A genomic clone encoding a novel proliferation-dependent histone H2A.1 mRNA enriched in the poly(A)+ fraction

1990 ◽  
Vol 10 (6) ◽  
pp. 2848-2854
Author(s):  
L Fecker ◽  
P Ekblom ◽  
M Kurkinen ◽  
M Ekblom
Keyword(s):  
Genomic Sequence ◽  
Genomic Clone ◽  
Polyadenylation Signal ◽  
Histone H2a ◽  
Hairpin Loop ◽  
Coding Region ◽  
Genomic Clones ◽  
Histone Mrnas ◽  
Cellulose Column

Replication-dependent histone mRNAs are prime examples of nonpolyadenylated mRNAs. We isolated and characterized cDNAs and a genomic clone for a replication-dependent histone H2A.1 mRNA which segregated into the poly(A)+ fraction during mRNA isolation through an oligo(dT)-cellulose column. However, the results of sequencing of the genomic clone suggested that the mRNA did not contain a poly(A) tail. Instead, the genomic sequence revealed a nonterminal oligo(A) tract directly upstream from the typical 3'-terminal hairpin loop of replication-dependent histone mRNAs. The nonterminal oligo(A) tract consisted of 14 adenylate residues interrupted by one guanylate residue (A4GA10). We concluded that this short oligo(A) stretch mediated binding of the mRNA to oligo(dT) even after stringent washes with 0.1 M NaCl, indicating that rather short oligo(A) sequences can ensure binding to oligo(dT)-cellulose. The cDNA and genomic clones contained an AAATAAG sequence at the end of the coding region. It has been suggested that this sequence contains a polyadenylation signal in some yeast and mouse transcripts, but it does not function as a polyadenylation signal in the histone transcript described in this paper.

scholarly journals A genomic clone encoding a novel proliferation-dependent histone H2A.1 mRNA enriched in the poly(A)+ fraction.

1990 ◽  
Vol 10 (6) ◽  
pp. 2848-2854 ◽  
Author(s):  
L Fecker ◽  
P Ekblom ◽  
M Kurkinen ◽  
M Ekblom
Keyword(s):  
Genomic Sequence ◽  
Genomic Clone ◽  
Polyadenylation Signal ◽  
Histone H2a ◽  
Hairpin Loop ◽  
Coding Region ◽  
Genomic Clones ◽  
Histone Mrnas ◽  
Cellulose Column

Replication-dependent histone mRNAs are prime examples of nonpolyadenylated mRNAs. We isolated and characterized cDNAs and a genomic clone for a replication-dependent histone H2A.1 mRNA which segregated into the poly(A)+ fraction during mRNA isolation through an oligo(dT)-cellulose column. However, the results of sequencing of the genomic clone suggested that the mRNA did not contain a poly(A) tail. Instead, the genomic sequence revealed a nonterminal oligo(A) tract directly upstream from the typical 3'-terminal hairpin loop of replication-dependent histone mRNAs. The nonterminal oligo(A) tract consisted of 14 adenylate residues interrupted by one guanylate residue (A4GA10). We concluded that this short oligo(A) stretch mediated binding of the mRNA to oligo(dT) even after stringent washes with 0.1 M NaCl, indicating that rather short oligo(A) sequences can ensure binding to oligo(dT)-cellulose. The cDNA and genomic clones contained an AAATAAG sequence at the end of the coding region. It has been suggested that this sequence contains a polyadenylation signal in some yeast and mouse transcripts, but it does not function as a polyadenylation signal in the histone transcript described in this paper.

scholarly journals Characterization of Tomato Necrotic Spot Virus, a Subgroup 1 Ilarvirus Causing Necrotic Foliar, Stem, and Fruit Symptoms in Tomatoes in the United States

