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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
..., the Polycomb landscape of differentiated cell types remains unexplored. Differentiated cells comprise the majority of the gut epithelium and directly impact both tissue and whole organismal aging. Using single-cell chromatin profiling of the Drosophila intestine, we identify cell type–specific chromatin...
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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
...-cell identity and activity.ResultsUsing a GSC and CySC tumor model for genomic studiesOur understanding of the transcriptional, chromatin, and replication landscapes of Drosophila GSCs is limited owing to their small number in wild-type testes (Fig. 1A; Supplemental Fig. S1A). GSCs were underrepresented...
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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: Evaluation of N⁶-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes
- Brian M. Debo,
- Benjamin J. Mallory,
- and Andrew B. Stergachis
Genome Res. March 2023 33: 427-434; Published in Advance February 14, 2023, doi:10.1101/gr.276696.122
...(Greer et al. 2015), Drosophila melanogaster (Zhang et al. 2015), Mus musculus (Koziol et al. 2016; Wu et al. 2016; Li et al. 2020), Homo sapiens (Wu et al. 2016; Xie et al. 2018), and others (Luo and He 2017). The level of DNA-m6A in eukaryotes has been reported to vary from as low as 6 ppm (i.e., six m...
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Research: CTCF looping is established during gastrulation in medaka embryos
- Ryohei Nakamura,
- Yuichi Motai,
- Masahiko Kumagai,
- Candice L. Wike,
- Haruyo Nishiyama,
- Yoichiro Nakatani,
- Neva C. Durand,
- Kaori Kondo,
- Takashi Kondo,
- Tatsuya Tsukahara,
- Atsuko Shimada,
- Bradley R. Cairns,
- Erez Lieberman Aiden,
- Shinichi Morishita,
- and Hiroyuki Takeda
Genome Res. June 2021 31: 968-980; Published in Advance May 18, 2021, doi:10.1101/gr.269951.120
...absent until gastrulation, local chromatin interaction is not uniform at blastula stage; that is, contact domain boundaries and small domains are beginning to form.Blocking of ZGA has been shown to inhibit contact domain establishment in human embryos but not in mouse or Drosophila (Du et al. 2017; Hug...
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Resource: Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns
- Jamie C. Kwasnieski,
- Terry L. Orr-Weaver,
- and David P. Bartel
Genome Res. July 2019 29: 1188-1197; Published in Advance June 24, 2019, doi:10.1101/gr.242164.118
...1986; Shermoen and O'Farrell 1991) or the size of the alternative isoforms that can be produced (Sandler et al. 2018).Experiments monitoring incorporation of α-P32-UTP into nascent transcripts of Drosophila embryos first detect transcription during nuclear cycle (NC) 11 (Edgar and Schubiger 1986...
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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
...the wondering stage (Supplemental Movie S1 in comparison to the scramble control shown in Supplemental Movie S2). FASN1 and FASN2 encode the two major fatty acid synthases in Drosophila (Chung et al. 2014; Garrido et al. 2015; Gramates et al. 2022). Fatty acids profiling (C14–C30) showed that heptadecanoic (17...
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Research: Transcriptional programs mediating neuronal toxicity and altered glial–neuronal signaling in a Drosophila knock-in tauopathy model
- Hassan Bukhari,
- Vanitha Nithianandam,
- Rachel A. Battaglia,
- Anthony Cicalo,
- Souvarish Sarkar,
- Aram Comjean,
- Yanhui Hu,
- Matthew J. Leventhal,
- Xianjun Dong,
- and Mel B. Feany
Genome Res. April 2024 34: 590-605; Published in Advance April 10, 2024, doi:10.1101/gr.278576.123
...Transcriptional programs mediating neuronal toxicity and altered glial–neuronal signaling in a Drosophila knock-in tauopathy model Hassan Bukhari1,2, Vanitha Nithianandam1,2, Rachel A. Battaglia1,2, Anthony Cicalo2,3,4, Souvarish Sarkar1, Aram Comjean5, Yanhui Hu5, Matthew J. Leventhal6,7, Xianjun...
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Resource: Small RNA expression and miRNA modification dynamics in human oocytes and early embryos
- Pauliina Paloviita,
- Christel Hydén-Granskog,
- Dawit A. Yohannes,
- Priit Paluoja,
- Juha Kere,
- Juha S. Tapanainen,
- Kaarel Krjutškov,
- Timo Tuuri,
- Urmo Võsa,
- and Sanna Vuoristo
Genome Res. August 2021 31: 1474-1485; doi:10.1101/gr.268193.120
...Drosophila, sea urchin, and mouse embryos (Fernandez-Valverde et al. 2010; Lee et al. 2014; Yang et al. 2016). To date sRNAs have not been sequenced in human developmental stages coinciding with embryo activation (EGA), the initiation of embryonic transcription, that peaks at the eight-cell stage...
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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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