Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genes, Overlapping”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 865 records · Page 48Linked to original sources
PubMed1989

Overlapping redundant septuplets identical with regulatory elements of HIV-1 and SV40.

Overlapping redundant short oligomers in DNA sequences of retroviruses and papovaviruses have been identified. For each sequence, a search procedure determines the 5% short oligomers of the same length with the highest ratios of observed to expected occurrences based on singlet composition of the sequence. These short oligomers are referred to as compositionally-assessed redundant sequence elements (COARSEs). A pair of COARSEs overlapping by at least one base is considered to be a COARSE overlap. Most COARSE overlaps of the 7th order (overlapping septuplets) are found in long terminal repeats of retroviruses and in the regulatory control regions of papovaviruses SV40, BK and JC. Many of the 7th order COARSE overlaps in HIV-1 and SV40 are identical with regulatory elements determined experimentally. On the contrary, very few of the most frequently occurring oligomer overlaps, which are defined differently from COARSE overlaps, are present in the regulatory regions of retroviruses and papovaviruses. Examining DNA sequences of other genomes by the COARSE overlap method may identify putative regulatory regions.

Base Sequence↗
PubMed1991

Diversity of coding strategies in influenza viruses.

Influenza viruses have exploited a variety of strategies to increase their genome coding capacities. These include unspliced, spliced, alternatively spliced and bicistronic mRNAs, translation from overlapping reading frames and a coupled stop-start translation of tandem cistrons.

Base Sequence↗
PubMed2005

LHON/MELAS overlap syndrome associated with a mitochondrial MTND1 gene mutation.

Pathogenic point mutations in the mitochondrial MTND1 gene have previously been described in association with two distinct clinical phenotypes -- Leber hereditary optic neuropathy (LHON) and mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). Here we report the first heteroplasmic mitochondrial DNA (mtDNA) point mutation (3376G>A) in the MTND1 gene associated with an overlap syndrome comprising the clinical features of both LHON and MELAS. Muscle histochemistry revealed subtle mitochondrial abnormalities, while biochemical analysis showed an isolated complex I deficiency. Our findings serve to highlight the growing importance of mutations in mitochondrial complex I structural genes in MELAS and its associated overlap syndromes.

Adult↗
PubMed1984

Dissection of overlapping functions within the adenovirus type 5 E1A gene.

The adenovirus E1A gene encodes multiple, overlapping mRNAs whose products function both to regulate mRNA levels during the lytic cycle of the virus and to facilitate transformation of non-permissive cells. To assign specific functions to the E1A gene products, two adenovirus type 5 variants have been constructed. Mutants dl347 and 348 carry cloned segments corresponding to the E1A 12 and 13S mRNAs, respectively, in place of the normal E1A gene. The variants produced the predicted E1A-specific mRNAs and polypeptides. Both viruses grew efficiently in HeLa cells. Although the 13S mRNA products were more effective, the products of either mRNA species could stimulate the accumulation of mRNAs from additional transcription units. Both viruses could induce the formation of transformed foci in an established rat cell line. Neither virus could transform primary rat embryo cells at normal frequency, and the dl347 foci which were induced were incomplete or abortive transformants. Thus, functions encoded by both 12S and 13S mRNAs are required for efficient and complete transformation of primary rat cells.

Adenoviridae↗
PubMed1984

Nucleotide sequence reveals overlap between T4 phage genes encoding dihydrofolate reductase and thymidylate synthase.

We have determined the nucleotide sequence of a 1075-base-pair HindIII fragment of the T4 phage genome. This fragment contains the structural gene (frd) for dihydrofolate reductase and part of the gene (td) encoding thymidylate synthase. The fragment contains a 579-base-pair open reading frame, encoding a 193-residue polypeptide with a calculated mass of 21,603 Da, in agreement with our reported subunit molecular mass of 23,000. The deduced amino acid sequence shows partial homology with other dihydrofolate reductases, with most of the identities lying in regions known to be involved in substrate binding and catalysis. The 3' end of the coding strand overlaps the coding region for thymidylate synthase; the sequence - ATGA -includes an opal terminator for the frd gene and an initiating triplet for the td gene. The deduced amino acid sequence from this initiating ATG is identical, for the first 20 residues, with the NH2-terminal 20 residues reported for the td protein (M. Belfort , A. Moelleken , G. F. Maley , and F. Maley (1983) J. Biol. Chem. 258, 2045-2051). The sequenced HindIII fragment was transferred into a high expression plasmid vector for large scale production of homogeneous T4 dihydrofolate reductase. The experimentally determined sequence of 20 residues at the NH2-terminus of this protein is identical with that deduced from the nucleotide sequence for T4 dihydrofolate reductase.

