Bernard G. Forget

The structure and evolution of the human β-globin gene family

Argiris Efstratiadis Department of Biological Chemistry Harvard Medical School Boston, Massachusetts 02115 James W. Posakony, Tom Maniatis, Richard M. Lawn* and Catherine O’Connell+ Division of Biology California Institute of Technology Pasadena, California 91125 Richard A. Spritz, Jon K. DeRiel,# Bernard G. Forget and Sherman M. Weissman Departments of Genetics and Internal Medicine Yale University School of Medicine New Haven, Connecticut 06510 Jerry L. Slightom, Ann E. Blechl and Oliver Smithies Laboratory of Genetics University of Wisconsin Madison, Wisconsin 53706 Francisco E. Baralle, Carol C. Shoulders and Nicholas J. ProudfootQ MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 2QH, England Summary We present the results of a detailed comparison of the primary structure of human p-like globin genes and their flanking sequences. Among the se- quences located 5’ to these genes are two highly conserved regions which include the sequences ATA and CCAAT located 31 2 1 and 77 + 10 bp, respectively, 5’ to the mRNA capping site. Similar sequences are found in the corresponding locations in most other eucaryotic structural genes. Calcula- tion of the divergence times of individual @like globin gene pairs provides the first description of the evolutionary relationships within a gene family based entirely on direct nucleotide sequence com- parisons. In addition, the evolutionary relationship of the embryonic e-globin gene to the other human P-like globin genes is defined for the first time. Finally, we describe a model for the involvement of short direct repeat sequences in the generation of deletions in the noncoding and coding regions of B-like globin genes during evolution.

Molecular Basis of Hereditary Persistence of Fetal Hemoglobin

Abstract: Increased levels of fetal hemoglobin (HbF) can ameliorate the clinical course of inherited disorders of β‐globin gene expression, such as β thalassemia and sickle cell anemia. In a group of disorders called hereditary persistence of fetal hemoglobin (HPFH), expression of the γ‐globin gene of HbF persists at high levels in adult erythroid cells. Molecular studies of the HPFH syndromes have identified several important regulatory elements for the normal pattern of γ‐globin gene expression. Deletion as well as nondeletion types of HPFH have been identified. The nondeletion types of HPFH are characterized by the presence of point mutations, in the promoter region of one or another γ‐globin gene, that are thought to alter interactions between various transcription factors and the promoter. The deletion types of HPFH are thought to deregulate the normal developmental pattern of γ‐globin gene expression due to the juxtaposition of normally distant cis‐acting factors into the vicinity of the γ genes. These findings have provided us with a more sophisticated understanding of the molecular basis for the persistent γ‐gene expression in these syndromes and point to certain strategies for potential future attempts at gene therapy for β‐globin gene disorders.

RNA of low molecular weight in KB cells infected with adenovirus type 2

Chromatographic analysis on methylated albumin—kieselguhr columns of newly formed, radioactive RNA from KB cells infected with adenovirus type 2 revealed an unusual radioactive component which was eluted following 4 s RNA. This RNA was present predominantly in the 100,000 g ribosomal supernatant cell fraction, and was distinguished from 4 s, 16 s and 28 s RNAs on the basis of its behavior on methylated albumin columns, base composition, sedimentation velocity and behavior on Sephadex G100 columns. This RNA component has certain characteristics in common with a “5 s” RNA associated with ribosomes from uninfected KB cells and a variety of other organisms. The effect of deoxy-fluorouridine and actinomycin D on the metabolism of this unusual RNA suggests that DNA synthesis and transcription of DNA into RNA are required for its formation.

Reverse transcription and direct amplification of cellular RNA transcripts by Taq polymerase.

We report the ability of Taq polymerase to directly transcribe RNA templates in vitro. We have made use of this finding to develop a single-step protocol for amplification of RNA transcripts. The method was shown to require only subnanogram amounts of total cellular RNA as starting material. A microassay was developed in which RNA can be extracted from one drop of blood or 1000 cultured cells, and analyzed for the expression of a specific gene.

Marrow Stem Cells Shift Gene Expression and Engraftment Phenotype with Cell Cycle Transit

We studied the genetic and engraftment phenotype of highly purified murine hematopoietic stem cells (lineage negative, rhodamine-low, Hoechst-low) through cytokine-stimulated cell cycle. Cells were cultured in interleukin (IL)-3, IL-6, IL-11, and steel factor for 0 to 48 h and tested for engraftment capacity in a lethally irradiated murine competitive transplant model. Engraftment showed major fluctuations with nadirs at 36 and 48 h of culture and recovery during the next G1. Gene expression of quiescent (0 h) or cycling (48 h) stem cells was compared with lineage positive cells by 3′ end PCR differential display analysis. Individual PCR bands were quantified using a 0 to 9 scale and results were visually compared using color-coded matrices. We defined a set of 637 transcripts expressed in stem cells and not expressed in lineage positive cells. Gene expression analyzed at 0 and 48 h showed a major shift from “stem cell genes” being highly expressed at 0 h and turned off at 48 h, while “cell division” genes were turned on at 48 h. These observations suggest stem cell gene expression shifts through cell cycle in relation to cell cycle related alterations of stem cell phenotype. The engraftment defect is related to a major phenotypic change of the stem cell.

