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Abstract
Thalassemia syndromes are common monogenic disorders and represent a significant health issue worldwide. In this review, the authors elaborate on fundamental genetic knowledge about thalassemias, including the structure and location of globin genes, the production of hemoglobin during development, the molecular lesions causing α-, β-, and other thalassemia syndromes, the genotype-phenotype correlation, and the genetic modifiers of these conditions. In addition, they briefly discuss the molecular techniques applied for diagnosis and innovative cell and gene therapy strategies to cure these conditions.
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Affiliation(s)
- Nicolò Tesio
- Department of Clinical and Biological Sciences, San Luigi Gonzaga University Hospital, University of Torino, Regione Gonzole, 10, 10043 Orbassano, Turin, Italy. https://twitter.com/nicolotesio
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA.
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Sen D, Roy P, Nandy A, Basak SC, Das S. Graphical representation methods: How well do they discriminate between homologous gene sequences? Chem Phys 2018; 513:156-164. [PMID: 32287864 PMCID: PMC7116999 DOI: 10.1016/j.chemphys.2018.07.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/21/2018] [Indexed: 01/05/2023]
Abstract
Graphical representation methods constitute a class of alignment-free techniques for comparative study of biomolecular sequences. In this brief commentary, we study how well some of these methods can discriminate among closely related genes.
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Affiliation(s)
- Dwaipayan Sen
- Centre for Interdisciplinary Research and Education, Jodhpur Park, Kolkata 700068, India
| | - Proyasha Roy
- Centre for Interdisciplinary Research and Education, Jodhpur Park, Kolkata 700068, India
| | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, Jodhpur Park, Kolkata 700068, India
| | - Subhash C Basak
- Department of Chemistry & Biochemistry, University of Minnesota Duluth, 5013 Miller Trunk Highway, Duluth, MN 55811, USA
| | - Sukhen Das
- Physics Department, Jadavpur University, Jadavpur, Kolkata 700032, India
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Al-Amodi AM, Ghanem NZ, Aldakeel SA, Ibrahim Al Asoom L, Rafique Ahmed N, Almandil NB, Naserullah ZA, Al-Jarrash S, Shakil Akhtar M, AbdulAzeez S, Al-Ali AK, Borgio JF. Hemoglobin A 2 (HbA 2) has a measure of unreliability in diagnosing β-thalassemia trait (β-TT). Curr Med Res Opin 2018; 34:945-951. [PMID: 29383950 DOI: 10.1080/03007995.2018.1435520] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Detection of β-thalassemia trait or carriers (β-TT) depends significantly on an increase in Hemoglobin A2 (HbA2) levels, which is found at low levels (<3%) in normal healthy individuals and elevated levels (≥3.5%) in β-TT individuals. The study was designed to evaluate the reliability of the diagnostic parameter HbA2 in the differentiation of β-TT and non-β-TT in Saudis. METHODS The widely used high performance liquid chromatography (Variant II Bio-Rad) was used to measure HbA2 levels in blood. Sanger sequencing was used to screen the variation in globin genes (HBB, HBD, HBA1, and HBA2). All the study subjects were divided into βTT and non-βTT (wild) categories based on the presence or absence of HBB variations and further sub-divided into false positive, true positive, false negative, and true negative, based on HbA2 values. RESULTS Out of 288 samples, 96 had HBB gene mutations. Of the 96 β-TT samples, sickle cell trait (SCT) samples (n = 58) were excluded, while the remaining (38 β-TT) were included in the detailed analysis: seven subjects with the HBB mutation had normal HbA2 (<3%), and three were borderline (3.1-3.9%). The remainder (n = 28) had an elevated HbA2 level (>4%). Based on HbA2 analysis alone, both these groups would be incorrectly diagnosed as normal. Similarly, of the 189 non-β-TT samples, 179 had normal HbA2, eight had borderline HbA2, and two had a HbA2 level above 4%. Based on HbA2 analysis alone, borderline and >4% HbA2 individuals, negative for β-TT, can be incorrectly diagnosed as carriers. CONCLUSION Given the percentage of samples falling in the HbA2 "borderline" and "normal" categories, it can be concluded that HbA2 has a measure of unreliability in the diagnosis of β-thalassemia carriers.
