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Methods: Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
- Steven G. Kuntz,
- Erich M. Schwarz,
- John A. DeModena,
- Tristan De Buysscher,
- Diane Trout,
- Hiroaki Shizuya,
- Paul W. Sternberg,
- and Barbara J. Wold
Genome Res. December 2008 18: 1955-1968; Published in Advance November 3, 2008, doi:10.1101/gr.085472.108
...bodywall muscle was abolished. Scale bars,10 microns. Ultraconserved elements Hox clusters are evolutionarily ancient, sharing a common origin for all bilaterians ( Garcia-Fernandez 2005 ; Lemons and McGinnis 2006 ), meaning that some cis -regulatory elements in C. elegans ceh-13/lin-39 might be conserved...
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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
...2007; Engstrom et al. 2007; Kikuta et al. 2007). Nevertheless, it is unclear whether long-range cis-regulatory interactions may have had an impact on architecture over deeper evolutionary distances (i.e., across different phyla) (Koonin 2009). Iroquois (Iro/Irx) genes encode highly conserved homeobox...
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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
...(for a recent review, see Wanninger 2024). There are many other examples of highly conserved microsyntenies across metazoans, in many cases related to the functional constraints imposed by cis-regulatory elements on the coordinated transcription of nearby genes. This includes genomic regulatory blocks...
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Letter: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
- Andrew L. Hufton,
- Susanne Mathia,
- Helene Braun,
- Udo Georgi,
- Hans Lehrach,
- Martin Vingron,
- Albert J. Poustka,
- and Georgia Panopoulou
Genome Res. November 2009 19: 2036-2051; Published in Advance August 24, 2009, doi:10.1101/gr.093237.109
...in transgenic zebrafish assays—including examples from vertebrates and amphioxus—and find that the majority are functional enhancers. We find that PCNEs are enriched around genes with ancient synteny conservation, and that this association is strongest for extragenic PCNEs, suggesting that cis -regulatory...
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Research: Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution
- Gang Li,
- Brian W. Davis,
- Terje Raudsepp,
- Alison J. Pearks Wilkerson,
- Victor C. Mason,
- Malcolm Ferguson-Smith,
- Patricia C. O'Brien,
- Paul D. Waters,
- and William J. Murphy
Genome Res. September 2013 23: 1486-1495; Published in Advance June 20, 2013, doi:10.1101/gr.154286.112
...483: 82–86. Irimia M, Tena JJ, Alexis M, Fernandez-Minan A, Maeso I, Bogdanovic O, de la Calle-Mustienes E, Roy SW, Gomez-Skarmeta JL, Fraser HB. 2012. Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome Res 22: 2356–2367. Kaiser VB, Bachtrog D...
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Research: Chromatin architecture transitions from zebrafish sperm through early embryogenesis
- Candice L. Wike,
- Yixuan Guo,
- Mengyao Tan,
- Ryohei Nakamura,
- Dana Klatt Shaw,
- Noelia Díaz,
- Aneasha F. Whittaker-Tademy,
- Neva C. Durand,
- Erez Lieberman Aiden,
- Juan M. Vaquerizas,
- David Grunwald,
- Hiroyuki Takeda,
- and Bradley R. Cairns
Genome Res. June 2021 31: 981-994; Published in Advance May 18, 2021, doi:10.1101/gr.269860.120
...chromatin shows extensive remodeling during embryonic development, and although the cleavage-stage embryos of most species lack structure before zygotic activation (pre-ZGA), zebrafish has been reported to have structure. Here, we aimed to determine the chromosomal architecture in paternal/sperm zebrafish...
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