New mutations of locus control region in Saudi sickle patients

Sickle cell anemia (SCA) is a common hematological disease affecting humans. Detection of a single base pair mutation in β-globin gene is an important diagnostic tool for SCA. The aim was to study the molecular survey of locus control regions (LCR) in Saudi patients with sickle cell anemia, and to identify the genetic variables and their clinical manifestations.MethodologyBlood samples from 69 unrelated sickle cell disease patients were obtained from the KKUH, Riyadh between 2017–2019. In this study, the DNA was extracted and PCR was performed. Additional PCR amplifications reactions covering the LCR were performed by using another different set of primers. Seven specific primer pairs were used to amplify seven regions in the locus control region (LCR) of β globin family. The generated fragments were sequenced to identify the possible alterations in this region.ResultsThe results gained from sequencing experiments revealed a wide range of genomic alterations. A total of 69 gene alterations have been recognized in the locus control region;- The first fragment LCR-HS1 shows 20 alterations; The second fragment LCR-HS2 revealed six changes; The third fragment LCR-HS3 shows many changes; The fifth LCR-HS5 region revealed four changes; The sixth fragment LCR-HS6 revealed eight changes; The seventh LCR-HS7 fragment demonstrates ten changes.ConclusionIt clear that this study has successfully identified LCR mutations for random Saudi patients with SCD. The above results should be taken further to set up management strategies to improve outcomes.     

Prenatal and post-natal screening of β-thalassemia and hemoglobin E genes in Thailand using denaturing high performance liquid chromatography

We have developed methods based on PCR and denaturing high performance liquid chromatography (DHPLC) for rapid identifications of common β-thalassemia mutations found in Thailand. The β-globin gene was separately amplified by PCR on four different fragments covering eight most common β-thalassemia mutations including nucleotide ?28 A-G, codon 17 (A-T), IVSI-1 (G-T), IVSI-5 (G-C), codon 26 (G-A or Hb E), codons 41/42 (–TTCT), codons 71/72 (+A) and IVSII-654 (C-T). After PCR amplification, heteroduplex was generated by denaturation at 95 °C for 5 min followed by a slow reduction in temperature to 25 °C at 0.03 °C/s. Analysis of heteroduplex was done on an automated WAVE Nucleic Acid Fragment Analysis System. Specific DHPLC profile for each mutation was demonstrated which could be used in screening for all eight β-thalassemia mutations. Further validation was done on 42 pre- and post-natal DNA samples which demonstrated 100 % accuracy as compared to the result obtained with conventional PCR assays. In a remaining case with an unknown mutation, a different DHPLC profile was noted on one of the amplified fragment. Further DNA sequencing of this fragment revealed a T-G transversion at the IVSI-116, a previously un-described mutation in Thai population. The DHPLC assay developed should prove useful for rapid screening of known and unknown β-thalassemia mutations during carrier screening and pre-natal diagnosis which would facilitate an ongoing prevention and control program of thalassemia.     

人同源异型盒基因Hu-1位点的RFLPs研究

用12种限制性核酸内切酶分别对4至104条人类染色体进行酶谱分析,以寻找Hu-1基因附近的限制性酶切多态位点,仅发现了Bg 1Ⅱ酶的一个多态性位点。表现为Bg 1Ⅱ酶谱中除3.6kb片段外,杂合子型尚具6.3及6.6kb两种片段,而纯合子型则只有6.3或6.6kb一种片段。在所检查的104条染色体中6.6kb片段出现的频率为3.88％,而6.3kb片段出现的频率为96.12％。经统计分析,计算出Hu-1基因及其附近的核苷酸变异率为0.0017,大体上与人β珠蛋白基因簇及人α-1-抗胰蛋白酶基因的核苷酸变异率相似。文中对本工作的意义进行了初步讨论。     

