乌鳢globin基因家族的鉴定及在鳃和鳃上器官中的表达模式分析

为了探究珠蛋白(Globin)在具有耐低氧和空气呼吸能力的乌鳢(Channa argus)中发挥的作用,本文对乌鳢的globin基因家族进行研究。在基因组中鉴定得到18个globin基因,分属于Hb、Mb、Ngb和Cygb四个亚家族,其中Hb亚家族拷贝数最多,达14个,其余各亚家族仅有1~2个拷贝。系统进化分析表明,乌鳢globin基因与硬骨鱼类聚为一枝,在进化上较为保守。对乌鳢globin基因结构分析得到4种保守结构域和5个motif。利用转录组测序技术对仔稚鱼(受精后3~8 d)和幼鱼(4月龄)的鳃和鳃上器官中globin基因进行表达量检测。在仔稚鱼中,hbae1(包括hbae1.1、hbae1.2和hbae1.3)、hbb2(包括hbb2.1、hbb2.2和hbb2.4)和hbaa的表达量在鳃上器官发育过程中呈显著升高趋势,而hba1和hbb1的表达量则显著降低。在幼鱼中,在空气暴露胁迫后,hbb2.2和cygb的表达量在鳃和鳃上器官中均发生显著变化,hbae1.1、hbae1.2和hbba的表达量在鳃中发生显著变化,hbae1.3和hbb2.1的表达量在鳃上器官中发生显著变化。这些在鳃上器官发育过程中和空气暴露胁迫中表达量出现显著变化的globin基因可能在乌鳢空气呼吸及低氧胁迫中发挥了生物学功能。

Globin-like蛋白质折叠类型识别

蛋白质折叠类型识别是蛋白质结构研究的重要内容.以SCOP中的Globin-like折叠为研究对象,选择其中序列同一性小于25%的17个代表性蛋白质为训练集,采用机器和人工结合的办法进行结构比对,产生序列排比,经过训练得到了适合Globin-like折叠的概形隐马尔科夫模型(profile HMM)用于该折叠类型的识别.以Astral1.65中的68057个结构域样本进行检验,识别敏感度为99.64%,特异性100%.在折叠类型水平上,与Pfam和SUPERFAMILY单纯使用序列比对构建的HMM相比,所用模型由多于100个归为一个,仍然保持了很高的识别效果.结果表明:对序列相似度很低但具有相同折叠类型的蛋白质,可以通过引入结构比对的方法建立统一的HMM模型,实现高准确率的折叠类型识别.

Co-Inheritance of Beta &Delta-Globin Gene (HbYialousa) Mutations in an Iranian <i>β</i>-Thalassemia Carrier

Introduction: Beta-thalassemia is characterized by absence or reduced synthesis of the β-globin. Carriers of β-thalas- semia, typically have microcytic hypochromic anemia and elevated hemoglobin HbA2 and normal HbF level. On the other hand carriers of severe alpha-thalassemia also have similar CBC parameters to that of β-thalassemia with normal HbA2 level. Co-presence of mutations in the β-globin and delta-globin genes (point mutations or deletions) usually give normal HbA2 and elevated HbF level. We report a β-thal carrier with normal level of HbA2 and increased level of HbF who had a point mutation in CD39 on the beta-globin gene and a point mutation in CD27 on the δ-globin gene named Hb-Yialousa. Materials & Methods: An individual with low hematological indices, normal HbA2 and elevated HbF was referred to our center as routine premarital screening program. Mutations in the β-globin and δ-globin genes were screened using ARMS and sequencing methods. Results: The mutation in β- and δ-globin genes were identified as CD39 and CD27 (HbYialousa) respectively. No point mutation or deletion in α-globin gene was identified. Discussion: We showed that normal HBA2 with elevated HbF level is due to co-inheritance of delta-globin gene mutation with mutation in the β-globin gene. When screening for β-thalassemia, one has to either rule out presence of α-globin gene mutation of mutation in the delta-globin gene.

