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At least 1,009 records · Page 56Linked to original sources
PubMed1988

The structural genes for alpha 1 and alpha 2 chains of human type IV collagen are divergently encoded on opposite DNA strands and have an overlapping promoter region.

Many of the genes of simple organisms with small genomes are encoded on opposite DNA strands so that the genes either overlap or one gene is nested within another gene (Normark, S., Bergström, S., Edlund, T., Grundström, T., Jaurin, B., Lindberg, F.P., and Olsson, D. (1983) Annu. Rev. Genet. 17, 499-525; Chen, C., Malone, T., Beckendorf, S.K., and Davis, R.L. Nature (1987) 329, 721-724). In contrast, most of the genes of complex organisms are dispersed in the genome in widely separated locations. Here, we report that the genes for the alpha 1 and alpha 2 chains of human type IV collagen are encoded on opposite DNA strands from loci that are so closely located that they may be separated by as little as 42 base pairs. The results provide the first description of two structural genes from a complex organism that code for two polypeptide chains of the same protein molecule but have overlapping 5'-flanking regions.

Amino Acid Sequence↗
PubMed1988

Mouse homeobox gene transcripts occupy different but overlapping domains in embryonic germ layers and organs: a comparison of Hox-3.1 and Hox-1.5.

By use of in situ hybridization experiments, the mouse homeobox genes Hox-3.1 and Hox-1.5 are compared in the temporal and spatial patterns of their embryonic transcripts. Transcripts of both genes are first detected at about 7 1/2 days, although the appearance of Hox-3.1 transcripts apparently follows Hox-1.5 after a small delay. Hox-3.1 and Hox-1.5 transcripts occupy domains which are different, although overlapping, along the anteroposterior axis of the embryo. The domains are first established within the ectoderm and mesoderm germ layers at 7 1/2-8 days, but subsequently they persist within the nervous system, the prevertebral column and within at least some of the organs (the thyroid, lung, stomach, mesonephric and metanephric kidneys) at 12 1/2 days. In discussion, two different mechanisms are considered by which positional information might first be generated within the germ layers.

Animals↗
PubMed2002

Regulation of the overlapping pic/set locus in Shigella flexneri and enteroaggregative Escherichia coli.

Most strains of Shigella flexneri 2a and enteroaggregative Escherichia coli carry a highly conserved chromosomal locus which encodes a 109-kDa secreted mucinase (called Pic) and, on the opposite strand in overlapping fashion, an oligomeric enterotoxin called ShET1, encoded by the setA and setB genes. Here, we characterize the genetic regulation of these overlapping genes. Our data suggest that pic and the setBA loci are transcribed as complementary 4-kb mRNA species. The major pic promoter is maximally activated at 37 degrees C in exponential growth phase. Our data suggest that the setB gene is transcribed from a promoter which lies more than 1.5 kb upstream of the setB structural gene; setA may be transcribed via readthrough of the setB transcript and possibly by its own promoter. The long leader of the setB gene provides a strong silencing effect on setB transcription. The signals which provide relief from setB silencing are not clear, but significant induction is observed in a continuous anaerobic culture of human fecal bacteria, suggesting that some complex characteristics of the human intestine act to lift repression of setB expression. Our studies provide the first insights into the mechanisms affecting expression of this unusual virulence locus.

Colon↗
PubMed2000

Coding in the noncoding DNA strand: A novel mechanism of gene evolution?

The question whether the noncoding DNA strand had or still has the capability for encoding functional polypeptides has been addressed in several articles. The theoretical background of the views advocating this idea arose from two groups of findings. One of them was based on various observations implying that the genetic code was adapted for double-strand coding. The other group of theories arose from the observation of gene-length overlapping open reading frames (O-ORFs) on the antisense DNA strand in a number of genes. In fact, the above theories, which I term selectionist, conceive a novel conception of gene evolution, proposing that new genes can be created by the utilization of antisense DNA strand. In contrast, neutralist theory claims that the O-ORFs are mere by-products of evolutionary processes acting to create special codon usage and base distribution patterns in the coding sequences.

