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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...A chromosome-scale epigenetic map of the Hydra reveals conserved regulators of cell state Jack F. Cazet1, Stefan Siebert1,2, Hannah Morris Little1, Philip Bertemes3, Abby S. Primack1, Peter Ladurner3, Matthias Achrainer3, Mark T. Fredriksen4, R. Travis Moreland4, Sumeeta Singh4, Suiyuan Zhang4...
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Research: Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
- Nikolaos Vakirlis,
- Véronique Sarilar,
- Guénola Drillon,
- Aubin Fleiss,
- Nicolas Agier,
- Jean-Philippe Meyniel,
- Lou Blanpain,
- Alessandra Carbone,
- Hugo Devillers,
- Kenny Dubois,
- Alexandre Gillet-Markowska,
- Stéphane Graziani,
- Nguyen Huu-Vang,
- Marion Poirel,
- Cyrielle Reisser,
- Jonathan Schott,
- Joseph Schacherer,
- Ingrid Lafontaine,
- Bertrand Llorente,
- Cécile Neuvéglise,
- and Gilles Fischer
Genome Res. July 2016 26: 918-932; Published in Advance May 31, 2016, doi:10.1101/gr.204420.116
...Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus Nikolaos Vakirlis 1 , 6 , Véronique Sarilar 2 , 6 , Guénola Drillon 1 , 6 , Aubin Fleiss 1 , Nicolas Agier...
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Research: Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes
- Stephen R. Voss,
- D. Kevin Kump,
- Srikrishna Putta,
- Nathan Pauly,
- Anna Reynolds,
- Rema J. Henry,
- Saritha Basa,
- John A. Walker,
- and Jeramiah J. Smith
Genome Res. August 2011 21: 1306-1312; Published in Advance April 11, 2011, doi:10.1101/gr.116491.110
...groups present lower chromosome numbers and smaller sizes (Duellman and Trueb 1986; Sessions 2008). In the absence of amphibian comparative gene maps, it has not been possible to test for the presence of ancestral tetrapod chromosomes in amphibian s. It also has not been possible to exploit amphibians...
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Resource: Extensive alternative polyadenylation during zebrafish development
- Igor Ulitsky,
- Alena Shkumatava,
- Calvin H. Jan,
- Alexander O. Subtelny,
- David Koppstein,
- George W. Bell,
- Hazel Sive,
- and David P. Bartel
Genome Res. October 2012 22: 2054-2066; Published in Advance June 21, 2012, doi:10.1101/gr.139733.112
...in five different stages of zebrafish development and in three adult tissues. These data allowed us to accuratelymap 39UTRs for over 79% of zebrafish protein-coding genes, define the C-terminal sequence of 640 proteins, and identifywidespread alternative polyadenylation affecting transcripts from 55...
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LETTER: A Comparative Map of the Zebrafish Genome
- Ian G. Woods,
- Peter D. Kelly,
- Felicia Chu,
- Phuong Ngo-Hazelett,
- Yi-Lin Yan,
- Hui Huang,
- John H. Postlethwait,
- and William S. Talbot
Genome Res. December 1, 2000 10: 1903-1914; doi:10.1101/gr.164600
...putative human orthologs for 804 zebrafish genes and ESTs. Map comparisons revealed 139 new conserved syntenies, in which two or more genes are on the same chromosome in zebrafish and human. Although some conserved syntenies are quite large, there were changes in gene order within conserved groups...
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LETTER: The Zebrafish Annexin Gene Family
- Steven A. Farber,
- Robert A. De Rose,
- Eric S. Olson,
- and Marnie E. Halpern
Genome Res. June 2003 13: 1082-1096; doi:10.1101/gr.479603
...on a single ancestral chromosome that split after divergence of mammalian and zebrafish s. The mapping results for zebrafish anx11 genes are more clear-cut, indicating that both paralogs are surrounded by genes with human orthologs that map to the same region on human chromosome 10 ( Fig. 4F ). These mapping...
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Methods: MAVID: Constrained Ancestral Alignment of Multiple Sequences
- Nicolas Bray and
- Lior Pachter
Genome Res. April 2004 14: 693-699; doi:10.1101/gr.1960404
...on the pairwise protein alignments of the predicted genes. During a MAVID alignment of ancestral sequences in the progressive multiple alignment, position r from sequence 1 maps to position u in the ancestral sequence A, and position s maps to position v in the ancestral sequence B (solid lines). Even though...
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LETTER: Genetic variation in the zebrafish
- Victor Guryev,
- Marco J. Koudijs,
- Eugene Berezikov,
- Stephen L. Johnson,
- Ronald H.A. Plasterk,
- Fredericus J.M. van Eeden,
- and Edwin Cuppen
Genome Res. April 2006 16: 491-497; Published in Advance March 13, 2006, doi:10.1101/gr.4791006
.... , 2000 The zebrafish book: A guide for the laboratory use of zebrafish (Danio rerio), 4th ed. University of Oregon Press Eugene, OR. ↵ Woods I.G. , Wilson C. , Friedlander B. , Chang P. , Reyes D.K. , Nix R. , Kelly P.D. , Chu F. , Postlethwait J.H. , Talbot W.S. ( 2005 ) The zebrafish gene map defines...
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ARTICLE: Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates
- Yoichiro Nakatani,
- Hiroyuki Takeda,
- Yuji Kohara,
- and Shinichi Morishita
Genome Res. September 2007 17: 1254-1265; Published in Advance July 25, 2007, doi:10.1101/gr.6316407
...) A medaka gene map: The trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping . Genome Res. 14 : 820 – 828 . ↵ Ohno, S. ( 1970 ) Evolution by gene duplication ( Springer-Verlag , New York ). ↵ Olmo, E. ( 2005 ) Rate of chromosome changes and speciation in reptiles . Genetica...
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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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