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Pena R, Lopes P, Gaspar G, Miranda A, Faustino P. Ancestry of the major long-range regulatory site of the α-globin genes in the Portuguese population with the common 3.7 kb α-thalassemia deletion. Mol Biol Rep 2024; 51:612. [PMID: 38704770 PMCID: PMC11070386 DOI: 10.1007/s11033-024-09530-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 04/05/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND The α-Major Regulatory Element (α-MRE), also known as HS-40, is located upstream of the α-globin gene cluster and has a crucial role in the long-range regulation of the α-globin gene expression. This enhancer is polymorphic and several haplotypes were identified in different populations, with haplotype D almost exclusively found in African populations. The purpose of this research was to identify the HS-40 haplotype associated with the 3.7 kb α-thalassemia deletion (-α3.7del) in the Portuguese population, and determine its ancestry and influence on patients' hematological phenotype. METHODS AND RESULTS We selected 111 Portuguese individuals previously analyzed by Gap-PCR to detect the presence of the -α3.7del: 50 without the -α3.7del, 34 heterozygous and 27 homozygous for the -α3.7del. The HS-40 region was amplified by PCR followed by Sanger sequencing. Four HS-40 haplotypes were found (A to D). The distribution of HS-40 haplotypes and genotypes are significantly different between individuals with and without the -α3.7del, being haplotype D and genotype AD the most prevalent in patients with this deletion in homozygosity. Furthermore, multiple correspondence analysis revealed that individuals without the -α3.7del are grouped with other European populations, while samples with the -α3.7del are separated from these and found more closely related to the African population. CONCLUSION This study revealed for the first time an association of the HS-40 haplotype D with the -α3.7del in the Portuguese population, and its likely African ancestry. These results may have clinical importance as in vitro analysis of haplotype D showed a decrease in its enhancer activity on α-globin gene.
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Affiliation(s)
- Rita Pena
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, Lisboa, 1649-016, Portugal
| | - Pedro Lopes
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, Lisboa, 1649-016, Portugal
| | - Gisela Gaspar
- Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal
| | - Armandina Miranda
- Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal
| | - Paula Faustino
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, Lisboa, 1649-016, Portugal.
- Grupo Ecogenética e Saúde Humana, Faculdade de Medicina, Instituto de Saúde Ambiental, Universidade de Lisboa, Lisboa, Portugal.
- Laboratório Associado TERRA, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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2
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Nie H, Crooijmans RPMA, Bastiaansen JWM, Megens HJ, Groenen MAM. Regional regulation of transcription in the chicken genome. BMC Genomics 2010; 11:28. [PMID: 20074332 PMCID: PMC2817690 DOI: 10.1186/1471-2164-11-28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 01/14/2010] [Indexed: 12/02/2022] Open
Abstract
Background Over the past years, the relationship between gene transcription and chromosomal location has been studied in a number of different vertebrate genomes. Regional differences in gene expression have been found in several different species. The chicken genome, as the closest sequenced genome relative to mammals, is an important resource for investigating regional effects on transcription in birds and studying the regional dynamics of chromosome evolution by comparative analysis. Results We used gene expression data to survey eight chicken tissues and create transcriptome maps for all chicken chromosomes. The results reveal the presence of two distinct types of chromosomal regions characterized by clusters of highly or lowly expressed genes. Furthermore, these regions correlate highly with a number of genome characteristics. Regions with clusters of highly expressed genes have higher gene densities, shorter genes, shorter average intron and higher GC content compared to regions with clusters of lowly expressed genes. A comparative analysis between the chicken and human transcriptome maps constructed using similar panels of tissues suggests that the regions with clusters of highly expressed genes are relatively conserved between the two genomes. Conclusions Our results revealed the presence of a higher order organization of the chicken genome that affects gene expression, confirming similar observations in other species. These results will aid in the further understanding of the regional dynamics of chromosome evolution. The microarray data used in this analysis have been submitted to NCBI GEO database under accession number GSE17108. The reviewer access link is: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=tjwjpscyceqawjk&acc=GSE17108
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Affiliation(s)
- Haisheng Nie
- Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, 6709 PG, Wageningen, the Netherlands
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3
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Klochkov D, Rincón-Arano H, Ioudinkova ES, Valadez-Graham V, Gavrilov A, Recillas-Targa F, Razin SV. A CTCF-dependent silencer located in the differentially methylated area may regulate expression of a housekeeping gene overlapping a tissue-specific gene domain. Mol Cell Biol 2006; 26:1589-97. [PMID: 16478981 PMCID: PMC1430243 DOI: 10.1128/mcb.26.5.1589-1597.2006] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The tissue-specific chicken alpha-globin gene domain represents one of the paradigms, in terms of its constitutively open chromatin conformation and the location of several regulatory elements within the neighboring housekeeping gene. Here, we show that an 0.2-kb DNA fragment located approximately 4 kb upstream to the chicken alpha-globin gene cluster contains a binding site for the multifunctional protein factor CTCF and possesses silencer activity which depends on CTCF binding, as demonstrated by site-directed mutagenesis of the CTCF recognition sequence. CTCF was found to be associated with this recognition site in erythroid cells but not in lymphoid cells where the site is methylated. A functional promoter directing the transcription of the apparently housekeeping ggPRX gene was found 120 bp from the CTCF-dependent silencer. The data are discussed in terms of the hypothesis that the CTCF-dependent silencer stabilizes the level of ggPRX gene transcription in erythroid cells where the promoter of this gene may be influenced by positive cis-regulatory signals activating alpha-globin gene transcription.