Incidence of Sickle Cell Disease and Other Hemoglobinopathies in Burkina Faso: Results of a Five-Year Systematic Neonatal Screening (2015-2019) in Four Urban Hospitals

Hemoglobinopathies, mainly Sickle cell disease (SCD), are the most common monogenic disorders in Africa. In Burkina Faso, data on these diseases are scarce, mainly hospital-based in Ouagadougou and its surroundings. In order to assess the incidence and allelic frequencies of the main hemoglobinopathies in newborns in Burkina Faso, we conducted a cross-sectional study from 2015 to 2019 in four hospitals. The study included babies of both sexes, regardless of ethnic group and parents’ hemoglobin status. It was a newborn screening and hemoglobin variants were detected using isoelectric focusing on cord blood samples and confirmed using hemoglobin electrophoresis by high-performance liquid chromatography. The proportions and cumulative incidences of the different hemoglobinopathies were computed. Hardy-Weinberg equilibrium law was applied to calculate genotypic and allelic frequencies. The significant level was p < 0.05. Out of 11,337 newborns included, 47.8% were males and 60.2% were from Bobo-Dioulasso. Abnormal hemoglobin was found in 27.1%, representing a cumulative incidence of 1:4 newborns. The incidence of SCD was 1.9% (1:53 newborns) with 27.9% of homozygous SS. Homozygous CC and compound heterozygous Cβ-Thalassemia accounted for 1.1%. SCD cases were 1.51 times higher in Bobo-Dioulasso (OR = 1.51;95% CI [1.09 - 2.10]: p = 0.013). The observed genotype frequencies were significantly different from the expected ones (p 0.001). The βS and βC alleles represented 5.1 and 9.9%, respectively. This study showed a high incidence of hemoglobinopathies. Such results raise the question of control strategies for these hemoglobinopathies in our country.

Intragenic and intergenic sequences regulating the expression of the 5'-to-5' linked adult α-and β-globin genes from large yellow croaker Pseudosciaena crocea

One adult α-globin gene and one β-globin gene have been cloned from the large yellow croaker Pseudosciaena crocea. Linkage analysis indicated that the α- and β-globin genes were oriented head-to-head relative to each other. To identify the regulatory elements present in the intergenic and intragenic regions of the globin complex, the intergenic region alone or together with the β-globin gene first intron was cloned into the luciferase-reporter vector pGL3-Basic respectively, and the chimeric constructs were tran- siently transfected into Vero cells and primary fish erythrocytes. The intergenic region cannot support the high-level expression of luciferase. However, the promoter activity of the intergenic region was strongly stimulated by the positive regulatory elements （PRE） located in the β-globin gene intron 1. Thus, it is proposed that the intergenic promoters and intragenic PRE were necessary for the effective expression of the linked α- and β-globin genes.

Identification and characterization of adult alpha-and beta-globin genes and their genomic arrangement in Pseudosciaena crocea

The α- and β-globin genes from Pseudosciaena crocea were cloned by rapid amplification of cDNA 3 ＇-end （ 3 ＇-RACE）. The cDNA of the α-globin is 595 bp with the ATG start codon located at Position 37, the TAA stop codon at Position 469 and the AATAAA polyadenylation signal at Position 560, which codifies 145 amino acids. The entire open reading frame of the β-globin gene is 447 bp long, which encodes 148 amino acids. Amino acid identity of the α- globin or β-globin gene compared with those reported in other fish species, ranged from 31.9% to 76.4%. When comparing with human α- and β-globins, three important alterations in the structural regions can be noted： ct39 Thr→Gln, α113 His→Tyr and β117 His→Lys. The α-globin has a unique inserted amino acid residue in the 47th position. To understand the process of globin gene duplication and identify the regulatory elements present in the intergenic and intragenic regions of globin genes, the genomic arrangement of α- and β-globin genes was investigated. The results showed that the orientation of the two genes was head-to-head relative to each other. The intergenic region between the translation initiation codons of the linked α- and β-globin genes contains classical promoter elements and the length of it is much shorter than that reported in other fish.

Application of α-globin 3′hypervariable region to gene diagnosis of adult polycystic kidney disease

Seventy-four members from 9 adult polycystic kidney disease(APKD)familieswere analysed with Southern blot and 3′hypervariable region/Pvu Ⅱ,3′HVR/Bgl ⅡRFLPs.The results showed that 3′ HVR fragments were highly polymorphic.Theheterozygote frequencies of Pvu Ⅱ,Bgl Ⅱ and PvuⅡ+Bg1Ⅱ fragments were 92%,84.7%and 98.6%,respectively.The maximum lod score for linkage between 3′HVR and APKDwas 9.71 at a recombination fraction 0.045.We successfully applied 3′HVR probe to thegene diagnosis of 17 symptomatic patients and 7 patients in the presymptomatic stage.

