Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “noncoding genome”

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 1,027 records · Page 57Linked to original sources
PubMed2005

Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in atlantic salmon (Salmo salar L.).

The prediction that selection affects the genome in a locus-specific way also affecting flanking neutral variation, known as genetic hitchhiking, enables the use of polymorphic markers in noncoding regions to detect the footprints of selection. However, as the strength of the selective footprint on a locus depends on the distance from the selected site and will decay with time due to recombination, the utilization of polymorphic markers closely linked to coding regions of the genome should increase the probability of detecting the footprints of selection as more gene-containing regions are covered. The occurrence of highly polymorphic microsatellites in the untranslated regions of expressed sequence tags (ESTs) is a potentially useful source of gene-associated polymorphisms which has thus far not been utilized for genome screens in natural populations. In this study, we searched for the genetic signatures of divergent selection by screening 95 genomic and EST-derived mini- and microsatellites in eight natural Atlantic salmon, Salmo salar L., populations from different spatial scales inhabiting contrasting natural environments (salt-, brackish, and freshwater habitat). Altogether, we identified nine EST-associated microsatellites, which exhibited highly significant deviations from the neutral expectations using different statistical methods at various spatial scales and showed similar trends in separate population samples from different environments (salt-, brackish, and freshwater habitats) and sea areas (Barents vs. White Sea). We consider these ESTs as the best candidate loci affected by divergent selection, and hence, they serve as promising genes associated with adaptive divergence in Atlantic salmon. Our results demonstrate that EST-linked microsatellite genome scans provide an efficient strategy for discovering functional polymorphisms, especially in nonmodel organisms.

Animals↗
PubMed2006

Characteristic length scale of electric transport properties of genomes.

A tight-binding model together with a statistical method are used to investigate the relation between the sequence-dependent electric transport properties and the sequences of protein-coding regions of complete genomes. A correlation parameter Omega is defined to analyze the relation. For some particular propagation length w max, the transport behaviors of the coding and noncoding sequences are very different and the correlation reaches its maximal value Omega max. w max and Omega max are characteristic values for each species. A possible reason for the difference between the features of transport properties in the coding and noncoding regions is the mechanism of DNA damage repair processes together with natural selection.

Computer Simulation↗
PubMed2002

Nucleotide sequence shows that Bean leafroll virus has a Luteovirus-like genome organization.

The complete nucleotide sequence of the Bean leafroll virus (BLRV) genomic RNA and the termini of its smallest subgenomic RNAs were determined to better understand its mechanisms of gene expression and replication and its phylogenetic position within the Luteoviridae: The number and placement of open reading frames (ORFs) within the BLRV genome was Luteovirus-like. The nucleotide and predicted amino acid sequences of BLRV were most similar to those of Soybean dwarf virus (SbDV). Phylogenetic analyses employing the neighbour-joining method and sister-scanning analysis indicated that the BLRV nonstructural proteins were closely related to those of Barley yellow dwarf virus-PAV (BYDV-PAV), a luteovirus: The region surrounding the frameshift at the junction between ORFs 1 and 2 also contained sequences very similar to those of BYDV-PAV and a Dianthovirus, Red clover necrotic mosaic virus. Similar analyses showed that the structural proteins were most similar to those of the Polerovirus genus. The 3'-noncoding regions downstream of ORF5 contained sequences similar to translational control elements identified in the BYDV-PAV genome. These data suggest that BLRV, like SbDV, is derived either through selection from a common ancestor with BYDV-PAV or that BLRV is the product of two recombination events between luteovirus-like and polerovirus-like ancestors where the 5' 2900 nt and 3' 700 nt of the BLRV genome are from a Luteovirus and the intervening sequences are derived from a Polerovirus:

3' Untranslated Regions↗
PubMed2025

Widespread induction of SINE-RNA expression in the mouse brain following transient focal ischemia.

