K27me3 is detectable at both inactive and active gene loci (DeLuca et al. 2020).In contrast, in CySC-like cells, H3K27me3 is most...
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Research: Shared evolutionary trajectories of three independent neo-sex chromosomes in Drosophila
- Masafumi Nozawa,
- Yohei Minakuchi,
- Kazuhiro Satomura,
- Shu Kondo,
- Atsushi Toyoda,
- and Koichiro Tamura
Genome Res. November 2021 31: 2069-2079; Published in Advance October 21, 2021, doi:10.1101/gr.275503.121
...relatively stringent gene-by-gene DC as shown in D. miranda (Nozawa et al. 2018).View larger version: In this window In a new window Figure 3. Relationship between the functionality of neo-Y-linked genes and the DC of neo-X-linked homologs in the larva, pupa, adult, and testis of Drosophila miranda (A), D...
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Research: Evidence for the fixation of gene duplications by positive selection in Drosophila
- Margarida Cardoso-Moreira,
- J. Roman Arguello,
- Srikanth Gottipati,
- L.G. Harshman,
- Jennifer K. Grenier,
- and Andrew G. Clark
Genome Res. June 2016 26: 787-798; Published in Advance April 12, 2016, doi:10.1101/gr.199323.115
...of the polymorphic phase of the evolution of new genes in Drosophila melanogaster. Utilizing five distinct globally dispersed populations, we combine whole- sequencing data with gene expression profiles to (1) describe the diversity and abundance of new genes segregating in these five populations, (2) understand...
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Research: Haploid selection drives new gene male germline expression
- Julia B. Raices,
- Paulo A. Otto,
- and Maria D. Vibranovski
Genome Res. July 2019 29: 1115-1122; Published in Advance June 20, 2019, doi:10.1101/gr.238824.118
...from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci 103: 9935–9939. doi:10.1073/pnas.0509809103 ↵Long M, VanKuren NW, Chen S, Vibranovski MD. 2013. New gene evolution: Little did we know. Annu Rev Genet 47: 307–333. doi:10...
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Resource: Comparative validation of the D. melanogaster modENCODE transcriptome annotation
- Zhen-Xia Chen,
- David Sturgill,
- Jiaxin Qu,
- Huaiyang Jiang,
- Soo Park,
- Nathan Boley,
- Ana Maria Suzuki,
- Anthony R. Fletcher,
- David C. Plachetzki,
- Peter C. FitzGerald,
- Carlo G. Artieri,
- Joel Atallah,
- Olga Barmina,
- James B. Brown,
- Kerstin P. Blankenburg,
- Emily Clough,
- Abhijit Dasgupta,
- Sai Gubbala,
- Yi Han,
- Joy C. Jayaseelan,
- Divya Kalra,
- Yoo-Ah Kim,
- Christie L. Kovar,
- Sandra L. Lee,
- Mingmei Li,
- James D. Malley,
- John H. Malone,
- Tittu Mathew,
- Nicolas R. Mattiuzzo,
- Mala Munidasa,
- Donna M. Muzny,
- Fiona Ongeri,
- Lora Perales,
- Teresa M. Przytycka,
- Ling-Ling Pu,
- Garrett Robinson,
- Rebecca L. Thornton,
- Nehad Saada,
- Steven E. Scherer,
- Harold E. Smith,
- Charles Vinson,
- Crystal B. Warner,
- Kim C. Worley,
- Yuan-Qing Wu,
- Xiaoyan Zou,
- Peter Cherbas,
- Manolis Kellis,
- Michael B. Eisen,
- Fabio Piano,
- Karin Kionte,
- David H. Fitch,
- Paul W. Sternberg,
- Asher D. Cutter,
- Michael O. Duff,
- Roger A. Hoskins,
- Brenton R. Graveley,
- Richard A. Gibbs,
- Peter J. Bickel,
- Artyom Kopp,
- Piero Carninci,
- Susan E. Celniker,
- Brian Oliver,
- and Stephen Richards
Genome Res. July 2014 24: 1209-1223; Published in Advance July 1, 2014, doi:10.1101/gr.159384.113
...transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura . We also describe conservation of four distinct core promoter...
