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Aspden JL, Wallace EW, Whiffin N. Not all exons are protein coding: Addressing a common misconception. CELL GENOMICS 2023; 3:100296. [PMID: 37082142 PMCID: PMC10112331 DOI: 10.1016/j.xgen.2023.100296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Exons are regions of DNA that are transcribed to RNA and retained after introns are spliced out. However, the term "exon" is often misused as synonymous to "protein coding," including in some literature and textbook definitions. In contrast, only a fraction of exonic sequences are protein coding (<30% in humans). Both exons and introns are also present in untranslated regions (UTRs) and non-coding RNAs. Misuse of the term exon is problematic, for example, "whole-exome sequencing" technology targets <25% of the human exome, primarily regions that are protein coding. Here, we argue for the importance of the original definition of an exon for making functional distinctions in genetics and genomics. Further, we recommend the use of clearer language referring to coding exonic regions and non-coding exonic regions. We propose the use of coding exome sequencing, or CES, to more appropriately describe sequencing approaches that target primarily protein-coding regions rather than all transcribed regions.
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Affiliation(s)
- Julie L. Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
- LeedsOmics, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Edward W.J. Wallace
- Institute for Cell Biology and Centre for Engineering Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nicola Whiffin
- Big Data Institute, University of Oxford, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Corresponding author
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Tefferi A. Genomics Basics: DNA Structure, Gene Expression, Cloning, Genetic Mapping, and Molecular Tests. Semin Cardiothorac Vasc Anesth 2016; 10:282-90. [PMID: 17200086 DOI: 10.1177/1089253206294343] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genomics is the study of the structure and function of the human genome including genes and their surrounding DNA sequences. The over 3 billion base pairs of the human genome have now been sequenced and approximately 25 000 genes acknowledged. However, only 1% of the entire genome has been assigned to protein coding and decades more work is anticipated to define the functional relevance of noncoding DNA as well as the basis and consequences of sequence variations among individuals. For medical scientists, the focus remains on discovering both disease-causing and disease-susceptibility genes. For pharmaceutical companies, the opportunity to develop molecularly targeted therapy is not going unnoticed. For the practicing physician, the prospect of genomic medicine that incorporates molecular diagnosis and pathogenesis-targeted therapy requires basic understanding of terminology and concepts in molecular biology and the corresponding laboratory tests.
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Affiliation(s)
- Ayalew Tefferi
- Division of Hematology, Mayo Clinic, Rochester, MN 55905, USA.
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Harrisson CM. The arrangement of chromatin in the interphase nucleus with reference to cell differentiation and repression in higher organisms. Tissue Cell 2009; 3:523-50. [PMID: 18631569 DOI: 10.1016/s0040-8166(71)80001-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/1971] [Indexed: 10/22/2022]
Abstract
HeLa cells were grown as monolayer cultures in Spinner medium and given 12-minute pulse labels of (3)H thymidine. Synchronous crops of cells labelled in the last minutes of S showed a metaphase pattern of chromosomes hot-labelled close to the kinetochores (centromeres). Such cells in subsequent stages of interphase showed a concentration of label at the nuclear envelope. A control experiment with cells labelled in the first minutes of S yielded chromosomes labelled at the tips and in the nucleolar organizers. These cells showed label concentrated in the central area of the nucleus in the next interphase. The results are compatible with the view that the kinetochore regions of chromosomes are attached to the nuclear envelope in interphase. The significance of these results is considered with reference to interpreting DNA replication patterns, the segregation of chromosomes, eukaryote differentiation and repression, and the rationale for chromosome numbers. It is argued that the nuclear envelope serves as a 'repressor organelle' in higher organisms, and that DNA methylation may be involved in the control of RNA transcription, and hence gene expression.