Codon↗
PubMed1990

Nucleotide sequence of the Caulobacter crescentus flaF and flbT genes and an analysis of codon usage in organisms with G + C-rich genomes.

The Caulobacter crescentus flaFG region encodes trans-acting, regulatory factors that modulate flagellin synthesis during flagellum biogenesis. In this study, sequence analysis and experiments utilizing a promoterless cat gene demonstrated that the flaF and flbT genes have overlapping transcripts with the same orientation. In addition, the 5' ends of the flgL and flbA genes were located. A sequence resembling an Rho-factor-independent terminator was found in the 3' region of the flaF gene. This region was uniquely A + T-rich and the encoded mRNA contained an inverted repeat sequence which could form a stable stem-loop structure followed by nine U-residues. The codon usage of C. crescentus genes was examined and indicated a preference for specific codons from each of the synonymous codon groups. Furthermore, comparison to the codon usage of other organisms with G + C-rich genomes indicated a strong preference for the same codons preferred by C. crescentus.

Amino Acid Sequence↗
PubMed2006

Expression of TFAP2beta and TFAP2gamma genes in Xenopus laevis.

The embryonic expression patterns of two additional members of the transcription factor TFAP2 family in Xenopus laevis, TFAP2beta and TFAP2gamma, are described. Both genes share overlapping expression domains with the previously characterized TFAP2alpha in this species, although differences exist. All three genes are expressed in the neural crest (NC) region at late gastrula to early neurula stages. TFAP2alpha and TFAP2gamma are also expressed in outer, epidermal cells, while TFAP2beta is essentially NC-specific. All three are induced by Wnt/beta-catenin -- BMP signals and all bind to a consensus TFAP2 recognition site from an epidermal keratin gene.

Amino Acid Sequence↗
PubMed2005

Validation and application of a high fidelity mRNA linear amplification procedure for profiling gene expression.

The need for microgram quantities of RNA for microarray experiments has hindered application of this novel technology in cell types/tissue samples with limited abundance of RNA. In this study, potential application of T7-based linear RNA amplification was investigated for use in gene expression profiling experiments where starting material is limited. Yield and integrity of amplified antisense RNA (aaRNA), microarray hybridization intensities, and fidelity of differential gene expression detected were determined for arrays generated for unamplified versus amplified RNA from the same homogenous starting pools. Total RNA was extracted from bovine spleen and fetal ovary, serially diluted to concentrations ranging from 2 microg to 500 pg and amplified. Quality and quantity of total input RNA and aaRNA were assessed by spectrophotometry, gel electrophoresis and bioanalyzer. In experiment 1, we determined the optimal amounts of aaRNA generated from 20, 40, 200 ng and 2 microg input total RNA for use in cDNA synthesis, labeling and array hybridization that would yield robust and consistent hybridization signals on a bovine oocyte cDNA microarray. In experiment 2, comparison of microarray hybridization intensities and fidelity of differential gene expression between aaRNA generated from 2, 20 and 40 ng input total RNA versus unamplified RNA (uRNA) were conducted. The hybridization intensities for each of the 7000 spots per slide for microarrays conducted using aaRNA versus uRNA were highly correlated (2 ng = 0.84, 20 ng = 0.88, 40 ng = 0.90; P < 0.01). The false positive rate was low and similar (4.0% versus 4.4%) for arrays done with uRNA and aaRNA. Ninety-seven ESTs were detected as differentially expressed in the fetal ovary versus spleen at > 1.5- or < 0.5-fold using uRNA (P < 0.05). However, the number of genes detected in arrays using aaRNA was approximately 1.5-2.5 times greater than with uRNA. Approximately, 65-70% of differentially expressed genes were common between uRNA and aaRNA arrays. Relative fold-expression (Cy3/Cy5 ratios) for 25 overlapping abundant genes was comparable for uRNA versus aaRNA arrays with 2 and 20 ng total RNA as input. Results demonstrate that T7-based linear amplification of small amounts of input RNA and use of aaRNA in microarray experiments retains fidelity of detection of differential gene expression that is relatively comparable to experiments done with uRNA and provides a potentially viable approach to facilitate gene expression profiling using limited amounts of starting material.

