scholarly journals Identification of the principal promoter sequence of the c-H-ras transforming oncogene: deletion analysis of the 5'-flanking region by focus formation assay.

1987 ◽  
Vol 7 (8) ◽  
pp. 2933-2940 ◽  
Author(s):  
H Honkawa ◽  
W Masahashi ◽  
S Hashimoto ◽  
T Hashimoto-Gotoh
Keyword(s):  
Dna Sequences ◽  
Promoter Sequence ◽  
Ras Oncogene ◽  
Coding Region ◽  
Focus Formation ◽  
S1 Nuclease ◽  
Protein Coding ◽  
Consensus Sequences ◽  
Flanking Region ◽  
Virus C

A number of deletion mutants were isolated, including 5', 3', and internal deletions in the 5'-flanking region of the human cellular oncogene related to the Harvey sarcoma virus (c-H-ras), and their transforming activities were examined in NIH 3T3 cells. DNA sequences which could not be detected without losing transforming activity were localized to a relatively short stretch upstream of the region which showed homology to the 5'-flanking region of v-H-ras oncogene. S1 nuclease analysis indicated that there were two clusters of mRNA start sites at positions that were about 1,371 and 1,298 base pairs upstream of the first coding ATG. The minimum region required for promoter function was estimated to be a 51-base-pair-long (or less) DNA segment. The promoter was GC rich (78%) and did not contain the consensus sequences that are usually observed in PolII-directed promoters but contained a GC box within which one of the mRNA start sites was included. In addition, two sets of positive and negative elements seemed to be located between the promoter and the protein-coding region, which appeared to influence positively and negatively, respectively, the efficiency of transformation with the c-H-ras oncogene.

Identification of the principal promoter sequence of the c-H-ras transforming oncogene: deletion analysis of the 5'-flanking region by focus formation assay

1987 ◽  
Vol 7 (8) ◽  
pp. 2933-2940
Author(s):  
H Honkawa ◽  
W Masahashi ◽  
S Hashimoto ◽  
T Hashimoto-Gotoh
Keyword(s):  
Dna Sequences ◽  
Promoter Sequence ◽  
Ras Oncogene ◽  
Coding Region ◽  
Focus Formation ◽  
S1 Nuclease ◽  
Protein Coding ◽  
Consensus Sequences ◽  
Flanking Region ◽  
Virus C

A number of deletion mutants were isolated, including 5', 3', and internal deletions in the 5'-flanking region of the human cellular oncogene related to the Harvey sarcoma virus (c-H-ras), and their transforming activities were examined in NIH 3T3 cells. DNA sequences which could not be detected without losing transforming activity were localized to a relatively short stretch upstream of the region which showed homology to the 5'-flanking region of v-H-ras oncogene. S1 nuclease analysis indicated that there were two clusters of mRNA start sites at positions that were about 1,371 and 1,298 base pairs upstream of the first coding ATG. The minimum region required for promoter function was estimated to be a 51-base-pair-long (or less) DNA segment. The promoter was GC rich (78%) and did not contain the consensus sequences that are usually observed in PolII-directed promoters but contained a GC box within which one of the mRNA start sites was included. In addition, two sets of positive and negative elements seemed to be located between the promoter and the protein-coding region, which appeared to influence positively and negatively, respectively, the efficiency of transformation with the c-H-ras oncogene.

Human DNA sequences homologous to a protein coding region conserved between homeotic genes of Drosophila

Cell ◽  
1984 ◽  
Vol 38 (3) ◽  
pp. 667-673 ◽  
Author(s):  
Michael Levine ◽  
Gerald M. Rubin ◽  
Robert Tjian
Keyword(s):  
Dna Sequences ◽  
Homeotic Genes ◽  
Coding Region ◽  
Protein Coding ◽  
Human Dna

scholarly journals Hormonally mediated negative regulation of human pro-opiomelanocortin gene expression after transfection into mouse L cells.