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Affiliation(s)
- Denis Klochkov
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology of the Russian Academy of Sciences, 34/5 Vavilov Street, 117334 Moscow, Russia
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4
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Nakagawa T, Guichard A, Castro CP, Xiao Y, Rizen M, Zhang HZ, Hu D, Bang A, Helms J, Bier E, Derynck R. Characterization of a human Rhomboid homolog, p100hRho/RHBDF1, which interacts with TGF-α family ligands. Dev Dyn 2005; 233:1315-31. [PMID: 15965977 DOI: 10.1002/dvdy.20450] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The activity of the TGF-alpha-like ligand Spitz in Drosophila depends on Rhomboid, a seven-transmembrane spanning protein that resides in the Golgi and acts as a serine protease to cleave Spitz, thereby releasing the soluble ligand. Several rhomboids in Drosophila have been implicated in the processing of TGF-alpha-like ligands, and consequent EGF receptor activation. The larger number of TGF-alpha-like ligands in vertebrates raises the possibility that they too might be subject to regulation by rhomboid-like proteins. We present the cDNA cloning and polypeptide sequence of an atypically long human rhomboid, which, based on the absence of critical residues for serine protease activity, is not predicted to act as a serine protease. We examined its tissue distribution, in comparison with TGF-alpha and the TGF-alpha-related protein HB-EGF, and the EGF/TGF-alpha receptor, in mouse embryo. This rhomboid, named p100(hRho) or RHBDF1, is a seven-transmembrane protein with a long N-terminal cytoplasmic extension that comprises half of the polypeptide sequence, and is found in the endoplasmic reticulum and Golgi, but not on the cell surface. It is expressed as two forms with different lengths, forms dimers and interacts with TGF-alpha ligands through a luminal interaction with the EGF core ectodomain. Finally, we evaluated the function of p100(hRho)/RHBDF1 in Drosophila, demonstrating that the short, but not the full-length form has functional activity. The characterization of this protein extends our understanding of the rhomboid family of regulatory proteins.
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Affiliation(s)
- Takatoshi Nakagawa
- Department of Cell and Tissue Biology, Program in Cell Biology, University of California at San Francisco, San Francisco, California 94143-0512, USA
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5
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Gribnau J, Hochedlinger K, Hata K, Li E, Jaenisch R. Asynchronous replication timing of imprinted loci is independent of DNA methylation, but consistent with differential subnuclear localization. Genes Dev 2003; 17:759-73. [PMID: 12651894 PMCID: PMC196021 DOI: 10.1101/gad.1059603] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genomic imprinting in mammals marks the two parental alleles resulting in differential gene expression. Imprinted loci are characterized by distinct epigenetic modifications such as differential DNA methylation and asynchronous replication timing. To determine the role of DNA methylation in replication timing of imprinted loci, we analyzed replication timing in Dnmt1- and Dnmt3L-deficient embryonic stem (ES) cells, which lack differential DNA methylation and imprinted gene expression. Asynchronous replication is maintained in these ES cells, indicating that asynchronous replication is parent-specific without the requirement for differential DNA methylation. Imprinting centers are required for regional control of imprinted gene expression. Analysis of replication fork movement and three-dimensional RNA and DNA fluorescent in situ hybridization (FISH) analysis of the Igf2-H19 locus in various cell types indicate that the Igf2-H19 imprinting center differentially regulates replication timing of nearby replicons and subnuclear localization. Based on these observations, we suggest a model in which cis elements containing nonmethylation imprints are responsible for the movement of parental imprinted loci to distinct nuclear compartments with different replication characteristics resulting in asynchronous replication timing.