Plant Disease ◽  
2019 ◽  
Vol 103 (6) ◽  
pp. 1391-1396 ◽  
Author(s):  
Sara A. Bratsch ◽  
Samuel Grinstead ◽  
Tom C. Creswell ◽  
Gail E. Ruhl ◽  
Dimitre Mollov
Keyword(s):  
Genomic Sequence ◽  
The United States ◽  
Amino Acid Identity ◽  
Necrotic Spot ◽  
Coding Region ◽  
Spot Virus ◽  
Protein Coding ◽  
Serological Characterization ◽  
Necrotic Spots

The genomic, biological, and serological characterization of tomato necrotic spot virus (ToNSV), a virus first described infecting tomato in California, was completed. The complete genomic sequence identified ToNSV as a new subgroup 1 ilarvirus distinct from the previously described tomato-infecting ilarviruses. We identified ToNSV in Indiana in 2017 and 2018 and in Ohio in 2018. The coat protein coding region of the isolates from California, Indiana, and Ohio have 94 to 98% identity, while the same isolates had 99% amino acid identity. ToNSV is serologically related to TSV, a subgroup 1 ilarvirus, and shows no serological relationship to ilarviruses in the other subgroups. In tomato, ToNSV caused symptoms of necrotic spots and flecks on leaves, necrotic streaking on stems, and necrotic spots and circular patterns on fruit resulting in a yield loss of 1 to 13%. These results indicate that ToNSV is a proposed new subgroup 1 ilarvirus causing a necrotic spotting disease of tomato observed in California, Indiana, and Ohio.

scholarly journals Genetic characterization of a Marek’s disease virus strain isolated in Japan

2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Shiro Murata ◽  
Yuka Machida ◽  
Masayoshi Isezaki ◽  
Naoya Maekawa ◽  
Tomohiro Okagawa ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Virus ◽  
Genomic Sequence ◽  
Marek's Disease Virus ◽  
Marek's Disease ◽  
Marek’S Disease Virus ◽  
Marek’S Disease ◽  
Coding Region ◽  
Japanese Strain ◽  
Genetic Characteristics

Abstract Background Marek’s disease virus (MDV) causes malignant lymphomas in chickens (Marek’s disease, MD). MD is currently controlled by vaccination; however, MDV strains have a tendency to develop increased virulence. Distinct diversity and point mutations are present in the Meq proteins, the oncoproteins of MDV, suggesting that changes in protein function induced by amino acid substitutions might affect MDV virulence. We previously reported that recent MDV isolates in Japan display distinct mutations in Meq proteins from those observed in traditional MDV isolates in Japan, but similar to those in MDV strains isolated from other countries. Methods To further investigate the genetic characteristics in Japanese field strains, we sequenced the whole genome of an MDV strain that was successfully isolated from a chicken with MD in Japan. A phylogenetic analysis of the meq gene was also performed. Results Phylogenetic analysis revealed that the Meq proteins in most of the Japanese isolates were similar to those of Chinese and European strains, and the genomic sequence of the Japanese strain was classified into the Eurasian cluster. Comparison of coding region sequences among the Japanese strain and MDV strains from other countries revealed that the genetic characteristics of the Japanese strain were similar to those of Chinese and European strains. Conclusions The MDV strains distributed in Asian and European countries including Japan seem to be genetically closer to each other than to MDV strains from North America. These findings indicate that the genetic diversities of MDV strains that emerged may have been dependent on the different vaccination-based control approaches.

Identifying Novel Blood Proteins and Protein Isoforms Using Tandem Mass Spectra.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1616-1616
Author(s):  
Damian Fermin ◽  
Baxter B. Allen ◽  
Thomas W. Blackwell ◽  
Rajasree Menon ◽  
Marcin Adamski ◽  
...  
Keyword(s):  
Human Genome ◽  
Genomic Sequence ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Protein Isoforms ◽  
Blood Protein ◽  
Tandem Mass ◽  
Blood Proteins ◽  
Coding Region ◽  
Significant Alignment

