In silico study on RNA structures of intronic mutations of beta-globin gene

Background: Mutation of the beta-globin gene (HBB) interferes with primary mRNA transcription, leading to beta-thalassemia disease. The IVS1nt1 and IVS1nt5 mutations were reported as two of the most prevalent intronic mutations associated with beta-thalassemia major. These mutations may affect the mRNA structure of the human beta-globin (HBB) gene. However, the mechanism by which variation in HBB alters the mRNA structure remains unclear. The objective of this study was to unveil the secondary and tertiary conformation difference of the mutants compared to the wildtype using in silico analysis. Methods: The sequence of HBB was obtained from Ensemble database and mutated manually at nucleotides 143 (IVS1nt1G>T) and 147 (IVS1nt5G>C). The RNA secondary and tertiary structure were performed by ViennaRNA Web Services and 3dRNA v2.0, respectively. Results and Discussion: The results revealed the unique folding characteristics of each mutations for the secondary and tertiary structures. Based on the structure, unwanted folding occurred in the IVS1nt1G>T and IVS1nt5G>C mRNA structures compared to the wild-type structure. This finding was supported by the results of centroid-based analysis and RNA structure analysis, indicating that the larger loops in IVS1nt1 and IVS1nt5 result in an unstable structure. Our study found that intronic mutations affect the mRNA structure of HBB by altering its folding mechanism.

In silico study on RNA structures of intronic mutations of beta-globin gene

Background: Mutation of the beta-globin gene (HBB) interferes with primary mRNA transcription, leading to beta-thalassemia disease. The IVS1nt1 and IVS1nt5 mutations were reported as two of the most prevalent intronic mutations associated with beta-thalassemia major. These mutations may affect the mRNA structure of the human beta-globin (HBB) gene. However, the mechanism by which variation in HBB alters the mRNA structure remains unclear. The objective of this study was to unveil the secondary and tertiary conformation difference of the mutants compared to the wildtype using in silico analysis. Methods: The sequence of HBB was obtained from Ensemble database and mutated manually at nucleotides 143 (IVS1nt1G>T) and 147 (IVS1nt5G>C). The RNA secondary and tertiary structure were performed by ViennaRNA Web Services and RNA Composer, respectively. Results and Discussion: The results revealed the unique folding characteristics of each mutations for the secondary and tertiary structures. Based on the structure, unwanted folding occurred in the IVS1nt1G>T and IVS1nt5G>C mRNA structures compared to the wild-type structure. This finding was supported by the results of centroid-based analysis and RNA structure analysis, indicating that the larger loops in IVS1nt1 and IVS1nt5 result in an unstable structure. Our study found that intronic mutations affect the mRNA structure of HBB by altering its folding mechanism.

Mutation in thalassemia syndrome and clinical manifestation

Introduction: Thalassemia intermedia is a term used to define a group of patients with β thalassemia in whom the clinical severity of the disease is somewhere between the mild symptoms of the β thalassemia trait and the severe manifestations of β thalassemia major. Thalassemia intermedia shows considerable heterogeneity in phenotype and molecular basis. Objectives: The aim of this study was to identify the common mutations of beta globin gene and the relationship between genotypes and phenotypes in thalassemia intermedia patients in Mazandaran province, in the north of Iran. Patients and Methods: Fifty unrelated thalassemia intermedia patients, based on clinical and hematological characteristics including age of diagnosis, age of first blood transfusion, history of blood transfusion, mean corpuscular volume (MCV), mean cell hemoglobin (MCH), hemoglobin values, and liver and spleen status were selected. DNA of peripheral blood was extracted and common mutations in beta globin gene were analyzed by reverse dot blot (RDB) method. Results: Our study showed that 30 patients (60%) had blood transfusion. There was no obvious hepatomegaly in any of the subjects, however 40 patients (80%) showed splenomegaly among which 34 cases (68%) underwent splenectomy. Mutations analysis indicated that HBB:c.315+1G>A [IVS II-1 (G>A)] mutation was the dominant mutation and has been widely associated with the phenotypic manifestations of thalassemia intermedia patients. Conclusion: It is important to comprehend the molecular basis of thalassemia intermedia and the association between genotype and phenotype in different ethnic groups. Therefore a careful evaluation of genetic, molecular, hematological and clinical aspects is necessary to differentiate thalassemia intermedia in patients at presentation.

In silico study on RNA structures of intronic mutations of beta-globin gene

Background: Mutation of the beta-globin gene (HBB) interferes with primary mRNA transcription, leading to beta-thalassemia disease. The IVS1nt1 and IVS1nt5 mutations were reported as two of the most prevalent intronic mutations associated with beta-thalassemia major. These mutations may affect the mRNA structure of the human beta-globin (HBB) gene. However, the mechanism by which variation in HBB alters the mRNA structure remains unclear. The objective of this study was to unveil the secondary and tertiary conformation difference of the mutants compared to the wildtype using in silico analysis. Methods: The sequence of HBB was obtained from Ensemble database and mutated manually at nucleotides 143 (IVS1nt1G>T) and 147 (IVS1nt5G>C). The RNA secondary and tertiary structure were performed by ViennaRNA Web Services and RNA Composer, respectively. Results and Discussion: The results revealed the unique folding characteristics of each mutations for the secondary and tertiary structures. Based on the structure, unwanted folding occurred in the IVS1nt1G>T and IVS1nt5G>C mRNA structures compared to the wild-type structure. This finding was supported by the results of centroid-based analysis and RNA structure analysis, indicating that the larger loops in IVS1nt1 and IVS1nt5 result in an unstable structure. Our study found that intronic mutations affect the mRNA structure of HBB by altering its folding mechanism.

Prediction of RNA Secondary Structure at IVS1 Mutation of Beta Globin Gene

Background: Beta globin gene is responsible for producing beta globin chains that stabilize the structure and function of hemoglobin. This gene expression is controlled by complex interactions of transcriptions factors and its regulatory elements in a specific manner. Disturbed beta globin genes may result in hemoglobinopathies, mainly sickle cell disease and beta thalassemia. It seems interesting that several mutations occurring in intronic region results in severe symptoms to beta thalassemia patients, such an IVS1nt5 G>C. This research aimed to analyze RNA structural alteration effected by intronic mutation of beta thalassemia. Methods: The most prevalent mutation of beta thalassemia in Indonesia was obtained from Ithanet. The RNA secondary structure of IVS1nt5 G>C and beta globin gen (HBB) wildtype were performed by RNAStructure, along with probknot prediction. Results: The result showed that intronic mutation caused conformational change in beta globin secondary structure, either for max expect or base pairing probability approach. The mutant had bigger and more loops that diminished the protein stability. Thus, the structure might undergo dysfunction. Conclusion: The comprehensive structural-functional significance of these findings needs further study.