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  1. Research: Heterodimerization of TFAP2 pioneer factors drives epigenomic remodeling during neural crest specification
    • Megan Rothstein and
    • Marcos Simoes-Costa
    Genome Res. January 2020 30: 35-48; Published in Advance December 17, 2019, doi:10.1101/gr.249680.119
    ...development. Our results show that TFAP2A activates distinct sets of genomic regions during induction of the neural plate border and specification of neural crest cells. Genomic occupancy analysis revealed that the repertoire of TFAP2A targets depends upon its dimerization with paralogous proteins TFAP2C...
  2. Perspective: Insights into neural crest development and evolution from genomic analysis
    • Marcos Simões-Costa and
    • Marianne E. Bronner
    Genome Res. July 2013 23: 1069-1080; doi:10.1101/gr.157586.113
    ...this process. Furthermore, comparative genomic analyses are providing important insights about the evolution of the neural crest and the origins of the vertebrate clade. Here, we will present a synopsis of the current state of the field of neural crest biology from a gene regulatory perspective and will also...
  3. Resource: A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
    • Jing Liu,
    • Zongji Wang,
    • Jing Li,
    • Luohao Xu,
    • Jiaqi Liu,
    • Shaohong Feng,
    • Chunxue Guo,
    • Shengchan Chen,
    • Zhanjun Ren,
    • Jinpeng Rao,
    • Kai Wei,
    • Yuezhou Chen,
    • Erich D. Jarvis,
    • Guojie Zhang,
    • and Qi Zhou
    Genome Res. March 2021 31: 497-511; Published in Advance January 6, 2021, doi:10.1101/gr.271569.120
    ...species (Sacerdot et al. 2018). Direct supporting evidence for the hypothesis came from genomic comparisons of chicken versus the amphibians Mexican axolotl and Western clawed frog (Voss et al. 2011), the spotted gar fish (Braasch et al. 2016), and the invertebrate amphioxus (Simakov et al. 2020...
  4. LETTER: The amphioxus genome illuminates vertebrate origins and cephalochordate biology
    • Linda Z. Holland,
    • Ricard Albalat,
    • Kaoru Azumi,
    • Èlia Benito-Gutiérrez,
    • Matthew J. Blow,
    • Marianne Bronner-Fraser,
    • Frederic Brunet,
    • Thomas Butts,
    • Simona Candiani,
    • Larry J. Dishaw,
    • David E.K. Ferrier,
    • Jordi Garcia-Fernàndez,
    • Jeremy J. Gibson-Brown,
    • Carmela Gissi,
    • Adam Godzik,
    • Finn Hallböök,
    • Dan Hirose,
    • Kazuyoshi Hosomichi,
    • Tetsuro Ikuta,
    • Hidetoshi Inoko,
    • Masanori Kasahara,
    • Jun Kasamatsu,
    • Takeshi Kawashima,
    • Ayuko Kimura,
    • Masaaki Kobayashi,
    • Zbynek Kozmik,
    • Kaoru Kubokawa,
    • Vincent Laudet,
    • Gary W. Litman,
    • Alice C. McHardy,
    • Daniel Meulemans,
    • Masaru Nonaka,
    • Robert P. Olinski,
    • Zeev Pancer,
    • Len A. Pennacchio,
    • Mario Pestarino,
    • Jonathan P. Rast,
    • Isidore Rigoutsos,
    • Marc Robinson-Rechavi,
    • Graeme Roch,
    • Hidetoshi Saiga,
    • Yasunori Sasakura,
    • Masanobu Satake,
    • Yutaka Satou,
    • Michael Schubert,
    • Nancy Sherwood,
    • Takashi Shiina,
    • Naohito Takatori,
    • Javier Tello,
    • Pavel Vopalensky,
    • Shuichi Wada,
    • Anlong Xu,
    • Yuzhen Ye,
    • Keita Yoshida,
    • Fumiko Yoshizaki,
    • Jr-Kai Yu,
    • Qing Zhang,
    • Christian M. Zmasek,
    • Pieter J. de Jong,
    • Kazutoyo Osoegawa,
    • Nicholas H. Putnam,
    • Daniel S. Rokhsar,
    • Noriyuki Satoh,
    • and Peter W.H. Holland
    Genome Res. July 2008 18: 1100-1111; Published in Advance June 18, 2008, doi:10.1101/gr.073676.107
    ...The amphioxus genome illuminates vertebrate origins and cephalochordate biology Linda Z. Holland 1 , 40 , Ricard Albalat 2 , Kaoru Azumi 3 , Èlia Benito-Gutiérrez 2 , Matthew J. Blow 4 , Marianne Bronner-Fraser 5 , Frederic...
  5. Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
    • Ni-Chen Chang,
    • Quirze Rovira,
    • Jonathan Wells,
    • Cédric Feschotte,
    • and Juan M. Vaquerizas
    Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
    ...), was discovered as a specific marker of the neural crest (Rubinstein et al. 2000; Luo et al. 2001). Despite these observations, BHIKHARI elements have not been characterized further, and there is a general dearth of information regarding the genomic characteristics and expression of individual TE families...
    OPEN ACCESS ARTICLE
  6. 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
    ...important insights into the origin and evolution of chordates as well as vertebrates. However, because this genomic data has not yet been mapped onto chromosomes, important biological questions including regulation of gene expression at the -wide level cannot yet be addressed. Here, we report the molecular...
  7. PERSPECTIVE: Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis
    • Weiyang Shi,
    • Michael Levine,
    • and Brad Davidson
    Genome Res. December 2005 15: 1668-1674; doi:10.1101/gr.3768905
    ...The Ciona intestinalis assembly and annotation is provided by the Joint Genome Institute at http://.jgi-psf.org/ciona4/ciona4.home.html . The newly released assembly version 2.0 contains 141 M base pairs of non-N sequences (A. Sidow, pers. comm.) and is a significant improvement over the original version 1...
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