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Pseudogenes: Four Decades of Discovery. Methods Mol Biol 2021. [PMID: 34165705 DOI: 10.1007/978-1-0716-1503-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
A pseudogene is defined as a genomic DNA sequence that looks like a mutated or truncated version of a known functional gene. Nearly four decades since their first discovery it has been estimated that between ~12,000 and ~20,000 pseudogenes exist in the human genome. Early efforts to characterize functions for pseudogenes were unsuccessful, thus they were considered functionless relics of evolutionary selection, junk DNA or genetic fossils. Remarkably, an increasing number of pseudogenes have been reported to be expressed as RNA transcripts above and beyond levels considered accidental or spurious transcription. There is emerging evidence that some expressed pseudogene transcripts have biological functions and should be defined as a subclass of functional long noncoding RNAs (lncRNA). In this introductory chapter, I briefly summarize the history and the current knowledge of pseudogenes, and highlight the emerging functions of some pseudogenes in human biology and disease. This second iteration of Pseudogenes in Methods in Molecular Biology highlights new methodological approaches to investigate this intriguing family of lncRNAs and the extent of their biological function.
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Cytogenetic markers using single-sequence probes reveal chromosomal locations of tandemly repetitive genes in scleractinian coral Acropora pruinosa. Sci Rep 2021; 11:11326. [PMID: 34059722 PMCID: PMC8167085 DOI: 10.1038/s41598-021-90580-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/13/2021] [Indexed: 02/04/2023] Open
Abstract
The short and similar sized chromosomes of Acropora pose a challenge for karyotyping. Conventional methods, such as staining of heterochromatic regions, provide unclear banding patterns that hamper identification of such chromosomes. In this study, we used short single-sequence probes from tandemly repetitive 5S ribosomal RNA (rRNA) and core histone coding sequences to identify specific chromosomes of Acropora pruinosa. Both the probes produced intense signals in fluorescence in situ hybridization, which distinguished chromosome pairs. The locus of the 5S rDNA probe was on chromosome 5, whereas that of core histone probe was on chromosome 8. The sequence of the 5S rDNA probe was composed largely of U1 and U2 spliceosomal small nuclear RNA (snRNA) genes and their interspacers, flanked by short sequences of the 5S rDNA. This is the first report of a tandemly repetitive linkage of snRNA and 5S rDNA sequences in Cnidaria. Based on the constructed tentative karyogram and whole genome hybridization, the longest chromosome pair (chromosome 1) was heteromorphic. The probes also hybridized effectively with chromosomes of other Acropora species and population, revealing an additional core histone gene locus. We demonstrated the applicability of short-sequence probes as chromosomal markers with potential for use across populations and species of Acropora.
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Protein-Coding Genes' Retrocopies and Their Functions. Viruses 2017; 9:v9040080. [PMID: 28406439 PMCID: PMC5408686 DOI: 10.3390/v9040080] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 12/11/2022] Open
Abstract
Transposable elements, often considered to be not important for survival, significantly contribute to the evolution of transcriptomes, promoters, and proteomes. Reverse transcriptase, encoded by some transposable elements, can be used in trans to produce a DNA copy of any RNA molecule in the cell. The retrotransposition of protein-coding genes requires the presence of reverse transcriptase, which could be delivered by either non-long terminal repeat (non-LTR) or LTR transposons. The majority of these copies are in a state of “relaxed” selection and remain “dormant” because they are lacking regulatory regions; however, many become functional. In the course of evolution, they may undergo subfunctionalization, neofunctionalization, or replace their progenitors. Functional retrocopies (retrogenes) can encode proteins, novel or similar to those encoded by their progenitors, can be used as alternative exons or create chimeric transcripts, and can also be involved in transcriptional interference and participate in the epigenetic regulation of parental gene expression. They can also act in trans as natural antisense transcripts, microRNA (miRNA) sponges, or a source of various small RNAs. Moreover, many retrocopies of protein-coding genes are linked to human diseases, especially various types of cancer.
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Shidhi PR, Suravajhala P, Nayeema A, Nair AS, Singh S, Dhar PK. Making novel proteins from pseudogenes. Bioinformatics 2015; 31:33-9. [PMID: 25236460 DOI: 10.1093/bioinformatics/btu615] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
MOTIVATION Recently, we made synthetic proteins from non-coding DNA of Escherichia coli. Encouraged by this, we asked: can we artificially express pseudogenes into novel and functional proteins? What kind of structures would be generated? Would these proteins be stable? How would the organism respond to the artificial reactivation of pseudogenes? RESULTS To answer these questions, we studied 16 full-length protein equivalents of pseudogenes. The sequence-based predictions indicated interesting molecular and cellular functional roles for pseudogene-derived proteins. Most of the proteins were predicted to be involved in the amino acid biosynthesis, energy metabolism, purines and pyrimidine biosynthesis, central intermediary metabolism, transport and binding. Interestingly, many of the pseudogene-derived proteins were predicted to be enzymes. Furthermore, proteins showed strong evidence of stable tertiary structures. The prediction scores for structure, function and stability were found to be favorable in most of the cases. IMPACT To our best knowledge, this is the first such report that predicts the possibility of making functional and stable proteins from pseudogenes. In future, it would be interesting to experimentally synthesize and validate these predictions.
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Affiliation(s)
- P R Shidhi
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India
| | - Prashanth Suravajhala
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India
| | - Aysha Nayeema
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India
| | - Achuthsankar S Nair
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India
| | - Shailja Singh
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India
| | - Pawan K Dhar
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India
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5
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Li W, Yang W, Wang XJ. Pseudogenes: pseudo or real functional elements? J Genet Genomics 2013; 40:171-7. [PMID: 23618400 DOI: 10.1016/j.jgg.2013.03.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/04/2013] [Accepted: 03/04/2013] [Indexed: 11/24/2022]
Abstract
Pseudogenes are genomic remnants of ancient protein-coding genes which have lost their coding potentials through evolution. Although broadly existed, pseudogenes used to be considered as junk or relics of genomes which have not drawn enough attentions of biologists until recent years. With the broad applications of high-throughput experimental techniques, growing lines of evidence have strongly suggested that some pseudogenes possess special functions, including regulating parental gene expression and participating in the regulation of many biological processes. In this review, we summarize some basic features of pseudogenes and their functions in regulating development and diseases. All of these observations indicate that pseudogenes are not purely dead fossils of genomes, but warrant further exploration in their distribution, expression regulation and functions. A new nomenclature is desirable for the currently called 'pseudogenes' to better describe their functions.