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Affiliation(s)
- Joost Gribnau
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
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6
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Harteveld CL, Muglia M, Passarino G, Kielman MF, Bernini LF. Genetic polymorphism of the major regulatory element HS-40 upstream of the human alpha-globin gene cluster. Br J Haematol 2002; 119:848-54. [PMID: 12437670 DOI: 10.1046/j.1365-2141.2002.03917.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The highly conserved 350-bp major regulatory element HS-40 (or alphaMRE) upstream of the human alpha-globin gene cluster is involved in the regulation of alpha-globin gene expression. The study of alphaMRE differences between human populations and the evolution of alphaMRE sequences in mammals may lead to a better understanding of the function and importance of this element in the regulation of expression of the downstream alpha-cluster. Denaturing gradient gel electrophoresis was used to determine the sequence heterogeneity of the alphaMRE region in 276 unrelated individuals, representing seven different populations. Furthermore, we analysed the alpha major regulatory elements of chimpanzee, orang-utan and rhesus monkeys and compared them with the equivalent human and murine sequences. Six different alphaMRE haplotypes (labelled A to F) were found in humans. Haplotype frequencies between the seven populations showed a gradual shift to a higher haplotype A distribution from west to east, being the highest in Indonesians. The African sample shows the largest divergence in haplotypes. Five out of six different haplotypes were present, three of which were exclusively found in Africans. The high prevalence of the haplotype A in humans, together with the conservation of this haplotype in apes, suggests that it is the ancestral one. The alphaMRE fragment appears to be a highly polymorphic marker, which could be used in combination with the regular markers in the alpha-cluster to extend the haplotype and to follow segregation of alpha-thalassaemia genes in population studies more accurately.
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Affiliation(s)
- Cornelis L Harteveld
- Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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7
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Yong PJ, Marion SA, Barrett IJ, Kalousek DK, Robinson WP. Evidence for imprinting on chromosome 16: The effect of uniparental disomy on the outcome of mosaic trisomy 16 pregnancies. ACTA ACUST UNITED AC 2002; 112:123-32. [PMID: 12244544 DOI: 10.1002/ajmg.10702] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although a number of infants with maternal uniparental disomy of chromosome 16 (upd(16)mat) have been reported, the evidence for imprinting on chromosome 16 is not yet conclusive. To test the hypothesis that upd(16)mat has a distinct phenotype, which would support the existence of imprinted gene(s) on chromosome 16, statistical analysis was performed on a large series (n = 83) of mosaic trisomy 16 cases with molecular determination of uniparental disomy status. The incidence of upd(16)mat was 40%, which is consistent with the expected one third from random chromosome loss during trisomy rescue (P = 0.262). In pairwise comparisons, upd(16)mat was found to be associated with fetal growth restriction (P = 0.029) and with increased risk of major malformation (RR = 1.43; P = 0.053). Regression modeling showed that the effect of upd(16)mat on fetal/neonatal weight and malformation is independent of the degree of trisomy detected in the fetus. Regression modeling to control for the degree of trisomy detected in the placenta was not possible due to limited sample size. We conclude that upd(16)mat is associated with more severe growth restriction, and possibly, with higher risk of malformation. Our hypothesis is that imprinted gene(s) exist on chromosome 16 and that abnormal expression of these gene(s) in upd(16)mat cells during development results in decreased cell proliferation. Although we do not advocate prenatal testing for upd(16), studies on the long-term outcome of upd(16)mat neonates is necessary for counseling purposes.