1985 ◽  
Vol 5 (9) ◽  
pp. 2443-2453 ◽  
Author(s):  
A Israel ◽  
S N Cohen
Keyword(s):  
Simian Virus 40 ◽  
Simian Virus ◽  
Negative Regulation ◽  
Coding Region ◽  
Transient Expression Assay ◽  
S1 Nuclease ◽  
Protein Coding ◽  
Pomc Gene ◽  
Simplex Virus ◽  
Nuclease Mapping

We report results indicating that expression and hormonally controlled negative regulation of the human pro-opiomelanocortin (POMC) gene in mouse fibroblasts can be accomplished by the placement nearby of a simian virus 40 enhancer sequence. Expression resulting from correctly initiated transcription required the enhancer in cis both in cells stably transfected with the POMC gene and in a transient expression assay with constructs that fused that POMC promoter region to the protein-coding region of the herpes simplex virus thymidine kinase (TK) gene. Negative regulation of POMC transcription by glucocorticoids was demonstrated in transiently infected cells by assaying for TK activity encoded by the POMC-TK fusion constructs and by quantitative S1 nuclease mapping. The sequences responsible for such regulation were shown to be contained within a DNA segment that extends 670 base pairs upstream from the cap site for POMC mRNA.

scholarly journals Coding and functional defect region prediction of placental protein in an embryo cell of first trimester using ANN approach

2018 ◽  
Vol 7 (1.9) ◽  
pp. 167
Author(s):  
Bipin Nair B J ◽  
Rahul Reghunath
Keyword(s):  
Dna Sequences ◽  
Energy Levels ◽  
Threshold Energy ◽  
First Trimester ◽  
Embryo Cell ◽  
Cell Protein ◽  
Coding Region ◽  
Protein Coding ◽  
Functional Region ◽  
Functional Regions

The protein coding and functional regions in DNA sequences has become an exciting task in bioinformatics. In particular, the coding region has a 3-base periodicity, which helps for exon identification. Many signal processing tools and techniques have been successfully applied to identify tasks, but still need to be improved in this direction. In our work, we employ ANN classifier to predict coding and functional region of proteinin human embryo cell protein in first trimester, and evaluate their performances according to the comparison energy levels of coding region. The obtained from the threshold energy level, results show that in a box plot finally predict the mutation.

scholarly journals An unusual adenine phosphoribosyltransferase pseudogene is syntenic with its functional gene and is flanked by highly polymorphic DNAs.

1986 ◽  
Vol 6 (12) ◽  
pp. 4161-4167 ◽  
Author(s):  
M K Dush ◽  
J A Tischfield ◽  
S A Khan ◽  
E Feliciano ◽  
J M Sikela ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Ecori Fragment ◽  
Chromosome 8 ◽  
Functional Gene ◽  
Direct Repeats ◽  
Coding Region ◽  
Adenine Phosphoribosyltransferase ◽  
Protein Coding ◽  
Dna Library ◽  
Processed Pseudogenes

A mouse adenine phosphoribosyltransferase (aprt) pseudogene that had previously been recovered from a BALB/c sperm DNA library possessed several unusual features. Its nucleotide sequence, like that of other processed pseudogenes, was colinear with its corresponding mRNA, but it was truncated at its 3' end and lacked a poly(A) tail. The pseudogene was 82% homologous with corresponding regions of the functional gene and had incurred mutations that included transitions, transversions, deletions, and a point insertion. Even though the pseudogene was truncated within the protein-coding region of the corresponding functional gene, it was flanked at both ends by 13-base-pair direct repeats. Curiously, the direct repeats exhibited homology to APRT mRNA at the site of pseudogene divergence. The pseudogene appeared to be common to BALB/c and A/J mice, but it was contained on a 3-kilobase EcoRI fragment in the former strain and a 4.5-kilobase EcoRI fragment in the latter. The BALB/c and apparently the A/J pseudogene both mapped to chromosome 8, which also contains the functional aprt gene. The DNA sequences immediately surrounding the pseudogene in the two strains appeared to be similar, suggesting that the BALB/c and A/J pseudogenes are allelic. However, DNA sequences more distal to the pseudogene in the two strains appeared to vary. Thus, the EcoRI polymorphism was not due to simple loss of an EcoRI site, but was more complex. The pattern of flanking restriction sites was different for each of several enzymes, consistent with extensive DNA rearrangement. Double digests of BALB/c and A/J genomic DNAs revealed complex polymorphisms on both sides of the pseudogene. The results were consistent with insertion, deletion, or other rearrangement of DNA sequences that flank the pseudogene and suggest that this region of mouse chromosome 8 may be a region active for mutation or recombination.

scholarly journals Structure and tissue-specific expression of the Drosophila melanogaster organellar-type Ca2+-ATPase gene

1995 ◽  
Vol 310 (3) ◽  
pp. 757-763 ◽  
Author(s):  
A Magyar ◽  
E Bakos ◽  
A Váradi
Keyword(s):  
Drosophila Melanogaster ◽  
Transcription Initiation ◽  
Initiation Site ◽  
Drosophila Genome ◽  
Coding Region ◽  
Specific Expression ◽  
S1 Nuclease ◽  
Protein Coding ◽  
Atpase Gene ◽  
High Level