一个α,β地中海贫血复合家系β珠蛋白基因的进一步研究

 前文~[1]曾报道广西一个α,β地中海贫血复合家系的血红蛋白组成及α珠蛋白基因分析结果,并讨论了各成员可能的β珠蛋白基因结构情况。本文利用先进的PCR即基因扩增技术,结合特异寡核苷酸探针斑点杂交及扩增后直接测定DNA序列的技术,进一步研究并彻底搞请了该家系各成员的β珠蛋白基因结构情况。结果显示:母亲及两个弟弟都是编码子41—42TTCT四个碱基缺失造成框架位移所致β地中海贫血的杂合子。父亲与先证者的β基因均属正常。前三个成员均为α地贫复合β地贫,其α与β珠蛋白链合成的不均衡状态得到改善,贫血症状也明显轻。     

Insertion of disease-causing mutations in BACs by homologous recombination in Escherichia coli

We have used GET Recombination, an inducible homologous recombination system for Escherichia coli, to insert one of the most common thalassaemia mutations into the intact β-globin locus in a second generation BAC vector. We first inserted a PCR fragment carrying the tetracycline resistance gene (TetR) into the β-globin gene. All recombinant clones examined contained the TetR gene at the correct target site. Next, a PCR fragment with the IVS I-110 G→A splicing mutation but no selectable marker was used to replace the TetR gene in a second round of GET Recombination. Recombinant clones were selected by plating on medium containing chlorotetracycline and fusaric acid. Although counterselection for the TetR gene is not very efficient, four recombinant colonies with the IVS I-110 mutation were identified among 480 clones screened. Analysis of the recombinant clones did not show any other modifications or rearrangements. Thus the TetR gene can be used in combination with GET Recombination to introduce point mutations and other modifications in BACs without leaving behind any operational sequences, in order to generate accurate cell and transgenic mouse models for various diseases.     

A comparison of methods for DNA extraction from paraffin-embedded tissue for microsatellite instability analysis by polymerase chain reaction

In a prospective study, nuclear DNA was extracted from colorectal tumours and normal mucosa which had been fixed in buffered formalin and embedded into paraffin. DNA-extraction was performed using three different methods: a commercial kit which was not especially created for this use; a known fast procedure without DNA-cleaning steps; and a more conventional DNA-preparation protocol with DNA-cleaning. Using the polymerase chain reaction (PCR), DNA was amplified by being targeted onto two β-globin fragments with different lengths (536 bp and 989 bp) and (CA)n repeats localized on chromosome 5q (D5S346) and chromosome 17p (TP53CA) with a length of about 100 bp for detection of microsatellite instability. The success rate of microsatellite amplification was 100% with all methods. The 536 bp β-globin fragment could be amplified with a success rate ranging from 40% to 100%. The amplification of the 989 bp β-globin fragment was unsuccessful. Significant differences were observed between the three methods in the final DNA concentration and DNA yield. In microsatellite instability studies of paraffin-embedded tissues, the investigator can expect a high success rate of nearly 100% using any of the described methods.     

Isolation and sequence analysis of a hybrid delta-globin pseudogene from the brown lemur

The β-globin gene cluster of the brown lemur, a prosimian, is very short and contains a single ?-, γ- and β-globin gene, with an additional β-related gene sequence between the γ- and β-globin genes. Brown lemur DNA was cloned into the bacteriophage vector λL47.1 and a recombinant was isolated which contained an 11 × 10³ base insert including the β-globin gene and the additional putative β-globin pseudogene. The nucleotide sequence of this β-related gene was completely determined. A complete gene sequence was found, containing four frameshift mutations sufficient to establish its pseudogene status. The gene was interrupted by two intervening sequences with sizes and locations typical of mammalian β-related globin genes. The pseudogene sequence was compared in detail with human ?-, γ-, δ- and β-globin genes. The beginning of the pseudogene, from the 5′ flanking region to the second exon, was homologous to the corresponding regions of the human ?- and γ-globin genes. In contrast, the second intron, third exon and 3′ flanking region showed a remarkably close homology to the δ-globin, but not β-globin, gene of man. This suggests that the δ-globin gene is not the product of a recent gene duplication, but instead is present in most or all primates. This gene has been silenced on at least two separate occasions in primate evolution (in lemurs and in old world monkeys). In addition, the 5′ end of the lemur ψδ gene appears to have exchanged sequences with an ?- or γ-globin gene, and an analogous exchange with the β-globin gene seems to have occurred recently in the human δ-globin gene. The evolution and function of the δ-globin gene are discussed.     

