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Resource: Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells
- Bony De Kumar,
- Mark E. Parrish,
- Brian D. Slaughter,
- Jay R. Unruh,
- Madelaine Gogol,
- Christopher Seidel,
- Ariel Paulson,
- Hua Li,
- Karin Gaudenz,
- Allison Peak,
- William McDowell,
- Brian Fleharty,
- Youngwook Ahn,
- Chengqi Lin,
- Edwin Smith,
- Ali Shilatifard,
- and Robb Krumlauf
Genome Res. August 2015 25: 1229-1243; Published in Advance May 29, 2015, doi:10.1101/gr.184978.114
...-occupancy of paused Pol II and H3K4me3 has predictive value for future gene expression in ES cells and Drosophila (Gaertner et al. 2012). Hence, the presence of Pol II and H3K4me3 over Hox genes, such as Hoxa3, Hoxa5, and Hoxa13 suggests that they too may be induced by regulation of elongation of paused polymerases...
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Research: An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
- Ignacio Maeso,
- Manuel Irimia,
- Juan J. Tena,
- Esther González-Pérez,
- David Tran,
- Vydianathan Ravi,
- Byrappa Venkatesh,
- Sonsoles Campuzano,
- José Luis Gómez-Skarmeta,
- and Jordi Garcia-Fernàndez
Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111
...pattern of amphioxus Sowah differs widely from those of Irx genes (Fig. 3A–D; Kaltenbach et al. 2009; Irimia et al. 2010), suggesting distinct regulations, and thus, that Sowah and Irx genes are not likely to share major transcriptional enhancers. A comparable situation is found in Drosophila, where...
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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
.... 7 : 1072 -1084. ↵ Negre, B., Casillas, S., Suzanne, M., Sánchez-Herrero, E., Akam, M., Nefedov, M., Barbadilla, A., de Jong, P., and Ruiz, A. 2005 . Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex. Genome Res. 15 : 692 -700...
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PERSPECTIVE: Drosophila melanogaster: A case study of a model genomic sequence and its consequences
- Michael Ashburner and
- Casey M. Bergman
Genome Res. December 2005 15: 1661-1667; doi:10.1101/gr.3726705
.... Science 287 : 2196 -2204. ↵ Negre, B., Casillas, S., Suzanne, M., Sanchez-Herrero, E., Akam, M., Nefedov, M., Barbadilla, A., De Jong, P.J., and Ruiz, A. 2005 . Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex. Genome Res. 15 : 692 -700...
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Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- Peter O. Mulhair,
- Liam Crowley,
- Douglas H. Boyes,
- Amber Harper,
- Owen T. Lewis,
- Darwin Tree of Life Consortium,
- and Peter W.H. Holland
Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
...conservation of other TADs in lepidopteran s. Outside the Hox gene cluster, the general structure of TADs across this chromosome appears similar to the pattern observed in Drosophila, with TADs representing condensed internal interactions and larger compartments showing long-range interactions between...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...ancestor of metazoans (Simakov et al. 2022). The most famous example of conserved microsynteny in animals is the Hox cluster, which contains genes that regulate axial patterning during embryogenesis and whose ancestry can be traced back to the origin of bilaterian animals hundreds of millions of years ago...
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