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Affiliation(s)
- Amani M Al-Amodi
- a Department of Genetic Research , Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Neda Z Ghanem
- a Department of Genetic Research , Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Sumayh A Aldakeel
- a Department of Genetic Research , Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Lubna Ibrahim Al Asoom
- b Department of Physiology, College of Medicine , Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Nazish Rafique Ahmed
- b Department of Physiology, College of Medicine , Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Noor B Almandil
- c Department of Clinical Pharmacy Research , Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | | | - Sana Al-Jarrash
- d Dammam Maternity and Child Hospital , Dammam , Saudi Arabia
| | - Mohammed Shakil Akhtar
- e Department of Biochemistry , Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Sayed AbdulAzeez
- a Department of Genetic Research , Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Amein K Al-Ali
- e Department of Biochemistry , Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - J Francis Borgio
- a Department of Genetic Research , Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
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Abstract
Across the expanse of vertebrate evolution, each species produces multiple forms of hemoglobin in erythroid cells at appropriate times and in the proper amounts. The multiple hemoglobins are encoded in two globin gene clusters in almost all species. One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. This preservation of synteny may reflect the presence of a powerful enhancer of globin gene expression in the NPRL3 gene. Despite substantial divergence in noncoding DNA sequences among mammals, several epigenetic features of the globin gene regulatory regions are preserved across vertebrates. The preserved features include multiple DNase hypersensitive sites, at least one of which is an enhancer, and binding by key lineage-restricted transcription factors such as GATA1 and TAL1, which in turn recruit coactivators such as P300 that catalyze acetylation of histones. The maps of epigenetic features are strongly correlated with activity in gene regulation, and resources for accessing and visualizing such maps are readily available to the community of researchers and students.
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Affiliation(s)
- Sjaak Philipsen
- Department of Cell Biology Ee1071b, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institute for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.
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Abstract
Thalassemia is a disorder of hemoglobin characterized by reduced or absent production of one of the globin chains in human red blood cells with relative excess of the other. Impaired synthesis of β-globin results in β-thalassemia, whereas defective synthesis of α-globin leads to α-thalassemia. Despite being a monogenic disorder, thalassemia exhibits remarkable clinical heterogeneity that is directly related to the intracellular imbalance between α- and β-like globin chains. Novel insights into the genetic modifiers have contributed to the understanding of the correlation between genotype and phenotype and are being explored as therapeutic pathways to cure this life-limiting disease.
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Affiliation(s)
- Sachith Mettananda
- Molecular Hematology Unit, Medical Research Council (MRC), Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; Department of Paediatrics, Faculty of Medicine, University of Kelaniya, Thalagolla Road, Ragama 11010, Sri Lanka
| | - Douglas R Higgs
- Molecular Hematology Unit, Medical Research Council (MRC), Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; National Institute for Health Research, Oxford Biomedical Research Centre, Blood Theme, Oxford University Hospitals, Headington, Oxford OX3 9DU, UK.
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Shaulov A, Filon D, Rund D. Haplotype analysis of α-thalassemia chromosomes reveals heterogeneity and multiple founders in Ashkenazi Jews. Eur J Med Genet 2016; 59:555-558. [PMID: 27771472 DOI: 10.1016/j.ejmg.2016.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/16/2016] [Indexed: 11/19/2022]
Abstract
α-Thalassemia (α-thal) is among the world's most common single gene disorders, generally attributed to a selective advantage of heterozygotes against malaria mortality. A high frequency of -α3.7 deletion heterozygosity has been previously reported in Ashkenazi Jews despite lack of obvious malarial selection pressure in this population. Using haplotype and -α3.7 subtype analysis we analyzed a subset of -α3.7 homozygotes from various Israeli ethnic groups. We found a high frequency of the common Ia haplotype in Yemenite Jews and Arabs (54% and 13% respectively). Ashkenazi Jews exhibited a high frequency of IIIb alleles (67%) previously reported only in Aboriginal Australians and not found in other Israeli ethnicities. Both Yemenites and Ashkenazim carried the rare IIh alleles (18% and 15% respectively). These results may suggest multiple founder effects in Ashkenazi Jews as well a common founder for both Yemenite and Ashkenazi Jews.