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Affiliation(s)
- Wen Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Rochon D, Siegel A. Chloroplast DNA transcripts are encapsidated by tobacco mosaic virus coat protein. Proc Natl Acad Sci U S A 2010; 81:1719-23. [PMID: 16593435 PMCID: PMC344990 DOI: 10.1073/pnas.81.6.1719] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Preparations of tobacco mosaic virus contain pseudovirions, particles resembling virions but containing host rather than viral RNA. The encapsidated host RNA was found to be composed of discrete-sized species derived from a large portion of the chloroplast genome except that very little, if any, ribosomal RNA is present. Pseudovirions contain the same chloroplast DNA transcripts as those detected in extracts from uninfected leaves, although not always in the same relative amounts. Several strains of tobacco mosaic virus were tested and all were found to contain pseudovirions, with the U2 strain containing more than the others.
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Affiliation(s)
- D Rochon
- Biology Department, Wayne State University, Detroit, MI 48202
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Abstract
Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. Rather, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity. Pseudogenes are involved in gene conversion or recombination with functional genes. Pseudogenes exhibit evolutionary conservation of gene sequence, reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes or DNA sequences that have functional roles. We first review the Drosophila literature and then extend the discussion to the various functional features identified in the pseudogenes of other organisms. A pseudogene that has arisen by duplication or retroposition may, at first, not be subject to natural selection if the source gene remains functional. Mutant alleles that incorporate new functions may, nevertheless, be favored by natural selection and will have enhanced probability of becoming fixed in the population. We agree with the proposal that pseudogenes be considered as potogenes, i.e., DNA sequences with a potentiality for becoming new genes.
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Affiliation(s)
- Evgeniy S Balakirev
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697-2525, USA.
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Clinton JM, Chansky HA, Odell DD, Zielinska-Kwiatkowska A, Hickstein DD, Yang L. Characterization and expression of the human gene encoding two translocation liposarcoma protein-associated serine-arginine (TASR) proteins. Gene 2002; 284:141-7. [PMID: 11891055 DOI: 10.1016/s0378-1119(02)00382-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Translocation liposarcoma protein (TLS)-associated serine-arginine (TASR)-1 and -2 are two newly identified serine-arginine splicing factors. Our recent studies suggest that disruption of TASR-mediated pre-mRNA splicing is involved in the pathogenesis of human leukemia and sarcomas. The mRNA transcripts for TASR-1 and -2 share an identical sequence at the 5' untranslated region (5' UTR) and in part of the coding region; however the other regions of the transcripts diverge from each other and it was not clear whether the differences resulted from alternative splicing or transcription from two distinct genes. Here we describe the assignment of both TASR cDNAs to the same 16 kb DNA segment located on chromosome 1. Despite the presence of at least three retroposed products of TASR-1 mRNA in the human genome, only the 16 kb structural TASR gene on chromosome 1 is actively transcribed. In addition, multiple polyadenylation sites and a rare U12-type intron were found within the TASR gene. Transcription initiation site of the TASR gene was determined by primer extension; analysis of the TASR promoter revealed that it lacks the TATA box but contains a GC-rich sequence. When cloned into a luciferase reporter and transfected into human cells, the TASR promoter construct generated luciferase activity that was at least 2000 fold greater than the promoterless plasmid. Northern blot analysis showed that at least five different TASR-1 and -2 transcripts are expressed in a broad range of human tissues.
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Affiliation(s)
- Jeremiah M Clinton
- Department of Orthopedics and Sports Medicine, University of Washington School of Medicine, 1660 South Columbian Way, GMR 151, Seattle, WA 98108, USA
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Satoh H, Inokuchi N, Nagae Y, Okazaki T. Molecular cloning and characterization of two sets of alpha-theta genes in the rat alpha-like globin gene cluster. Gene 1999; 230:91-9. [PMID: 10196478 DOI: 10.1016/s0378-1119(99)00055-4] [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: 10/18/2022]
Abstract
The highly heterogeneous rat hemoglobin system was investigated at the gene level. Two regions of the alpha-like globin gene cluster from a Wistar rat were isolated. Four lambda Dash recombinant clones carrying rat alpha-like globin genes were localized on two distinct gene regions. A region of approximately 16kb was found to contain the 5'-IIalpha1-psi theta 1-3' loci, and another of approximately 24kb the 5'-IIalpha2-psi theta2-psiI alpha3-3' loci. Both IIalpha1 and IIalpha2 are considered to be active, coding the IIalpha-globin chain. The nt sequences of IIalpha1 and IIalpha2 are identical except for six nt in the non-coding region. The psiI alpha3 locus is a truncated pseudogene. The putative promoter region of an alpha-like globin gene is joined directly to the third exon, homologous to that of Ialpha-globin cDNA. psi theta1 and psi theta2 are also pseudogenes, as evidenced by several deletions located in the protein-coding regions of these loci. The psi theta1 and psi theta2 loci exhibit extensive homology, but the restriction maps of these genes and their flanking regions differ considerably. Genomic Southern blot analyses of the total liver DNA from six rats showed the existence of three theta-globin-related genes, including psi theta1 and psi theta2. These results indicate that the two gene regions investigated are not allelic variants, but may be generated by block duplication. This is the first report of the existence of rodent theta-globin genes.
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Affiliation(s)
- H Satoh
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo 113, Japan.
