Open Access Research article

Using BAC transgenesis in zebrafish to identify regulatory sequences of the amyloid precursor protein gene in humans

Leighcraft A Shakes1, Hansen Du2, Hope M Wolf13, Charles Hatcher1, Derek C Norford1, Patricia Precht2, Ranjan Sen2 and Pradeep K Chatterjee1*

Author Affiliations

1 Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA

2 Laboratory of Molecular Biology and Immunology, National Institute on Aging, Biomedical Research Center, 251 Bay View Blvd., Suite 100, Baltimore, MD, 21224, USA

3 Present address: Department of Chemistry, University of North Carolina at Chapel-Hill, Chapel-Hill, NC, 27599, USA

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BMC Genomics 2012, 13:451  doi:10.1186/1471-2164-13-451

Published: 4 September 2012

Additional files

Additional file 1:

Figure S1. The E. coli expressed DNA-binding protein domain common to members within gene family, shown in green (A) E4BP4/ NFIL3, or red (B) Fkd. The corresponding DNA sequence that was amplified using the PCR primers is underlined.

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Additional file 2:

Figure S2. Sequences of primers, analyzed using pDRWN32 software, used to probe chromatin immune-precipitates with H3K9Ac or control IgG antibody.

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Additional file 3:

Figure S3. Sequences of primers used to detect E4BP4/ NFIL3 mRNA levels in the human cell line SHSY5Y using RT-PCR.

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Additional file 4:

Figure S4. Sequence of intron 1 enhancer is indicated in black letters, and the sequences of predicted transcription factor (TF) binding sites indicated in colored letters. The long arrows indicate the location and directionality of PCR primers used to delete specific transcription factor binding sites. The thick short underlines within the SOX5 site indicate point mutations introduced that leave the overlapping E4BP4 site intact.

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Additional 5:

Figure S5. Locations of putative binding sites of E4BP4 and XFD1 in zebrafish appb (from Figure 4) and human APP (from Figure 6A) are tabulated in the top and bottom panels respectively.

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