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Affiliation(s)
- C M Harrisson
- Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
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Tefferi A, Wieben ED, Dewald GW, Whiteman DAH, Bernard ME, Spelsberg TC. Primer on medical genomics part II: Background principles and methods in molecular genetics. Mayo Clin Proc 2002; 77:785-808. [PMID: 12173714 DOI: 10.4065/77.8.785] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The nucleus of every human cell contains the full complement of the human genome, which consists of approximately 30,000 to 70,000 named and unnamed genes and many intergenic DNA sequences. The double-helical DNA molecule in a human cell, associated with special proteins, is highly compacted into 22 pairs of autosomal chromosomes and an additional pair of sex chromosomes. The entire cellular DNA consists of approximately 3 billion base pairs, of which only 1% is thought to encode a functional protein or a polypeptide. Genetic information is expressed and regulated through a complex system of DNA transcription, RNA processing, RNA translation, and posttranslational and cotranslational modification of proteins. Advances in molecular biology techniques have allowed accurate and rapid characterization of DNA sequences as well as identification and quantification of cellular RNA and protein. Global analytic methods and human genetic mapping are expected to accelerate the process of identification and localization of disease genes. In this second part of an educational series in medical genomics, selected principles and methods in molecular biology are recapped, with the intent to prepare the reader for forthcoming articles with a more direct focus on aspects of the subject matter.
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Affiliation(s)
- Ayalew Tefferi
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, Minn 55905, USA
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FLAVELL R, SABO D, BANDLE E, WEISSMANN C. Site-directed Mutagenesis : Generation of an Extracistronic Mutation in Bacteriophage Qβ RNA. Mol Biol 1989. [DOI: 10.1016/b978-0-12-131200-8.50038-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Iserentant D, Fiers W. Secondary structure of the 5' end of bacteriophage MS2 RNA Methoxyamine and kethoxal modification. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 102:595-604. [PMID: 118878 DOI: 10.1111/j.1432-1033.1979.tb04277.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To refine the secondary structure model of the 5' end of the bacteriophage MS2 genome, 32P-labeled MS2 RNA was partially digested with T1 RNase or with Cm-RNase and the 5'-end fragment was isolated, renatured and submitted to treatment with methoxyamine or kethoxal. The resulting modified RNA was digested with T1 RNase and the products were separated by minifingerprinting. Methoxyamine-induced modification of exposed cytidines was detected by differential mobility of modified oligonucleotides, while kethoxal-induced alteration of exposed guanosines was monitored by resistance to T1 ribonuclease digestion. The positions of the modified residues are discussed in terms of an improved secondary structure model proposed for the 5' end of the viral RNA. The structure itself is discussed in relation to sequence conservation and biological function.
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7
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Leung DW, Browning KS, Heckman JE, RajBhandary UL, Clark JM. Nucleotide sequence of the 5' terminus of satellite tobacco necrosis virus ribonucleic acid. Biochemistry 1979; 18:1361-6. [PMID: 427118 DOI: 10.1021/bi00574a036] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Treatment of the RNA of satellite tobacco necrosis virus (STNV) with phosphomonoesterase followed by heat denaturation and treatment with polynucleotide kinase in the presence of [gamma-32P]ATP yields a STNV [5'-32P]RNA containing a homogeneous 5' terminus. Analyses of this STNV [5'-32P]RNA yield the sequence of the first 42 nucleotides from the 5'terminus of STNV RNA. This nucleotide sequence contains the translation initiation AUG codon starting at position 30 from the 5' terminus as indicated by match of subsequent nucleotides with the genetic code assignments for the N-terminal amino acids of STNV coat protein in the 5'-terminal sequence ppAGUAAAGACAGGAAACUU-UACUGACUAACAUGGCAAAACAAC. An interesting feature of this sequence is its potential to form a hairpin loop structure involving perfect Watson-Crick base pairing between the first seven nucleotides and nucleotides at positions 16--22.