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12
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Jellie AM, Tate WP, Trotman CN. Evolutionary history of introns in a multidomain globin gene. J Mol Evol 1996; 42:641-7. [PMID: 8662016 DOI: 10.1007/bf02338797] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Artemia hemoglobin contains two subunits that are similar or different chains of nine globin domains. The domains are ancestrally related and are presumed to be derived from copies of an original single-domain parent gene. Since the gene copies have remained in the same environment for several hundred million years they provide an excellent model for the investigation of intron stability. The cDNA for one of the two types of nine-domain subunit (domains T1-T9) has been sequenced. Comparison with the corresponding genomic DNA reveals a total of 17 intradomain introns. Fourteen of the introns are in locations on the protein that are conventional in globins of other species. In eight of the nine domains an intron corresponds to the B helix, amino acid B12, following the second nucleotide (phase 2), and in six domains a G-helix intron is located between G6 and G7 (phase 0). The consistency of this pattern is supportive of the introns having been inherited from a single-domain parent gene. The remaining three introns are in unconventional locations. Two occur in the F helix, either in amino acid F3 (phase 1) in domain T3, or between F2 and F3 (phase 0) in domain T6. The two F introns strengthen an interpretation of intron inheritance since globin F introns are rare, and in domains T3 and T6 they replace rather than supplement the conventional G introns, as though displacement from G to F occurred before that part of the gene became duplicated. It is inferred that one of the F introns subsequently moved by one nucleotide. Similarly, the third unconventional intron location is the G intron in domain T4 which is in G6, phase 2, one nucleotide earlier than the other G introns. Domain T4 is also unusual in lacking a B intron. The pattern of introns in the Artemia globin gene supports a concept of general positional stability but the exceptions, where introns have moved out of reading frame, or have moved by several codons, or have been deleted, suggest that intron displacements can occur after inheritance from an ancient source.
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Affiliation(s)
- A M Jellie
- Department of Biochemistry, University of Otago, Box 56, Dunedin, New Zealand
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Pászty C, Mohandas N, Stevens ME, Loring JF, Liebhaber SA, Brion CM, Rubin EM. Lethal alpha-thalassaemia created by gene targeting in mice and its genetic rescue. Nat Genet 1995; 11:33-9. [PMID: 7550311 DOI: 10.1038/ng0995-33] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Mutations at the alpha-globin locus are the most common class of mutations in humans, with deletion of all four adult alpha-globin genes resulting in the perinatal lethal condition haemoglobin Barts hydrops fetalis. Using gene targeting in mice, we have deleted a 16 kilobase region encompassing both adult alpha-globin genes. Animals homozygous for this deletion become hydropic and die late in gestation mimicking humans with hydrops fetalis. Introduction of a human alpha-globin transgene rescued these animals from perinatal death thus demonstrating the utility of this murine model in the development of cellular and gene based approaches for treating this human genetic disease.
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Affiliation(s)
- C Pászty
- Human Genome Center, Lawrence Berkeley Laboratory, University of California, Berkeley 94720, USA
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Pohajdak B, Dixon B. A commentary on: 'unexpected intron location in non-vertebrate globin genes', by: Moens et al. (FEBS letters, 312 (1992) 105-109). FEBS Lett 1993; 320:281-3; discussion 284-7. [PMID: 8096468 DOI: 10.1016/0014-5793(93)80603-r] [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: 01/28/2023]
Abstract
We are submitting this commentary in order to prevent the confusion which Moens et al. may provoke in the minds of readers. Our comments are intended to point out the exclusion of some major issues and some errors which may mislead readers of this paper.
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Affiliation(s)
- B Pohajdak
- Department of Biology, Dalhouse University, Halifax, Nova Scotia, Canada
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Amariglio N, Rechavi G. Insertional mutagenesis by transposable elements in the mammalian genome. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 1993; 21:212-218. [PMID: 8385004 DOI: 10.1002/em.2850210303] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Several mammalian repetitive transposable genetic elements were characterized in recent years, and their role in mutagenesis is delineated in this review. Two main groups have been described: elements with symmetrical termini such as the murine IAP sequences and the human THE 1 elements and elements characterized by a poly-A rich tail at the 3' end such as the SINE and LINE sequences. The characteristic property of such mobile elements to spread and integrate in the host genome leads to insertional mutagenesis. Both germline and somatic mutations have been documented resulting from the insertion of the various types of mammalian repetitive transposable genetic elements. As foreseen by Barbara McClintock, such genetic events can cause either the activation or the inactivation of specific genes, resulting in their identification via an altered phenotype. Several disease states, such as hemophilia and cancer, are the result of this apparent aspect of genome instability.
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Affiliation(s)
- N Amariglio
- Department of Hematology, Chaim Sheba Medical Center, Tel-Hashomer, Israel
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Dixon B, Walker B, Kimmins W, Pohajdak B. A nematode hemoglobin gene contains an intron previously thought to be unique to plants. J Mol Evol 1992; 35:131-6. [PMID: 1501253 DOI: 10.1007/bf00183224] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Hemoglobin genes from plants and animals both have a characteristic chromosomal organization. Plant hemoglobin genes contains a unique intron inserted into the heme-binding domain of exon 2. This intron has not been previously reported in animal globin genes, and its loss was hypothesized to have occurred early in the evolution of hemoglobins. We report here a unique six-intron, seven-exon internally duplicated nematode hemoglobin gene that contains an intron equivalent to the plant central intron in its first repeat. This nematode hemoglobin gene has lost both the central and the normal third intron in its second repeat. The nematode globin also contains a unique intron between its secretory peptide leader sequence and its coding sequence, which is absent in other extracellular invertebrate globin genes. Possible models to explain the head-to-tail duplication of this gene are discussed.
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Affiliation(s)
- B Dixon
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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Abdallah B, Hourdry J, Krieg PA, Denis H, Mazabraud A. Germ cell-specific expression of a gene encoding eukaryotic translation elongation factor 1 alpha (eEF-1 alpha) and generation of eEF-1 alpha retropseudogenes in Xenopus laevis. Proc Natl Acad Sci U S A 1991; 88:9277-81. [PMID: 1924391 PMCID: PMC52697 DOI: 10.1073/pnas.88.20.9277] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We have studied by in situ hybridization the expression of the genes encoding the somatic form and the oocyte form of Xenopus laevis eEF-1 alpha. The somatic form of eEF-1 alpha (eEF-1 alpha S) mRNA is virtually undetectable in male and female germ cells of the adult gonad but is very abundant in embryonic cells after the neurula stage. In contrast, another form of eEF-1 alpha (eEF-1 alpha O) mRNA is highly concentrated in oogonia and in previtellogenic oocytes but is undetectable in eggs and embryos. eEF-1 alpha O mRNA is also present in spermatogonia and spermatocytes of adult testis. The latter finding identifies eEF-1 alpha O mRNA as a germ cell-specific gene product. Although germ cells contain very little eEF-1 alpha S mRNA, several eEF-1 alpha S retropseudogenes exist in X. laevis chromosomes. These genes are thought to arise in germ cells from reverse transcription of mRNA and subsequent integration of the cDNA copies into chromosomal DNA. We suggest that eEF-1 alpha S pseudogenes are generated in primordial germ cells of the embryo before they differentiate into oogonia or spermatogonia.