Fannin-Lubbock-I [α2β2119(GLY>ASP)], a rare mutation in the beta-globin gene,has been detected for the first time in a Hindu Brahmin family in West Bengal,India

This study aims to describe the hemoglobin Fannin-Lubbock-I, which has a rare mutation substituting the amino acid glycine with aspartic acid at codon 119 of the β-globin chain. A Bengalee Hindu Brahmin family from Kolkata in West Bengal was the focus of this study. Molecular analysis using ARMS-PCR and direct DNA sequencing revealed the presence of a GGC > GAC mutation in codon 119 of the β-globin gene in a heterozygote state in three women of the same family. This is the first report of the hemoglobin Fannin-Lubbock-I from India. Our results will help to identify this mutation, which is relatively infrequent in our population.     

A fusion gene in man: DNA sequence analysis of the abnormal globin gene of Hemoglobin Miyada

An abnormal globin gene from a patient heterozygous for Hemoglobin Miyada was cloned and sequenced. The results indicated that the 5′ flanking region and the 5′ side of the gene were identical to those of a β-globin gene and that the 3′ side was identical to that of a γ-globin gene. The part of the gene identical to a β-globin gene shifted to the part identical to the δ-globin gene somewhere in a homologous sequence region between the third nucleotide of the 17th codon and the second nucleotide of the 22nd codon of these two genes. Thus, results of analysis of the nucleotide sequence support the idea that the abnormal globin gene of Hemoglobin Miyada was generated as a fusion gene by unequal crossing over between a β- and a δ-globin gene.     

The rabbit beta-globin gene contains a large large insert in the coding sequence

We have used the rabbit β-globin DNA plasmid PβG1 (Maniatis et al., 1976) labeled with ³²P as a filter hybridization probe for DNA fragments containing the β-globin gene in restriction endonuclease digests of rabbit liver DNA. The β-globin DNA fragments we detect appear to contain the gene, present in PβG1 DNA, which codes for adult rabbit β-globin. These fragments have been ordered into a physical map of cleavage sites within and neighboring the structural gene in the rabbit genome (Jeffreys and Flavell, 1977). A detailed analysis of β-globin DNA fragments produced by cleavage with restriction endonucleases which are known to cut the β-globin gene has now shown that the β-globin structural gene is not contiguous in rabbit liver DNA, but is interrupted by a 600 base pair DNA segment inserted somewhere within the coding sequence for amino acid residues 101–120 of the 146 residue β-globin chain. Otherwise, the map of cleavage sites within the gene is co-linear with that deduced from the sequence of rabbit β-globin messenger RNA. Preliminary analysis indicates that this insert is also present in the β-globin gene in rabbit brain, kidney, spleen, bone marrow and sperm, and in erythroid cells isolated from the marrow of an anemic rabbit. The insert appears, therefore, to be a general property of the rabbit β-globin gene, even in tissues in which this gene is active, which suggests that the insert is not involved in inactivating the gene in nonerythroid tissues.     

Mitochondrial DNA analysis of Scottish populations of Arctic charr, Salvelinus alpinus (L.)

Mitochondrial DNA analysis of a total of 82 individuals from seven Scottish populations of Arctic charr ( Salvelinus alpinus L.) using restriction fragment length polymorphism and direct nucleotide sequencing of the cytochrome b gene revealed little variation within or between populations. One of 19 restriction enzymes showed a polymorphism that was present in three of the seven populations. Only one nucleotide substitution was detected in a 288 base pair segment of the cytochrome b gene examined in 26 fish. Approximately 4% of the mitochondrial genome was surveyed with these complementary procedures.     