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Sabo DL, Domingo E, Bandle EF, Flavell RA, Weissmann C. A guanosine to adenosine transition in the 3' terminal extracistronic region of bacteriophage Q beta RNA leading to loss of infectivity. J Mol Biol 1977; 112:235-52. [PMID: 875018 DOI: 10.1016/s0022-2836(77)80141-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Vournakis JN, Flashner MS, Katopes M, Kitos GA, Vamvakopoulos NC, Sell MS, Wurst RM. Structural studies on intact and deadenylylated rabbit globin mRNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1977; 19:233-52. [PMID: 1019346 DOI: 10.1016/s0079-6603(08)60922-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Jou WM, Fiers W. Studies on the bacteriophages MS2. XXXIII. Comparison of the nucleotide sequences in related bacteriophage RNAs. J Mol Biol 1976; 106:1047-60. [PMID: 978743 DOI: 10.1016/0022-2836(76)90352-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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12
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Bastin M, Dasgupta R, Hall TC, Kaesberg P. Similarity in structure and function of the 3'-terminal region of the four brome mosaic viral RNAs. J Mol Biol 1976; 103:737-45. [PMID: 940163 DOI: 10.1016/0022-2836(76)90206-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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13
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Domingo E, Flavell RA, Weissmann C. In vitro site-directed mutagenesis: generation and properties of an infectious extracistronic mutant of bacteriophage Qbeta. Gene 1976; 1:3-25. [PMID: 1052322 DOI: 10.1016/0378-1119(76)90003-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
An infectious extracistronic mutant of phage Qbeta has been prepared by site-directed mutagenesis. Qbeta RNA minus strands containing the mutagenic base analog N4-hydroxy-CMP instead of UMP at position 39 from the 5' end were synthesized in vitro and used as template for Qbeta replicase to synthesize one generation of plus strands. E. coli spheroplasts were infected with the newly synthesized plus strands and phage recovered from single plaques. RNA sequence analysis revealed that four out of the eighteen phage clones analyzed contained RNA with an A leads to G transition at position 40 from the 3' end (which corresponds to position 39 of the minus strand). Thus, the viability of phage Qbeta does not depend on a unique nucleotide sequence in the 3'-extracistronic RNA segment. Upon in vivo propagation of mutant 40, spontaneous true revertants arose with high frequency and overgrew the parental clone within about 10 passages, indicating a selective disadvantage of the extracistronic mutant. Replication of mixtures of wild type and mutant RNA in vitro resulted in a decrease of the proportion of mutated RNA in the progeny plus strands. The fact that Qbeta RNA containing an A leads to G transition in nucleotide--40 of Qbeta RNA is less efficiently replicated in vitro may explain the selective disadvantage of the mutant phage in vivo. The preparation of an infectious mutated RNA by site-directed mutagenesis shows that the method is suitable to produce specific nucleotide exchanges without impairing the biological competence of the RNA.
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Favre A, Morel C, Scherrer K. The secondary structure and poly(A) content of globin messenger RNA as a pure RNA and in polyribosome-derived ribonucleoprotein complexes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 57:147-57. [PMID: 1175639 DOI: 10.1111/j.1432-1033.1975.tb02285.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The conformation in solution of duck and rabbit globin mRNA, and of the duck mRNA in the mRNA - protein particle, has been investigated by optical methods and also by the use of the dye ethidium bromide which becomes highly fluorescent when intercalated into the double-stranded regions of a nucleic acid. On the basis of the properties of this dye and on the ability of homopolyribonucleotides to form double-stranded structures we have, in addition, developed a simple and sensitive assay for the detection and quantitisation of sequences rich in a particular residue that may be present in an RNA chain. In solution, 45 to 60% of the nucleotides of duck globin nRNA were found to be in bihelical regions. A similar degree of secondary structure was found in rabbit globin mRNA (this paper), as well as in calf lens mRNA and mRNAs from ewe mammary gland (other results). All samples of globin mRNA examined in this work containeda sequence of poly(A), which has poly(U) binding properties similar to that of synthetic poly(a): no specific interaction between the poly(A) sequence and the rest of the molecules can be detected. The fraction of adenosine residues within these poly(A) segments represents 4% in rabbit mRNA and 8 to 9% in duck mRNA. An additional adenosine-rich segment interspersed with guanosine and possibly other residues, was also detected in one duck mRNA sample. The RNA in the duck mRNA - protein particle is also highly structured. The melting profile in the range of 20 to 65 degrees C is quite similar to that of free mRNA and the ability of ethidium bromide to intercalate is reduced to the extent of 70%. Yet the dichroic spectra of free and bound mRNA are significantly distinct. These data suggest that free and protein-bound mRNA May have a very similar degree of secondary structure but with distinct detailed conformation in bihelical regions (change in base tilting for example). Direct evidence has been obtained that proteins stick to the poly(A) segment in the particle since the fraction of adenosine residues detectable by our poly(u) titration procedure is reduced to 50% of that observed in the free mRNA.