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Affiliation(s)
- B Abdallah
- Centre de Génétique Moléculaire, Laboratoire propre du Centre National de la Recherche Scientifique associé à l'Université P. et M. Curie (Paris VI), Gif-sur-Yvette, France
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Carter CA, Murphy G, Fabre JW. A polymorphic HLA-DPA-like locus, unlinked to the rat major histocompatibility complex. Immunogenetics 1991; 34:277-80. [PMID: 1680811 DOI: 10.1007/bf00215267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- C A Carter
- Institute of Child Health, London and Blond McIndoe Centre, Queen Victoria Hospital, Sussex, England
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19
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Matsuo Y, Yokoyama S. Cloning and sequencing of a processed pseudogene derived from a human class III alcohol dehydrogenase gene. Am J Hum Genet 1990; 46:85-91. [PMID: 2294756 PMCID: PMC1683552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Current information on the molecular structure of human alcohol dehydrogenase (ADH) genes is fragmentary. To characterize all ADH genes, we have isolated 63 ADH clones from human genomic libraries made from one individual. Fifty-nine clones have been classified into five previously known loci: ADH1 (18 clones), ADH2 (20 clones), and ADH3 class I (16 clones), ADH4 class II (4 clones), and ADH5 class III (1 clone). Sequencing of one of the remaining four unclassified clones, SY lambda ADHE38, about 1.1 kb in length, shows no introns and three frameshift mutations in the coding region, with a total of 10 internal termination codons. When its deduced amino acid sequence was compared with those of the class I, class II, and class III ADHs, the proportions of identical amino acids were 56.7%, 55.5%, and 88.7%, respectively, suggesting that the processed pseudogene was derived from an ADH5 gene. The duplication event seems to have occurred about 3.5 million years ago, and the pseudogene has undergone a rapid change since then.
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Affiliation(s)
- Y Matsuo
- Department of Ecology, Ethology, and Evolution, University of Illinois, Urbana-Champaign 61820
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20
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Rebbe NF, Hickman WS, Ley TJ, Stafford DW, Hickman S. Nucleotide Sequence and Regulation of a Human 90-kDa Heat Shock Protein Gene. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)63803-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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21
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Uetsuki T, Naito A, Nagata S, Kaziro Y. Isolation and Characterization of the Human Chromosomal Gene for Polypeptide Chain Elongation Factor-1α. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83619-5] [Citation(s) in RCA: 130] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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22
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Marks J. Molecular micro- and macroevolution in the primate alpha-globin gene family. Am J Hum Biol 1989; 1:555-566. [DOI: 10.1002/ajhb.1310010506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/1988] [Accepted: 02/01/1989] [Indexed: 11/08/2022] Open
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23
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Borst DE, Redmond TM, Elser JE, Gonda MA, Wiggert B, Chader GJ, Nickerson JM. Interphotoreceptor Retinoid-binding Protein. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)85061-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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24
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A group of type I keratin genes on human chromosome 17: characterization and expression. Mol Cell Biol 1988. [PMID: 2451124 DOI: 10.1128/mcb.8.2.722] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human type I keratins K16 and K14 are coexpressed in a number of epithelial tissues, including esophagus, tongue, and hair follicles. We determined that two genes encoding K16 and three genes encoding K14 were clustered in two distinct segments of chromosome 17. The genes within each cluster were tightly linked, and large parts of the genome containing these genes have been recently duplicated. The sequences of the two K16 genes showed striking homology not only within the coding sequences, but also within the intron positions and sequences and extending at least 400 base pairs 5' upstream and 850 base pairs 3' downstream from these genes. Despite the strong homologies between these two genes, only one of the genes encoded a protein which assembled into keratin filaments when introduced into simple epithelial cells. While there were no obvious abnormalities in the sequence of the other gene, its promoter seemed to be significantly weaker, and even a hybrid gene with the other gene's promoter gave rise to a much reduced mRNA level after gene transfection. To demonstrate that the functional K16 gene that we identified was in fact responsible for the K16 expressed in human tissues, we made a polyclonal antiserum which recognized our functional K16 gene product in both denatured and filamentous form and which was specific for bona fide human K16.
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25
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Rosenberg M, RayChaudhury A, Shows TB, Le Beau MM, Fuchs E. A group of type I keratin genes on human chromosome 17: characterization and expression. Mol Cell Biol 1988; 8:722-36. [PMID: 2451124 PMCID: PMC363198 DOI: 10.1128/mcb.8.2.722-736.1988] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The human type I keratins K16 and K14 are coexpressed in a number of epithelial tissues, including esophagus, tongue, and hair follicles. We determined that two genes encoding K16 and three genes encoding K14 were clustered in two distinct segments of chromosome 17. The genes within each cluster were tightly linked, and large parts of the genome containing these genes have been recently duplicated. The sequences of the two K16 genes showed striking homology not only within the coding sequences, but also within the intron positions and sequences and extending at least 400 base pairs 5' upstream and 850 base pairs 3' downstream from these genes. Despite the strong homologies between these two genes, only one of the genes encoded a protein which assembled into keratin filaments when introduced into simple epithelial cells. While there were no obvious abnormalities in the sequence of the other gene, its promoter seemed to be significantly weaker, and even a hybrid gene with the other gene's promoter gave rise to a much reduced mRNA level after gene transfection. To demonstrate that the functional K16 gene that we identified was in fact responsible for the K16 expressed in human tissues, we made a polyclonal antiserum which recognized our functional K16 gene product in both denatured and filamentous form and which was specific for bona fide human K16.