Ischemic stroke triggers rapid transcriptional changes in the brain, including the induction of noncoding RNAs, which are well-established regulators of post-stroke pathophysiology. Among the numerous classes of noncoding RNAs, short interspersed nuclear element RNAs (SINE-RNAs) are transcribed by Pol III and reported to be upregulated in various paradigms of cellular stress. In the ischemic brain, Pol III-driven gene expression is not well-studied and the expression of SINE-RNAs is virtually unmapped. In the current study, we used a mouse model of transient focal ischemia to evaluate for the first time post-stroke SINE-RNA expression in the cerebral cortex on a genome-wide scale. We observed SINE-RNA induction as early as 0 to 3 h of reperfusion and peak expression at 6 h of reperfusion, with 335 SINE-RNAs induced at this timepoint as compared to sham controls. Many of these transcripts remained induced through later timepoints during the acute phase of reperfusion (24 h). Fluorescence in situ hybridization against the SINE-RNAs, combined with immunohistochemistry for cell-type markers, revealed that these RNAs are localized to the nuclei of post-ischemic neurons and microglia in the ipsilateral cortex and hippocampus in both males and females. Further, we found that SINE-RNA expression was recapitulated in vitro following oxygen-glucose deprivation in HT22 hippocampal neurons, showing that they are reproducibly expressed in neurons in both in vivo and in vitro models of ischemia. Together, this is the first study to map genome-wide SINE-RNA expression in the post-ischemic brain and reveals a new layer of the noncoding transcriptome that may play a role in the post-stroke pathophysiology.

Animals↗
PubMed2006

Patterns of sequence conservation in presynaptic neural genes.

BACKGROUND: The neuronal synapse is a fundamental functional unit in the central nervous system of animals. Because synaptic function is evolutionarily conserved, we reasoned that functional sequences of genes and related genomic elements known to play important roles in neurotransmitter release would also be conserved. RESULTS: Evolutionary rate analysis revealed that presynaptic proteins evolve slowly, although some members of large gene families exhibit accelerated evolutionary rates relative to other family members. Comparative sequence analysis of 46 megabases spanning 150 presynaptic genes identified more than 26,000 elements that are highly conserved in eight vertebrate species, as well as a small subset of sequences (6%) that are shared among unrelated presynaptic genes. Analysis of large gene families revealed that upstream and intronic regions of closely related family members are extremely divergent. We also identified 504 exceptionally long conserved elements (> or =360 base pairs, > or =80% pair-wise identity between human and other mammals) in intergenic and intronic regions of presynaptic genes. Many of these elements form a highly stable stem-loop RNA structure and consequently are candidates for novel regulatory elements, whereas some conserved noncoding elements are shown to correlate with specific gene expression profiles. The SynapseDB online database integrates these findings and other functional genomic resources for synaptic genes. CONCLUSION: Highly conserved elements in nonprotein coding regions of 150 presynaptic genes represent sequences that may be involved in the transcriptional or post-transcriptional regulation of these genes. Furthermore, comparative sequence analysis will facilitate selection of genes and noncoding sequences for future functional studies and analysis of variation studies in neurodevelopmental and psychiatric disorders.

Animals↗
PubMed1992

Essential role of duplications of short motif sequences in the genomic evolution of Bombyx mori.

The Bombyx fibroin gene has a discrete mosaic structure of various repetitive sequences, which may have evolved through various repeating arrangements. Detailed sequence analysis of the fibroin gene containing coding and noncoding regions revealed that the whole sequence could be arranged as an array of short repetitive sequences. A portion of the intron of the fibroin gene is one of interspersed repetitive elements. We cloned a 1.5-kb DNA fragment of the Bombyx genome that contains interspersed elements homologous to the intron sequence. Sequence comparison between the intron and the 1.5-kb fragment shows that partial duplication has frequently occurred in evolutionary progress, and the resultant repetitive blocks of short motif sequences are abundant in the genome. These facts suggest that tandem duplication of the short motif sequence is an important rearrangement in genomic evolution of the fibroin gene.