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Affiliation(s)
- Adir Shaulov
- Department of Hematology, Hadassah - Hebrew University Hospital, Jerusalem, Israel.
| | - Dvora Filon
- Department of Hematology, Hadassah - Hebrew University Hospital, Jerusalem, Israel
| | - Deborah Rund
- Department of Hematology, Hadassah - Hebrew University Hospital, Jerusalem, Israel
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Martyn GE, Quinlan KGR, Crossley M. The regulation of human globin promoters by CCAAT box elements and the recruitment of NF-Y. Biochim Biophys Acta Gene Regul Mech 2016; 1860:525-536. [PMID: 27718361 DOI: 10.1016/j.bbagrm.2016.10.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/01/2023]
Abstract
CCAAT boxes are motifs found within the proximal promoter of many genes, including the human globin genes. The highly conserved nature of CCAAT box motifs within the promoter region of both α-like and β-like globin genes emphasises the functional importance of the CCAAT sequence in globin gene regulation. Mutations within the β-globin CCAAT box result in β-thalassaemia, while mutations within the distal γ-globin CCAAT box cause the Hereditary Persistence of Foetal Haemoglobin, a benign condition which results in continued γ-globin expression during adult life. Understanding the transcriptional regulation of the globin genes is of particular interest, as reactivating the foetal γ-globin gene alleviates the symptoms of β-thalassaemia and sickle cell anaemia. NF-Y is considered to be the primary activating transcription factor which binds to globin CCAAT box motifs. Here we review recruitment of NF-Y to globin CCAAT boxes and the role NF-Y plays in regulating globin gene expression. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Gabriella E Martyn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia.
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Nefedochkina AV, Petrova NV, Ioudinkova ES, Kovina AP, Iarovaia OV, Razin SV. Characterization of the enhancer element of the Danio rerio minor globin gene locus. Histochem Cell Biol 2016; 145:463-73. [PMID: 26847176 DOI: 10.1007/s00418-016-1413-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2016] [Indexed: 12/23/2022]
Abstract
In Danio rerio, the alpha- and beta-globin genes are present in two clusters: a major cluster located on chromosome 3 and a minor cluster located on chromosome 12. In contrast to the segregated alpha- and beta-globin gene domains of warm-blooded animals, in Danio rerio, each cluster contains both alpha- and beta-globin genes. Expression of globin genes present in the major cluster is controlled by an erythroid-specific enhancer similar to the major regulatory element of mammalian and avian alpha-globin gene domains. The enhancer controlling expression of the globin genes present in the minor locus has not been identified yet. Based on the distribution of epigenetic marks, we have selected two genomic regions that might harbor an enhancer of the minor locus. Using transient transfection of constructs with a reporter gene, we have demonstrated that a ~500-bp DNA fragment located ~1.7 Kb upstream of the αe4 gene possesses an erythroid-specific enhancer active with respect to promoters present in both the major and the minor globin gene loci of Danio rerio. The identified enhancer element harbors clustered binding sites for GATA-1, NF-E2, and EKLF similar to the enhancer of the major globin locus on chromosome 3. Both enhancers appear to have emerged as a result of independent evolution of a duplicated regulatory element present in an ancestral single alpha-/beta-globin locus that existed before teleost-specific genome duplication.
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Affiliation(s)
- Anastasia V Nefedochkina
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow, Russia, 119334.,Molecular Biology Department, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Natalia V Petrova
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow, Russia, 119334
| | - Elena S Ioudinkova
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow, Russia, 119334
| | - Anastasia P Kovina
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow, Russia, 119334.,Molecular Biology Department, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Olga V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow, Russia, 119334
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow, Russia, 119334. .,Molecular Biology Department, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia, 119992.
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García-González E, Recillas-Targa F. A regulatory element affects the activity and chromatin structure of the chicken α-globin 3' enhancer. Biochim Biophys Acta 2014; 1839:1233-41. [PMID: 25239823 DOI: 10.1016/j.bbagrm.2014.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 09/09/2014] [Accepted: 09/10/2014] [Indexed: 11/19/2022]
Abstract
Gene promoters are frequently insufficient to drive the spatiotemporal patterns of gene expression during cell differentiation and organism development. Enhancers convey these properties through diverse mechanisms, including long-distance interactions with target promoters via their association with specific transcription factors. Despite unprecedented progress in the knowledge of enhancer mechanisms of action, there are still many unanswered questions. In particular, the contribution of an enhancer's local chromatin configuration to its mechanism of action is not completely understood. Here we describe a novel regulatory element, the Upstream Enhancer Element (UEE), which modulates the activity of the chicken α-globin 3' enhancer by regulating its chromatin structure, specifically by positioning a nucleosome upstream of the core enhancer. This element binds nuclear factors and confers a more restricted activation on the α-globin 3' enhancer, suggesting a progressive/rheostatic model for enhancer activity. Our results suggest that the UEE activity contributes to the positioning of a nucleosome that is necessary for the α-globin 3' enhancer activation.
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Affiliation(s)
- Estela García-González
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Ciudad de México, DF, Mexico
| | - Félix Recillas-Targa
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Ciudad de México, DF, Mexico.
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