Amino Acid Sequence↗
PubMed1999

Cig30 and Pitx3 genes are arranged in a partially overlapping tail-to-tail array resulting in complementary transcripts.

The mouse Cig30 gene codes for a 30-kDa membrane glycoprotein, which appears to have a role in the recruitment of brown adipose tissue. To elucidate the structure of the Cig30 gene, we have isolated a lambda phage genomic DNA clone containing the entire mouse gene and found that Cig30 consists of four exons that are spread over 4 kilobase pairs of genomic sequence. Using a fluorescence in situ hybridization assay and interspecific backcross panel mapping, we have localized the Cig30 locus to the distal region of mouse chromosome 19, between the Tlx1 and Ins1 loci. Sequencing of the corresponding lambda clone to completion revealed that the insert contained yet another gene in the opposite orientation. It turned out to be the newly identified homeobox gene Pitx3. Interestingly, the genes are very tightly linked, so that the 3' ends of their transcripts are complementary. Thus, our results provide evidence for bidirectional transcription of a several hundred base pair-long DNA region as a result of the extremely tight linkage between Cig30 and Pitx3.

Acetyltransferases↗
PubMed1993

TATA-binding protein and the retinoblastoma gene product bind to overlapping epitopes on c-Myc and adenovirus E1A protein.

Using a protein binding assay, we show that the amino-terminal 204 amino acids of the c-Myc protein interact directly with a key component of the basal transcription factor TFIID, the TATA box-binding protein (TBP). Essentially the same region of the c-Myc protein also binds the product of the retinoblastoma gene, the RB protein. c-Myc protein coimmunoprecipitates with TBP in lysates of mammalian cells, demonstrating that the proteins are also complexed in vivo. A short peptide that spans the RB binding site of the E7 protein of human papilloma virus type 16 interferes with the binding of c-Myc to TBP. The same peptide also blocks binding of adenovirus E1A protein to TBP, suggesting that c-Myc and E1A bind to RB and TBP through overlapping epitopes. Furthermore, we show that binding of RB to E1A prevents association of E1A with TBP. Our data suggest that one of the functions of RB and RB-like proteins is to prevent interaction of viral and cellular oncoproteins, such as c-Myc and E1A, with TBP.

Adenosine Triphosphate↗
PubMed2003

The murine Ten-m/Odz genes show distinct but overlapping expression patterns during development and in adult brain.

The mouse TEN-M/ODZ proteins belong to a new family of type II transmembrane proteins with unknown function. The family consists of four members, which are expressed highly in brain and less in many other tissues. In the present study we have generated specific RNA probes and antibodies to characterize the expression of the 4 Ten-m/Odz genes in the developing and adult central nervous system (CNS) of mice. Ten-m/Odz3 and Ten-m/Odz4 mRNAs were first detectable at E7.5, Ten-m/Odz2 expression started at the 37 somite (E 10.5) stage, while Ten-m/Odz1 mRNA is not found before E15.5. In the adult mouse CNS mRNAs of the 4 Ten-m/Odzs were expressed in distinct patterns, which partially overlapped. Immunostaining and in situ hybridization localized proteins and mRNAs of Ten-m/Odzs in adjacent areas suggesting that TEN-M/ODZ proteins might be transported from the cell body along the axon or that they are shed from the cell surface and diffuse into distant regions.

Animals↗
PubMed1985

Transcriptional organization of the convergent overlapping dnaQ-rnh genes of Escherichia coli.