Association of Xmn1 −158 γG variant with severity and HbF levels in β-thalassemia major and sickle cell anaemia

Haemoglobinopathies including β-thalassemia and sickle cell anaemia (SCA) are considered to be classical monogenic diseases. There is considerable clinical variability between patients inheriting identical β-globin mutations. The reasons for this variability are not well understood. Previous studies have suggested that a variety of genetic determents influence different clinical phenotypes. The genetic variants that modulate HbF levels have a very strong impact on ameliorating the clinical phenotype. In the present study 6,500 blood samples from suspected cases were analysed using HPLC, ARMS-PCR, RDB techniques. Patients with β-thalassemia and SCA were classified into mild, moderate, severe according to the severity score based on Hb levels, age of onset, age at which patients received their first blood transfusion, the degree of growth retardation and splenectomy. Patients with β-thalassemia and SCA were analysed for Xmn1 polymorphism and association between this polymorphism and severity of β-thalassemia and SCA was evaluated. We found a significant difference in genotypic and allelic frequencies of Xmn1 polymorphism between mild and moderate and mild and severe cases. There was a significant difference in high and low percentage of HbF in CC, CT and TT bearing individuals. The TT bearing individuals were found to have a high percentage of HbF in β-thalassemia as well as SCA. This study confirms that increased γ^G-globin expression associated with Xmn1 polymorphism ameliorates the clinical severity in β-thalassemia as well as SCA in the study population.     

Main regulatory element (MRE) of the <Emphasis Type="Italic">Danio rerio</Emphasis> α/β-globin gene domain exerts enhancer activity toward the promoters of the embryonic-larval and adult globin genes

In warm-blooded vertebrates, the α- and β-globin genes are organized in domains of different types and are regulated in different fashion. In cold-blooded vertebrates and, in particular, the tropical fish Danio rerio, the α- and β-globin genes form two gene clusters. A major D. rerio globin gene cluster is in chromosome 3 and includes the α- and β-globin genes of embryonic-larval and adult types. The region upstream of the cluster contains c16orf35, harbors the main regulatory element (MRE) of the α-globin gene domain in warm-blooded vertebrates. In this study, transient transfection of erythroid cells with genetic constructs containing a reporter gene under the control of potential regulatory elements of the domain was performed to characterize the promoters of the embryonic-larval and adult α- and β-globin genes of the major cluster. Also, in the 5th intron of c16orf35 in Danio rerio was detected a functional analog of the warm-blooded vertebrate MRE. This enhancer stimulated activity of the promoters of both adult and embryonic-larval α- and β-globin genes.     

The Cretan type of non-deletional hereditary persistence of fetal hemoglobin [Aγ–158C→T] results from two independent gene conversion events

We report a new type of non-deletional hereditary persistence of fetal hemoglobin that is due to a C→T transition at position –158, relative to the Cap site of the human Aγ-globin gene. This mutation was identified in three unrelated adult cases presenting slightly elevated levels of fetal hemoglobin (Hb F), i.e. 2.9–5.1%, and normal hematological indices. Our sequencing results, from both polymerase chain reaction-amplified and subcloned DNA fragments, indicate that the Aγ–158C→T mutation occurred by two independent gene conversion events in the three cases studied. In addition, hematological and molecular data, including restriction fragment length polymorphism haplotyping in the β-globin gene cluster, extended haplotype analysis inside the γ-globin gene region and routine analysis of three tandem repeat loci (D1S80, 3′-HVR/apoB and F8vWf), led us to conclude that the Aγ–158C→T mutation in one of the three cases occurred recently in the parental germ line (P=99.47%), representing the first example of a de novo gene conversion event identified in humans. Received: 10 November 1997 / Accepted: 10 February 1998     

