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Research: Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome
- Keerthi T. Chathoth and
- Nicolae Radu Zabet
Genome Res. April 2019 29: 613-625; Published in Advance February 1, 2019, doi:10.1101/gr.246710.118
...on the positive strand; dashed lines, the expression levels on the negative strand. For that, we mapped the expression levels of the genes to the corresponding strand using the FlyBase annotation (see Methods) (dos Santos et al. 2015).Looking into the poly(A) RNA levels, in both embryonic and neuronal cells, we...
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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...along the DNA's right-handed axis. Either owing to drag force or owing to immobilization inside of transcription factories (Papantonis et al. 2010), Pol II cannot rotate freely, causing the DNA molecule to rotate instead, thereby generating torsional stress (Liu and Wang 1987). In this theory, called...
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Resource: Gene expression networks in the Drosophila Genetic Reference Panel
- Logan J. Everett,
- Wen Huang,
- Shanshan Zhou,
- Mary Anna Carbone,
- Richard F. Lyman,
- Gunjan H. Arya,
- Matthew S. Geisz,
- Junwu Ma,
- Fabio Morgante,
- Genevieve St. Armour,
- Lavanya Turlapati,
- Robert R.H. Anholt,
- and Trudy F.C. Mackay
Genome Res. March 2020 30: 485-496; Published in Advance March 6, 2020, doi:10.1101/gr.257592.119
.... melanogaster sequences in Repbase (Jurka et al. 2005). The remaining sequences that did not align to any of the databases above were then aligned to the D. melanogaster (BDGP5) and known transcriptome (FlyBase v5.57) using STAR v2.4.0e (Dobin et al. 2013). Libraries with fewer than 5 million reads uniquely...
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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
...for batch effect in these analyses because of the absence of a factorial two-way nonparametric test. Embryos differed in os-piRNA expression from oocytes and zygotes, and in conventional piRNA expression from oocytes (FDR < 0.05), whereas for miRNAs the expression difference between oocytes and embryos...
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Research: Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation
- Andrew J. Tock,
- Daniel M. Holland,
- Wei Jiang,
- Kim Osman,
- Eugenio Sanchez-Moran,
- James D. Higgins,
- Keith J. Edwards,
- Cristobal Uauy,
- F. Chris H. Franklin,
- and Ian R. Henderson
Genome Res. September 2021 31: 1614-1628; Published in Advance August 23, 2021, doi:10.1101/gr.273672.120
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Research: Clustering of Drosophila housekeeping promoters facilitates their expression
- Marc Corrales,
- Aránzazu Rosado,
- Ruggero Cortini,
- Joris van Arensbergen,
- Bas van Steensel,
- and Guillaume J. Filion
Genome Res. July 2017 27: 1153-1161; Published in Advance April 18, 2017, doi:10.1101/gr.211433.116
...that transcription proceeds in “factories” (Rieder et al. 2012). It is possible that multiple active genes coalesce into compact structures where transcription is most efficient. However, it still remains to be determined whether the contacts activating the reporters are pairwise or involve multiple genes...
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Research: Hormone-control regions mediate steroid receptor–dependent genome organization
- François Le Dily,
- Enrique Vidal,
- Yasmina Cuartero,
- Javier Quilez,
- A. Silvina Nacht,
- Guillermo P. Vicent,
- José Carbonell-Caballero,
- Priyanka Sharma,
- José Luis Villanueva-Cañas,
- Roberto Ferrari,
- Lara Isabel De Llobet,
- Gaetano Verde,
- Roni H.G. Wright,
- and Miguel Beato
Genome Res. January 2019 29: 29-39; Published in Advance December 14, 2018, doi:10.1101/gr.243824.118
...the cell population, these hubs of regulatory regions might serve as a reservoir of factors to facilitate transcription in a permissive environment. They may correspond to specialized transcription factories (Xu and Cook 2008) or to active hubs previously described for other steroid receptors (Hakim et al...
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Perspective: Epigenomics and the structure of the living genome
- Nir Friedman and
- Oliver J. Rando
Genome Res. October 2015 25: 1482-1490; doi:10.1101/gr.190165.115
.... A similar question arises from 3C-based assays, where any genomic locus that exhibits interactions with two or more other regions in ensemble measurements could, in principle, result from locus X interacting in a cluster (e.g., a “transcription factory”) with both locus Y and Z in the same cell...
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Resource: MicroRNA programs in normal and aberrant stem and progenitor cells
- Christopher P. Arnold,
- Ruoying Tan,
- Baiyu Zhou,
- Si-Biao Yue,
- Steven Schaffert,
- Joseph R. Biggs,
- Regis Doyonnas,
- Miao-Chia Lo,
- John M. Perry,
- Valérie M. Renault,
- Alessandra Sacco,
- Tim Somervaille,
- Patrick Viatour,
- Anne Brunet,
- Michael L. Cleary,
- Linheng Li,
- Julien Sage,
- Dong-Er Zhang,
- Helen M. Blau,
- Caifu Chen,
- and Chang-Zheng Chen
Genome Res. May 2011 21: 798-810; Published in Advance March 30, 2011, doi:10.1101/gr.111385.110
....g., TRIM-NHL proteins like mouse TRIM32 and fly Brat and Mei-P26) regulate the self-renewal of tissue-specific SCs (TSCs) (Neumuller et al. 2008; Hammell et al. 2009; Schwamborn et al. 2009). Loss of DICER1 or Drosha (also known as RNASEN), enzymes essential for miRNA biogenesis, affects the proliferation...
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Method: Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
- Wei-Jen Chung,
- Phaedra Agius,
- Jakub O. Westholm,
- Michael Chen,
- Katsutomo Okamura,
- Nicolas Robine,
- Christina S. Leslie,
- and Eric C. Lai
Genome Res. February 2011 21: 286-300; Published in Advance December 22, 2010, doi:10.1101/gr.113050.110
.... Unexpectedly, we uncovered examples of clustered mirtrons in both fly and worm genomes, including a &lt;8-kb region in C. elegans harboring eight distinct mirtrons. Altogether, we demonstrate that discovery of functional mirtrons, unlike canonical miRNAs, is amenable to computational methods independent...
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