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Phylogenetic footprinting of hypersensitive site 3 of the beta-globin locus
control region
DA Shelton, L Stegman, R Hardison, W Miller, JH Bock, JL Slightom, M Goodman and DL Gumucio
Department of Anatomy and Cell Biology, University of Michigan Medical
School, Ann Arbor 48109-0616, USA.
Hypersensitive site 3 (HS3) of the beta-like globin locus control region
has been implicated as an important regulator of the beta-like globin
genes, but the trans factors that bind HS3 have only been partially
characterized. Using a five-species alignment (human, galago, rabbit, goat,
and mouse) that represents 370 million years of evolution, we have
identified 24 phylogenetic footprints in the HS3 core and surrounding
regions. Probes corresponding to the human sequence at each footprint have
been used in binding studies to identify the nuclear factors that bind
within and near these conserved sequence elements. Among the high-affinity
interactions observed were several binding sites for proteins with
repressor activity, including YY1, CCAAT displacement protein, and G1/G2
complexes (uncharacterized putative repressors) and several binding sites
for the stage selector protein. To complement this analysis, orthologous
galago sequences were also used to derive probes and the pattern of
proteins binding to human and galago probes was compared. Binding
interactions differing between these two species could be responsible for
the different expression patterns shown by the two gamma genes (galago
gamma is embryonic; human gamma is fetal). Alternatively, binding
interactions that are conserved in the two species may be important in the
regulation of common expression patterns (eg, repression of gamma in adult
life).
Volume 89,
Issue 9,
pp. 3457-3469,
05/01/1997
Copyright © 1997 by The American Society of Hematology
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