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15
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Klämbt D. A model for messenger RNA sequences maximizing secondary structure due to code degeneracy. J Theor Biol 1975; 52:57-65. [PMID: 1152488 DOI: 10.1016/0022-5193(75)90039-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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16
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Hofstetter H, Monstein HJ, Weissmann C. The readthrough protein A1 is essential for the formation of viable Q beta particles. BIOCHIMICA ET BIOPHYSICA ACTA 1974; 374:238-51. [PMID: 4611493 DOI: 10.1016/0005-2787(74)90366-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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Flavell RA, Sabo DL, Bandle EF, Weissmann C. Site-directed mutagenesis: generation of an extracistronic mutation in bacteriophage Q beta RNA. J Mol Biol 1974; 89:255-72. [PMID: 4444051 DOI: 10.1016/0022-2836(74)90517-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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19
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Rensing UF, Coulson A, Schoenmakers JG. A sequence of 54 nucleotides from the A-protein cistron of coliphage-R17 RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 41:431-8. [PMID: 4361645 DOI: 10.1111/j.1432-1033.1974.tb03284.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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20
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Porter AG, Hindley J, Billeter MA. A sequence of 83 nucleotides containing the replicase cistron ribosome binding site of phage Qbeta RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 41:413-20. [PMID: 4593581 DOI: 10.1111/j.1432-1033.1974.tb03282.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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21
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Marotta CA, Levy CC, Weissman SM, Varricchio F. Preferred sites of digestion of a ribonuclease from Enterobacter sp. in the sequence analysis of Bacillus stearothermophilus 5S ribonucleic acid. Biochemistry 1973; 12:2901-4. [PMID: 4719125 DOI: 10.1021/bi00739a020] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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22
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Arrand JR, Hindley J. Nucleotide sequence of a ribosome binding site on RNA synthesized in vitro from coliphage T7. NATURE: NEW BIOLOGY 1973; 244:10-3. [PMID: 4578422 DOI: 10.1038/newbio244010a0] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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23
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Silverman PM. Replication of RNA viruses: specific binding of the Q RNA polymerase to Q RNA. Arch Biochem Biophys 1973; 157:222-33. [PMID: 4716954 DOI: 10.1016/0003-9861(73)90408-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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24
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Abstract
Treatment of insect polyribosomes with 1 M KCl released a messenger ribonucleoprotein with a pronounced 16S peak. Phenol extraction resulted in a defined peak of 10S RNA, which was judged as mRNA by the following criteria: it showed specificity for binding to ribosomes, and the formation of initiation complex was dependent on protein initiation factors, GTP, mRNA, and aminoacyl-tRNA. The complex directed protein synthesis upon the addition of elongation factors. mRNA was treated with phosphatase and phosphorylated at the 5'-end with [(32)P]cyanoethylphosphate. [(32)P]mRNA was digested by T1 ribonuclease to completion and chromatographed on DEAE-cellulose. The only fragment with (32)P was 15 nucleotides long; it was treated with pancreatic ribonuclease and fingerprinted. Fractions of AC, AAC, and AAAC were found. Initiation signal AUG or GUG in these mRNAs does not begin immediately at the 5'-end and may be at a distance greater than 15 nucleotides. Alkaline hydrolysis of mRNAs labeled in vivo with [(14)C]adenosine revealed Ap and pppAp. Alkaline hydrolysis of mRNA labeled with (32)P at the 5'-terminus resulted in pAp. Hence, these results suggest that in a heterogeneous population of mRNAs from insects, all start with A and have sequence homology at the 5'-termini. This sequence may reflect the signal for RNA polymerase on the gene or may promote the binding of mRNA to ribosomes.
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25
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Rensing UF, Coulson A, Thompson EO. Nucleotide sequences of similar size from the coliphage R17 genome. Biochem J 1973; 131:605-10. [PMID: 4720715 PMCID: PMC1177508 DOI: 10.1042/bj1310605] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A sequence of 33 nucleotides from the coliphage R17 RNA genome was determined. It constitutes the main component of a mixture of fragments that migrate together on electrophoresis in a separation according to molecular weight. Fragments of comparable chain length from 3' end of RNA from coliphage R17, from a region preceding and overlapping the coat-protein cistron ribosome binding site and from the beginning of the A-protein cistron, were also found and characterized. ;Hairpin'-like secondary structures are proposed for the longer fragments, one of which appears to have a tetranucleotide excised in the loop region.
