Functional sites in HS2 of the beta-globin LCR


Information on in vivo footprints and site-directed mutations tested in transgenic mice and transfected cells were combined to establish a set of experimentally-verified functional sites in HS2 of the beta-globin locus control region (LCR). Additional information on binding sites was also brought into the assignments. If nucleotides identified as important by in vivo footprints are part of a binding site for a protein, or class of proteins, implicated as binding at that site (e.g. by in vitro binding assays or mutagenesis), then the entire consensus binding site for that protein was included in the list of functional sites.


Region   examined:   11240   11510

The functional nucleotides are:

The coordinates are for the sequence file starting 5' to HS5. Coordinates in the GenBank file HUMHBB can be obtained by subtracting 2687.



References for in vivo footprints in HS2:

Data from Reddy and Shen 1991 (human), Ikuta and Kan 1991 (human), Reddy and Shen 1993 (mouse), Reddy et al 1994. All data from Figures are included, even if the positions were not mentioned in the text (this is particularly true for some data from Reddy and Shen 1993 for the conserved CACC box and the E box). Interestingly, some of these regions show up as results in Reddy et al. 1994.


References for mutagenesis studies:

Data are from Caterina et al. 1994 (transgenic mice), Lam and Bresnick 1996, Elnitski et al. 1997 (transiently transfected K562 cells). Many other papers contain mutational analysis, but these three papers implicate a fairly long region that covers the sites mutated by lots of labs.