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At least 919 records · Page 51Linked to original sources
PubMed1996

Typing of Mycobacterium avium isolates by PCR.

A Mycobacterium avium typing method based on PCR amplification of genomic sequences located between the recently described repetitive elements IS1245 and IS1311 was developed. This method was applied to a set of epidemiologically related and unrelated strains and compared with restriction fragment length polymorphism analysis with IS1245 as the probe. This PCR typing consists of a rapid and simple technique, providing a reproducible M. avium characterization as discriminant as restriction fragment length polymorphism analysis.

AIDS-Related Opportunistic Infections↗
PubMed2001

Comparative genomic sequencing reveals a strikingly similar architecture of a conserved syntenic region on human chromosome 11p15.3 (including gene ST5) and mouse chromosome 7.

Comparative genomics is a superior way to identify phylogenetically conserved features like genes or regions involved in gene regulation. The comparison of extended orthologous chromosomal regions should also reveal other characteristic traits essential for chromosome or gene function. In the present study we have sequenced and compared a region of conserved synteny from human chromosome 11p15.3 and mouse chromosome 7. In human, this region is known to contain several genes involved in the development of various disorders like Beckwith-Wiedemann overgrowth syndrome and other tumor diseases. Furthermore, in the neighboring chromosome region 11p15.5 extensive imprinting of genes has been reported which might extend to region 11p15.3. The analysis of approximately 730 kb in human and 620 kb in mouse led to the identification of eleven genes. All putative genes found in the mouse DNA were also present in the same order and orientation in the human chromosome. However, in the human DNA one putative gene of unknown function could be identified which is not present in the orthologous position of the mouse chromosome. The sequence similarity between human and mouse is higher in transcribed and exon regions than in non-transcribed segments. Dot plot analysis, however, reveals a surprisingly well-conserved sequence similarity over the entire analyzed region. In particular, the positions of CpG islands, short regions of very high GC content in the 5' region of putative genes, are similar in human and mouse. With respect to base composition, two distinct segments of significantly different GC content exist as well in human as in the mouse. With a GC content of 45% the one segment would correspond to "isochore H1" and the other segment (39% GC in human, 40% GC in mouse) to "isochore L1/L2". The gene density (one gene per 66 kb) is slightly higher than the average calculated for the complete human genome (one gene per 90 kb). The comparison of the number and distribution of repetitive elements shows that the proportion of human DNA made up by interspersed repeats (43.8%) is significantly higher than in the corresponding mouse DNA (30.1%). This partly explains why the human DNA is longer between the landmark genes used to define the orthologous positions in human and mouse.

Animals↗
PubMed1985

L1 sequences in HeLa extrachromosomal circular DNA: evidence for circularization by homologous recombination.

Subcloned probes of the L1 family of repetitive elements were used to isolate L1-carrying clones from a plasmid library of HeLa cell extrachromosomal circular DNA. One clone was analyzed in detail by restriction mapping, cross-hybridization to L1 probes, and base sequence analysis. In addition to approximately the 3' half of a full-sized L1 element, this clone carried 390 base pairs of non-L1 sequence that is single copy in the HeLa genome. A HeLa genomic clone of this unique chromosomal region was isolated and the sequence organization of the circle clone was compared with the linear chromosomal region from which it was ultimately derived. We discuss possible mechanisms of circular DNA formation and propose homologous intrachromosomal recombination between 9-base-pair direct repeats to be most likely in this case.

Chromosome Deletion↗
PubMed2003

Comparative analysis of vertebrate dystrophin loci indicate intron gigantism as a common feature.

The human DMD gene is the largest known to date, spanning > 2000 kb on the X chromosome. The gene size is mainly accounted for by huge intronic regions. We sequenced 190 kb of Fugu rubripes (pufferfish) genomic DNA corresponding to the complete dystrophin gene (FrDMD) and provide the first report of gene structure and sequence comparison among dystrophin genomic sequences from different vertebrate organisms. Almost all intron positions and phases are conserved between FrDMD and its mammalian counterparts, and the predicted protein product of the Fugu gene displays 55% identity and 71% similarity to human dystrophin. In analogy to the human gene, FrDMD presents several-fold longer than average intronic regions. Analysis of intron sequences of the human and murine genes revealed that they are extremely conserved in size and that a similar fraction of total intron length is represented by repetitive elements; moreover, our data indicate that intron expansion through repeat accumulation in the two orthologs is the result of independent insertional events. The hypothesis that intron length might be functionally relevant to the DMD gene regulation is proposed and substantiated by the finding that dystrophin intron gigantism is common to the three vertebrate genes.