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Abstract
1. A sequence of 73 nucleotides of the RNA genome from coliphage R17 was determined. It can be read through in only one translational frame. The fragment is not part of the coatprotein cistron (Min Jou et al., 1972), nor does it come from the untranslated sequences described previously (Steitz, 1969; Nichols, 1970; Cory et al., 1970; de Wachter et al., 1971; Contreras et al., 1971; Cory et al., 1972). It contains two sequences of 23 and 24 nucleotides, 22 of which are identical. This kind of reiteration is the first one found in bacteriophage nucleic acid. 2. Improved conditions were found and tested for blocking oligonucleotides with carbodi-imide and cleaving by ribonuclease A at cytidylate residues. 3. A synthetic medium is described which allows labelling in vivo with (32)P to give specific radioactivities higher than those obtained in the procedures used previously.
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Rensing UF, Schoenmakers GG. A sequence of 50 nucleotides from coliphage R17 RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 33:8-18. [PMID: 4347963 DOI: 10.1111/j.1432-1033.1973.tb02648.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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28
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August JT, Eoyang L, Franze de Fernández MT, Hayward WS, Kuo CH, Silverman PM. Host proteins in the replication of bacteriophage RNA. BASIC LIFE SCIENCES 1973; 1:29-41. [PMID: 4589683 DOI: 10.1007/978-1-4684-0877-5_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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29
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Hindley J. Structure and strategy in phage RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1973; 26:269-321. [PMID: 4575322 DOI: 10.1016/0079-6107(73)90021-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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30
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Porter AG, Hindley J. Characterization of extended sequences around the coat and replicase cistron ribosome binding sites in phage Q RNA. FEBS Lett 1972; 26:139-44. [PMID: 4564654 DOI: 10.1016/0014-5793(72)80560-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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31
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Adams JM, Cory S, Spahr PF. Nucleotide sequences of fragments of R17 bacteriophage RNA from the region immediately preceding the coat-protein cistron. EUROPEAN JOURNAL OF BIOCHEMISTRY 1972; 29:469-79. [PMID: 4563341 DOI: 10.1111/j.1432-1033.1972.tb02011.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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32
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Jeppesen PG, Barrell BG, Sanger F, Coulson AR. Nucleotide sequences of two fragments from the coat-protein cistron of bacteriophage R17 ribonucleic acid. Biochem J 1972; 128:993-1006. [PMID: 4566195 PMCID: PMC1173988 DOI: 10.1042/bj1280993h] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Bacteriophage R17 RNA was labelled with (32)P and was subjected to partial digestion with ribonuclease T(1). The products were fractionated by ionophoresis on polyacrylamide gel. Two fragments were purified and their nucleotide sequences determined by methods involving complete and further partial digestion with ribonucleases A and T(1). Fragment 20 had a sequence that coded for the amino acids in positions 32-53 of the coat protein of the bacteriophage. Fragment 20X, on further purification in 7m-urea, gave rise to two smaller nucleotides whose sequences coded for the amino acids in positions 56-66 and 67-76 of the coat protein. The sequence of the two fragments was such that they could be written in the form of loops stabilized by base-pairing.
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Robinson JW. Properties of the ribonucleic acid bacteriophage ZIK-1 coat protein and its synthesis in an Escherichia coli cell-free system. Biochem J 1972; 128:481-9. [PMID: 4564257 PMCID: PMC1173800 DOI: 10.1042/bj1280481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The coat protein subunit of the RNA bacteriophage ZIK/1 has a molecular weight of 12100 and does not contain histidine, methionine and cysteine. The amino acid composition of the coat protein is different from that of other RNA bacteriophage coat proteins. Bacteriophage ZIK/1 belongs to a class of RNA bacteriophages distinct from the f2 type, which lack histidine in their coat proteins, and the Qbeta type, which lack histidine and methionine. Bacteriophage ZIK/1 RNA is an efficient template in the Escherichia coli cell-free system producing coat protein as the major product and a number of non-coat proteins. This result is similar to that obtained with RNA from f2-type bacteriophages. It is probable that the genomes of RNA bacteriophages are structurally similar and that differences between the types of RNA bacteriophage arise from minor differences in RNA sequence.