Complete nucleotide sequence of the human δ-globin gene

Abstract We present the complete nucleotide sequence of the human δ-globin gene. The general DNA sequence organization of the δ-globin gene is similar to that of other known globin genes. We have been unable to identify unambiguously the structural basis of the low level of expression characteristic of the δ-globin gene.

An Alternate Promoter Directs Expression of a Truncated, Muscle-specific Isoform of the Human Ankyrin 1 Gene

Ankyrin 1, an erythrocyte membrane protein that links the underlying cytoskeleton to the plasma membrane, is also expressed in brain and muscle. We cloned a truncated, muscle-specific ankyrin 1 cDNA composed of novel 5′ sequences and 3′ sequences previously identified in the last 3 exons of the human ankyrin 1 erythroid gene. Northern blot analysis revealed expression restricted to cardiac and skeletal muscle tissues. Deduced amino acid sequence of this muscle cDNA predicted a peptide of 155 amino acids in length with a hydrophobic NH2 terminus. Cloning of the corresponding chromosomal gene revealed that the ankyrin 1 muscle transcript is composed of four exons spread over ∼10 kilobase pairs of DNA. Reverse transcriptase-polymerase chain reaction of skeletal muscle cDNA identified multiple cDNA isoforms created by alternative splicing. The ankyrin 1 muscle promoter was identified as a (G + C)-rich promoter located >200 kilobase pairs from the ankyrin 1 erythroid promoter. An ankyrin 1 muscle promoter fragment directed high level expression of a reporter gene in cultured C2C12 muscle cells, but not in HeLa or K562 (erythroid) cells. DNA-protein interactions were identified in vitro at a single Sp1 and two E box consensus binding sites contained within the promoter. A MyoD cDNA expression plasmid transactivated an ankyrin 1 muscle promoter fragment/reporter gene plasmid in a dose-dependent fashion in both HeLa and K562 cells. A polyclonal antibody raised to human ankyrin 1 muscle-specific sequences reacted with peptides of 28 and 30 kDa on immunoblots of human skeletal muscle.

Structure and Organization of the Human Ankyrin-1 Gene BASIS FOR COMPLEXITY OF PRE-mRNA PROCESSING

Ankyrin-1 (ANK-1) is an erythrocyte membrane protein that is defective in many patients with hereditary spherocytosis, a common hemolytic anemia. In the red cell, ankyrin-1 provides the primary linkage between the membrane skeleton and the plasma membrane. To gain additional insight into the structure and function of this protein and to provide the necessary tools for further genetic studies of hereditary spherocytosis patients, we cloned the human ANK-1 chromosomal gene. Characterization of theANK-1 gene genomic structure revealed that the erythroid transcript is composed of 42 exons distributed over ∼160 kilobase pairs of DNA. Comparison of the genomic structure with the protein domains reveals a near-absolute correlation between the tandem repeats encoding the membrane-binding domain of ankyrin with the location of the intron/exon boundaries in the corresponding part of the gene. Erythroid stage-specific, complex patterns of alternative splicing were identified in the region encoding the regulatory domain of ankyrin-1. Novel brain-specific transcripts were also identified in this region, as well as in the “hinge” region between the membrane-binding and spectrin-binding domains. Utilization of alternative polyadenylation signals was found to be the basis for the previously described, stage-specific 9.0- and 7.2-kilobase pair transcripts of theANK-1 gene.

Defect in messenger RNA for human hemoglobin synthesis in beta thalassemia

Functional messenger RNA for human hemoglobin synthesis was prepared from reticulocyte lysates of patients with homozygous beta thalassemia and sickle cell anemia. The messenger RNA stimulated the synthesis of human globin chains by a cell-free system derived from Krebs mouse ascites cells. In the presence of beta thalassemia messenger RNA, the system synthesized much less beta chain than alpha chain whereas in the presence of sickle cell anemia messenger RNA, nearly equal amounts of alpha and beta chains were synthesized. The beta/alpha synthetic ratios obtained in the cell-free system were similar to those obtained by incubating intact beta thalassemia and sickle cell anemia reticulocytes in the presence of radioactive leucine. The experiments provide direct evidence of a defect in messenger RNA for beta chains as a cause for the decreased synthesis of beta chains observed in beta thalassemia.

Absence of messenger RNA and gene DNA for β-globin chains in hereditary persistence of fetal hemoglobin

The relative amounts of alpha-amd beta-globin mRNA and globin gene DNA were measured in reticulocyte RNA and lymphocyte DNA of an individual with homozygous hereditary persistence of fetal hemoglobin whose red blood cells contain 100% fetal hemoglobin (hb F: alpha2gamma2.) Molecular hybridization assays used as probes full-length DNA copies of human alpha- and beta-globin messenger RNA. The results of these hybridization assays demonstrated the expected amounts of alpha-globin mRNA and gene DNA, but absence of beta-globin mRNA and absence of beta-globin gene DNA. In the individual studied, hereditary persistence of fetal hemoglobin is associated with total deletion of the beta-globin structural gene.