Amino Acid Sequence↗
PubMed1999

Short sequence repeats in microbial pathogenesis and evolution.

Repetitive DNA is ubiquitous in microbial genomes. Different classes of short sequence repeats (SSRs) have been identified and demonstrated to be generally heterogeneous in a locus-dependent manner, reflected in variation in the number of repeat units present at a given genomic site or by sequence heterogeneity among individual units. Both types of variability can be used to assess intra-species genetic diversity. Repeat variability often affects the coding potential of the region in which the repetitive element is located. This implies that determination of the primary structure of variable numbers of tandem repeats can be used for epidemiological identification purposes, and also for the analysis of gene function. Precise assessment of SSR structure can also generate insight into the regulation of gene expression. Together, DNA repeat analysis in microbial species provides information on both functional and evolutionary aspects of genetic diversity among microbial isolates.

Candida albicans↗
PubMed2001

Species-specific evolution of repeated DNA sequences in great apes.

DNA sequencing reveals that the genomes of the human, gorilla and chimpanzee share more than 98% homology. Comparative chromosome painting and gene mapping have demonstrated that only a few rearrangements of a putative ancestral mammalian genome occurred during great ape and human evolution. However, interspecies representational difference analysis (RDA) of the gorilla between human and gorilla revealed gorilla-specific DNA sequences. Cloning and sequencing of gorilla-specific DNA sequences indicate that there are repetitive elements. Gorilla-specific DNA sequences were mapped by fluorescence in-situ hybridization (FISH) to the subcentromeric/centromeric regions of three pairs of gorilla submetacentric chromosomes. These sequences could represent either ancient sequences that got lost in other species, such as human and orang-utan, or, more likely, recent sequences which evolved or originated specifically in the gorilla genome.

Animals↗
PubMed1995

A small-insert bovine genomic library highly enriched for microsatellite repeat sequences.

A bovine genomic phagemid library was constructed with randomly sheared DNA. Enrichment of this single-stranded DNA library with CA or GT primers resulted in 45% positive clones. The 14% of positive clones with (CA.GT) > 12, and not containing flanking repetitive elements, were sequenced, and the efficiency of marker production was compared with random M13 bacteriophage libraries. Primer sequences and genotyping information are presented for 390 informative bovine microsatellite markers. The genomic frequency for 11 tri- and tetranucleotide repeats was estimated by hybridization to a lambda genomic library. Only GCT, GGT, and GGAT were estimated to have a frequency of > 100 per genome. Enrichment of the phagemid library for these repeats failed to provide a viable source of microsatellite markers in the bovine. Comparison of map interval lengths between 100 markers from the enriched library prepared from randomly sheared DNA and M13 bacteriophage libraries prepared from Mbo1 restriction digests suggested no bias in skeletal genomic coverage based on source of small insert DNA. In conclusion, enrichment of the bovine phagemid library provides a sufficient source of microsatellites so that small repeat lengths and flanking repetitive sequences common in the bovine can be eliminated, resulting in a high percentage of informative markers.

Animals↗
PubMed2005

Noncoding DNA and the teem theory of inheritance, emotions and innate behaviour.

The evolutionary function of noncoding 'junk' DNA remains one of the most challenging mysteries of genetics. Here a new model of DNA is proposed to explain this function. The hypothesis asserts the DNA molecule contains not one, but two separate modes of inheritance. In addition to exons that code for proteins and physical traits, it is argued noncoding repetitive elements code for the inheritance of emotions and innate behaviour in metazoans. That is to say, noncoding DNA functions as the medium of a second, hitherto unknown evolutionary process that genetically archives adaptive information, configured as emotions and acquired during the life of an organism, into an inheritable form. This second evolutionary process, here called 'Teemosis', is a selectionist process, but paradoxically, because it does not affect physical traits, it has no maladaptive Lamarckian consequences. The medical implications of the hypothesis are discussed.

Animals↗
PubMed1997

Sequence analysis of two genomic regions containing the KIT and the FMS receptor tyrosine kinase genes.