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Affiliation(s)
- M Rosenberg
- Department of Molecular Genetics, University of Chicago, Illinois 60637
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26
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Serero S, Maire P, Nguyen VC, Cohen-Haguenauer O, Gross MS, Jégou-Foubert C, de Tand MF, Kahn A, Frézal J. Localization of the active gene of aldolase on chromosome 16, and two aldolase A pseudogenes on chromosomes 3 and 10. Hum Genet 1988; 78:167-74. [PMID: 2828224 DOI: 10.1007/bf00278190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Southern blot analysis of human genomic DNA hybridized with a coding region aldolase A cDNA probe (600 bases) revealed four restriction fragments with EcoRI restriction enzyme: 7.8 kb, 13 kb, 17 kb and greater than 30 kb. By human-hamster hybrid analysis (Southern technique) the principal fragments, 7.8 kb, 13 kb, greater than 30 kb, were localized to chromosomes 10, 16 and 3 respectively. The 17-kb fragment was very weak in intensity; it co-segregated with the greater than 30-kb fragment and is probably localized on chromosome 3 with the greater than 30-kb fragment. Analysis of a second aldolase A labelled probe protected against S1 nuclease digestion by RNAs from different hybrid cells, indicated the presence of aldolase A mRNAs in hybrid cells containing only chromosome 16. Under the stringency conditions used, the EcoRI sequences detected by the coding region aldolase A cDNA probe did not correspond to aldolase B or C. The 7.8-kb and greater than 30-kb EcoRI sequences, localized respectively on chromosomes 10 and 3, correspond to aldolase A pseudogenes; the 13-kb EcoRI sequence localized on chromosome 16 corresponds to the aldolase active gene. The fact that the aldolase A gene and pseudogenes are located on three different chromosomes supports the hypothesis that the pseudogenes originated from aldolase A mRNAs, copied into DNA and integrated in unrelated chromosomal loci.
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Affiliation(s)
- S Serero
- Clinique et Unité de Recherches de Génétique Médicale (INSERM U12), Hôpital des Enfants-Malades, Paris, France
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27
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Kuff EL, Lueders KK. The intracisternal A-particle gene family: structure and functional aspects. Adv Cancer Res 1988; 51:183-276. [PMID: 3146900 DOI: 10.1016/s0065-230x(08)60223-7] [Citation(s) in RCA: 281] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- E L Kuff
- Laboratory of Biochemistry, National Cancer Institute, Bethesda, Maryland. 20892
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28
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Adra CN, Ellis NA, McBurney MW. The family of mouse phosphoglycerate kinase genes and pseudogenes. SOMATIC CELL AND MOLECULAR GENETICS 1988; 14:69-81. [PMID: 2829366 DOI: 10.1007/bf01535050] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The mammalian genome contains two genes encoding phosphoglycerate kinase; the pgk-1 gene is X-linked and is expressed in all cells except sperm, while the pgk-2 gene is expressed exclusively in sperm cells. The mouse genome contains no pseudogenes derived from pgk-2. On the other hand, the genomes of Balb/c and C3H/He strain mice contain six other regions with sequences homologous to those of pgk-1 cDNA. These pgk-related sequences are likely derived from the pgk-1 gene by retroposition because all are located on autosomal chromosomes and because none appear to be interrupted by introns. Two of the presumed pseudogenes contain sequences homologous to all regions of the pgk-1 cDNA while the other four genomic regions were truncated at the 5', 3', or both ends. One of the truncated pseudogenes was sequenced. Its pgk-related sequence was not flanked by direct repeats, suggesting that loss of the 5' and/or 3' ends of this retrogene may have occurred following its integration into the genome. Our evidence suggests that pgk-1-derived retroposons arose initially more than 100 million years ago and have continued to arise until so recently that some are unique to different mouse strains.
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Affiliation(s)
- C N Adra
- Department of Medicine, University of Ottawa, Canada
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29
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Human U1 RNA pseudogenes may be generated by both DNA- and RNA-mediated mechanisms. Mol Cell Biol 1987. [PMID: 6085956 DOI: 10.1128/mcb.2.7.815] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of cloned human genomic loci homologous to the small nuclear RNA U1 established that such sequences are abundant and dispersed in the human genome and that only a fraction represent bona fide genes. The majority of genomic loci bear defective gene copies, or pseudogenes, which contain scattered base mismatches and in some cases lack the sequence corresponding to the 3' end of U1 RNA. Although all of the U1 genes examined to date are flanked by essentially identical sequences and therefore appear to comprise a single multigene family, we present evidence for the existence of at least three structurally distinct classes of U1 pseudogenes. Class I pseudogenes had considerable flanking sequence homology with the U1 gene family and were probably derived from it by a DNA-mediated event such as gene duplication. In contrast, the U1 sequence in class II and III U1 pseudogenes was flanked by single-copy genomic sequences completely unrelated to those flanking the U1 gene family; in addition, short direct repeats flanked the class III but not the class II pseudogenes. We therefore propose that both class II and III U1 pseudogenes were generated by an RNA-mediated mechanism involving the insertion of U1 sequence information into a new chromosomal locus. We also noted that two other types of repetitive DNA sequences in eucaryotes, the Alu family in vertebrates and the ribosomal DNA insertions in Drosophila, bore a striking structural resemblance to the classes of U1 pseudogenes described here and may have been created by an RNA-mediated insertion event.
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30
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Rubinstein WS, Gordon JW. Restriction enzyme evidence for Alu sequence-mediated dispersion of microinjected genes in transgenic mice. DEVELOPMENTAL GENETICS 1987; 8:233-47. [PMID: 2844459 DOI: 10.1002/dvg.1020080407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A human bacteriophage clone containing adult beta-globin genes with four Alu sequences was microinjected to produce transgenic mice. Southern blot analysis on the spleen of a transgenic mouse revealed an unusual hybridization pattern that suggested extensive dispersion of human DNA throughout the mouse genome. This pattern was reproducible using several restriction enzymes, including a noncutting enzyme. The hybridization pattern was not observed in other tissues, and sequences were not detected in progeny using the bacteriophage probe. However, hybridization of spleen DNA of offspring against a human Alu probe revealed genetic transmission of human Alu sequences. The results suggest dispersion of microinjected Alu sequences throughout the genome.