Retroviral mediated human β-globin gene transfer and expression in vitro

Retroviral mediated gene transfer of humanglobin gene into hematopoietic stem cells is apromising approach for thalassemia gene therapy.Major problem of the transferred globin gene was lowlevel expression of the gene with its proximal cis-acting sequence. The locus control region (LCR) ofthe human β-globin gene cluster consists of four majorDNase I hypersensitive sites (HS). When linked

Trans-acting factors from the human fetal liver bindingto the human ε-globin gene silencer

The developmental stage-specific silencing of the human ε-globin gene during embryonic life is controlled, inpart, by the silencer (-392bp～-177bp) upstream of thisgene. In order to elucidate its role, the nuclear extractfrom the human fetal liver has been prepared and the interactions between trans-acting factors and this silencerelement have been examined. By using DNasel footprinting assay, a major protected region from -278bp to -235bpwithin this silencer element was identified. Furthermore,we found in gel mobility shift assay and Southwestern blotting assay that there were at least four trans-acting factors (MW ≈ 32, 28, 26 and 22kD) in the nuclear extractisolated from the human fetal liver, which could specifically bind to this region. Our results suggested that thesetrans-acting factors might play an important role in silencing the human embryonic ε-globin gene expression at thefetal stage through the interactions with this silencer.

Chromatin-binding in vivo of the erythroid kruppel-like factor,EKLF,in the murine globin loci

EKLF 是一 erythroid 特定，锌为在在权威的系的 erythroid 房间的基因的哺乳动物的贝它滴的激活的包含手指的抄写因素必需品。我们准备了对西方的弄污和免疫降水(IP ) 质量合适的 polyclonal 反老鼠 EKLF 抗体，并且使用了它在老鼠 erythroid 开发期间定义 EKLF 蛋白质的表示模式。我们也为 chromatin-immunoprecipitation (薄片) 使用了这抗体试金。EKLF 被发现以一种 DMSO 可诱导的方式在老鼠 erythroleukemia 房间(MEL ) 在老鼠 beta-major-globin 倡导者和 beta-LCR 的 HS2 地点在 vivo 绑。象三另外的蛋白质一样的 EKLF 的 导致DMSO 的绑定，也就是 RNA 聚合酶 II ，乙酰 ated 嘘一 H3 ，和 methylated 嘘一 H3 ，没在 CB3 被废除，但是显著地降低了，一根 导出MEL 的房间线与 p45/NF-E2 空表示，在 loci 为哺乳动物的滴的激活需要的一个 充实erythroid 的因素。有趣地，在 vivo 的 EKLF 的绑定也在地点在鼠标象 alpha 一样滴被检测，在成年高山哈在倡导者和它的远在上游的规章的元素 alpha-MRE (HS26 ) 的滴。这研究提供直接证据为在在在基因的像贝它的滴聚类的老鼠的主要规章的元素的 vivo EKLF 有约束力数据也在基因规定在哺乳动物的滴关于 EKLF 染色质相互作用的角色有有趣的含意。

PREDOMINANT EXPRESSION OF HUMAN Aγ-IN CONTRAST WITH β-GLOBIN GENE IN MEL CELLS TRANSFECTED WITH THE CONSTRUCT μLCRAγψβδ

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A stage-specific protein factor binding to a CACCC motif in both human β-globin gene promoter and 5'-HS2region

The DNasel hypersensitive site 2 (HS2) of human β-globin locus control region (LCR) is required fOr the high level expression of human d-globin genes. In the present study, a stage-specific protein factor (LPF-β) was identified in the nuclear extract prepared from mouse fetal liver at d 18 of gestation, which could bind to the HS2 region of humanβ-globin LCRt We also found that the shift band of LPF-βfactor could be competed by humanβ-globin promoter. However, it couldn’t be competed by human E-globin promoter or by human Aβ-globin promoter. Furthermore, our data demonstrated that the binding-sequence of LPF-d factor is 5’CACACCCTA 3’,which is located at the HS2 region ofβ-LCR (from -10845 to -10853 bp) and humanβ-globin promoter (from -92 to -84 bp). We speculated that these regions containing the CACCC box in both the humallβ-globin promoter and HS2 might function as stage selector elements in the regulation of humanβd-globin switching and the LPF-βfactor might be a stage-specific protein factor involved in the regulation of humanβ-globin gene expression.

