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Research: Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
- Yi Liao,
- Xinwen Zhang,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. March 2021 31: 397-410; Published in Advance February 9, 2021, doi:10.1101/gr.266130.120
...million years of divergence, showed that ∼30%–40% of their s retain conserved TADs. Comparative genomic analysis of 17 Drosophila species revealed that chromosomal rearrangement breakpoints are enriched at TAD boundaries but depleted within TADs. Additionally, genes within conserved TADs show lower...
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Research: Age-dependent chromosomal distribution of male-biased genes in Drosophila
- Yong E. Zhang,
- Maria D. Vibranovski,
- Benjamin H. Krinsky,
- and Manyuan Long
Genome Res. November 2010 20: 1526-1533; Published in Advance August 26, 2010, doi:10.1101/gr.107334.110
...pseudoobscura: Chromosomal, gene, and ciselement evolution. Genome Res 15: 1–18. Ruby JG, Stark A, JohnstonWK, Kellis M, Bartel DP, Lai EC. 2007. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res 17: 1850–1864. Smyth GK. 2004. Linear...
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Research: Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification
- Robert K. Arthur,
- Lijia Ma,
- Matthew Slattery,
- Rebecca F. Spokony,
- Alexander Ostapenko,
- Nicolas Nègre,
- and Kevin P. White
Genome Res. July 2014 24: 1115-1124; Published in Advance July 1, 2014, doi:10.1101/gr.162008.113
...specification, and differentiation. However, evolutionary patterns of key modifications that regulate gene expression in differentiating organisms have not been examined. Here we mapped the genomic locations of the repressive mark histone 3 lysine 27 trimethylation (H3K27me3) in four species of Drosophila...
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Research: The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species
- Jingping Yang,
- Edward Ramos,
- and Victor G. Corces
Genome Res. November 2012 22: 2199-2207; Published in Advance August 15, 2012, doi:10.1101/gr.142125.112
...regulated. Conservation and diversity of BEAF-32 insulators across the Drosophila species Since BEAF-32 appears to functionally separate close head-to-head genes, gain or loss of BEAF-32 binding during evolution may prevent or allow adjacent genes to be affected by neighboring regulatory sequences, leading...
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RESOURCE: Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis
- Eiichi Shoguchi,
- Takeshi Kawashima,
- Yutaka Satou,
- Makoto Hamaguchi,
- Tadasu Sin-I,
- Yuji Kohara,
- Nik Putnam,
- Daniel S. Rokhsar,
- and Nori Satoh
Genome Res. February 2006 16: 297-303; Published in Advance December 14, 2005, doi:10.1101/gr.4156606
.... Methods Mol. Biol. 132 : 185 -219. ↵ Richards, S., Liu, Y., Bettencourt, B.R., Hradecky, P., Letovsky, S., Nielsen, R., Thornton, K., Hubisz, M.J., Chen, R., Meisel, R.P., et al. 2005 . Comparative sequencing of Drosophila pseudoobscura : Chromosomal, gene, and cis -element evolution. Genome Res. 15 : 1...
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Research: The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomes
- Emily J. Brown and
- Doris Bachtrog
Genome Res. July 2014 24: 1125-1137; Published in Advance May 19, 2014, doi:10.1101/gr.172155.114
...) (see Fig. 3B,C). This is consistent with the known mechanism of dosage compensation in Drosophila, whereby the MSL complex targets actively transcribed genes along the X chromosome by recognizing H3K36me3 and then inducing H4K16 acetylation Sex-specific chromatin landscape of Drosophila Genome Research...
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Research: Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila
- Marcin von Grotthuss,
- Michael Ashburner,
- and José M. Ranz
Genome Res. August 2010 20: 1084-1096; Published in Advance July 2, 2010, doi:10.1101/gr.103713.109
...that are susceptible to breakage. The balance between these two mechanisms is still poorly understood. Drosophila species have very dynamic genomes and, therefore, can be very informative. We compared the gene organization of the main five chromosomal elements (Muller's elements A–E) of nine Drosophila species...
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RESOURCE: A BAC-based physical map of the Drosophila buzzatii genome
- Josefa González,
- Michael Nefedov,
- Ian Bosdet,
- Ferran Casals,
- Oriol Calvete,
- Alejandra Delprat,
- Heesun Shin,
- Readman Chiu,
- Carrie Mathewson,
- Natasja Wye,
- Roger A. Hoskins,
- Jacqueline E. Schein,
- Pieter de Jong,
- and Alfredo Ruiz
Genome Res. June 2005 15: 885-892; doi:10.1101/gr.3263105
..., R., Thornton, K., Hubisz, M.J., Chen, R., Meisel, R.P., et al. 2005 . Comparative sequencing of Drosophila pseudoobscura : Chromosomal, gene, and cis -element evolution. Genome Res. 15 : 1 -18. ↵ Ruiz, A. and Wasserman, M. 1993 . Evolutionary cytogenetics of the Drosophila buzzatii species complex...
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12 Drosophila Genomes/Letter: Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
- J. Graham Ruby,
- Alexander Stark,
- Wendy K. Johnston,
- Manolis Kellis,
- David P. Bartel,
- and Eric C. Lai
Genome Res. December 2007 17: 1850-1864; Published in Advance November 7, 2007, doi:10.1101/gr.6597907
...the descriptions of about half of those that had been previously annotated. These results provided insights into miRNA evolution, biogenesis, and expression in insects. When combined with improved target prediction, which used information from all 12 sequenced Drosophila s ( Drosophila 12 Genomes Consortium 2007...
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Letter: General gene movement off the X chromosome in the Drosophila genus
- Maria D. Vibranovski,
- Yong Zhang,
- and Manyuan Long
Genome Res. May 2009 19: 897-903; Published in Advance February 27, 2009, doi:10.1101/gr.088609.108
.... 38: 735–742. Richards, S., Liu, Y., Bettencourt, B.R., Hradecky, P., Letovsky, S., Nielsen, R., Thornton, K., Hubisz, M.J., Chen, R., Meisel, R.P., et al. 2005. Comparative sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Res. 15: 1– 18. Schaeffer, S...

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