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Affiliation(s)
- W S Rubinstein
- Department of Biochemistry, Mt. Sinai School of Medicine, New York, NY 10029
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31
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Human Genomics 1986: Toward a Complete Gene Map and Nucleotide Sequence of the Human Genome. Hum Genet 1987. [DOI: 10.1007/978-3-642-71635-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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32
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Abstract
A family of transposable genetic elements in the genome of the frog, Xenopus laevis, is described. They are designated Tx1. Transposability of the elements was deduced by characterization of a chromosomal locus which is polymorphic for the presence or absence of a Tx1 element. Nucleotide sequence analysis suggested that Tx1 elements show target site specificity, as they are inserted at the pentanucleotide TTTAA in all four cases that were examined. The elements appear to have 19-base-pair (bp) inverted terminal repeats, and they are flanked by 4-bp target duplications (TTAA), although the possibility that they do not create target site duplications is discussed. Tx1 elements have several unusual characteristics: the central portion of each element is comprised of a variable number of two types of 393-bp repeating units; the rightmost 1,000 bp of the element contains separate regions potentially capable of forming bends, left-handed Z-form DNA, and alternative stem-loop structures. Comparisons among single frogs suggest that germ line transposition is relatively infrequent and that variations in numbers of internal repeats accumulate quite slowly at any locus.
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33
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RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon. Mol Cell Biol 1986. [PMID: 2427930 DOI: 10.1128/mcb.5.8.2090] [Citation(s) in RCA: 156] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rats and mice have two, equally expressed, nonallelic genes encoding preproinsulin (genes I and II). Cytological hybridization with metaphase chromosomes indicated that both genes reside on rat chromosome I but are approximately 100,000 kilobases apart. In mice the two genes reside on two different chromosomes. DNA sequence comparisons of the gene-flanking regions in rats and mice indicated that the preproinsulin gene I has lost one of the two introns present in gene II, is flanked by a long (41-base) direct repeat, and has a remnant of a polydeoxyadenylate acid tract preceding the downstream direct repeat. These structural features indicated that gene I was generated by an RNA-mediated duplication-transposition event involving a transcript of gene II which was initiated upstream from the normal capping site. Sequence divergence analysis indicated that the pair of the original gene and its retroposed, but functional, counterpart (which appeared about 35 million years ago) is maintained by strong negative selection operating primarily on the segments encoding the chains of the mature hormone, whereas the segments encoding the parts of the polypeptide that are eliminated during processing and also the introns and the flanking regions are evolving neutrally.
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34
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Abstract
The insulin 1, but not the insulin 2, locus is polymorphic (i.e., exhibits allelic variation) in rats. Restriction enzyme analysis and hybridization studies showed that the polymorphic region is 2.2 kilobases upstream of the insulin 1 coding region and is due to the presence or absence of an approximately 2.7-kilobase repeated DNA element. DNA sequence determination showed that this DNA element is a member of a long interspersed repeated DNA family (LINE) that is highly repeated (greater than 50,000 copies) and highly transcribed in the rat. Although the presence or absence of LINE sequences at the insulin 1 locus occurs in both the homozygous and heterozygous states, LINE-containing insulin 1 alleles are more prevalent in the rat population than are alleles without LINEs. Restriction enzyme analysis of the LINE-containing alleles indicated that at least two versions of the LINE sequence may be present at the insulin 1 locus in different rats. Either repeated transposition of LINE sequences or gene conversion between the resident insulin 1 LINE and other sequences in the genome are possible explanations for this.
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35
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Royer-Pokora B, Kunkel LM, Monaco AP, Goff SC, Newburger PE, Baehner RL, Cole FS, Curnutte JT, Orkin SH. Cloning the gene for an inherited human disorder--chronic granulomatous disease--on the basis of its chromosomal location. Nature 1986; 322:32-8. [PMID: 2425263 DOI: 10.1038/322032a0] [Citation(s) in RCA: 580] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The gene that is abnormal in the X-linked form of the phagocytic disorder chronic granulomatous disease has been cloned without reference to a specific protein by relying on its chromosomal map position. The transcript of the gene is expressed in the phagocytic lineage of haematopoietic cells and is absent or structurally abnormal in four patients with the disorder. The nucleotide sequence of complementary DNA clones predicts a polypeptide of at least 468 amino acids with no homology to proteins described previously.
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36
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Alsip GR, Konkel DA. A processed chicken pseudogene (CPS1) related to the ras oncogene superfamily. Nucleic Acids Res 1986; 14:2123-38. [PMID: 3083400 PMCID: PMC339647 DOI: 10.1093/nar/14.5.2123] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We describe the first polyA-containing processed pseudogene reported in the chicken. It includes a 0.52 kb open reading frame which could encode a 175 amino acid protein. The putative protein shows extensive homology to the ras oncogene superfamily, being most closely related to the yeast protein YP2. It is one of the two most divergent members of the ras superfamily yet described and is the most homologous of any ras-related protein to the G-protein alpha-transducin. The chicken genome contains at least one other gene highly homologous to CPS1; at least one member of the CPS1 family is active, but only early in chicken development. This pattern of expression, and the presence of mutations in regions known to activate human c-ras genes to oncogenicity, suggest that CPS1 may represent a new oncogene family.
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37
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Garrett JE, Carroll D. Tx1: a transposable element from Xenopus laevis with some unusual properties. Mol Cell Biol 1986; 6:933-41. [PMID: 3022140 PMCID: PMC367594 DOI: 10.1128/mcb.6.3.933-941.1986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A family of transposable genetic elements in the genome of the frog, Xenopus laevis, is described. They are designated Tx1. Transposability of the elements was deduced by characterization of a chromosomal locus which is polymorphic for the presence or absence of a Tx1 element. Nucleotide sequence analysis suggested that Tx1 elements show target site specificity, as they are inserted at the pentanucleotide TTTAA in all four cases that were examined. The elements appear to have 19-base-pair (bp) inverted terminal repeats, and they are flanked by 4-bp target duplications (TTAA), although the possibility that they do not create target site duplications is discussed. Tx1 elements have several unusual characteristics: the central portion of each element is comprised of a variable number of two types of 393-bp repeating units; the rightmost 1,000 bp of the element contains separate regions potentially capable of forming bends, left-handed Z-form DNA, and alternative stem-loop structures. Comparisons among single frogs suggest that germ line transposition is relatively infrequent and that variations in numbers of internal repeats accumulate quite slowly at any locus.
