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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
...cells to re-enter the cell cycle partially restores a youthful H3K27me3 landscape, suggesting that DNA replication may rejuvenate chromatin structure (Yang et al. 2023). However, even mitotically active somatic stem cells display age-related increases in Polycomb repression: Aged Drosophila intestinal...
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Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
- Irmgard U. Haussmann,
- Thomas C. Dix,
- David W.J. McQuarrie,
- Veronica Dezi,
- Abdullah I. Hans,
- Roland Arnold,
- and Matthias Soller
Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
...of the sgRNA/Cas9 complex to scan the DNA for target sites.When we analyzed the cleavage efficiencies of sgRNAs used in Drosophila (Ren et al. 2014), we observed a good overlap with the ability of those sgRNAs to adopt the correct structure and having a high cleavage efficiency. Further refinement...
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Research: ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm
- Marta Bozek,
- Roberto Cortini,
- Andrea Ennio Storti,
- Ulrich Unnerstall,
- Ulrike Gaul,
- and Nicolas Gompel
Genome Res. May 2019 29: 771-783; Published in Advance April 8, 2019, doi:10.1101/gr.242362.118
...) followed by a 3×FLAG tag (Sigma). Expression of the nuclear tag was driven by selected enhancers of Drosophila gap and pair-rule genes (amplified from genomic DNA, genomic coordinates as in Segal et al. 2008) that were separated by a 69-bp linker from the basal promoter: either Hs43 (Thummel and Pirrotta...
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Research: Drosophila poised enhancers are generated during tissue patterning with the help of repression
- Nina Koenecke,
- Jeff Johnston,
- Qiye He,
- Samuel Meier,
- and Julia Zeitlinger
Genome Res. January 2017 27: 64-74; Published in Advance November 14, 2016, doi:10.1101/gr.209486.116
...in the first place? Broad regions of H3K27me3 are catalyzed from specific nucleation sites in the DNA called Polycomb Responsive Elements (PREs) (Simon et al. 1993;Muller andKassis 2006). InDrosophila, Polycombgroup proteins are recruited to PREs by a combination of DNA-binding factors, including GAGA factor...
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Research: Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors
- Bradford H. Casey,
- Rahul K. Kollipara,
- Karine Pozo,
- and Jane E. Johnson
Genome Res. April 2018 28: 484-496; Published in Advance March 2, 2018, doi:10.1101/gr.224360.117
...related factors retain specificity, especially when they recognize the same DNA motifs, is not understood. We address this paradox using basic helix-loop-helix (bHLH) transcription factors ASCL1, ASCL2, and MYOD1, crucial mediators of lineage specification. In vivo, these factors recognize the same DNA...
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Method: Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
- Daniel Marbach,
- Sushmita Roy,
- Ferhat Ay,
- Patrick E. Meyer,
- Rogerio Candeias,
- Tamer Kahveci,
- Christopher A. Bristow,
- and Manolis Kellis
Genome Res. July 2012 22: 1334-1349; Published in Advance March 28, 2012, doi:10.1101/gr.127191.111
...a machine-learning framework to combine both functional and physical regulatory interactions (Fig. 1). The physical TF–DNA regulatory interactions consist of (1) evolutionarily conserved instances of TF binding site motifs across 12 Drosophila s (Kheradpour et al. 2007; Stark et al. 2007) for 139 TFs...
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Research: The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo
- Rahul Satija and
- Robert K. Bradley
Genome Res. April 2012 22: 656-665; Published in Advance January 13, 2012, doi:10.1101/gr.130682.111
..., Zhou S, Bell M, Lipsick JS, Botchan MR. 2002. Role for a Drosophila Myb-containing protein complex in site-specific DNA replication. Nature 420: 833–837. Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB. 2002. Exploiting transcription factor binding site clustering...