Animals↗
PubMed2004

The DNA sequence and comparative analysis of human chromosome 10.

The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence.

Animals↗
PubMed2006

Distinctive profiles of gene expression in the human nucleus accumbens associated with cocaine and heroin abuse.

Drug abuse is thought to induce long-term cellular and behavioral adaptations as a result of alterations in gene expression. Understanding the molecular consequences of addiction may contribute to the development of better treatment strategies. This study utilized high-throughput Affymetrix microarrays to identify gene expression changes in the post-mortem nucleus accumbens of chronic heroin abusers. These data were analyzed independently and in relation to our previously reported data involving human cocaine abusers, in order to determine which expression changes were drug specific and which may be common to the phenomenon of addiction. A significant decrease in the expression of numerous genes encoding proteins involved in presynaptic release of neurotransmitter was seen in heroin abusers, a finding not seen in the cocaine-abusing cohort. Conversely, the striking decrease in myelin-related genes observed in cocaine abusers was not evident in our cohort of heroin subjects. Overall, little overlap in gene expression profiles was seen between the two drug-abusing cohorts: out of the approximately 39,000 transcripts investigated, the abundance of only 25 was significantly changed in both cocaine and heroin abusers, with nearly one-half of these being altered in opposite directions. These data suggest that the profiles of nucleus accumbens gene expression associated with chronic heroin or cocaine abuse are largely unique, despite what are thought to be common effects of these drugs on dopamine neurotransmission in this brain region. A re-examination of our current assumptions about the commonality of molecular mechanisms associated with substance abuse seems warranted.

Adult↗
PubMed1996

SRK, the stigma-specific S locus receptor kinase of Brassica, is targeted to the plasma membrane in transgenic tobacco.

The S locus receptor kinase (SRK) gene is one of two S locus genes required for the self-incompatibility response in Brassica. We have identified the product of the SRK6 gene in B. oleracea stigmas and have shown that it has characteristics of an integral membrane protein. When expressed in transgenic tobacco, SRK6 is glycosylated and targeted to the plasma membrane. These results provide definitive biochemical evidence for the existence in plants of a plasma membrane-localized transmembrane protein kinase with a known cell-cell recognition function. The timing of SRK expression in stigmas follows a time course similar to that previously described for another S locus-linked gene, the S locus glycoprotein (SLG) gene, and correlates with the ability of stigmas to mount a self-incompatibility response. Based on SRK6 promoter studies, the site of gene expression overlaps with that of SLG and exhibits predominant expression in the stigmatic papillar cells. Although reporter gene studies indicated that the SRK promoter was active in pollen, SRK protein was not detected in pollen, suggesting that SRK functions as a cell surface receptor exclusively in the papillar cells of the stigma.

Base Sequence↗
PubMed1986

Nucleotide sequence of the small double-stranded RNA segment of bacteriophage phi 6: novel mechanism of natural translational control.

The lipid-containing bacteriophage phi 6 has a genome composed of three segments of double-stranded RNA. We determined the nucleotide sequence of a cDNA copy of the smallest RNA segment. The coding sequences of the four proteins on this segment were identified. These sequences were clustered. Three of the genes had overlapping initiation-termination codons. All noncoding sequences were at the ends of the molecule. The genes of the small double-stranded RNA segment comprised two translational polarity groups. We propose that the translational coupling is the result of an inability of ribosomes to bind independently to two of the four genes. Translation of these genes occurred when ribosomes were delivered to them by translation of an upstream gene.

Bacteriophages↗
PubMed2004

P2 growth restriction on an rpoC mutant is suppressed by alleles of the Rz1 homolog lysC.