γ-珠蛋白基因表达调控机制与临床应用

成人体内的血红蛋白是由2个 α-珠蛋白和2个β-珠蛋白组成的四聚体,负责氧气的运输。珠蛋白基因在基因组中成簇分布,其表达受到多种顺式作用元件和反式作用因子的共同调控,具有高度的组织特异性和发育时序性。β-地中海贫血和镰刀型细胞贫血是两种最常见的由于β-珠蛋白基因突变引起的常染色体隐性遗传病。γ-珠蛋白是一种主要在胎儿时期表达的类β-珠蛋白,同样具有载氧功能,但编码该蛋白的基因在上述贫血患者中却保持完好。因此,临床上优选的治疗方案之一是重新激活患者体内沉默的γ-珠蛋白基因的表达来弥补缺损的β-珠蛋白,从而缓解临床症状。目前已有多种能提高γ-珠蛋白基因表达的药物,在临床上用于治疗β-地中海贫血和镰刀型细胞贫血。随着基因组编辑技术的发展,针对这两种贫血的精准基因治疗研究也在进行中。本文着重介绍了参与γ-珠蛋白基因调控的转录因子和表观遗传修饰分子,以及目前相关的β-地中海贫血和镰刀型细胞贫血的临床治疗药物和手段,以期为深入阐明γ-珠蛋白基因的转录表达分子调控机制提供参考。     

Meiotic recombination in an Irish family with beta-thalassaemia

Using the technique of allele-specific priming of the polymerase chain reaction (PCR), the C-T substitution in codon 39 was identified as the cause of -thalassaemia in an Irish family. Analysis of the restriction fragment length polymorphisms (RFLPs) in the -globin gene cluster established linkage of the -thalassaemia mutation to a particular -haplotype but indicated that a recombinational event had occurred in the paternal chromosome in the younger of two affected children. Non-paternity was excluded by DNA fingerprinting analysis with hypervariable minisatellite probes. This is the fourth case of recombination in the -globin gene cluster to be reported. The event has occurred 5 of the polymorphic RsaI site at position-550 bp upstream of the -globin gene mRNA Cap site, within the 9.1-kb region that has been shown to be a hot spot for recombination in the -globin gene cluster.     

脊髓小脑共济失调第7型的临床特征及基因突变研究

对一脊髓小脑性共济失调(Spinocerebellar ataxia, SCA)家系的患者进行临床特征及相关基因突变研究。对该家系进行详细的病史采集, 并对患者行视力、眼底血管造影、眼底拍照、视觉诱发电位、视网膜电图以及头颅MRI等辅助检查; 采用聚合酶链反应分别扩增SCA1、SCA2、SCA3、SCA6、SCA7、SCA17及DRPLA基因的CAG重复序列, 用8%变性聚丙烯酰胺凝胶电泳及直接测序进行突变分析。结果2名患者主要表现为小脑性共济失调、视力下降、眼底视网膜色素变性、小脑和脑干萎缩; 并存在SCA7基因的突变, 而未发现SCA1、SCA2、SCA3、SCA6、SCA17及DRPLA基因突变。说明该家系为SCA7突变家系, SCA7基因中CAG三核苷酸重复拷贝数的异常扩增是其致病原因。     

CTCF-dependent enhancer blockers at the upstream region of the chicken alpha-globin gene domain

The eukaryotic genome is partitioned into chromatin domains containing coding and intergenic regions. Insulators have been suggested to play a role in establishing and maintaining chromatin domains. Here we describe the identification and characterization of two separable enhancer blocking elements located in the 5′ flanking region of the chicken α-globin domain, 11–16 kb upstream of the embryonic α-type π gene in a DNA fragment harboring a MAR (matrix attachment region) element and three DNase I hypersensitive sites (HSs). The most upstream enhancer blocking element co-localizes with the MAR element and an erythroid-specific HS. The second enhancer blocking element roughly co-localizes with a constitutive HS. The third erythroid-specific HS present within the DNA fragment studied harbors a silencing, but not an enhancer blocking, activity. The 11 zinc-finger CCCTC-binding factor (CTCF), which plays an essential role in enhancer blocking activity in many previously characterized vertebrate insulators, is found to bind the two α-globin enhancer blocking elements. Detailed analysis has demonstrated that mutation of the CTCF binding site within the most upstream enhancer blocking element abolishes the enhancer blocking activity. The results are discussed with respect to special features of the tissue-specific α-globin gene domain located in a permanently open chromatin area.