Animals↗
PubMed1988

Deletion of DNA sequences flanking an Mr 19,000 zein gene reduces its transcriptional activity in heterologous plant tissues.

Analysis of a series of clones containing deletions in the 5' noncoding sequence of a gene encoding an Mr 19,000 zein allowed identification of a region required for maximal transcription. Transcriptional activity was assayed in two heterologous plant systems. In one system, the Ti plasmid was used to introduce the modified zein genes into the sunflower genome. In the other system, electroporation was used to transform carrot protoplasts with plasmids containing the zein genes. For the electroporation experiments, the 5' noncoding sequences from the zein clones were linked to the protein coding sequence of chloramphenicol acetyl transferase. The results showed that an upstream sequence, delimited by nucleotides -337 and -125 with respect to the mRNA cap site, is required for maximal transcription of the gene. In contrast, very low levels of transcription were directed by constructs that contained 125 bp of 5' noncoding sequence that included the CAAT and TATA boxes, suggesting that the additional sequences (-337 to -125) further 5' exert a quantitative effect on transcription. Examination of the additional 5' sequences showed five regions that share homology with the SV40 enhancer core sequence.

Base Sequence↗
PubMed2004

Analysis of the serotype and genotype correlation of VP1 and the 5' noncoding region in an epidemiological survey of the human enterovirus B species.

The sequence identity of the enterovirus VP1 gene has been shown to correlate with the serotype concept. Enterovirus molecular typing methods are therefore often based on sequencing of the VP1 genomic region and monophyletic clustering of VP1 sequences of a homologous serotype. For epidemiological surveillance, 342 enterovirus samples obtained from patients with aseptic meningitis in Belgium from 1999 to 2002 were first diagnosed as being enterovirus positive by amplification of the 5' noncoding region (5'NCR) by reverse transcription (RT)-PCR. Subsequently, samples were molecularly typed by RT-nested PCR amplification and sequencing of a portion of the VP1 gene. Phylogenetic analyses were performed to investigate enteroviral evolution and to examine the serotype and genotype correlation of the two genomic regions. Our typing results demonstrated echovirus 30, echovirus 13, echovirus 18, and echovirus 6 to be the most predominant types. Echoviruses 13 and 18 were considered to be emerging human serotypes since 2000 and 2001, respectively, as they had been rarely reported before. Several serotypes existed as multiple genotypes (subtypes) from 1999 to 2002, but genomic differences mainly resided at synonymous sites; these results strongly suggest that the subtypes exhibit similar antigenic properties. Phylogenetic analyses confirmed that VP1 is an adequate region for molecular typing. Serotype-specific clusters are not observed commonly in phylogenetic trees based on the 5'NCR, and the phylogenetic signal in the 5'NCR was found to be particularly low. However, some substructure in the 5'NCR tree made a tentative prediction of the enterovirus type possible and was therefore helpful in PCR strategies for VP1 (e.g., primer choice), provided some background knowledge on the local spectrum of enteroviruses already exists.

Base Sequence↗
PubMed1984

Localization and analysis of bovine papillomavirus type 1 transforming functions.

Bovine papillomavirus type 1 (BPV-1) or cloned BPV-1 DNA can transform susceptible rodent cells, and the viral DNA remains as a stable extrachromosomal plasmid in the transformed cells. The transforming region of the BPV-1 genome has previously been localized to a specific fragment comprising 69% of the genome, which also contains the elements sufficient for extrachromosomal plasmid maintenance. To define more precisely the viral DNA sequences which are involved in cellular transformation, we have tested the ability of defined deletion mutants of BPV-1 DNA to morphologically transform mouse C127 cells. Cells containing the mutated DNAs have been examined for anchorage independence and tumorigenicity in nude mice. Several distinct regions of the BPV-1 genome were found to influence expression of the viral transformation functions. A transcriptional regulatory region located in the noncoding region 5' to the early open reading frames is essential for transcriptional activity and transformation. A transcriptional enhancer element, located 3' to the polyadenylation site for the viral RNAs expressed in transformed cells, has previously been shown to be essential for transformation (Lusky et al., Mol. Cell. Biol., 3:1108-1122, 1983). Deletion mutants affecting the E2 open reading frame, particularly the NH2 half, are significantly impaired in their ability to transform, suggesting that the E2 gene product is an important transforming protein of BPV-1. Mutants lacking the E6 and E7 open reading frames are still able to induce transformation but at a lowered efficiency, and the transformants have altered characteristics. Mutations localized within the E1 open reading frame do not significantly affect the transforming functions but result in the integration of the viral genome in the transformed cells, implicating the E1 gene product in stable plasmid replication and maintenance.