Escherichia coli strain 397c carries a temperature-sensitive mutation, rpoC397, that removes the last 50 amino acids of the RNA polymerase beta' subunit and is nonpermissive for plating of bacteriophage P2. P2 gor mutants productively infect 397c and define a new gene, lysC, encoded by a reading frame that extensively overlaps the P2 lysis accessory gene, lysB. The unusual location of lysC with respect to lysB is reminiscent of the Rz/Rz1 lysis gene pair of phage lambda. Indeed, coexpression of lysB and lysC complemented the growth defect of lambda Rz/Rz1 null mutants, indicating that the LysB/C pair is similar to Rz/Rz1 in both gene arrangement and function. Cells carrying the rpoC397 mutation exhibited an early onset of P2-induced lysis, which was suppressed by the gor mutation in lysC. We propose that changes in host gene expression resulting from the rpoC397 mutation result in changes in the composition of the bacterial cell wall, making the cell more susceptible to P2-mediated lysis and preventing accumulation of progeny phage sufficient for plaque formation.

Amino Acid Sequence↗
PubMed1992

Sequence and in vitro expression of the M2 gene of turkey rhinotracheitis pneumovirus.

Negative-stranded virion RNA and oligonucleotide primers complementary to fusion (F) protein gene sequences were used to generate cDNA clones, revealing that the gene 5'-proximal to the F protein corresponded to the M2 (22K) gene, as in respiratory syncytial (RS) virus. The transcription start signal, GGGACAAGU, was identical to that of the F and matrix (M) proteins of turkey rhinotracheitis virus (TRTV). There were two sequences with the potential to function as transcription termination/poly(A) signals, located at nucleotides 751 to 762 and 777 to 787; 15 clones derived from mRNA indicated that the first of these sequences formed the major signal. Part of the next downstream (5') gene was sequenced; unlike mammalian pneumoviruses the TRTV M2 gene did not overlap the beginning of the 5'-proximal gene. Northern blotting indicated that infected Vero cells contained less M2 mRNA than F mRNA and that about half of the M2 mRNA was present as a F-M2 dicistronic mRNA. The M2 gene contained two overlapping open reading frames (ORFs 1 and 2), as with RS virus. ORF 1 comprised 558 nucleotides with the coding potential for a 186 amino acid polypeptide, M(r) 20959, eight or nine residues shorter than for human RS virus strains. The overall amino acid identity was 40%, the N-terminal one-third of the proteins sharing 62% of residues, the remainder 29%. A hydropathy plot of the TRTV M2 protein had close similarity to that of the M2 or RS virus. The protein was predicted to have a basic character with no N-terminal signal sequence or other major highly hydrophobic sequences. In vitro translation of a transcript comprising both ORFs 1 and 2 produced a single product of apparent M(r) 23000, corresponding to the M2 product of ORF 1. Site-directed mutagenesis confirmed that this product was derived from ORF 1 and that frameshifting was not involved. The second ORF was expressed only from a transcript which lacked the AUG codons of ORF 1 and, although occupying a similar position to that in the RS virus M2 gene, had virtually no amino acid identity in its 73 residue length and was approximately 25% shorter than the corresponding RS virus ORF 2. The hydropathy plot of the potential products of the second ORFs of TRTV and RS virus showed little resemblance. Taken together these results suggest that ORF 2 is unlikely to be expressed in vivo.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1979

Overlap hybridization screening: isolation and characterization of overlapping DNA fragments surrounding the leu2 gene on yeast chromosome III.

A set of four plasmids containing overlapping segments comprising a total of about 30 kbp of cloned DNA from chromosome III of yeast (Saccharomyces cerevisiae) has been isolated and characterized by restriction endonuclease analyses and DNA:DNA hybridizations. Colony hybridization was carried out with labeled pYe(leu2)10, a plasmid carrying the yeast leu2 gene, to a bank of bacterial colonies containing recombinant plasmids constructed from the vector ColE1 and random fragments of yeast DNA. This resulted in the detection of two plasmids, pYe11G4 and pYe40C3, with DNA inserts which partially overlap the original cloned segment and contain additional DNA extending in opposite directions on the chromosome. By carrying out a second round of colony hybridization with pYe40C3, the cloned region was further extended in one direction. A region of DNA that is repeated at least ten times in the yeast genome was identified by hybridization of pYe11G4 to an EcoRI digest of total yeast DNA. The procedure described in this paper should allow the isolation of large sections of chromosomes, including non-transcribed regions, surrounding cloned genes.