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38
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A unique element resembling a processed pseudogene. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)42420-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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39
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Young JA, Trowsdale J. A processed pseudogene in an intron of the HLA-DP beta 1 chain gene is a member of the ribosomal protein L32 gene family. Nucleic Acids Res 1985; 13:8883-91. [PMID: 3866218 PMCID: PMC318958 DOI: 10.1093/nar/13.24.8883] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A sequence in an intron of the human HLA-DP beta 1 gene was identified by its homology to the gene encoding ribosomal protein L32 (rpL32). It lacked introns indicating that it was derived from a processed rpL32 mRNA transcript. A human cDNA clone encoding rpL32 was isolated and compared to this human pseudogene and to several related mouse sequences, one of which is contained in an intron of the murine dihydrofolate reductase gene. Comparison of these sequences revealed that they were more related within species than between, suggesting that they became inserted in the genome after man and mouse diverged.
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40
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Mellor J, Malim MH, Gull K, Tuite MF, McCready S, Dibbayawan T, Kingsman SM, Kingsman AJ. Reverse transcriptase activity and Ty RNA are associated with virus-like particles in yeast. Nature 1985; 318:583-6. [PMID: 2415827 DOI: 10.1038/318583a0] [Citation(s) in RCA: 164] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Ty element of yeast represents a class of eukaryotic transposons that show remarkable structural similarity to retroviral proviruses. Recently, these comparisons have been strengthened by a series of observations on the yeast Ty element: Ty transposes via an RNA intermediate; it contains a sequence (Fig. 1) which, when translated, is homologous to a conserved region found in all reverse transcriptases; a fusion protein encoded by Ty is produced by a frameshift event that is directly analogous to the production of Pr180gag-pol in a retrovirus such as Rous sarcoma virus. Here we identify the reverse transcriptase activity that, until now, has been presumed to mediate Ty transposition and show that it is sequestered in virus-like particles that also contain Ty RNA.
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41
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Characterization of the functional gene and several processed pseudogenes in the human triosephosphate isomerase gene family. Mol Cell Biol 1985. [PMID: 4022011 DOI: 10.1128/mcb.5.7.1694] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The functional gene and three intronless pseudogenes for human triosephosphate isomerase were isolated from a recombinant DNA library and characterized in detail. The functional gene spans 3.5 kilobase pairs and is split into seven exons. Its promoter contains putative TATA and CCAAT boxes and is extremely rich in G and C residues (76%). The pseudogenes share a high degree of homology with the functional gene but contain mutations that preclude the synthesis of an active triosephosphate isomerase enzyme. Sequence divergence calculations indicate that these pseudogenes arose approximately 18 million years ago. We present evidence that there is a single functional gene in the human triosephosphate isomerase gene family.
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42
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Lakshmikumaran MS, D'Ambrosio E, Laimins LA, Lin DT, Furano AV. Long interspersed repeated DNA (LINE) causes polymorphism at the rat insulin 1 locus. Mol Cell Biol 1985; 5:2197-203. [PMID: 3016521 PMCID: PMC366944 DOI: 10.1128/mcb.5.9.2197-2203.1985] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The insulin 1, but not the insulin 2, locus is polymorphic (i.e., exhibits allelic variation) in rats. Restriction enzyme analysis and hybridization studies showed that the polymorphic region is 2.2 kilobases upstream of the insulin 1 coding region and is due to the presence or absence of an approximately 2.7-kilobase repeated DNA element. DNA sequence determination showed that this DNA element is a member of a long interspersed repeated DNA family (LINE) that is highly repeated (greater than 50,000 copies) and highly transcribed in the rat. Although the presence or absence of LINE sequences at the insulin 1 locus occurs in both the homozygous and heterozygous states, LINE-containing insulin 1 alleles are more prevalent in the rat population than are alleles without LINEs. Restriction enzyme analysis of the LINE-containing alleles indicated that at least two versions of the LINE sequence may be present at the insulin 1 locus in different rats. Either repeated transposition of LINE sequences or gene conversion between the resident insulin 1 LINE and other sequences in the genome are possible explanations for this.
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43
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Horiuchi Y, Honjo T, Ono M. IgE heavy chain constant region genes in atopic dermatitis and senile erythroderma patients. Immunogenetics 1985; 22:241-6. [PMID: 2995248 DOI: 10.1007/bf00404483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
By Southern hybridization using a genomic DNA fragment carrying a human IgE heavy chain constant region gene (C epsilon) as a probe, we analyzed the organization of human C epsilon genes and their flanking regions in 23 atopic dermatitis and 6 senile erythroderma patients with elevated serum IgE levels, and 6 atopic dermatitis patients with normal IgE levels. On Bam HI, Hind III, and Eco RI digestions, we detected three hybridizable fragments containing three human C epsilon genes, C epsilon 1, C epsilon 2, and C epsilon 3, respectively, in all leukocyte DNAs. These fragments were almost identical in size among patients and healthy donors. Pst I digestion generated a genetic polymorphism. We, however, could find no correlation between this polymorphism and the disorders. It was concluded that among the patients and healthy donors, there was no marked difference in the organization of the functional C epsilon gene and its flanking region containing a class switch region. Our conclusion cannot rule out the presence of genetic abnormalities of this region in some atopic dermatitis patients which are not resolvable by our method. In the course of this study, we found a novel C epsilon-like gene in placenta DNA which differs from the three C epsilon genes commonly present in normal human DNA.
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44
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Soares MB, Schon E, Henderson A, Karathanasis SK, Cate R, Zeitlin S, Chirgwin J, Efstratiadis A. RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon. Mol Cell Biol 1985; 5:2090-103. [PMID: 2427930 PMCID: PMC366927 DOI: 10.1128/mcb.5.8.2090-2103.1985] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rats and mice have two, equally expressed, nonallelic genes encoding preproinsulin (genes I and II). Cytological hybridization with metaphase chromosomes indicated that both genes reside on rat chromosome I but are approximately 100,000 kilobases apart. In mice the two genes reside on two different chromosomes. DNA sequence comparisons of the gene-flanking regions in rats and mice indicated that the preproinsulin gene I has lost one of the two introns present in gene II, is flanked by a long (41-base) direct repeat, and has a remnant of a polydeoxyadenylate acid tract preceding the downstream direct repeat. These structural features indicated that gene I was generated by an RNA-mediated duplication-transposition event involving a transcript of gene II which was initiated upstream from the normal capping site. Sequence divergence analysis indicated that the pair of the original gene and its retroposed, but functional, counterpart (which appeared about 35 million years ago) is maintained by strong negative selection operating primarily on the segments encoding the chains of the mature hormone, whereas the segments encoding the parts of the polypeptide that are eliminated during processing and also the introns and the flanking regions are evolving neutrally.
