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Open Access Highly Accessed Research article

Cooperative activation of Xenopus rhodopsin transcription by paired-like transcription factors

Sarah E Reks, Vera McIlvain, Xinming Zhuo and Barry E Knox*

Author Affiliations

Departments of Neuroscience & Physiology, Ophthalmology and Biochemistry & Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA

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BMC Molecular Biology 2014, 15:4  doi:10.1186/1471-2199-15-4

Published: 6 February 2014

Additional files

Additional file 1: Table S3:

Characterization of Xenopus promoter sequences. Nucleotide composition and number of ATTA sites of the different Xenopus rhodopsin promoter lengths used in this study: XOP(−5361/+41), XOP(−503/+41) and XOP(−145/+41).

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Additional file 2: Figure S1:

Effect of cis-element deletions on Xenopus rhodopsin promoter activity. Comparison of luciferase activities in lysates from cells transfected with WT XOP(−503/+41), Ret1∆(−503/+41), BAT1∆(−503/+41) or Ret1/BAT1∆ (−503/+41) alone or with LNrl-Otx5. Activities are presented as mean RLU ± S.E.M. (n = 6).

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Additional file 3: Figure S2:

Mutational analysis of Pax-like cis-elements in the RPP with 5′ upstream sequences: Effect on Otx5-LNrl activation. Cells were transiently transfected with a plasmid containing a wild type promoter (XOP(−5361/+41)) or a mutation in cis-element (s) (m1-m10, see Figure4A) in the absence (No TF) or presence of Otx5-LNrl. Activities in cell lysates are presented as mean ± S.E.M (n = 6-8). Promoter basal activity (RLU) is shown in parentheses.

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Additional file 4: Figure S3:

Expression of Rax transcription factors in Xenopus laevis. (A) RT-PCR was performed using total RNA (1 μg) from embryo heads (stages 35/36 and 39/40) or adult retinas and primers to amplify histone H4 and the three Rx paralogs (xRax1b, 2a and 2b). (B) Quantitative analysis of Rax expression levels in adult retinas by qRT-PCR.

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Additional file 5: Figure S4:

Deletion analysis of Pax-like cis-elements in the RPP: Effect on Rax2b co-activation. Comparison of luciferase activities in lysates from cells transfected with WT XOP(−503/+41), Ret1∆(−503/+41), BAT1∆(−503/+41) or Ret1/BAT1∆ (−503/+41) alone or with LNrl-Otx5-Rax2b. Activities are presented as mean RLU ± S.E.M. (n = 6).

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Additional file 6: Figure S5:

Mutational analysis of Pax-like cis-elements in the RPP with 5′ upstream sequences: Effect on Rax2b co-activation. Comparison of luciferase activity in lysates from cells transfected with XOP(−5361/+41) or XOP(−5361/+41) containing RPP mutants (see Figure 4A) alone with Otx5-LNrl or with Otx5-LNrl-Rax2b. Activities are presented as mean RLU ± S.E.M. (n = 6-8). Promoter basal activity (RLU) is shown in parentheses.

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Additional file 7: Table S1:

Accession numbers of tetrapod rhodopsin proximal promoters.

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Additional file 8:

Alignment of tetrapod rhodopsin proximal promoters.

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Additional file 9: Table S2:

List of primers used in this study.

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