The transcriptional organization was determined for the DNA polymerase III epsilon subunit (dnaQ) and the ribonuclease H (rnh) genes, which are closely spaced and organized in a face-to-face system (Maki, H., Horiuchi, T., and Sekiguchi, M. (1983) Proc. Natl. Acad. Sci. U. S. A. 80, 7137-7141). Nuclease S1 mapping revealed that transcription starts from a single promoter for rnh and two promoters for dnaQ and proceeds in opposite directions. The 5' terminus of the rnh RNA overlaps about 100 and 20 nucleotide sequences with the 5' terminus of the dnaQ-1 and dnaQ-2 RNA, respectively. The levels of in vivo transcription for the three RNA species increased altogether by more than 10-fold in cells carrying a multicopy plasmid with intact dnaQ-rnh genes, keeping the relative level for the convergent transcription units nearly constant.

DNA Polymerase III↗
PubMed2026

Auditing bacterial dark-gene screens for superimposed open reading frame artefacts: A multi-layer analysis of Rv2438A in Mycobacterium tuberculosis.

Essentiality and knockdown-vulnerability screens can promote spurious bacterial open reading frames when those frames overlap essential genes, because such a frame inherits its neighbour's signals undiluted and therefore satisfies the screen's criteria better than a genuine small gene. We present a multi-layer audit that tests this failure mode across genome annotation, transposon mutagenesis, CRISPR interference, homology, transcript mapping, proteomics, and population variation. We apply it to Rv2438A, a 92-codon conserved hypothetical open reading frame of Mycobacterium tuberculosis ranked first by our own dark-gene target screen. Rv2438A is superimposed on the essential NAD synthetase locus nadE: 44% lies within its coding sequence on the opposite strand, and the remainder covers its promoter and transcription start site. Consequently, three of five Himar1 sites lie within nadE, no CRISPRi guide can target Rv2438A without binding nadE, and the cross-species hit maps to the same nadE start junction. Rv2438A lacks its own transcription start site and is absent from every proteomic dataset that detects nadE. A genome-wide scan identifies six short, overlapping, uncharacterised loci among 3907 annotated genes, but only Rv2438A combines overlap and essentiality with non-detection across all proteomic datasets; rare genome-wide, it ranked first among screen hits. We provide an implementable audit workflow and a codon-position control, but measure the control's sensitivity as only two of five genes with attested protein, limiting it to confirmatory use. Overlap coordinates and neighbour-specific experimental resolution should therefore be reported before bacterial dark genes are prioritised.

CRISPR interference↗
PubMedDate not supplied

Partial overlap of Ir gene-controlled responses to two proteins of limited relatedness: hen egg-white lysozyme and human lysozyme.

The plaque-forming cell (PFC) response to human lysozyme (HUL) is regulated by an Ir gene(s) located within the major histocompatibility complex of the mouse. Mice of H-2a, H-2k, H-2v and H-2r haplotypes respond to HUL, whereas mice with H-2b, H-2d, H-2q, H-2s and H-2u haplotypes fail to generate substantial anti-HUL PFC responses. In contrast, only mice carrying the H-2b and H-2s haplotypes are non-responders to the distantly related hen eggwhite lysozyme (HEL). The major genetic control of the anti-HUL PFC response maps to the I-A subregion of the H-2 complex with perhaps a minor influence by a gene mapping to the right of the I-B subregion. HUL and HEL induce a cross-reactive suppressor cell, directed against a particular determinant found on both lysozymes. Once generated, these antigen-specific suppressor cells can affect the in vitro primary response to either lysozyme conjugated to sheep red blood cells. Despite this overlap, the strain distribution pattern of responsiveness is different for the two lysozymes. In the discussion, this was attributed to the MHC-related failure to process and/or present HEL to the HEL/HUL cross-reactive suppressor T cell in H-2q, d and u strains.

Animals↗
PubMed1992

A novel transcript overlapping the myelin basic protein gene.

