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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...sox17 expression 219 has not been reported in the zebrafish lateral line, either in literature providing detailed in situ 220 hybridisation analysis of sox17 (Chung et al. 2011), or in whole embryo single-cell RNA-seq 221 timecourse datasets including Daniocell (Sur et al. 2023). These resources do...
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Research: Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network
- Nicolas Chassaing,
- Erica E. Davis,
- Kelly L. McKnight,
- Adrienne R. Niederriter,
- Alexandre Causse,
- Véronique David,
- Annaïck Desmaison,
- Sophie Lamarre,
- Catherine Vincent-Delorme,
- Laurent Pasquier,
- Christine Coubes,
- Didier Lacombe,
- Massimiliano Rossi,
- Jean-Louis Dufier,
- Helene Dollfus,
- Josseline Kaplan,
- Nicholas Katsanis,
- Heather C. Etchevers,
- Stanislas Faguer,
- and Patrick Calvas
Genome Res. April 2016 26: 474-485; Published in Advance February 18, 2016, doi:10.1101/gr.196048.115
...in the zebrafish myotome. Dashed blue lines indicate measurement position (at the midpoint between the proximal hindgut and the anus) used for phenotypic scoring of embryo batches. (C) All six nonsynonymous PTCH1 variants identified in ODA cases were pathogenic as indicated by the inability of mutant m...
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Method: Discovery and assessment of conserved Pax6 target genes and enhancers
- Pedro Coutinho,
- Sofia Pavlou,
- Shipra Bhatia,
- Kevin J. Chalmers,
- Dirk A. Kleinjan,
- and Veronica van Heyningen
Genome Res. August 2011 21: 1349-1359; Published in Advance May 26, 2011, doi:10.1101/gr.124115.111
...-specific antibodies with chromatin from 28-hpf zebrafish embryos. We selected two putative pax6 BSs for each of five genes that show differential expression in pax6MO and control embryos, plus two novel predicted BSs within the pax6a locus. As a positive control, we used the pax6 BS in the sox2 enhancer N3...
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12 Drosophila Genomes/Letter: Genomic regulatory blocks underlie extensive microsynteny conservation in insects
- Pär G. Engström,
- Shannan J. Ho Sui,
- Øyvind Drivenes,
- Thomas S. Becker,
- and Boris Lenhard
Genome Res. December 2007 17: 1898-1908; Published in Advance November 7, 2007, doi:10.1101/gr.6669607
...et al. 2000 ; Sumiyama and Ruddle 2003 ; Kimura-Yoshida et al. 2004 ; Milewski et al. 2004 ), followed by systematic studies in zebrafish, Xenopus , and mouse ( de la Calle-Mustienes et al. 2005 ; Shin et al. 2005 ; Woolfe et al. 2005 ; Pennacchio et al. 2006 ). Genome-wide analyses of HCNE sequences...
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ARTICLE: Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis
- Gayle K. McEwen,
- Adam Woolfe,
- Debbie Goode,
- Tanya Vavouri,
- Heather Callaway,
- and Greg Elgar
Genome Res. April 2006 16: 451-465; Published in Advance March 13, 2006, doi:10.1101/gr.4143406
...as previously described. Functional analysis of dCNEs To assess whether the dCNEs are likely to have a regulatory role during development, we tested their ability to up-regulate a GFP reporter in zebrafish embryos, as described previously ( Woolfe et al. 2005 ). We chose five two-member dCNE families that had...
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REPORT: Organization of Mouse Iroquois Homeobox Genes in Two Clusters Suggests a Conserved Regulation and Function in Vertebrate Development
- Thomas Peters,
- Renate Dildrop,
- Katrin Ausmeier,
- and Ulrich Rüther
Genome Res. October 1, 2000 10: 1453-1462; doi:10.1101/gr.144100
...subdivision of the neural plate in the chick embryo. Mech. Dev. 87 : 203 – 206 . ↵ Grillenzoni N. , van Helden J. , Dambly-Chaudiere C. , Ghysen A. ( 1998 ) The iroquois complex controls the somatotopy of Drosophila notum mechanosensory projections. Development 125 : 3563 – 3569 . ↵ Haldi M.L. , Strickland C...
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Resource: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
- Michal Pawlak,
- Katarzyna Z. Kedzierska,
- Maciej Migdal,
- Karim Abu Nahia,
- Jordan A. Ramilowski,
- Lukasz Bugajski,
- Kosuke Hashimoto,
- Aleksandra Marconi,
- Katarzyna Piwocka,
- Piero Carninci,
- and Cecilia L. Winata
Genome Res. March 2019 29: 506-519; Published in Advance February 13, 2019, doi:10.1101/gr.244491.118
...accessibility in isolated cardiomyocytes (CMs) from wild-type zebrafish embryos at developmental stages corresponding to heart tube morphogenesis, looping, and maturation. We identified genetic regulatory modules driving crucial events of heart development that contained key cardiac TFs and are associated...
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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
...tools for targeted functional studies, particularly in chicken and zebrafish embryos, given the new approaches for efficient and rapid integration of transgenes in these embryos (Fisher et al. 2006; Yokota et al. 2011). Cis-regulatory analysis can also provide insights into how differences between...
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Research: Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
- Metewo Selase Enuameh,
- Yuna Asriyan,
- Adam Richards,
- Ryan G. Christensen,
- Victoria L. Hall,
- Majid Kazemian,
- Cong Zhu,
- Hannah Pham,
- Qiong Cheng,
- Charles Blatti,
- Jessie A. Brasefield,
- Matthew D. Basciotta,
- Jianhong Ou,
- Joseph C. McNulty,
- Lihua J. Zhu,
- Susan E. Celniker,
- Saurabh Sinha,
- Gary D. Stormo,
- Michael H. Brodsky,
- and Scot A. Wolfe
Genome Res. June 2013 23: 928-940; Published in Advance March 7, 2013, doi:10.1101/gr.151472.112
...are functional in vivo Overall, pairs of ZFAs with compatible specificity for five of six ZFN target sites were successfully constructed (Fig. 6; Supplemental Fig. 15). The activity of ZFNs constructed from these ZFAs was determined in zebrafish embryos (Meng et al. 2008). Often, equal concentrations of m...

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