A 14 kb genomic clone covering the organellar-type Ca(2+)-ATPase gene of Drosophila melanogaster has been isolated and characterized. The sequence of a 7132 bp region extending from 1.1 kb 5′ upstream of the initiation ATG codon over the polyadenylation signal at the 3′ end has been determined. The gene consists of nine exons including one with an exceptional size of 2172 bp representing 72% of the protein coding region. Introns are relatively small (< 100 bp) except for the 3′ intron which has a size of 2239 bp, an exceptionally large size among Drosophila introns. Five of the introns are in the same positions in Drosophila, Artemia and rabbit SERCA1 Ca(2+)-ATPase genes. There is only one organellar-type Ca(2+)-ATPase gene in the Drosophila genome, as was shown by Southern-blot analysis [Váradi, Gilmore-Hebert and Benz (1989) FEBS Lett. 258, 203-207] and by chromosomal localization [Magyar and Váradi (1990) Biochem. Biophys. Res. Commun. 173, 872-877]. Primer extension and S1-nuclease assays revealed a potential transcription initiation site 876 bp upstream of the translation initiation ATG with a TATA-box 23 bp upstream of this site. Analysis of the 5′ region of the Drosophila organellar-type Ca(2+)-ATPase gene suggests the presence of potential recognition sequences of various muscle-specific transcription factors and shows a region with remarkable similarity to that in the rabbit SERCA2 gene. The tissue distribution of expression of the organellar-type Ca(2+)-ATPase gene has been studied by in situ RNA-RNA hybridization on microscopic sections. A low mRNA abundance can be detected in each tissue of adult flies, suggesting a housekeeping function for the gene. On the other hand a pronounced tissue specificity of expression has also been found as the organellar-type Ca(2+)-ATPase is expressed at a very high level in cell bodies of the central nervous system and in various muscles.

Molecular screening of both the promoter and the protein coding regions in the human ob gene in Japanese obese subjects with non-insulin-dependent diabetes mellitus

1997 ◽  
pp. 511-513 ◽  
Author(s):  
M Shigemoto ◽  
S Nishi ◽  
Y Ogawa ◽  
N Isse ◽  
N Matsuoka ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Promoter Region ◽  
Insulin Dependent Diabetes Mellitus ◽  
Dependent Diabetes Mellitus ◽  
Coding Region ◽  
Protein Coding ◽  
Ob Gene ◽  
Insulin Dependent ◽  
Obese Subjects ◽  
Flanking Region

OBJECTIVE: Although the molecular mechanism of obesity has been poorly understood, recent studies indicate that leptin plays a critical role in regulating both food intake and body weight. Because obesity decreases the sensitivity to insulin, the human ob gene is presumed to be one of the candidate genes for non-insulin-dependent diabetes mellitus (NIDDM) associated with obesity. Although the protein coding region in the ob gene has been screened for mutations, the promoter region and the non-coding first exon have not yet been studied. We investigated the involvement of the human ob gene, especially mutations at the promoter region and the non-coding first exon, in the development of NIDDM associated with obesity. SUBJECTS: The study group comprised 60 Japanese obese subjects with NIDDM (body mass index (BMI) 43.6 > or = BMI > or = 26.4, 29.0+/-0.41 (mean+/-S.E.M.)) and 24 obese individuals with impaired glucose tolerance (IGT) (30 > or = BMI > or = 26.4, 27.1+/-0.22). METHODS: Mutations at both the promoter region and all three exons in the human ob gene were screened by the single-stranded conformational polymorphism analysis. When aberrantly migrated bands were recognized, the PCR-amplified DNA fragment was directly sequenced. RESULTS: In the protein coding region a silent mutation in the second exon was detected. The non-coding first exon and the about 100 bp 5'-flanking region of the gene which contains a proximal CCAAT/enhancer-binding protein site were screened, but no mutations were found. CONCLUSION: These results suggest that no mutations in either the promoter region at the about 100 bp 5'-flanking region of the gene, or in any of the three exons, are involved in the development of NIDDM or IGT associated with obesity.