Myelin basic protein (MBP) is a major constituent of myelin synthesized by oligodendrocytes and Schwann cells. We have investigated the expression of mouse MBP RNAs outside the nervous system. Nuclease protection experiments indicate that RNAs containing exon 1 and not the six downstream exons of the MBP gene are transcribed in various hemopoietic tissues. We have isolated a hemopoietic MBP-related (HMBPR) cDNA clone from a mouse bone marrow cDNA library screened with an MBP cDNA probe. This clone contains exons 1a and 1b and a part of intron 1 of the MBP gene. An additional 5' region, encoded by at least three unidentified exons, lies upstream of exon 1a. The HMBPR clone corresponds to a 5-kb RNA expressed in bone marrow, spleen, thymus, and macrophagic cells. This transcript is expressed at a similar level in brain, although at a lower level than the classical 2-kb mRNA. These data indicate that a new transcript, overlapping the MBP transcription unit and controlled by a distinct promoter, is expressed in hemopoietic tissues. This RNA might encode a 21-kDa protein sharing a common domain with MBP.

Amino Acid Sequence↗
PubMed1990

Aspartokinase genes lysC alpha and lysC beta overlap and are adjacent to the aspartate beta-semialdehyde dehydrogenase gene asd in Corynebacterium glutamicum.

A 2.1 kb DNA fragment of the recombinant plasmid pCS2, isolated from an aminoethyl cysteine (AEC)-resistant and lysine-producing Corynebacterium glutamicum mutant strain, and which confers AEC resistance and lysine production on the wild-type G. glutamicum ATCC 13032 was analysed. DNA sequence analysis of this fragment revealed three large open reading frames (ORFs). The incomplete ORF1 does not contain the 5' end of the coding region. ORF2, which uses the same reading frame as ORF1, is identical to the 3' end of ORF1 and encodes a putative protein of 172 amino acids (aa) and of Mr 18,584. ORF3 encodes a putative protein of 344 aa and of Mr 36,275. The amino acid sequences deduced from ORF1 and ORF2 display strong homologies to those of the alpha- and beta-subunits of the Bacillus subtilis aspartokinase II. It is therefore proposed that the incomplete ORF1, termed lysC alpha, encodes part of the alpha-subunit of the C. glutamicum aspartokinase whereas the complete ORF2, termed lysC beta, encodes the beta-subunit of the same enzyme. ORF2 is responsible for AEC resistance and lysine production due to a feedback-resistant aspartokinase. The amino acid sequence deduced from ORF3, termed asd, is highly homologous to that of the Streptococcus mutans aspartate beta-semialdehyde dehydrogenase (ASD). Plasmids carrying the C. glutamicum asd gene complemented Escherichia coli asd mutants. Increase in ASD activity by a factor of 30-60 was measured for C. glutamicum cells harbouring high copy-number plasmids with the C. glutamicum asd gene.

Amino Acid Sequence↗
PubMed1997

Evidence for two types of subunits in the bacterioferritin of Magnetospirillum magnetotacticum.

In order to investigate the role of bacterioferritin (Bfr) in the biomineralization of magnetite by microorganisms, we have cloned and sequenced the bfr genes from M. magnetotacticum. The organism has two bfr genes that overlap by one nucleotide. Both encode putative protein products of 18 kDa, the expected size for Bfr subunits, and show a strong similarity to other Bfr subunit proteins. By scanning the DNA sequence databases, we found that a limited number of other organisms, including N. gonorrhea, P. aeruginosa, and Synechocystis PCC6803, also have two bfr genes. When the sequences of a number of microbial Bfrs are compared with each other, they fall into two distinct types with the organisms mentioned above having one of each type. Differences in heme- and metal-binding sites and ferroxidase activities of the two types of subunits are discussed.

Amino Acid Sequence↗
PubMed1989

Sequence of bacteriophage T3 DNA from gene 2.5 through gene 9.

The nucleotide sequence of bacteriophage T3 DNA, from gene 2.5 through gene 9 has been determined. In addition to regulatory sites, the sequence predicts 19 close-packed genes plus two genes that overlap, in a different reading frame, another gene. The majority of these genes are highly homologous to those in the corresponding region of bacteriophage T7. However, there are some genes that are present in one, but not the other, phage. These apparent deletions are almost exactly gene size and thus the close-packed organization of genes remains the same in T3 as in T7. The varying levels of homology between T3 and T7 DNAs, first noted by Davis and Hyman in their study of DNA heteroduplexes, are also demonstrated here by a comparison of T3 and T7 nucleotide sequences. Many regions of extremely high homology immediately abut sequences that have no apparent homology. These data suggest that bacteriophages T3 and T7 have recombined, both with each other and with other members of a pool of T7-like phages, during their co-evolution.

