Bioinformatic Tools for the Identification of MicroRNAs Regulating the Transcription Factors in Patients with β-Thalassemia

Abstract

β-thalassemia is a significant health issue worldwide, with approximately 7% of the world's population having defective hemoglobin genes. MicroRNAs (miRNAs) are short noncoding RNAs regulating gene expression at the post-transcriptional level by targeting multiple gene transcripts. The levels of fetal hemoglobin (HbF) can be increased by regulating the expression of the γ-globin gene using the suppressive effects of miRNAs on several transcription factors such as MYB, BCL11A, GATA1, and KLF. An early step in discovering miRNA:mRNA target interactions is the computational prediction of miRNA targets that can be later validated with wet-lab investigations. This review highlights some commonly employed computational tools such as miRBase, Target scan, DIANA-microT-CDS, miRwalk, miRDB, and micro-TarBase that can be used to predict miRNA targets. Upon comparing the miRNA target prediction tools, 4 main aspects of the miRNA:mRNA target interaction are shown to include a few common features on which most target prediction is based: conservation sites, seed match, free energy, and site accessibility. Understanding these prediction tools' usage will help users select the appropriate tool and interpret the results accurately. This review will, therefore, be helpful to peers to quickly choose a list of the best miRNAs associated with HbF induction. Researchers will obtain significant results using these bioinformatics tools to establish a new important concept in managing β-thalassemia and delivering therapeutic strategies for improving their quality of life.

Keywords: Bioinformatics; beta-thalassemia; gamma-globin; hemoglobinopathy; microRNAs.

Figure 1.

Role of transcription factors in switching the γ- to β-globin gene: HBS1 L: GTP-binding protein-myeloblastosis (HBS1L-MYB) are the transcription factors that regulate HbF levels on the locus control region (LCR) of the β-globin locus. BCL11A mainly interacts with transcription factors such as globin transcription factor (GATA), zinc finger protein (FOG1), and nucleosome remodeling and deacetylase (NuRD), acts as a regulator of HbF to HbA switching; KLF (EKLF1) (erythroid-specific Kruppel-like factor) activates the transcription of BCL11A by binding to its promoter region, thereby mediating the γ-globin to β-globin gene switching. By interacting with the HBG1 and HBG2 genes, LRF represses the synthesis of the γ-globin gene and maintains the density of nucleosomes, resulting in the silencing of the γ-globin gene.

Figure 2.

Biosynthesis of miRNAs:RNA polymerase II/III transcribes the miRNA gene to produce pri-miRNA, which is subsequently processed by Drosha to produce pre-miRNA. Pre-miRNAs are carried to the cytoplasm, where the enzyme Dicer acts on them to form mature miRNA duplexes (22 nucleotides). The RISC subsequently packs this into Ago protein, which is then unwound into a single strand in the RISC. One strand acts as a guide strand and results in the formation of a silencing complex at 3′ UTR of target mRNA for translational repression.

Figure 3.

Criteria for selection of miRNAs: Candidate miRNAs may be selected using the criteria shown in the figure.