Screening of Transcription Factors Involved in Fetal Hemoglobin Regulation Using Phylogenetic Footprinting

Abstract

Fetal hemoglobin (Hb F) is an important genetic modulator of the beta-hemoglobinopathies. The regulation of Hb F levels is influenced by transcription factors. We used phylogenetic footprinting to screen transcription factors that have binding sites in HBG1 and HBG2 genes' noncoding regions in order to know the genetic determinants of the Hb F expression. Our analysis showed 354 conserved motifs in the noncoding regions of HBG1 gene and 231 motifs in the HBG2 gene between the analyzed species. Of these motifs, 13 showed relation to Hb F regulation: cell division cycle-5 (CDC5), myelo-blastosis viral oncogene homolog (c-MYB), transcription factor CP2 (TFCP2), GATA binding protein 1 (GATA-1), GATA binding protein 2 (GATA-2), nuclear factor erythroid 2 (NF-E2), nuclear transcription factor Y (NF-Y), runt-related transcription factor 1 (RUNX-1), T-cell acute lymphocytic leukemia 1 (TAL-1), YY1 transcription factor (YY1), beta protein 1 (BP1), chicken ovalbumin upstream promoter-transcription factor II (COUP-TFII), and paired box 1 (PAX-1). The last three motifs were conserved only in the noncoding regions of the HBG1 gene. The understanding of genetic elements involved in the maintenance of high Hb F levels may provide new efficient therapeutic strategies in the beta-hemoglobinopathies treatment, promoting reduction in clinical complications of these genetic disorders.

Keywords: Hb F; beta-hemoglobinopathies; phylogenetic footprinting; transcription factors.

Figure 1

VISTA plots obtained from the comparison analysis of genomic sequences of the nonconding regions from the γ-globin genes. The plots contain genomic sequences of γ^A-globin and γ^G-globin genes from H. sapiens (gray arrow), P. troglodytes (line 1), P. abelli (line 2), M. mulatta (line 3), C. jacchus (line 4), C. apella (line 5), and T. syrichta (line 6), showing the patterns of peaks and valleys. In blue are represented γ-globin coding regions (exons) and in red are represented the noncoding regions (introns). The results indicate similarity conservation of coding and noncoding sequences greater than 70%, suggesting functionality for the noncoding regions.

Figure 2

Representation of the interaction between transcription factors and regulation of hematopoiesis, erythropoiesis, and the globin genes. The 13 transcription factors selected from in silico analysis are showed. The continuous arrows indicate elements that act as transcriptional activators. The dashed arrows indicate indirect activators. The bars show transcriptional repressors. Boxes without staining (NF-E4 and SSP) indicate factors that comprise protein complexes involved in globin regulation. The different colors of transcription factors represent different forms of action: dark green represents direct transcriptional activation, orange transcriptional activation mediated by the presence of specific mutations, light green indirect transcriptional activation, red transcriptional repression, and blue control of hematopoiesis and erythropoiesis and synthesis of globin chains. We used the Microsoft PowerPoint to elaborate this figure.