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Affiliation(s)
- P J Yong
- Experimental Medicine Programs, University of British Columbia, Canada
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8
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Tufarelli C, Frischauf AM, Hardison R, Flint J, Higgs DR. Characterization of a widely expressed gene (LUC7-LIKE; LUC7L) defining the centromeric boundary of the human alpha-globin domain. Genomics 2001; 71:307-14. [PMID: 11170747 DOI: 10.1006/geno.2000.6394] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have identified the first gene lying on the centromeric side of the alpha-globin gene cluster on human 16p13.3. The gene, called 16pHQG;16 (HGMW-approved symbol LUC7L), is widely transcribed and lies in the opposite orientation with respect to the alpha-globin genes. This gene may represent a mammalian heterochromatic gene, encoding a putative RNA-binding protein similar to the yeast Luc7p subunit of the U1 snRNP splicing complex that is normally required for 5' splice site selection. To examine the role of the 16pHQG;16 gene in delimiting the extent of the alpha-globin regulatory domain, we mapped its mouse orthologue, which we found to lie on mouse chromosome 17, separated from the mouse alpha-cluster on chromosome 11. Establishing the full extent of the human 16pHQG;16 gene has allowed us to define the centromeric limit of the region of conserved synteny around the human alpha-globin cluster to within an 8-kb segment of chromosome 16.
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MESH Headings
- Alternative Splicing
- Amino Acid Sequence
- Animals
- Blotting, Northern
- Blotting, Southern
- CHO Cells
- Cell Line
- Centromere/metabolism
- Centromere/ultrastructure
- Chromosomes, Human, Pair 16
- Chromosomes, Human, Pair 17
- Conserved Sequence
- Cricetinae
- Evolution, Molecular
- Exons
- Globins/chemistry
- Globins/genetics
- Humans
- Introns
- Mice
- Models, Genetic
- Molecular Sequence Data
- Protein Structure, Tertiary
- RNA Splicing
- RNA, Messenger/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Ribonucleoproteins, Small Nuclear/metabolism
- Sequence Homology, Amino Acid
- Telomere/metabolism
- Tissue Distribution
- Transcription, Genetic
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Affiliation(s)
- C Tufarelli
- MRC Molecular Haematology Unit, Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, United Kingdom
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9
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Abstract
alpha-Thalassaemias are genetic defects extremely frequent in some populations and are characterized by the decrease or complete suppression of alpha-globin polypeptide chains. The gene cluster, which codes for and controls the production of these polypeptides, maps near the telomere of the short arm of chromosome 16, within a G + C rich and early-replicating DNA region. The genes expressed during the embryonic (zeta) or fetal and adult stage (alpha 2 and alpha 1) can be modified by point mutations which affect either the processing-translation of mRNA or make the polypeptide chains extremely unstable. Much more frequent are the deletions of variable size (from approximately 3 to more than 100 kb) which remove one or both alpha genes in cis or even the whole gene cluster. Deletions of a single gene are the result of unequal pairing during meiosis, followed by reciprocal recombination. These unequal cross-overs, which produce also alpha gene triplications and quadruplications, are made possible by the high degree of homology of the two alpha genes and of their flanking sequences. Other deletions involving one or more genes are due to recombinations which have taken place within non-homologous regions (illegitimate recombinations) or in DNA segments whose homology is limited to very short sequences. Particularly interesting are the deletions which eliminate large DNA areas 5' of zeta or of both alpha genes. These deletions do not include the structural genes but, nevertheless, suppress completely their expression. Larger deletions involving the tip of the short arm of chromosome 16 by truncation, interstitial deletions or translocations result in the contiguous gene syndrome ATR-16. In this complex syndrome alpha-thalassaemia is accompanied by mental retardation and variable dismorphic features. The study of mutations of the 5' upstream flanking region has led to the discovery of a DNA sequence, localized 40 kb upstream of the zeta-globin gene, which controls the expression of the alpha genes (alpha major regulatory element or HS-40). In the acquired variant of haemoglobin H (HbH) disease found in rare individuals with myelodysplastic disorders and in the X-linked mental retardation associated with alpha-thalassaemia, a profound reduction or absence of alpha gene expression has been observed, which is not accompanied by structural alterations of the coding or controlling regions of the alpha gene complex. Most probably the acquired alpha-thalassaemia is due to the lack of soluble activators (or presence of repressors) which act in trans and affect the expression of the homologous clusters and are coded by genes not (closely) linked to the alpha genes. The ATR-X syndrome results from mutations of the XH2 gene, located on the X chromosome (Xq13.3) and coding for a transacting factor which regulates gene expression. The interaction of the different alpha-thalassaemia determinants results in three phenotypes: the alpha-thalassaemic trait, clinically silent and presenting only limited alterations of haematological parameters, HbH disease, characterized by the development of a haemolytic anaemia of variable degree, and the (lethal) Hb Bart's hydrops fetalis syndrome. The diagnosis of alpha-thalassaemia due to deletions is implemented by the electrophoretic analysis of genomic DNA digested with restriction enzymes and hybridized with specific molecular probes. Recently polymerase chain reaction (PCR) based strategies have replaced the Southern blotting methodology. The straightforward identification of point mutations is carried out by the specific amplification of the alpha 2 or alpha 1 gene by PCR followed by the localization and identification of the mutation with a variety of screening systems (denaturing gradient gel electrophoresis (DGGE), single strand conformation polymorphisms (SSCP)) and direct sequencing.
