Differential phylogenetic footprinting as a means to identify base changes responsible for recruitment of the anthropoid gamma gene to a fetal expression pattern

• Published in: The Journal of biological chemistry Vol. 269; no. 21; pp. 15371 - 15380
• Main Authors: GUMUCIO, D. L, SHELTON, D. A, BLANCHARD-MCQUATE, K, GRAY, T, TARLE, S, HEILSTEDT-WILLIMASON, H, SLIGHTOM, J. L, COLLINS, F, GOODMAN, M
• Format: Journal Article
• Language: English
• Published: Bethesda, MD American Society for Biochemistry and Molecular Biology 27-05-1994
• Subjects: Animals; Base Sequence; Binding Sites; Biological and medical sciences; Biological Evolution; Cells, Cultured; DNA-Binding Proteins - metabolism; Fetal Hemoglobin - genetics; Fundamental and applied biological sciences. Psychology; Galago; Gene Expression Regulation; Globins - genetics; Globins - metabolism; GTP-Binding Proteins - metabolism; HeLa Cells; Humans; Mice; Molecular and cellular biology; Molecular genetics; Molecular Sequence Data; Mutation; Phylogeny; Promoter Regions, Genetic; Sequence Homology, Nucleic Acid; Transcription. Transcription factor. Splicing. Rna processing; Tumor Cells, Cultured; Human; Embryo; Transcription; Transcription promoter; Monkey; Footprinting technique; Globin; Vertebrata; Mammalia; Development; Primates; Fetus; Regulatory sequence
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1016/S0021-9258(17)36616-4

Expression of the anthropoid (simian) gamma gene in fetal life contrasts with the exclusively embryonic expression pattern
of the gamma-like genes of other eutherian mammals. To elucidate the factors responsible for this change in expression pattern,
we utilized a strategy called differential phylogenetic footprinting (DPF). This strategy entails the following: (a) identification,
within regulatory regions, of the gamma promoter, of individual nucleotides that differ between human (fetal expression),
and galago (embryonic expression) gamma genes, (b) analysis of the effect of these nucleotide differences on the binding of
nuclear proteins to human and galago sequences, and (c) assessment of the functional consequences of these binding changes
in expression assays. The DPF analysis revealed several proteins that bind upstream from the CCAAT motif in the galago gamma
promoter but do not bind to the corresponding region of the human gamma promoter. In transfection assays, binding of these
proteins is associated with erythroid-specific repression of promoter strength. Binding sites for these proteins also occur
near the CCAAT box of other embryonically expressed genes, including rabbit, mouse, and dwarf lemur gamma genes and the human
epsilon globin gene. These data are consistent with the hypothesis that sequence changes near the proximal CCAAT box in the
ancestral simian gamma gene may have facilitated a novel expression pattern by reducing the binding of repressors that act
in the fetal stage.