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INSIGHT/OUTLOOK: Doubling the Rewards: Testis ESTs for Drosophila Gene Discovery and Spermatogenesis Expression Profile Analysis
- Barbara T. Wakimoto
Genome Res. December 1, 2000 10: 1841-1842; doi:10.1101/gr.169400
...: Testis ESTs for Drosophila Gene Discovery and Spermatogenesis Expression Profile Analysis Doubling the Rewards: Testis ESTs for Drosophila Gene Discovery and Spermatogenesis Expression Profile Analysis Barbara T. Wakimoto 1 University of Washington, Seattle, Washington 98195, USA One of the rewards...
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Research: Gene regulation and speciation in house mice
- Katya L. Mack,
- Polly Campbell,
- and Michael W. Nachman
Genome Res. April 2016 26: 451-461; Published in Advance February 1, 2016, doi:10.1101/gr.195743.115
...% of testable genes in comparisons betweenmouse subspecies. These results stand in contrast to those of McManus et al. (2010) and Coolon et al. (2014), both of whom found a large proportion of expression divergence to be the result of trans differences in Drosophila crosses. Elevated trans divergence...
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Research: Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
- Eugene Berezikov,
- Nicolas Robine,
- Anastasia Samsonova,
- Jakub O. Westholm,
- Ammar Naqvi,
- Jui-Hung Hung,
- Katsutomo Okamura,
- Qi Dai,
- Diane Bortolamiol-Becet,
- Raquel Martin,
- Yongjun Zhao,
- Phillip D. Zamore,
- Gregory J. Hannon,
- Marco A. Marra,
- Zhiping Weng,
- Norbert Perrimon,
- and Eric C. Lai
Genome Res. February 2011 21: 203-215; Published in Advance December 22, 2010, doi:10.1101/gr.116657.110
...few well-conserved Drosophila miRNA genes that have escaped discovery efforts. It remains plausible though, if not likely, that many of these conserved segments of the have been retained for functional or regulatory reasons other than miRNA production. We provide detailed analysis of the reads mapping...
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RESOURCE: High-Throughput Gene Discovery in the Rat
- Todd E. Scheetz,
- Jennifer J. Laffin,
- Brian Berger,
- Sara Holte,
- Susan A. Baumes,
- Robert Brown II,
- Shereen Chang,
- Justin Coco,
- Jim Conklin,
- Keith Crouch,
- Micca Donohue,
- Greg Doonan,
- Chris Estes,
- Mari Eyestone,
- Katrina Fishler,
- Jack Gardiner,
- Lankai Guo,
- Brad Johnson,
- Catherine Keppel,
- Rikki Kreger,
- Mark Lebeck,
- Rudy Marcelino,
- Vladan Miljkovich,
- Mindee Perdue,
- Ling Qui,
- Joshua Rehmann,
- Rebecca S. Reiter,
- Bridgette Rhoads,
- Kelly Schaefer,
- Christina Smith,
- Ivana Sunjevaric,
- Kurtis Trout,
- Ning Wu,
- Clayton L. Birkett,
- Jared Bischof,
- Barry Gackle,
- Allen Gavin,
- A. Jason Grundstad,
- Brian Mokrzycki,
- Chris Moressi,
- Brian O'Leary,
- Kevin Pedretti,
- Chad Roberts,
- Natalie L. Robinson,
- Michael Smith,
- Dylan Tack,
- Nishank Trivedi,
- Tamara Kucaba,
- Tom Freeman,
- Jim J.-C. Lin,
- Maria F. Bonaldo,
- Thomas L. Casavant,
- Val C. Sheffield,
- and M. Bento Soares
Genome Res. April 2004 14: 733-741; doi:10.1101/gr.1414204
...DNA clones has proven to be the most efficient and cost-effective strategy for gene discovery. EST-based gene discovery strategies are advantageous for a few reasons, not the least of which is that purely computational methods of gene prediction are notoriously inaccurate in higher eukaryotes, in which only...
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PERSPECTIVE: Drosophila melanogaster: A case study of a model genomic sequence and its consequences
- Michael Ashburner and
- Casey M. Bergman
Genome Res. December 2005 15: 1661-1667; doi:10.1101/gr.3726705
.... Computational identification of Drosophila microRNA genes. Genome Biol. 4 : R42 . ↵ Lerat, E., Rizzon, C., and Biemont, C. 2003 . Sequence divergence within transposable element families in the Drosophila melanogaster . Genome Res. 13 : 1889 -1896. ↵ Lewis, S.E. 2005 . Gene Ontology: Looking backwards...

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