Identification of the development stage-specific factors in mouse fetal liver binding to the human β-globin gene promoter

In order to elucidate the molecular mechanisms of globin gene expression during embryonic development, the nuclear extracts from mouse hematopoietic tissue at different stages of development have been prepared. By using DNase I footprinting and gel mobility shift assays, the binding of protein factors in these extracts to the human βglobin promoter was analyzed. The differences in the binding patterns of protein factors during development were observed. An erythroid-specific and stage-specific nuclear protein in the nuclear extract from d 18 mouse fetal liver was identified, which can bind to the sequence (from -66bp to -90bp) of human β-globin promoter. We therefore speculate that the function of this cis-acting element may be similar to stage selector element (SSE) in chieken βA- promoter.

ISOBUTYRAMIDE ACTIVATES TRANSCRIPTION OF HUMAN FETAL γ-AND MURINE EMBRYONIC εy-GLOBIN GENES

Objective. To examine the effect of isobutyramide synthesized in our laboratory on human and murine globin gene expression and to test cell toxicity ofthe drug.Methods. MEL cells were transfected with the recombinant construct μLCRAγψβδβand the stable transformants were cultured in the medium with different concentrations of isobutyramide. The experimental mice and rabbit were injected with different doses of isobutyramide. The globin mRNAs were analyzed by RNase protection assay. The hematological toxicity and electrolyte toxicity ofthe drug were tested.Results. An inducible and dose dependent expression of the human γ , β and mouse α globin gene was observed in the transfected MEL cells. The induction of the human γ globin gene is significant stronger than that of the β globin gene. With 2.5～5 mmol/L isobutyramide, the induction of the human γ globin gene is even more effective than that of mouse α globin gene. After a 15 day injection under the doses of 500～900mg·kg-1·d-1, the level of the mouse embryonic εy globin mRNA could be significantly induced up to 3～4 fold of that of uninjected controls. The changes of hemoglobin(Hb), RBC, hematocrit(HCT), WBC, derived from mice injected with different doses of isobutyramide at the interval of 24 hours for 2～4 weeks, were generally within the normal range. In rabbits injected with isobutyramide in the same regiment for 2 weeks, the concentration of blood K+, Na+, Cl-and CO2 were all within normal range and serum ionic osmotic pressure remained stable as well. Conclusion. Our results suggested that isobutyramide is a weak inducer ofcell differentiation, but it can selectively activate transcription of human γ globin gene at a certain degree, and it can act on early stages of erythroid progenitor differentiation in adult mice and activate transcription of embryonic εy-globin gene and have no hematological toxicity. Our results have further proved the potential value of isobutyramide in treatment of β-thalassemia and sickle cell disease.

Identification of a NF-кB site in the negative regulatory element (ε-NRAII) of human ε-globin gene and its binding protein NF-кB p50 in the nuclei of K562 cells

The developmental control of the human e-globin gene expression is mediated by transcription regulatory elements in the 5’ flanking DNA of this gene. Sequence analysis has revealed a DNA motif (GGGGAATTTGCT) similar to NF-кB consensus sequence resides in the negative regulatory element (-3028bp～ -2902bp, termed ε-NRAII) 5’ to the cap site of this gene. NRF DNA fragment (-3010bp～ -2986bp) containing the NF-кB motif similar sequence was synthesized and used in electrophoresis mobility shift assay (EMSA) and competitive analysis. Data showed that a protein factor from nuclear extracts of K562 cells specifically interacted with NRF DNA fragment. The synthetic NF DNA fragment (containing NF-кB consensus sequence) could competed for the protein binding, but MNF DNA fragment (mutated NF-кB motif) could not, suggesting that the binding protein is a member of NF-кB/Rel family. Western blot assay demonstrated that the molecular weight of NF-кB protein in the nuclei of K562 cells is 50ku. We suggested that NF-кB p50 may play an important role in the regulation of human c-globin gene expression.

Proteins binding to the 5'-flanking regulatory elements of the human β-globin gene^1

The binding of nuclear proteins prepared from mouse erythroid tissue in different developmental stages to the 5'-flanking regulatory elements of human β-globin gene,two negative control regions(NCR1,-610to-490 bp;NCR2,-338,to-233bp),was identified.Two stage specific protein factors corresponding to embryonic and fetal stages were found to be capable of binding to NCR2.These data provided evidence that the cis acting elements of the 5'-flanking region might be involved in the developmental control of β-globin gene and NCR2 might be responsible in art for the silence of β-glolbin gene in the embryonic and fetal stages.