Animals↗
PubMed1990

Compositional patterns in the nuclear genome of cold-blooded vertebrates.

DNA preparations obtained from 122 species of fishes, 5 species of amphibians, and 13 species of reptiles were investigated in their compositional properties by analytical equilibrium centrifugation in CsCl density gradients. These species represented 21 orders of Osteichthyes, 3 orders of Chondrichthyes, 2 orders of amphibians, and 3 orders of reptiles. Modal buoyant densities of fish DNAs ranged from 1.696 to 1.707 g/cm3, the vast majority of values falling, however, between 1.699 and 1.704 g/cm3, which is the range covered by the DNAs of amphibians and reptiles. In all cases, DNA bands in CsCl were only weakly asymmetrical and only very rarely were accompanied by separate satellite bands (mostly on the GC-rich side). Intermolecular compositional heterogeneities were low in the vast majority of cases, and, like CsCl band asymmetries, at least partially due to cryptic or poorly resolved satellites. The present findings indicate, therefore, that DNAs from cold-blooded vertebrates are characterized by a number of common properties, namely a very wide spectrum of modal buoyant densities, low intermolecular compositional heterogeneities, low CsCl band asymmetries, and, in most cases, small amounts of satellite DNAs. In the case of fish DNAs a negative correlation was found between the GC level and the haploid size (c value) of the genome. If polyploidization is neglected, this phenomenon appears to be mainly due to the fact that increases and decreases in GC are associated with contraction and expansion phenomena, respectively, of intergenic noncoding sequences, which are GC poor relative to coding sequences.

Amphibians↗
PubMed2006

Viral proteomics: a promising approach for understanding JC virus tropism.

The human polyomavirus JC virus (JCV) is responsible for the CNS demyelination observed in cases of progressive multifocal leukoencephalopathy. The JCV regulatory region (promoter) is a hypervariable, noncoding, nucleotide sequence positioned between the early and late protein-coding regions in the viral genome. Selective binding of cellular transcription factors to this promoter region participates in the control of viral tropism. Hence, further study of these proteins might provide new insights into JCV tropism and associated pathogenesis. This review gives an overview of viral proteomics - the study of all proteins expressed from the viral gene transcripts, and all the cellular proteins that play a role in JCV tropism. It also describes a new biochemical approach for studying relevant JCV promoter-binding proteins, which is an anchored-JCV transcriptional promoter (ATP) assay. An ATP assay utilizes the product of PCR-amplified JCV promoter sequences coupled with Sepharose beads in order to capture and isolate cellular nuclear proteins with specific promoter-binding affinity for analysis. Proteins that bind to JCV-ATPs can be eluted and subjected to proteomic analysis. Insights from this approach may improve the understanding of viral and cellular parameters that control JCV tropism.

Deoxyribonuclease I↗
PubMed1982

Nucleotide sequence of DNA from an altered-virulence isolate D/H of the cauliflower mosaic virus.