Abstract Blood is a complex fluid that samples all tissues in the human body. Despite complete sequence determination of the human genome, defining genes and gene products remains a challenge. Here, we apply tandem mass spectroscopy as new source of unbiased data to interrogate genomic sequence and identify novel protein coding sequences. A six-frame translation of the Human genome was used as the query database to search for novel blood proteins in the data from the HUPO PPP. Significance is assessed using a Poisson statistical model incorporating the length of the matching sequence and the frequency of spectrum matches observed in searching the database [Nat Biotech 2006 24(3):333–8]. Matches are binned by X!Tandem hyperscore, and statistics for each score class are considered independently. The overall probability that the matches to an ORF occurred at random is calculated as the product of the probability that the matches in each score category occurred at random. The expected number of random matches, E, is calculated as the product of the probability that an ORF match occurred at random multiplied by the number of ORFs searched. The confidence in an ORF identification is 1/(1+E). An open reading frame is considered significant if confidence is greater than 95%. Expanding recently published work [Genome Biol2006; 7(4):R35], we have identified 837 significant open reading frames coding for 18852 peptides falling within 914 exons of 413 genes. Out of 8856 candidate ORFs outside the boundaries of known genes, 3246 of them achieved a confidence >= 0.95. We also required the XG ORFs to be supported by at least 3 distinct ESTs. Twenty four of the XG ORFs were found to have a significant alignment to the mouse genome. Of these, 13 of the alignments encompassed a coding region for one of the diagnostic peptides associated with the ORF. Gene models for the XG ORFS were derived from the GENSCAN prediction made for their coding regions. This analysis suggests that alternative splicing of blood protein genes is common and that much remains to be learned about the protein constituents of blood.

scholarly journals Characterization of a Novel vpu-Harboring Simian Immunodeficiency Virus from a Dent's Mona Monkey (Cercopithecus mona denti)

2005 ◽  
Vol 79 (13) ◽  
pp. 8560-8571 ◽  
Author(s):  
Marie-Christine Dazza ◽  
Michel Ekwalanga ◽  
Monique Nende ◽  
Karhemere Bin Shamamba ◽  
Pitchou Bitshi ◽  
...  
Keyword(s):  
Simian Immunodeficiency Virus ◽  
Genomic Sequence ◽  
Democratic Republic Of Congo ◽  
Coding Region ◽  
Reading Frame ◽  
Immunodeficiency Virus ◽  
Primate Lentiviruses ◽  
Infected Cells ◽  
Mona Monkey ◽  
Hiv 1

ABSTRACT We report the identification of a new simian immunodeficiency virus (SIV), designated SIVden, in a naturally infected Dent's Mona monkey (Cercopithecus mona denti), which was kept as pet in Kinshasa, capital of the Democratic Republic of Congo. SIVden is genetically distinct from the previously characterized primate lentiviruses. Analysis of the full-length genomic sequence revealed the presence of a vpu open reading frame. This gene is also found in the virus lineage of human immunodeficiency virus type 1 (HIV-1) and chimpanzee immunodeficiency virus (SIVcpz) and was recently described in viruses isolated from Cercopithecus nictitans, Cercopithecus mona, and Cercopithecus cephus. The SIVden vpu coding region is shorter than the HIV-1/SIVcpz and the SIVgsn, SIVmon, and SIVmus counterparts. Unlike Pan troglodytes schweinfurthii viruses (SIVcpzPts) and Cercopithecus monkey viruses (SIVgsn, SIVmon, and SIVmus), the SIVden Vpu contains the characteristic DSGXES motif which was shown to be involved in Vpu-mediated CD4 and IκBα proteolysis in HIV-1 infected cells. Although it harbors a vpu gene, SIVden is phylogenetically closer to SIVdeb isolated from De Brazza's monkeys (Cercopithecus neglectus), which lacks a vpu gene, than to Cercopithecus monkey viruses, which harbor a vpu sequence.

scholarly journals Isolation and cloning of the raccoon (Procyon lotor) papillomavirus type 1 by using degenerate papillomavirus-specific primers

