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Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
- Lianne B Cohen,
- Tamara Hadzic,
- Caitlin Sauer,
- Julia R Gibbs,
- and Zeba Wunderlich
Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
...first binned enhancers by their 116 genomic region and found the majority (63.1%-64.3%) fall within intronic regions of the , 117 with a smaller group (25.3-25.7%) in intergenic regions. Similar genomic distributions of 118 Drosophila enhancers were previously found using STARR-seq (Arnold et al. 2013...
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Resource: Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster
- Matthew Slattery,
- Lijia Ma,
- Rebecca F. Spokony,
- Robert K. Arthur,
- Pouya Kheradpour,
- Anshul Kundaje,
- Nicolas Nègre,
- Alex Crofts,
- Ryan Ptashkin,
- Jennifer Zieba,
- Alexander Ostapenko,
- Sarah Suchy,
- Alec Victorsen,
- Nader Jameel,
- A. Jason Grundstad,
- Wenxuan Gao,
- Jennifer R. Moran,
- E. Jay Rehm,
- Robert L. Grossman,
- Manolis Kellis,
- and Kevin P. White
Genome Res. July 2014 24: 1224-1235; Published in Advance July 1, 2014, doi:10.1101/gr.168807.113
...IP experiments performed in duplicate or greater, 413,743 TRF-binding sites, and 50,336 unique TRF-binding regions. Genomic features targeted by transcriptional regulators Gene expression is controlled by regulatory DNA sequences and the TRFs that interact with these sequences. A significant amount of regulatory...
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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...et al. 2019; Teets et al. 2023). Neural events also control the production and release of prothoracicotropic hormone (PTTH), as well as the production of ecdysone (Ahmadi et al. 2021). Additionally, downstream genes, such as microRNAs regulated by ecdysone titers (e.g., let-7, miR-252, and miR-8–3p...
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ARTICLE: The Nuclear Receptor Superfamily Has Undergone Extensive Proliferation and Diversification in Nematodes
- Ann E. Sluder,
- Siuyien Wong Mathews,
- David Hough,
- Viravuth P. Yin,
- and Claude V. Maina
Genome Res. February 1, 1999 9: 103-120; doi:10.1101/gr.9.2.103
...predicted members of the nuclear receptor superfamily were isolated by PCR amplification of genomic DNA using degenerate primers corresponding to highly conserved regions of the NR DBD (see Materials and Methods). Amplification products were cloned and sequenced to identify eight candidate NR genes (Fig. 1...
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Resource: A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
- Desislava P. Staneva,
- Roberta Carloni,
- Tatsiana Auchynnikava,
- Pin Tong,
- Juri Rappsilber,
- A. Arockia Jeyaprakash,
- Keith R. Matthews,
- and Robin C. Allshire
Genome Res. November 2021 31: 2138-2154; Published in Advance August 18, 2021, doi:10.1101/gr.275368.121
...(Supplemental Fig. S5). Moreover, under our standard fixation and ChIP-seq conditions, no specific enrichment over any genomic region was detected for 45 of the YFP-tagged proteins, including several that showed clear nuclear localization (Supplemental Fig. S5; Supplemental Table S3).View larger version...
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Research: Phenotypically distinct female castes in honey bees are defined by alternative chromatin states during larval development
- Marek Wojciechowski,
- Robert Lowe,
- Joanna Maleszka,
- Danyal Conn,
- Ryszard Maleszka,
- and Paul J. Hurd
Genome Res. October 2018 28: 1532-1542; Published in Advance August 22, 2018, doi:10.1101/gr.236497.118
...immunoprecipitation (ChIP) and RNA samples from 96 h larval heads and identified thousands of genomic regions that show caste-specific chromatin states, many of which are linked to caste-specific gene transcription.ResultsHistone post-translational modifications in the honey bee associate with transcribed regions...
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Research: Genome-wide phosphoacetylation of histone H3 at Drosophila enhancers and promoters
- Wendy A. Kellner,
- Edward Ramos,
- Kevin Van Bortle,
- Naomi Takenaka,
- and Victor G. Corces
Genome Res. June 2012 22: 1081-1088; Published in Advance April 16, 2012, doi:10.1101/gr.136929.111
...state. Proc Natl Acad Sci 107: 21931–21936. Dekker J, Rippe K, Dekker M, Kleckner N. 2002. Capturing chromosome conformation. Science 295: 1306–1311. Gauhar Z, Sun LV, Hua S, Mason CE, Fuchs F, Li T-R, Boutros M, White KP. 2009. Genomic mapping of binding regions for the Ecdysone receptor protein...
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Research: Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation
- Maria Warnefors,
- Katharina Mössinger,
- Jean Halbert,
- Tania Studer,
- John L. VandeBerg,
- Isa Lindgren,
- Amir Fallahshahroudi,
- Per Jensen,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1961-1973; Published in Advance October 27, 2017, doi:10.1101/gr.225391.117
...transcribed from their own promoters (Ozsolak et al. 2008) and would require targeted sex-biased regulation, for example by hormones, to become differentially expressed between males and females. In Drosophila, hormonal regulation by ecdysone promotes sex-biased expression of the miRNA locus let-7-C, which...
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Resource: The mRNA-bound proteome of the early fly embryo
- Hans-Hermann Wessels,
- Koshi Imami,
- Alexander G. Baltz,
- Marcin Kolinski,
- Anastasia Beldovskaya,
- Matthias Selbach,
- Stephen Small,
- Uwe Ohler,
- and Markus Landthaler
Genome Res. July 2016 26: 1000-1009; Published in Advance April 28, 2016, doi:10.1101/gr.200386.115
...data from existing databases showed that mRNAs encoding RBPs are enriched in posterior regions of the early embryo, suggesting their general importance in posterior patterning and germ cell maturation.Post-transcriptional regulatory mechanisms play crucial roles in a wide variety of biological...
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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
...in any other line. Cherbas et al. 304 Genome Research www..org the cytoplasmic transducers and the main transcription factors that are regulated by the pathways (Supplemental Table S5). In general, ligands and receptors (but not cytoplasmic and transcription factor/DNA components) show differential...
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