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45
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Brown JR, Daar IO, Krug JR, Maquat LE. Characterization of the functional gene and several processed pseudogenes in the human triosephosphate isomerase gene family. Mol Cell Biol 1985; 5:1694-706. [PMID: 4022011 PMCID: PMC367288 DOI: 10.1128/mcb.5.7.1694-1706.1985] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The functional gene and three intronless pseudogenes for human triosephosphate isomerase were isolated from a recombinant DNA library and characterized in detail. The functional gene spans 3.5 kilobase pairs and is split into seven exons. Its promoter contains putative TATA and CCAAT boxes and is extremely rich in G and C residues (76%). The pseudogenes share a high degree of homology with the functional gene but contain mutations that preclude the synthesis of an active triosephosphate isomerase enzyme. Sequence divergence calculations indicate that these pseudogenes arose approximately 18 million years ago. We present evidence that there is a single functional gene in the human triosephosphate isomerase gene family.
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46
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Lawrence CB, McDonnell DP, Ramsey WJ. Analysis of repetitive sequence elements containing tRNA-like sequences. Nucleic Acids Res 1985; 13:4239-52. [PMID: 3839306 PMCID: PMC321785 DOI: 10.1093/nar/13.12.4239] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Several repetitive sequence elements from diverse species share extensive sequence homology with tRNA molecules. Analysis of the tRNA-like sequences within these elements suggest that they have originated from authentic tRNA sequences. Elements containing tRNA-like sequences can be divided into three distinct groups whose members share extensive sequence homology, have similar sequence organization and have unique species distribution. We suggest that these three groups represent independent examples of retroposon families that have originated from tRNAs.
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Michelson AM, Bruns GA, Morton CC, Orkin SH. The human phosphoglycerate kinase multigene family. HLA-associated sequences and an X-linked locus containing a processed pseudogene and its functional counterpart. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)88877-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Insertion of long interspersed repeated elements at the Igh (immunoglobulin heavy chain) and Mlvi-2 (Moloney leukemia virus integration 2) loci of rats. Proc Natl Acad Sci U S A 1985; 82:2857-61. [PMID: 2986141 PMCID: PMC397665 DOI: 10.1073/pnas.82.9.2857] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Restriction enzyme analysis of normal DNA derived from individual rats of the National Institutes of Health outbred Osborn-Mendel colony revealed that two independent single-copy loci, the Igh (immunoglobulin heavy chain) locus and the Mlvi-2 (Moloney leukemia virus integration 2) locus, a putative oncogene, are polymorphic (i.e., exhibit allelic variation). The polymorphism at both loci was due to the presence or absence of a long interspersed repeated DNA element (LINE). The LINE insertion in the Igh locus occurred in the joining (J) region, which is involved in the physiological rearrangement of this locus. The LINE insertion in the Mlvi-2 locus has occurred approximately 6 kilobases from the region of provirus integration in Moloney murine leukemia virus-induced rat thymomas. The two inserts are colinear with each other and with other randomly selected cloned copies of the rat LINE family, the general characteristics of which we also present. LINE insertion in the Mlvi-2 locus was observed in several rat strains, established from independent rat colonies, suggesting that LINE-containing Mlvi-2 alleles may be widespread in the rat population. LINE insertion in the Igh locus was observed in 1 of 27 rats. The detection of a LINE-related polymorphism at two nonselected loci indicates that LINEs are transposable. The presence or absence of these long (greater than 5 kilobases), highly transcribed elements at single-copy loci could have profound effects on gene activity. Furthermore, LINE-containing single-copy loci could be affected by homologous interaction between the resident LINE and any of the other 50,000 or so copies of these elements in the rat genome.
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Scarpulla RC. Association of a truncated cytochrome c processed pseudogene with a similarly truncated member from a long interspersed repeat family of rat. Nucleic Acids Res 1985; 13:763-75. [PMID: 2987808 PMCID: PMC341033 DOI: 10.1093/nar/13.3.763] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The cytochrome c multigene family of rat contains approximately 30 processed pseudogenes that represent genomic DNA copies of three alternate mRNAs. Here, the DNA sequence of an unusual processed pseudogene reveals that it has a complete 3' noncoding region including a short poly A tail but unlike the others is abruptly truncated at its 5' end, 19 amino acid codons from the translation terminator. At this position the pseudogene is fused through 17 consecutive adenylic acid residues to a 1.3 kb repetitive sequence. This repetitive element is flanked by direct repeats and represents a truncated member from a major long interspersed repeat family. The rat element is a composite of sequences observed in long interspersed repeats from both rodents and primates. Comparison to the equivalent mouse sequences shows that the 5' half of the repeat distal to the pseudogene has an open reading frame and is highly conserved whereas the half adjacent to the pseudogene is evolutionarily unstable. The proportion of cytochrome c pseudogene recombinant clones containing this repetitive DNA is 3 fold greater than observed in random isolates and may reflect a general tendency of processed pseudogenes to associate with other repetitive sequences in the genome.
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Processed pseudogenes for rat cytochrome c are preferentially derived from one of three alternate mRNAs. Mol Cell Biol 1985. [PMID: 6096691 DOI: 10.1128/mcb.4.11.2279] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three cytochrome c mRNAs (1,400, 1,100 and 700 nucleotides) are colinear with RC4, a gene that has introns and correctly encodes cytochrome c. A comparison of RC4 to six nonallelic clones isolated from the rat cytochrome c multigene family demonstrates that all three mRNAs are represented in the genome as processed pseudogenes. Four of the six pseudogenes are derived from the 1,100-nucleotide mRNA, and genomic hybridizations further establish that nearly all of the 30 or so gene family members are also genomic copies of this mRNA despite the equimolar ratio of the three messages in rat tissues. Thus, the surprising multiplicity of cytochrome c sequences in the rat genome is mainly accounted for by the selective use of the 1,100-nucleotide mRNA for the formation of processed pseudogenes. In contrast to 700- and 1,400-nucleotide species which are polyadenylated downstream from AAGUAAA and AAUUAAA, respectively, the 1,100-nucleotide mRNA uses the ubiquitous AAUAAA and also displays a unique stem and loop structure (delta G = -59.4 kJ) centered 37 base pairs upstream from this sequence.
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