2005 ◽  
Vol 86 (7) ◽  
pp. 2029-2033 ◽  
Author(s):  
Annabel Rector ◽  
Koenraad Van Doorslaer ◽  
Mads Bertelsen ◽  
Ian K. Barker ◽  
Rolf-Arne Olberg ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Procyon Lotor ◽  
Cutaneous Lesion ◽  
Open Reading Frames ◽  
Coding Region ◽  
Specific Primers ◽  
Entire Genome ◽  
Early Proteins ◽  
Late Protein

Partial sequences of a novel papillomavirus were amplified from a cutaneous lesion biopsy of a raccoon (Procyon lotor), by using PCR with degenerate papillomavirus-specific primers. The Procyon lotor papillomavirus type 1 (PlPV-1) DNA was amplified with long template PCR in two overlapping fragments, together encompassing the entire genome, and the complete PlPV-1 genomic sequence was determined. The PlPV-1 genome consists of 8170 bp, and contains the typical papillomaviral open reading frames, encoding five early proteins and two late capsid proteins. Besides the classical non-coding region (NCR1) between the end of L1 and the start of E6, PlPV-1 contains an additional non-coding region (NCR2) of 1065 bp between the early and late protein region, which has previously also been described for the canine oral papillomavirus (COPV) and the Felis domesticus papillomavirus (FdPV-1). Phylogenetic analysis places PlPV-1 together with COPV and FdPV-1 in a monophyletic branch which encompasses the Lambda papillomavirus genus.

scholarly journals Complete Genomic Sequence of the Virulent Salmonella Bacteriophage SP6

2004 ◽  
Vol 186 (7) ◽  
pp. 1933-1944 ◽  
Author(s):  
Aleisha T. Dobbins ◽  
Matthew George ◽  
Daryl A. Basham ◽  
Michael E. Ford ◽  
Jennifer M. Houtz ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Genomic Sequence ◽  
Bioinformatic Analysis ◽  
Complete Genomic Sequence ◽  
Coding Region ◽  
Gene Encoding ◽  
Serovar Typhimurium ◽  
The Right ◽  
Direct Terminal Repeat ◽  
Complete Genomic

ABSTRACT We report the complete genome sequence of enterobacteriophage SP6, which infects Salmonella enterica serovar Typhimurium. The genome contains 43,769 bp, including a 174-bp direct terminal repeat. The gene content and organization clearly place SP6 in the coliphage T7 group of phages, but there is ∼5 kb at the right end of the genome that is not present in other members of the group, and the homologues of T7 genes 1.3 through 3 appear to have undergone an unusual reorganization. Sequence analysis identified 10 putative promoters for the SP6-encoded RNA polymerase and seven putative rho-independent terminators. The terminator following the gene encoding the major capsid subunit has a termination efficiency of about 50% with the SP6-encoded RNA polymerase. Phylogenetic analysis of phages related to SP6 provided clear evidence for horizontal exchange of sequences in the ancestry of these phages and clearly demarcated exchange boundaries; one of the recombination joints lies within the coding region for a phage exonuclease. Bioinformatic analysis of the SP6 sequence strongly suggested that DNA replication occurs in large part through a bidirectional mechanism, possibly with circular intermediates.

Generation, characterization, and molecular cloning of the Noerg-1 mutation of rhodopsin in the mouse

2005 ◽  
Vol 22 (5) ◽  
pp. 619-629 ◽  
Author(s):  
LAWRENCE H. PINTO ◽  
MARTHA H. VITATERNA ◽  
KAZUHIRO SHIMOMURA ◽  
SANDRA M. SIEPKA ◽  
ERIN L. MCDEARMON ◽  
...  
Keyword(s):  
Autosomal Dominant ◽  
De Novo ◽  
Genomic Sequence ◽  
Outer Nuclear Layer ◽  
Dna Polymorphisms ◽  
Fundus Photography ◽  
Induced Mutations ◽  
Coding Region ◽  
Optomotor Response