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Affiliation(s)
- L F Bernini
- Institute of Human Genetics, Medical Faculty, University of Leiden, Sylvius Laboratory, The Netherlands
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10
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Buratovich MA, Phillips RG, Whittle JR. Genetic relationships between the mutations spade and Sternopleural and the wingless gene in Drosophila development. Dev Biol 1997; 185:244-60. [PMID: 9187086 DOI: 10.1006/dbio.1997.8562] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In Drosophila melanogaster, there are cases in which gene products contributing to the same developmental event may derive from closely adjacent transcription units and may even share cis-regulatory sequences. Correct recognition of such genomic organization is central to an understanding of developmental mechanisms. The adult phenotypes of combinations between the mutations spade, Sternopleural, and wingless suggest that they are lesions in functionally related genes within the same chromosomal region. wingless mutations fail to complement the recessive mutation spade. The spade mutation, as previously shown, behaves as a lesion in a regulatory site of wingless, sited 5' to the transcription unit, and is concerned with particular postembryonic functions of wingless. While showing wingless-like phenotypes in combination with Sternopleural, even lethal alleles of wingless complement the recessive lethality of Sternopleural alleles. Mutations in Sternopleural increase the severity of wingless phenotypes in many wingless-dependent processes during postembryonic development, and this interaction can occur when the only functional copies of Sp or wg are located in either opposing chromosomes or the same chromosome. This is inconsistent with previous attempts to define Sp as a regulatory allele of wg and explain the phenotypes that result from combinations of Sp and wg by means of transvection. We have analyzed a new EMS-induced allele of Sternopleural that is more severe than the original allele, which also argues for Sp being a separate, mutable genetic locus rather than a regulatory allele of wg. Finally, we have a revertant of Sternopleural (Sp[Rv1]) that behaves as a genetic null allele of wg, but causes ventral-to-dorsal transformations in combination with wg(P), which is not observed in combinations of wg null alleles with wg(P). Because wg(P) is the result of an inversion and because inversions inhibit transvection, the increased severity observed in Sp(Rv1)/wg(P) in comparison to wg(null)/Sp(Rv1) animals cannot be explained by an absence of transvection. Therefore, the two Sternopleural mutations most reasonably define an independent gene located 3' to the wingless gene and having strong functional synergism with it.
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Affiliation(s)
- M A Buratovich
- School of Biological Sciences, University of Sussex, Falmer, Brighton, United Kingdom
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11
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López-Alãnón DM, Lopez-Fernández LA, Castañeda V, Krimer DB, Del Mazo J. H3.3A variant histone mRNA containing an alpha-globin insertion: modulated expression during mouse gametogenesis correlates with meiotic onset. DNA Cell Biol 1997; 16:639-44. [PMID: 9174168 DOI: 10.1089/dna.1997.16.639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Replacement-variant H3.3 histones have been isolated and sequenced in different eukaryotes, but no functional H3.3A gene has been characterized in the mouse so far. We have cloned an H3.3A cDNA from a mouse fetal ovary library, differentially screened with testis versus somatic cDNA probes. We showed this gene contains a region homologous to the reverse and complementary alpha-globin gene. We believe such a structure could have been generated by retroposition during the evolution of both globin and histone gene families. The sequence coding for H3.3A is 76.6% homologous to the mouse H3.3B gene at the nucleotide level and differs in only one amino acid at the protein level. The high degree of homology between these genes and the H3.3 variant histones from other eukaryotes reveals the conservation of these replication-independent class of histones throughout evolution. Analysis of gene expression reveals a developmental regulation concurrent with meiotic progression, with the highest level of transcript detection coincident with meiotic onset during both oogenesis and spermatogenesis.
