Bioinformatic analyses of KLF1 variants detected in Argentinean population with hemoglobinopathies

Abstract

KLF1 is an erythroid essential transcription factor. Sequence variants (mainly nonsense or substitutions in its Zinc finger domains) lead to distinctive phenotypes. The lack of KLF1 can lead to an inefficient β-globin cluster switch, which can increase the HbF and HbA2 fractions. In consequence, variants mapping in this gene can alter the clinical course of β-thalassemia.Objectives: Perform structural predictive analyses of the missense variants detected in a group of Argentinean patients and carry out analyses to predict their impact as regulatory targets.Patients and methods: The DNA from 3 individuals with moderately increased levels of HbA2 and 20 patients with thalassemia intermedia or severe β-thalassemia carriers was obtained and KLF1 was amplified by PCR and sequenced by the Sanger method. Since KLF1 has not been crystallized, predictive models were built with RaptorX contact prediction, their potential as regulatory sites was analyzed with RegulomeDB and their impact on the splicing of the mRNA with ESEfinder. Results: Only 3 previously described missense variants with no or minor functional consequences were detected: rs112631212, rs2072597 and rs2072596. The first two could affect the structure locally, disrupting α-helixes. However, none affect the Zinc Finger domains. The second variant scored 0.3145 (2a category) in RegulomeDB 2.0. The latter 2 affect exonic splicing enhancers. Discussion: The structural analysis of the variants matches the lack of effect described. It is unlikely that they could affect the default splicing of the KLF1 mRNA, since these SNPs map far from the exon-exon junctions. rs2072597 was the most frequent variant (13/46 alleles) and it could impact its role as a regulatory target; the ZFX transcription factor motif is disrupted and ChIP assays have demonstrated that this factor interacts with this region in K562 cells. Although this effect may not inhibit KLF1 expression, it could induce changes in its expression levels.