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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: 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
...and 5 kb (Colby and Williams 1993). The 5-kb repeat unit has a 242-bp insert between H1 and H3 genes. These variants are present in a number of Drosophila species, indicating that their origin predates the speciation event (Strausbaugh and Weinberg 1982). Figure 3B shows the distribution of 5- and 4...
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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
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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Research: Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo
- Katharine N. Schulz,
- Eliana R. Bondra,
- Arbel Moshe,
- Jacqueline E. Villalta,
- Jason D. Lieb,
- Tommy Kaplan,
- Daniel J. McKay,
- and Melissa M. Harrison
Genome Res. November 2015 25: 1715-1726; Published in Advance September 2, 2015, doi:10.1101/gr.192682.115
...transcriptionally quiescent and undergoes significant chromatin remodeling. In Drosophila, the DNA-binding protein Zelda (also known as Vielfaltig) is required for this transition and for transcriptional activation of the zygotic . Open chromatin is associated with Zelda-bound loci, as well as more generally...
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Method: 2C-Cas9: a versatile tool for clonal analysis of gene function
- Vincenzo Di Donato,
- Flavia De Santis,
- Thomas O. Auer,
- Noé Testa,
- Héctor Sánchez-Iranzo,
- Nadia Mercader,
- Jean-Paul Concordet,
- and Filippo Del Bene
Genome Res. May 2016 26: 681-692; Published in Advance March 8, 2016, doi:10.1101/gr.196170.115
...cells (RGCs) in clonally derived cell populationsWe next wanted to test the utility of the 2C-Cas9 system in the analysis of a loss-of-function phenotype in cell clones. We chose to target the atonal bHLH transcription factor 7 (atoh7) gene because a characterized loss-of-function allele (lakritz) shows...
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Resource: The transcriptional diversity of 25 Drosophila cell lines
- Lucy Cherbas,
- Aarron Willingham,
- Dayu Zhang,
- Li Yang,
- Yi Zou,
- Brian D. Eads,
- Joseph W. Carlson,
- Jane M. Landolin,
- Philipp Kapranov,
- Jacqueline Dumais,
- Anastasia Samsonova,
- Jeong-Hyeon Choi,
- Johnny Roberts,
- Carrie A. Davis,
- Haixu Tang,
- Marijke J. van Baren,
- Srinka Ghosh,
- Alexander Dobin,
- Kim Bell,
- Wei Lin,
- Laura Langton,
- Michael O. Duff,
- Aaron E. Tenney,
- Chris Zaleski,
- Michael R. Brent,
- Roger A. Hoskins,
- Thomas C. Kaufman,
- Justen Andrews,
- Brenton R. Graveley,
- Norbert Perrimon,
- Susan E. Celniker,
- Thomas R. Gingeras,
- and Peter Cherbas
Genome Res. February 2011 21: 301-314; Published in Advance December 22, 2010, doi:10.1101/gr.112961.110
...San Francisco, California 94080, USA. Abstract Drosophila melanogaster cell lines are important resources for cell biologists. Here, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19...
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LETTER: Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex
- Bárbara Negre,
- Sònia Casillas,
- Magali Suzanne,
- Ernesto Sánchez-Herrero,
- Michael Akam,
- Michael Nefedov,
- Antonio Barbadilla,
- Pieter de Jong,
- and Alfredo Ruiz
Genome Res. May 2005 15: 692-700; doi:10.1101/gr.3468605
...) belong to the Drosophila subgenus (see Negre et al. 2003 for details). In order to ascertain the consequences of Drosophila HOM-C splits, we have carried out a genomic and functional characterization of the two splits present in D. buzzatii . We isolated and sequenced two BAC clones containing the lab...
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ARTICLE: Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless
- Edwin J. Ostrin,
- Yumei Li,
- Kristi Hoffman,
- Jing Liu,
- Keqing Wang,
- Li Zhang,
- Graeme Mardon,
- and Rui Chen
Genome Res. April 2006 16: 466-476; Published in Advance March 13, 2006, doi:10.1101/gr.4673006
...genes with no characterized role in eye development, shf and VhaPPA1–1, and two known RD genes that had not previously been characterized as direct targets of Ey, eyes absent ( eya ) and Optix. shf encodes a Drosophila homolog of Wnt-inhibitory factor-1 (WIF-1) and has recently been shown...
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Research: Evolution of a genomic regulatory domain: The role of gene co-option and gene duplication in the Enhancer of split complex
- Elizabeth J. Duncan and
- Peter K. Dearden
Genome Res. July 2010 20: 917-928; Published in Advance May 10, 2010, doi:10.1101/gr.104794.109
...intervening genes with no homology with Drosophila E(spl)-C genes. E(spl)-C in hemimetabolous insects The conclusion that E(spl) complexes are larger and more evolutionarily stable than previously thought led us to examine the newly sequenced s of the pea aphid (Acyrthosiphon pisum) and louse (Pediculus...
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LETTER: Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22
- Leonard Lipovich and
- Mary-Claire King
Genome Res. January 2006 16: 45-54; Published in Advance December 12, 2005, doi:10.1101/gr.3883606
...22) and to characterize their incidence, evolutionary conservation, and distribution along the genomic landscape of the chromosome. Results Characterization of known genes and novel TUs To catalog known genes and novel TUs, all genomic clones comprising the chr22 tiling path were subjected to a Perl...

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