The double-stranded DNA from the isolate D/H with an altered virulence of the cauliflower mosaic virus (CaMV) contains 8016 bp. The DNA is circular and possesses, like the DNA of most CaMV strains, three sequence interruptions. The comparison of its sequence with the previously published sequences of two other CaMV strains (Cabb-S and CM 1841) leads to the following conclusions: (1) The genetic organization of all three CaMV strains is identical with six potential genes (open reading frames) and two intergenic regions; (2) considered pairwise, the three DNAs differ from one another by only about 5% with base substitutions accounting for most of the changes although several deletions and insertions are also observed. The sequence differences among the three strains are spread in a uniform manner upon the genome except for the two intergenic regions, which are more highly conserved. The stability of the noncoding regions is probably linked to the fact that they carry sequences important for the initiation and termination of transcription. On the other hand, the sequence variation in the open reading frames has relatively little effect on the sequence of the corresponding polypeptides as changes occur preferentially in the third position of the reading frame triplets. It is anticipated that knowledge of the DNA sequences of several CaMV strains will facilitate construction of inter-strain recombinants which, once available, can be used to correlate gene structure and function.

Base Composition↗
PubMed1990

Structure and chromosome localization of the human eosinophil-derived neurotoxin and eosinophil cationic protein genes: evidence for intronless coding sequences in the ribonuclease gene superfamily.

Human genomic DNAs for the eosinophil granule proteins, eosinophil-derived neurotoxin (EDN) and eosinophil cationic protein (ECP), were isolated from genomic libraries. Alignment of EDN (RNS2) and ECP (RNS3) gene sequences demonstrated remarkable nucleotide similarities in noncoding sequences, introns, and flanking regions, as well as in the previously known coding regions. Detailed examination of the 5'-noncoding regions yielded putative TATA and CAAT boxes, as well as similarities to promoter motifs from unrelated genes. A single intron of 230 bases was found in the 5' untranslated region and we suggest that a single intron in this region and an intronless coding region are features common to many members of the RNase gene superfamily. The RNS2 and RNS3 genes were localized to the q24-q31 region of human chromosome 14. It is likely that these two genes arose as a consequence of a gene duplication event that took place approximately 25-40 million years ago and that a subset of anthropoid primates possess both of these genes or closely related genes.

Animals↗
PubMed2004

Genomic imprinting: CTCF protects the boundaries.

The DNA-binding protein CTCF, which acts as a chromatin 'insulator', regulates imprinting of the mammalian Igf2 and H19 genes in a methylation-sensitive manner. It has now been shown that CTCF is also required for protection against de novo methylation of the differentially methylated domain of H19 in the female germline.

CCCTC-Binding Factor↗
PubMed2003

The mouse zinc-fingers and homeoboxes (ZHX) family; ZHX2 forms a heterodimer with ZHX3.

Human zinc-fingers and homeoboxes (ZHX) 1, ZHX2 and ZHX3, members of the ZHX family, contain two Cys(2)-His(2)-type zinc-finger motifs and five homeodomains (HDs). These proteins not only form homodimers but heterodimers with ZHX1 as well and act as ubiquitous transcriptional repressors. The cloning of mouse ZHX2 and ZHX3 cDNAs and the corresponding genes from a 129 mouse genomic library are reported, along with an analysis of the heterodimerization of ZHX2 with ZHX3. The mouse ZHX2 and ZHX3 proteins consist of 836 and 951 amino acid residues, respectively. The similarity of amino acid sequences of each protein with those of human orthologue is 87.0% and 85.2%, respectively. An analysis of genomic clones revealed that an entire coding sequence and a portion of the 5'- and 3'-noncoding sequence of mouse ZHX2 cDNA are encoded by a single exon of the mouse ZHX2 gene as well as the mouse ZHX1 gene. In contrast, in the case of the mouse ZHX3 gene, the coding sequences of ZHX3 cDNA are separated by an intron. A 4.5-kb ZHX2 transcript, and three ZHX3 transcripts, 9.5-, 6.5- and 4.4-kb, are ubiquitously expressed, although their levels vary. Lastly, in vitro and in vivo protein-protein interaction assays revealed that ZHX2 is able to form a heterodimer with ZHX3 via a region containing each HD1.

Amino Acid Sequence↗