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Affiliation(s)
- D M López-Alãnón
- Department of Cell and Developmental Biology, Centro de Investigaciones Biológicas (C.S.I.C.), Madrid, Spain
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12
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Bouhassira EE, Kielman MF, Gilman J, Fabry MF, Suzuka S, Leone O, Gikas E, Bernini LF, Nagel RL. Properties of the mouse alpha-globin HS-26: relationship to HS-40, the major enhancer of human alpha-globin gene expression. Am J Hematol 1997; 54:30-9. [PMID: 8980258 DOI: 10.1002/(sici)1096-8652(199701)54:1<30::aid-ajh5>3.0.co;2-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
HS-26, the mouse homologue of HS-40, is the major regulatory element of the mouse alpha-globin gene locus. Like HS-40, HS-26 is located within an intron of a house-keeping gene; comparison of the nucleotide sequences of HS-26 and HS-40 reveals conservation of the sequences and positions of several DNA binding motifs in the 5' regions of both elements (3 GATA, 2 NFE-2, and 1 CACCC sites) and the absence in HS-26 of three CACCC sites and one GATA site that are present in the 3' region of HS-40, suggesting that the two elements might not be identical. We report here that when HS-26 is linked to a 1.5 kb Pstl human alpha-globin gene fragment, it has a weak enhancer activity in induced MEL cells and in transgenic embryos, and it does not have any detectable activity in adult transgenic mice. This suggests that HS-26 does not have Locus Control Region (LCR) activity but can act as an enhancer during the embryonic life when integrated at a permissive locus. To further test the importance of HS-26 at its natural locus, we have generated embryonic stem cells and chimeric animals in which 350 bp containing HS-26 have been replaced by a neomycin resistance gene by homologous recombination. The sizes of the chimeras' red cells were then estimated by measuring forward scattering on a FacsScan apparatus in hypotonic conditions. This revealed that a fraction of the chimeric animals' red cells were smaller than normal mouse red cells and were very similar to cells from mice heterozygous for alpha-thalassemia. Density gradient analysis also suggested the presence of thalassemic cells. These results indicated that despite its lack of LCR activity, HS-26 is important for the regulation of the mouse alpha-globin gene locus.
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Affiliation(s)
- E E Bouhassira
- Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York 10461, USA
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13
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Kielman MF, Barradeau S, Smits R, Harteveld CL, Bernini LF. Characterization and localization of the mProx1 gene directly upstream of the mouse alpha-globin gene cluster: identification of a polymorphic direct repeat in the 5'UTR. Mamm Genome 1996; 7:877-80. [PMID: 8995756 DOI: 10.1007/s003359900260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The alpha-globin major regulatory element (alpha MRE) positioned far upstream of the gene cluster is essential for the proper expression of the alpha-globin genes. Analysis of the human and mouse alpha-globin Upstream Flanking Regions (alpha UFR) has identified three nonglobin genes in the order Dist1-MPG-Prox1-alpha-globin. Further characterization of the whole region indicates that the alpha MRE and several other erythroid DNase HSSs are associated with the transcription unit of the Prox1 gene. In this paper we describe the characterization and localization of the mouse Prox1 cDNA and compare it with its human homolog, the -14 gene, and another human cDNA sequence named hProx1. Our results show a strong conservation between the -14 gene and the mouse Prox1 gene with the exception of the first exon of the mProx1 gene. This exon is absent in the -14 cDNA but is present and conserved in the human Prox1 cDNA, indicating that the human -14/hProx1 gene is alternatively spliced or transcribed. The mProx1 gene encodes a predicted protein of 491 amino acids (aa) whose function is not known. In the 5'UTR of this gene, a 35-bp repeat (VNTR) is positioned, which is highly polymorphic among laboratory inbred mice (Mus domesticus). Our results strongly suggest that the mProx1 VNTR arose during the divergence of M. spretus and M. domesticus. Besides its use in evolutionary studies and positional cloning, the mProx1 VNTR might be invaluable for monitoring the expression of a transgenic mProx1 gene. The cloning of the mProx1 gene will be helpful to analyze its possible role on alpha-globin as well on MPG expression in the mouse.