We performed genome-wide mutagenesis of C57BL/6J mice using the mutagen N-ethyl-N-nitrosourea (ENU) and screened the third generation (G3) offspring for visual system alterations using electroretinography and fundus photography. Several mice in one pedigree showed characteristics of retinal degeneration when tested at 12–14 weeks of age: no recordable electroretinogram (ERG), attenuation of retinal vessels, and speckled pigmentation of the fundus. Histological studies showed that the retinas undergo a photoreceptor degeneration with apoptotic loss of outer nuclear layer nuclei but visual acuity measured using the optomotor response under photopic conditions persists in spite of considerable photoreceptor loss. The Noerg-1 mutation showed an autosomal dominant pattern of inheritance in progeny. Studies in early postnatal mice showed degeneration to occur after formation of partially functional rods. The Noerg-1 mutation was mapped genetically to chromosome 6 by crossing C57BL/6J mutants with DBA/2J or BALB/cJ mice to produce an N2 generation and then determining the ERG phenotypes and the genotypes of the N2 offspring at multiple loci using SSLP and SNP markers. Fine mapping was accomplished with a set of closely spaced markers. A nonrecombinant region from 112.8 Mb to 115.1 Mb was identified, encompassing the rhodopsin (Rho) coding region. A single nucleotide transition from G to A was found in the Rho gene that is predicted to result in a substitution of Tyr for Cys at position 110, in an intradiscal loop. This mutation has been found in patients with autosomal dominant retinitis pigmentosa (RP) and results in misfolding of rhodopsin expressed in vitro. Thus, ENU mutagenesis is capable of replicating mutations that occur in human patients and is useful for generating de novo models of human inherited eye disease. Furthermore, the availability of the mouse genomic sequence and extensive DNA polymorphisms made the rapid identification of this gene possible, demonstrating that the use of ENU-induced mutations for functional gene identification is now practical for individual laboratories.

scholarly journals Structure, expression and duplication of genes which encode phosphoglyceromutase of Drosophila melanogaster.

Genetics ◽  
1994 ◽  
Vol 138 (2) ◽  
pp. 353-363
Author(s):  
P D Currie ◽  
D T Sullivan
Keyword(s):  
Molecular Evolution ◽  
Genomic Sequence ◽  
Glycolytic Enzyme ◽  
Coding Region ◽  
Subsequent Increase ◽  
Rnase Protection ◽  
Reading Frame ◽  
Isolation And Characterization ◽  
Genomic Regions

Abstract We report here the isolation and characterization of genes from Drosophila that encode the glycolytic enzyme phosphoglyceromutase (PGLYM). Two genomic regions have been isolated that have potential to encode PGLYM. Their cytogenetic localizations have been determined by in situ hybridization to salivary gland chromosomes. One gene, Pglym78, is found at 78A/B and the other, Pglym87, at 87B4,5 of the Drosophila polytene map. Pglym78 transcription follows a developmental pattern similar to other glycolytic genes in Drosophila, i.e., substantial maternal transcript deposited during oogenesis; a decline in abundance in the first half of embryogenesis; a subsequent increase in the second half of embryogenesis which continues throughout larval life; a decline in pupae and a second increase to a plateau in adults. This transcript has been mapped by cDNA and genomic sequence comparison, RNase protection, and primer extension. Using similar analyses transcripts of Pglym87 could not be detected. Pglym78 has two introns which interrupt the coding region, while the Pglym87 gene lacks introns. This and other features support a model of retrotransposition mediated gene duplication for the origin of Pglym87. The apparent absence of a complete, intact coding frame and transcript suggest that Pglym87 is a pseudogene. However, retention of reading frame and codon bias suggests that Pglym87 may retain coding function, or may have been inactivated recently, substantially after the time of duplication, or that the molecular evolution of Pglym87 is unusual. Similarities of the unusual molecular evolution of Pglym87 and other proposed pseudogenes are discussed.

Sign in / Sign up

Export Citation Format

Share Document