The 5'-flanking cis-acting elements of the human ε-globin gene associates with the nuclear matrix and binds to the nuclear matrix proteins

The nucleax mains attachment regions(MARs) and the binding nuclear matrix proteins in the 5’-flalildng cisacting elements of the humanε-globin gene have been examined. Using in vitro DNA-matrix binding assay,it has been shown that the positive stage-specific regulatory element (ε-PREII, -446bp-419bp) upstream of this gene could specifically associate with the nuclear matrix from K562 cells, indicating thatε-PREII mad be an erythroidspecilic facultstive MAR. In gel mobility shift assay and Southwestern blotting assal an eothroid-specific nuclear matrix protein (ε-NMPk) in K562 cells has been revealed to bind to this positive regulatory element (E-PREII). Furthermore, we demonstrated that the silencer (-392hp -177bp) uP8tream of the humanε-globin gene could associate with the nuclear matrices from K562, HEL and Raji cells. In addition, the nucleax matrix proteins prepared from these three cell lines could also bind to this silencer, suggesting that this silencer element linght be a constitutive nuclear mains attachment region (constitutive MAR). Our results demonstrated that the nucleax madrid and nuclear mains proteins lxilght play an important role in the regulation of the human 5-globin gene expression.

Studies on DNA-protein interactions in the upstream regulatory region of the human ε-globin gene promoter

The erythroid- and developmental stage-specific expression of the human ε-globin gene is controlled, in part,by the 5’-flanking DNA sequence of this gene. In the present study, we have used DNA-protein binding assays to identify trans-acting factors which regulate the temporal expression of the human ε-globin gene during development. Using gel mobility shift assays and DNasel footprinting assays, a nuclear protein factor (termed ε-SSF1) in the nuclear extracts from mouse haematopoietic tissues at d 11 and d 13 of gestation was identified. It could specifically bind to the positive control region (between -535 and -453bp) of the human ε-globin gene. We speculated that the E-SSF1 might be an erythroid- and developmental stage-specific activator. In addition, we found another nuclear protein factor (termed ε-R1) in the nuclear extract from mouse fetal liver at d 18 of gestation, which could strongly bind to the silencer region (between -392 and -177bp) of this gene. Therefore, we speculated that the ε-R1 might be an erythroid- and developmental stagespecific repressor. Our data suggest that both ε-SSF1 and ε-R1 might play important roles in developmental regulation of the human ε-globin gene expression during the early embryonic life. On the other hand, we observed that the binding patterns of nuclear proteins from three cell lines (K562, HEL and Raji) to these regulatory regions were partially different. These results suggest that different trans-acting factors in K562, HEL and Raji cells might be responsible for activating or silencing the human ε-globin gene in three different cell lines.

The interaction between the human β-globin locus control region and nuclear matrix

Our previous study showed that hydroxyurea (Hu) could induce HEL cells to express human β-globin gene. However the molecular mechanisms by which the expression of β-globin gene is activated and regulated are poorly understood. Here we show that the binding patterns between the core DNA sequences (HS2 core sequence -10681～ -10971 bp , HS3 core sequence -14991～ -14716 bp and HS4 core sequence -18586～ -18306 bp) of DNase I hypersensitive sites in the human/3-globin LCR and nuclear matrix proteins isolated from Hu induced and uninduced HEL cells are quite different. Results demonstrated that nuclear matrix proteins might play important roles in regulating the expression of human β-like globin genes through their interaction with HSs (HS2,HS3 and HS4 core sequences) in the LCR. Moreover, the results obtained from the in vitro DNA-matrix binding assay showed that the core DNA sequences of DNase I hypersensitive sites (HS2, HS3 and HS4) were unable to bind to the nuclear matrix isolated from uninduced HEL cells; in addition, HS2 core DNA sequence was capable of binding to the nuclear matrix prepared from Hu-induced HEL cells, while both HS3 and HS4 core DNA sequences could not do so. Results indicated that the HS2 core DNA sequence may be a functional MAR (matrix attachment region). We suggest that the HS2 core DNA sequence binding to the nuclear matrix in Hu-induced HEL cells may open the structure of chromatin to make the LCR accessible to the promoter of β-globin gene and to promote its transcription.