Open Access Highly Accessed Research article

Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression

Ana Ariza-Cosano1, Axel Visel23, Len A Pennacchio23, Hunter B Fraser4, José Luis Gómez-Skarmeta1*, Manuel Irimia45* and José Bessa1*

Author Affiliations

1 Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Ctra. Utrera Km 1, Seville, 41013, Spain

2 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA

3 U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA

4 Department of Biology, Stanford University, Stanford, CA, 94305, USA

5 The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada

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BMC Genomics 2012, 13:713  doi:10.1186/1471-2164-13-713

Published: 19 December 2012

Additional files

Additional file 1:

Comparison of expression patterns in mice and zebrafish driven by the tested CNEs.

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Additional file 2:

Comparison of expression patterns in mice and zebrafish driven by ancestral CNEs.

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Additional file 3:

4 way comparison of expression patterns driven by CNEs and corresponding target genes in zebrafish and mice.

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Additional file 4:

Graph representing the number of times expression is detected per anatomical domain, in mouse (orange) or zebrafish (blue) enhancer activity assays.

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Additional file 5:

Comparison of transient and stable transgenesis in zebrafish for the enhancer activity assay of the Hs200 CNE. A) Expression driven by Hs200 in 24hpf transient transgenic embryos is mostly detected in the forebrain. B) A stable transgenic line for the Hs200 CNE show strong expression in the forebrain but also a weaker reproducible expression in the midbrain and hindbrain in 24hpf embryos.

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Additional file 6:

Comparison of expression patterns in mice and zebrafish driven by mammal sequences reported in other datasets.

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Additional file 7:

Summary of expression patterns driven by CNEs in zebrafish and mice enhancer assays.

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Additional file 8:

GFP expression in a representative stable transgenic line for each CNE. Images of GFP expression from a representative line for each CNE in 48hpf stable transgenic embryos.

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Additional file 9:

Synteny, enhancer activity in mice and target gene expression in mice and zebrafish for the Hs215 and Hs335 CNEs. A) Relative position of Hs215 and Hs335 CNEs and their respective target genes isl1 and ntm. Hs335 is not detected by alignment in the zebrafish genome. B) Expression driven by the Hs215 enhancer in the eye, spinal cord, dorsal root ganglia and cranial nerve is shared by its target gene, islt1, in mice (C; inset is part of another section from the same embryo sowing expression in the eye) and zebrafish (D). E) Expression driven by the Hs335 enhancer in the spinal cord and limbs is shared with its corresponding target gene ntm (F; inset is part of another section from the same embryo sowing expression in the limb) but it does not coincide with the ntm ortholog in zebrafish (G).

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Additional file 10:

Genomic location of tested CNEs and respective target genes.

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Additional file 11:

In situ hybridization performed in 24hpf zebrafish embryos for gsx2 and znf423 genes. A) gsx2 expression is detected in hindbrain and forebrain at 24hpf and 48hpf (B). C) At 22hpf znf423 gene is expressed in the forebrain, hindbrain, eye and spinal cord. D) At 48hpf znf423 gene is detected in the forebrain, midbrain, hindbrain and eye.

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Additional file 12:

Enhancer activity of CNEs absent from the lineage of teleost fishes in mice and in zebrafish. A and B) Expression of Hs240 is shared by zebrafish and mice in the forebrain, being singularly expressed in the zebrafish hindbrain. C and D) The Hs426 enhancer shows similar expression in mice and zebrafish (otic vesicle, forebrain and hindbrain). E and F) A species specific expression of the Hs312 enhancer is observed in the hindbrain and midbrain of mice (E) being shared by zebrafish (F) in the spinalcord, limbs and forebrain. G and H) The expression of the H752 enhancer is shared by mice and zebrafish in muscle being mice specific for the dorsal root ganglia, trigeminal ganglion and spinal cord.

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