The KIT and FMS tyrosine kinase receptors, which are implicated in the control of cell growth and differentiation, stem through duplications from a common ancestor. We have conducted a detailed structural analysis of the two loci containing the KIT and FMS genes. The sequence of the approximately 90-kb KIT locus reveals the position and size of the 21 introns and of the 5' regulatory region of the KIT gene. The introns and the 3'-untranslated parts of KIT and FMS have been analyzed in parallel. Comparison of the two sequences shows that, while introns of both genes have extensively diverged in size and sequence, this divergence is, at least in part, due to intron expansion through internal duplications, as suggested by the discrete extant analogies. Repetitive elements as well as exon predictions obtained using the GRAIL and GENEFINDER programs are described in detail. These programs led us to identify a novel gene, designated SMF, immediately downstream of FMS, in the opposite orientation. This finding emphasizes the gene-rich characteristic of this genomic region.

Animals↗
PubMedDate not supplied

Repetitive exon 45/46-related sequences of human Ca2+ channel alpha1C subunit gene.

We found in the Ca2+ channel alpha1C subunit gene a new repetitive element of three paired exon 45/46-related sequences. We also identified a new exon 45/46-related sequence in the human genome and mapped it by fluorescence in situ hybridization to the 12p11.2 and 12p13.2-p13.1 bands. These positions are not recognized by DNA probes generated from the 5'- and 3'-terminal regions of the alpha1C gene. A possible existence of a new genomic homologue of the alpha1C subunit gene is discussed.

Base Sequence↗
PubMed1995

Genomic sequence comparison of the human and mouse XRCC1 DNA repair gene regions.

The XRCC1 (X-ray repair cross complementing) gene is involved in the efficient repair of DNA single-strand breaks formed by exposure to ionizing radiation and alkylating agents. The human gene maps to chromosome 19q13.2, and the mouse homologue maps to the syntenic region on chromosome 7. Two cosmids (approximately 38 kb each) containing the human and mouse genes were sequenced to an average 8-fold clonal redundancy. The XRCC1 gene spans a genomic distance of 26 kb in mouse and 31.9 kb in human. Both genes contain 17 exons, are 84% identical within the coding regions, and are 86% identical at the amino acid sequence level. Intron and exon lengths are highly conserved. For the human cosmid, a total of 43 Alu repetitive elements are present, a density of 1.1 Alu/kb, but due to clustering, the local density is as high as 1.8 Alu/kb. In addition, we observed a statistically significant bias for insertion of these elements in the 3'-5' orientation relative to the direction of XRCC1 transcription, predominantly in the second and third introns. This bias may indicate that XRCC1 is more accessible to Alu retroposition events during transcription than genes not expressed during spermatogenesis. The density of B1 and B2 elements in the mouse is 0.4/kb, integrated primarily in the 5'-3' orientation. The human chromosome 19-specific minisatellite PE670 was present in the same orientation in 3 introns in the human gene, and a similar repeat was found at 3 different locations in the mouse cosmid.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1988

Chromosome size polymorphism in Plasmodium falciparum can involve deletions of the subtelomeric pPFrep20 sequence.

The P. falciparum pPFrep20 repetitive element from the Palo Alto Uganda strain has been isolated and sequenced. The Palo Alto pPFrep20 repeat (pPFPArep20) has a clustered subtelomeric location and on chromosome 1 has been deleted from one end. Analysis of chromosome 1 from 5 other strains has revealed that pPFrep20 sequences have been deleted from one end in 3 of them. Thus, deletion of pPFrep20 appears to be a frequent event that could significantly contribute to chromosome size polymorphism in P. falciparum.

Animals↗
PubMed1988

The rat vitamin-D-dependent calcium-binding protein (9-kDa CaBP) gene. Complete nucleotide sequence and structural organization.

The structural organization of the entire rat vitamin-D-dependent calcium-binding protein (9-kDa CaBP) gene was determined by analysis of overlapping genomic clones isolated from a rat genomic library using the rat 9-kDa CaBP cDNA [Desplan C., Heidmann O., Lillie J., Auffray C. and Thomasset M. (1983) J. Biol. Chem. 258, 13502-13505]. These clones together span 30 kbp of rat genomic DNA, with the rat 9-kDa CaBP gene lying in the middle. The 9-kDa CaBP gene is 2.5 kbp long and contains three exons interrupted by two introns. The first exon contains almost the entire 5' untranslated region. The second exon codes for the calcium-binding site I, the third exon codes for site II and the 3' untranslated region. Therefore each of the calcium-binding domains is encoded by single, separate exons. The transcription initiation site was identified by S1 nuclease mapping and primer extension. A consensus sequence TATAAA is localized 31 bp upstream from the cap site and the 'CCAAT-box' lies upstream from the transcription start. Single (AC)25 and (AG)23 repeats are present in the second intron together with an Alu-like sequence. Repetitive elements are present 5 kbp upstream from the cap site and in the 3' flanking region. Comparison of the known rat CaBP sequences (9-kDa CaBP, 28-kDa CaBP, S100 protein) shows that the 9-kDa CaBP is more closely related to the S100 protein than to the 28-kDa CaBP. There is no evidence to indicate that 9-kDa CaBP has arisen from the 28-kDa CaBP.