Isolation and characterization of calmodulin genes from Xenopus laevis

1984 ◽  
Vol 4 (3) ◽  
pp. 507-513
Author(s):  
Y H Chien ◽  
I B Dawid
Keyword(s):  
Xenopus Laevis ◽  
Dna Sequences ◽  
Complete Analysis ◽  
Cdna Clones ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Isolation And Characterization ◽  
Electric Eel ◽  
Complete Protein

Two cDNAs derived from Xenopus laevis calmodulin mRNA have been cloned. Both cDNAs contain the complete protein-coding region and various lengths of untranslated segments. The two cDNAs encode an identical protein but differ from each other by 5% nucleotide substitutions. The 5' and 3' untranslated regions, to the extent available, are highly homologous between the two cDNAs. The predicted sequence of X. laevis calmodulin is identical to that of vertebrate calmodulins from mammals and chickens and shows one substitution compared with electric eel calmodulin. Genomic DNA sequences homologous to each of the two cDNA clones have been isolated and were shown to account for the major calmodulin-coding DNA sequences in X. laevis. These data suggest that X. laevis carries two active, nonallelic calmodulin genes. Although no complete analysis has been carried out, it appears that the X. laevis calmodulin genes are interrupted by at least four introns. The relative concentrations of calmodulin mRNA have been estimated in different embryonic stages and adult tissues and found to vary by up to a factor of 10. The highest levels of calmodulin mRNA were found in ovaries, testes, and brains. In these three tissues, the two calmodulin genes appear to be expressed at approximately equal levels.

scholarly journals IN-MACA-MCC: Integrated Multiple Attractor Cellular Automata with Modified Clonal Classifier for Human Protein Coding and Promoter Prediction

2014 ◽  
Vol 2014 ◽  
pp. 1-7
Author(s):  
Kiran Sree Pokkuluri ◽  
Ramesh Babu Inampudi ◽  
S. S. S. N. Usha Devi Nedunuri
Keyword(s):  
Cellular Automata ◽  
Dna Sequences ◽  
Promoter Prediction ◽  
Coding Region ◽  
Mathematical Methods ◽  
Protein Coding ◽  
Promoter Sequences ◽  
Specificity And Sensitivity ◽  
Average Accuracy ◽  
Proposed Model

Protein coding and promoter region predictions are very important challenges of bioinformatics (Attwood and Teresa, 2000). The identification of these regions plays a crucial role in understanding the genes. Many novel computational and mathematical methods are introduced as well as existing methods that are getting refined for predicting both of the regions separately; still there is a scope for improvement. We propose a classifier that is built with MACA (multiple attractor cellular automata) and MCC (modified clonal classifier) to predict both regions with a single classifier. The proposed classifier is trained and tested with Fickett and Tung (1992) datasets for protein coding region prediction for DNA sequences of lengths 54, 108, and 162. This classifier is trained and tested with MMCRI datasets for protein coding region prediction for DNA sequences of lengths 252 and 354. The proposed classifier is trained and tested with promoter sequences from DBTSS (Yamashita et al., 2006) dataset and nonpromoters from EID (Saxonov et al., 2000) and UTRdb (Pesole et al., 2002) datasets. The proposed model can predict both regions with an average accuracy of 90.5% for promoter and 89.6% for protein coding region predictions. The specificity and sensitivity values of promoter and protein coding region predictions are 0.89 and 0.92, respectively.

scholarly journals Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana

2017 ◽  
Author(s):  
Anuj Kumar ◽  
Aditi Chauhan ◽  
Mansi Sharma ◽  
Sai Kumar Kompelli ◽  
Vijay Gahlaut ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Full Length ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Regions ◽  
Mirna Genes ◽  
Genome Wide ◽  
Varying Length

AbstractSimple Sequence Repeats (SSRs), also known as microsatellites are short tandem repeats of DNA sequences that are 1-6 bp long. In plants, SSRs serve as a source of important class of molecular markers because of their hypervariabile and co-dominant nature, making them useful both for the genetic studies and marker-assisted breeding. The SSRs are widespread throughout the genome of an organism, so that a large number of SSR datasets are available, most of them from either protein-coding regions or untranslated regions. It is only recently, that their occurrence within microRNAs (miRNA) genes has received attention. As is widely known, miRNA themselves are a class of non-coding RNAs (ncRNAs) with varying length of 19-22 nucleotides (nts), which play an important role in regulating gene expression in plants under different biotic and abiotic stresses. In this communication, we describe the results of a study, where miRNA-SSRs in full length pre-miRNA sequences of Arabidopsis thaliana were mined. The sequences were retrieved by annotations available at EnsemblPlants using BatchPrimer3 server with miRNA-SSR flanking primers found to be well distributed. Our analysis shows that miRNA-SSRs are relatively rare in protein-coding regions but abundant in non-coding region. All the observed 147 di-, tri-, tetra-, penta- and hexanucleotide SSRs were located in non-coding regions of all the 5 chromosomes of A. thaliana. While we confirm that miRNA-SSRs were commonly spread across the full length pre-miRNAs, we envisage that such studies would allow us to identify newly discovered markers for breeding studies.

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