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Affiliation(s)
- M F Kielman
- Department of Human Genetics, Leiden University, The Netherlands
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Zhao QZ, Liang XL, Mitra S, Gourdon G, Alter BP. Cloning and characterization of the mouse alpha globin cluster and a new hypervariable marker. Mamm Genome 1996; 7:749-53. [PMID: 8854862 DOI: 10.1007/s003359900225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A 95-kb region of the mouse genome spanning the entire alpha-globin gene cluster was isolated as overlapping cosmid clones and characterized. In addition to the embryonic (zeta) and adult (alpha) genes, the cloned contig contains the complete N-methylpurine-DNA glycosylase (MPG) gene, the alpha-globin-positive regulatory element (mHS-26), and a previously unidentified hypervariable region (named the mouse alpha-HVR). In mice, the distance between the MPG gene and mHS-26 is approximately 18 kb; between the mHS-26 and the zeta-gene, approximately 26 kb; from the zeta-gene to the 5' end of the alpha-gene, approximately 16 kb; and the two alpha-genes are separated by approximately 12 kb. In human, the corresponding distances are approximately 27 kb, approximately 40 kb, approximately 19 kb, and approximately 3 kb respectively. The alpha-HVR is located approximately 18 kb upstream of the mouse zeta-globin gene transcription start site and contains a variable copy number tandem repeat (VNTR) array of a 35-bp sequence rich in (G+C) content. The unit sequence of the HVR shares the short core sequence with the HVRs identified in the human alpha-gene cluster. Thus, this HVR may be a valuable evolutionary marker, as well as a useful genetic marker for the mouse.
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Affiliation(s)
- Q Z Zhao
- Division of Pediatric Hematology/Oncology, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas 77555-0361, USA
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Kielman MF, Smits R, Bernini LF. Structure of the mouse 3-methyladenine DNA glycosylase gene and exact localization upstream of the alpha-globin gene cluster on chromosome 11. Mamm Genome 1995; 6:499-504. [PMID: 8589517 DOI: 10.1007/bf00356165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In this paper we describe the genomic organization of the mouse 3-Methyladenine DNA Glycosylase (MPG) gene and localize three putative regulatory elements around this gene. The MPG gene plays a key role in the excision repair of methylated adenine residues and has been localized upstream of the alpha-globin gene cluster in human and mouse. The human MPG gene has been fully characterized, whereas up to now only the cDNA sequence of the mouse MPG gene had been published. Here, we describe a detailed restriction map, the intron/exon structure, the CpG-rich putative promoter sequence, and the exact localization of the mouse MPG gene with respect to the murine alpha-globin gene cluster. Our analysis reveals a remarkable different exon/intron structure of the mouse MPG gene compared with its human homolog. Two prominent DNase hypersensitive sites (HSS) were found 0.1 and 1.5 kb upstream of the coding sequence. In addition to these elements, an erythroid prominent HSS was mapped at the intron/exon boundary of the last exon. The characterization and localization of the MPG gene in mouse makes it now possible to carry out transgenic and gene targeting experiments and are essential to understand the control of gene expression of the MPG gene in particular and of the whole region in general.
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Affiliation(s)
- M F Kielman
- Department of Human Genetics, State University Leiden, The Netherlands
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Datson NA, Duyk GM, Van Ommen JB, Den Dunnen JT. Specific isolation of 3'-terminal exons of human genes by exon trapping. Nucleic Acids Res 1994; 22:4148-53. [PMID: 7937140 PMCID: PMC331902 DOI: 10.1093/nar/22.20.4148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Exon trapping is a method to functionally clone expressed sequences from genomic DNA. We have previously developed the vector system pETV-SD2, which contains only a splice donor site (SD) followed by a LacZ gene, allowing trapping of internal exons of human genes by blue-white selection. We now describe the adaptation of the same system for the efficient trapping of 3'-terminal exons, by using different RT-PCR primers in a 3' RACE reaction. The addition of a T7 promoter to the RT-PCR products derived from pETV-SD2 allows their amplification in an isothermic amplification reaction called NASBA (nucleic acid sequence-based amplification reaction) and results in a strong signal from amplified 3' exons in addition to a great reduction of non-specific background. As a test for the system, 3' exon trapping was performed using a cosmid containing the alpha-globin gene cluster on chromosome 16. The 3'-terminal exons of the human alpha 1-, zeta 2-, and theta-globin genes were trapped, as well as a correctly spliced and polyadenylated sequence in the 3' flanking region of the alpha 1-globin gene. This exon appears to belong to a previously unidentified gene within the alpha-globin gene cluster. This 3' exon trapping strategy should facilitate the cloning of genes from large genomic regions.
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Affiliation(s)
- N A Datson
- Department of Human Genetics, Leiden University, The Netherlands
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