ZFIN ID: ZDB-LAB-101001-1
Chatterjee Lab
PI/Director: Chatterjee, Pradeep K.
Contact Person: Shakes, Leighcraft
Email: lshakes@nccu.edu
URL: http://ariel.acc.nccu.edu/Academics/BBRI/personnel/chatterjee.htm
Address: Rm 119, Biomedical/ Biotechnology Research Institute 700 George Street North Carolina Central University Durham, NC 27707
Country: United States
Phone: (919) 530-7007
Fax: (919) 530-7998
Line Designation: ncc

Show all 5 genomic features

About two-thirds of the highly conserved genome sequence between human and other vertebrates as divergent as the fish does not code for proteins, is distributed throughout the genome, and mostly located at large distances along the DNA from the start sites of genes. Part of this conserved non-coding DNA plays a role in regulating gene expression from large distances, and is believed to be essential to all vertebrate development. Conservation of gene regulatory function has also been demonstrated in the absence of sequence similarity, suggesting that structural features of DNA can be preserved at those sites despite their different sequence. In fact shape and solvent accessibility of non-coding DNA having similar function appear better preserved evolutionarily than sequence alone. All of these criteria make identification of functional non-coding DNA a real challenge.

We have developed a novel approach to “scan” Bacterial Artificial Chromosomes (BACs) with enhancer-traps to identify functional non-coding DNA in an unbiased and non-targeted manner. BACs are functionalized with enhancer-traps and expressed as transgenes in zebrafish. Using this approach we identified an intron enhancer that is poorly conserved, but required for expression of the Amyloid Precursor Protein (APPb) gene from zebrafish. Identifying functional non-coding DNA this way relies upon expressing genes in their chromosomal contexts in the appropriate tissues and levels reminiscent of their endogenous counterparts.

Shakes, Leighcraft Research Staff

Chatterjee, P.K. (2015) Directing Enhancer-Traps and iTol2 End-Sequences to Deleted BAC Ends with loxP- and lox511-Tn10 Transposons. Methods in molecular biology (Clifton, N.J.). 1227:99-122
Shakes, L.A., Wolf, H.M., Norford, D.C., Grant, D.J., Chatterjee, P.K. (2014) Harnessing mobile genetic elements to explore gene regulation. Mobile genetic elements. 4:e29759
Chatterjee, P.K., Shakes, L.A., Wolf, H.M., Mujalled, M.A., Zhou, C., Hatcher, C., Norford, D.C. (2013) Identifying Distal cis-acting Gene-Regulatory Sequences by Expressing BACs Functionalized with loxP-Tn10 Transposons in Zebrafish.. RSC Advances. 3:8604-8617
Shakes, L.A., Du, H., Wolf, H.M., Hatcher, C., Norford, D.C., Precht, P., Sen, R., and Chatterjee, P.K. (2012) Using BAC transgenesis in zebrafish to identify regulatory sequences of the amyloid precursor protein gene in humans. BMC Genomics. 13(1):451
Shakes, L.A., Abe, G., Eltayeb, M.A., Wolf, H.M., Kawakami, K., and Chatterjee, P.K. (2011) Generating libraries of iTol2-end insertions at BAC ends using loxP and lox511 Tn10 transposons. BMC Genomics. 12(1):351
Chatterjee, P.K., Shakes, L.A., Stennett, N., Richardson, V.L., Malcolm, T.L., and Harewood, K.R. (2010) Replacing the wild type loxP site in BACs from the public domain with lox66 using a lox66 transposon. BMC research notes. 3:38
Shakes, L.A., Malcolm, T.L., Allen, K.L., De, S., Harewood, K.R., and Chatterjee, P.K. (2008) Context dependent function of APPb enhancer identified using enhancer trap-containing BACs as transgenes in zebrafish. Nucleic acids research. 36(19):6237-6248