Base Sequence↗
PubMed1995

Structure and organization of the human glucose phosphate isomerase gene (GPI).

Two overlapping yeast artificial chromosome clones containing the human glucose 6-phosphate isomerase gene (GPI) have been isolated. PCR and direct sequencing were used to determine the exon/intron structure of the gene. The gene spans in excess of 40 kb and consists of 18 exons ranging in size from 44 to 153 bp. All splice sites conform to the GT/AG rule.

Animals↗
PubMed1997

An Escherichia coli gene divergently transcribed from a promoter overlapping the metA promoter.

The upstream region of the metA gene in Escherichia coli contains two promoters. We have identified by lacZ fusion an additional promoter in this region, and showed that it is transcribed in the opposite orientation from the metA gene. The putative translation product corresponds to a peptide of 147 amino acids-ORF19 by molecular mass. This peptide is probably not essential for growth, as an insertion mutant is viable.

Acyltransferases↗
PubMed2005

Toward the evaluation of function in genetic variability: characterizing human SNP frequencies and establishing BAC-transgenic mice carrying the human CYP1A1_CYP1A2 locus.

Interindividual differences in human CYP1A1 and CYP1A2 expression appear to be associated with variability in risk toward various types of environmental toxicity and cancer. These two genes are oriented head-to-head on human chromosome 15; the 23.3-kb spacer region might contain distinct regulatory regions for CYP1A1 and distinct regulatory regions for CYP1A2, or the regulatory regions for the two genes might overlap one another. From 24 unrelated subjects of five major, geographically-isolated subgroups, we resequenced both genes (all exons and all introns) plus some 3' flanking sequences and the entire spacer region (39.6 kb total); 85 SNPs were found, 49 of which were not currently in the National Center for Biotechnology Information (NCBI) database. Of the 57 double-hit SNPs, we carried out SNP-typing in 94 Africans, 96 Asians, and 83 Caucasians and found striking ethnic differences in SNP frequencies and haplotype evolution; the two CYP1A1 SNPs and the one CYP1A2 SNP that are most commonly used in epidemiological studies were shown not to be representative haplotype tag SNPs across these three human subgroups. Four BAC-transgenic mouse lines, carrying the human CYP1A2 and 15,190 bp of 5' flank, expressed only negligible basal or inducible CYP1A2 mRNA. A fifth BAC-transgenic mouse line, carrying both the human CYP1A1 and CYP1A2 genes and ample amounts of 3' flanking sequences, plus all of the spacer region--in the absence of the mouse Cyp1a1 or Cyp1a2 genes--expressed the human CYP1A1 and CYP1A2 mRNA, protein and enzyme activities in liver and nonhepatic tissues very similar to that of the mouse. Comparison of this hCYP1A1_1A2 transgenic line with hCYP1A1_1A2 lines carrying other common human haplotypes will enable us to evaluate function in human CYP1A1_CYP1A2 locus variability, with regard to toxicity and cancer caused by combustion products.

Animals↗
PubMed2001

Expression of Klf9 and Klf13 in mouse development.

Klf9 and Klf13 are members of the C(2)H(2) zinc finger family of transcription factors that are thought to be involved in regulating basal transcription. The mRNA localization of Klf9 and Klf13 during development was determined by in situ hybridization of mouse E8, E11, E13 and E16 embryo sections. The data showed that Klf9 and Klf13 are widely expressed at all the mouse embryo stages examined. Whilst the expression patterns of the two genes largely overlap there are differences in the localization or level of expression in some tissues. At E11, both genes are expressed in high levels in the cephalic mesenchyme whilst Klf13 and not Klf9 is expressed at high levels in the developing heart at E8 and E11. In the gut and bladder at E16, Klf13 is expressed in the epithelial cell layer whereas Klf9 is expressed in both the muscle and epithelial layers. Both Klf9 and Klf13 are expressed at high levels in the epidermis at E11, E13 and E16.

Animals↗