Amino Acid Sequence↗
PubMed2015

The transcription factor NFAT promotes exhaustion of activated CD8⁺ T cells.

During persistent antigen stimulation, CD8(+) T cells show a gradual decrease in effector function, referred to as exhaustion, which impairs responses in the setting of tumors and infections. Here we demonstrate that the transcription factor NFAT controls the program of T cell exhaustion. When expressed in cells, an engineered form of NFAT1 unable to interact with AP-1 transcription factors diminished T cell receptor (TCR) signaling, increased the expression of inhibitory cell surface receptors, and interfered with the ability of CD8(+) T cells to protect against Listeria infection and attenuate tumor growth in vivo. We defined the genomic regions occupied by endogenous and engineered NFAT1 in primary CD8(+) T cells and showed that genes directly induced by the engineered NFAT1 overlapped with genes expressed in exhausted CD8(+) T cells in vivo. Our data show that NFAT promotes T cell anergy and exhaustion by binding at sites that do not require cooperation with AP-1.

Animals↗
PubMed2006

Analysis of gene expression profiles in melanoma cells with acquired resistance against antineoplastic drugs.

Resistance to various antineoplastic agents is common in the clinical management of malignant melanoma. The biological mechanisms conferring these different drug-resistant phenotypes are still unclear. To identify potential factors mediating drug resistance to melanoma cells, the mRNA expression profiles of the parental drug-sensitive human melanoma cell line MeWo and four derived drug-resistant sublines with acquired resistance against four commonly used drugs for melanoma treatment (cisplatin, etoposide, fotemustine and vindesine) were analysed. We investigated cDNA arrays with 43,000 cDNA clones ( approximately 30,000 unique genes) to study the expression patterns of these cell lines. We were able to simultaneously extract new candidate genes associated with drug resistance in malignant melanoma and to correlate the present findings with previously described resistance-associated genes. Using hierarchical clustering and analysing the overlap of genes with altered expression, we detected similarities between the expression signatures related to cisplatin and fotemustine resistance. The resistance against vindesine required a minimal set of changes in gene expression relative to the parental MeWo cell line. Our study provides new data that may be used to obtain further insight into the resistance characteristics of malignant melanoma.

Cell Line, Tumor↗
PubMed2003

Transcriptional profiling of Arabidopsis tissues reveals the unique characteristics of the pollen transcriptome.

Pollen tubes are a good model for the study of cell growth and morphogenesis because of their extreme elongation without cell division. Yet, knowledge about the genetic basis of pollen germination and tube growth is still lagging behind advances in pollen physiology and biochemistry. In an effort to reduce this gap, we have developed a new method to obtain highly purified, hydrated pollen grains of Arabidopsis through flowcytometric sorting, and we used GeneChips (Affymetrix, Santa Clara, CA; representing approximately 8,200 genes) to compare the transcriptional profile of sorted pollen with those of four vegetative tissues (seedlings, leaves, roots, and siliques). We present a new graphical tool allowing genomic scale visualization of the unique transcriptional profile of pollen. The 1,584 genes expressed in pollen showed a 90% overlap with genes expressed in these vegetative tissues, whereas one-third of the genes constitutively expressed in the vegetative tissues were not expressed in pollen. Among the 469 genes enriched in pollen, 162 were selectively expressed, and most of these had not been associated previously with pollen. Their functional classification reveals several new candidate genes, mainly in the categories of signal transduction and cell wall biosynthesis and regulation. Thus, the results presented improve our knowledge of the molecular mechanisms underlying pollen germination and tube growth and provide new directions for deciphering their genetic basis. Because pollen expresses about one-third of the number of genes expressed on average in other organs, it may constitute an ideal system to study fundamental mechanisms of cell biology and, by omission, of cell division.

Arabidopsis↗