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36
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Temple GF, Housman DE. Separation and translation of the mRNAs coding for and chains of rabbit globin. Proc Natl Acad Sci U S A 1972; 69:1574-7. [PMID: 4504371 PMCID: PMC426751 DOI: 10.1073/pnas.69.6.1574] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
A method is presented to separate the mRNAs coding for alpha and beta globins of rabbit reticulocytes. 10S RNA was extracted from the light and heavy polysomes created by incubation of reticulocytes with L-O-methylthreonine, and assayed for mRNA activity in an ascites cell-free extract. Tryptic digests of the in vitro products demonstrated that the heavy polysomes yielded beta globin mRNA at least 90% free of alpha mRNA activity, and that the light polysomes yielded alpha mRNA at least 70% free of beta mRNA activity.
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Morrison MR, Paul J, Williamson R. The DNA-RNA hybridisation of ( 3 H) methylated mouse-globin mRNA in conditions of RNA excess. EUROPEAN JOURNAL OF BIOCHEMISTRY 1972; 27:1-9. [PMID: 4558855 DOI: 10.1111/j.1432-1033.1972.tb01803.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Padmanabhan R, Wu R. Nucleotide sequence analysis of DNA. IV. Complete nucleotide sequence of the left-hand cohesive end of coliphage 186 DNA. J Mol Biol 1972; 65:447-67. [PMID: 4554112 DOI: 10.1016/0022-2836(72)90201-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Kozak M, Nathans D. Translation of the genome of a ribonucleic acid bacteriophage. BACTERIOLOGICAL REVIEWS 1972; 36:109-34. [PMID: 4555183 PMCID: PMC378432 DOI: 10.1128/br.36.1.109-134.1972] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Nichols JL, Hay AJ, Joklik WK. 5'-terminal nucleotide sequence of reovirus mRNA synthesized in vitro. NATURE: NEW BIOLOGY 1972; 235:105-7. [PMID: 4501191 DOI: 10.1038/newbio235105a0] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Cory S, Adams JM, Spahr PF, Rensing U. Sequence of 51 nucleotides at the 3'-end of R17 bacteriophage RNA. J Mol Biol 1972; 63:41-56. [PMID: 5016970 DOI: 10.1016/0022-2836(72)90520-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Affiliation(s)
- V Ling
- Medical Research Council, Laboratory of Molecular Biology Hills Road, Cambridge, England
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McLachlan AD. Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551 . J Mol Biol 1971; 61:409-24. [PMID: 5167087 DOI: 10.1016/0022-2836(71)90390-1] [Citation(s) in RCA: 382] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Sanger F. Nucleotide sequences in bacteriophage ribonucleic acid. The eighth hopkins memorial lecture. Biochem J 1971; 124:833-43. [PMID: 5131010 PMCID: PMC1177270 DOI: 10.1042/bj1240833a] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Mangiarotti G, Schlessinger D, Kuwano M. Initiation of ribosome-dependent breakdown of T4-specific messenger RNA. J Mol Biol 1971; 60:441-52. [PMID: 5110312 DOI: 10.1016/0022-2836(71)90180-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Jeppesen PG. The nucleotide sequences of some large ribonuclease T 1 products from bacteriophage R17 ribonucleic acid. Biochem J 1971; 124:357-66. [PMID: 5158505 PMCID: PMC1177150 DOI: 10.1042/bj1240357] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A method of ;fingerprinting' high-molecular-weight (32)P-labelled RNA species, using a two-dimensional thin-layer-chromatographic separation of ribonuclease T(1) digestion products, has been applied to RNA from the Escherichia coli bacteriophage R17. The ;fingerprinting' technique, besides giving a unique pattern that can be used as a characterization of the RNA, has made it possible to isolate a number of the larger oligonucleotides and to determine their nucleotide sequences.
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Lebowitz P, Weissman SM, Radding CM. Nucleotide Sequence of a Ribonucleic Acid Transcribed in Vitro from λ Phage Deoxyribonucleic Acid. J Biol Chem 1971. [DOI: 10.1016/s0021-9258(18)61977-5] [Citation(s) in RCA: 132] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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