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ARTICLE: Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
- Stephen Richards,
- Yue Liu,
- Brian R. Bettencourt,
- Pavel Hradecky,
- Stan Letovsky,
- Rasmus Nielsen,
- Kevin Thornton,
- Melissa J. Hubisz,
- Rui Chen,
- Richard P. Meisel,
- Olivier Couronne,
- Sujun Hua,
- Mark A. Smith,
- Peili Zhang,
- Jing Liu,
- Harmen J. Bussemaker,
- Marinus F. van Batenburg,
- Sally L. Howells,
- Steven E. Scherer,
- Erica Sodergren,
- Beverly B. Matthews,
- Madeline A. Crosby,
- Andrew J. Schroeder,
- Daniel Ortiz-Barrientos,
- Catharine M. Rives,
- Michael L. Metzker,
- Donna M. Muzny,
- Graham Scott,
- David Steffen,
- David A. Wheeler,
- Kim C. Worley,
- Paul Havlak,
- K. James Durbin,
- Amy Egan,
- Rachel Gill,
- Jennifer Hume,
- Margaret B. Morgan,
- George Miner,
- Cerissa Hamilton,
- Yanmei Huang,
- Lenée Waldron,
- Daniel Verduzco,
- Kerstin P. Clerc-Blankenburg,
- Inna Dubchak,
- Mohamed A.F. Noor,
- Wyatt Anderson,
- Kevin P. White,
- Andrew G. Clark,
- Stephen W. Schaeffer,
- William Gelbart,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. January 2005 15: 1-18; doi:10.1101/gr.3059305
...Comparative genome sequencing of Drosophila pseudoobscura : Chromosomal, gene, and cis -element evolution Stephen Richards 1 , 15 , Yue Liu 1 , 2 , 3 , Brian R. Bettencourt 4 , Pavel Hradecky 4 , Stan Letovsky 4 , Rasmus Nielsen...
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Resource: Modeling transcriptional regulation of model species with deep learning
- Evan M. Cofer,
- João Raimundo,
- Alicja Tadych,
- Yuji Yamazaki,
- Aaron K. Wong,
- Chandra L. Theesfeld,
- Michael S. Levine,
- and Olga G. Troyanskaya
Genome Res. June 2021 31: 1097-1105; Published in Advance April 22, 2021, doi:10.1101/gr.266171.120
...with active transcription in Drosophila embryos during minute 20 of nuclear cycle 14 illustrate the distinct levels of transcriptional activation induced by each allele (Supplemental Fig. S6). Three replicates were imaged for each allele. (AU) Arbitrary units, which represent the intensity of the pixels...
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Research: Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality
- Daniel F. Simola,
- Lothar Wissler,
- Greg Donahue,
- Robert M. Waterhouse,
- Martin Helmkampf,
- Julien Roux,
- Sanne Nygaard,
- Karl M. Glastad,
- Darren E. Hagen,
- Lumi Viljakainen,
- Justin T. Reese,
- Brendan G. Hunt,
- Dan Graur,
- Eran Elhaik,
- Evgenia V. Kriventseva,
- Jiayu Wen,
- Brian J. Parker,
- Elizabeth Cash,
- Eyal Privman,
- Christopher P. Childers,
- Monica C. Muñoz-Torres,
- Jacobus J. Boomsma,
- Erich Bornberg-Bauer,
- Cameron R. Currie,
- Christine G. Elsik,
- Garret Suen,
- Michael A.D. Goodisman,
- Laurent Keller,
- Jürgen Liebig,
- Alan Rawls,
- Danny Reinberg,
- Chris D. Smith,
- Chris R. Smith,
- Neil Tsutsui,
- Yannick Wurm,
- Evgeny M. Zdobnov,
- Shelley L. Berger,
- and Jürgen Gadau
Genome Res. August 2013 23: 1235-1247; Published in Advance May 1, 2013, doi:10.1101/gr.155408.113
...selection compared with Drosophila without significantly reduced synteny. Correspondingly, ant genomes exhibit dramatic divergence of noncoding regulatory elements; however, extant conserved regions are enriched for novel noncoding RNAs and transcription factor–binding sites. Comparison of orthologous...

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