Amino Acid Sequence↗
PubMed1987

A highly abundant transcript in adult murine cerebellar granule cells contains repetitive sequences homologous to L1.

Cloned cDNA from adult mouse cerebellum composed of subsequences homologous to the L1Md consensus sequence (long interspersed repetitive element "LINE" family of the mouse) hybridizes specifically with large nuclear poly(A)+RNAs that are highly concentrated in the murine and rat cerebellum. These homogeneous L1-related transcripts were localized in the mouse CNS by in situ hybridization with 3H- and biotin-labeled DNA probes. They were found to hybridize to cerebellar granule cells specifically.

Animals↗
PubMed1994

A theory that may explain the Hayflick limit--a means to delete one copy of a repeating sequence during each cell cycle in certain human cells such as fibroblasts.

A model that may explain the limited division potential of certain cells such as human fibroblasts in culture is presented. The central postulate of this theory is that there exists, prior to certain key exons that code for materials needed for cell division, a unique sequence of specific repeating segments of DNA. One copy of such repeating segments is deleted during each cell cycle in cells that are not protected from such deletion through methylation of their cytosine residues. According to this theory, the means through which such repeated sequences are removed, one per cycle, is through the sequential action of enzymes that act much as bacterial restriction enzymes do--namely to produce scissions in both strands of DNA in areas that correspond to the DNA base sequence recognition specificities of such enzymes. After the first scission early in a replicative cycle, that enzyme becomes inhibited, but the cleavage of the first site exposes the closest site in the repetitive element to the action of a second restriction enzyme after which that enzyme also becomes inhibited. Then repair occurs, regenerating the original first site. Through this sequential activation and inhibition of two different restriction enzymes, only one copy of the repeating sequence is deleted during each cell cycle. In effect, the repeating sequence operates as a precise counter of the numbers of cell doubling that have occurred since the cells involved differentiated during development.

Base Sequence↗
PubMed1994

Selection of oligonucleotide probes and experimental conditions for multiplex hybridization experiments.

Different DNA probes hybridize under different conditions. I examine the constraints of the design of oligonucleotide probes that are meant to hybridize to different unique sites in human genomic DNA under a single set of hybridization conditions as a parallel array. In 522 kb of human genomic DNA, 75% of 12-base and 89% of 22-base are unique, as opposed to 90% and 100% as expected of unstructured DNA, and this is not due solely to repetitive elements in the DNA. Hybridization in TMAC to reduce A+T content effects on melting temperature allows only 90% of unique targets to be hybridized under one set of conditions if a 2 degrees C difference between matched and mismatched sequences is required. Standard hybridization conditions allow no more than 60% of unique probes to be used together. This suggests that probe, hybridization conditions, and instrument design for multiple-probe hybridization applications will be harder than previously suggested.

Base Composition↗
PubMed2004

Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

RNA editing by adenosine deamination generates RNA and protein diversity through the posttranscriptional modification of single nucleotides in RNA sequences. Few mammalian A-to-I edited genes have been identified despite evidence that many more should exist. Here we identify intramolecular pairs of Alu elements as a major target for editing in the human transcriptome. An experimental demonstration in 43 genes was extended by a broader computational analysis of more than 100,000 human mRNAs. We find that 1,445 human mRNAs (1.4%) are subject to RNA editing at more than 14,500 sites, and our data further suggest that the vast majority of pre-mRNAs (greater than 85%) are targeted in introns by the editing machinery. The editing levels of Alu-containing mRNAs correlate with distance and homology between inverted repeats and vary in different tissues. Alu-mediated RNA duplexes targeted by RNA editing are formed intramolecularly, whereas editing due to intermolecular base-pairing appears to be negligible. We present evidence that these editing events can lead to the posttranscriptional creation or elimination of splice signals affecting alternatively spliced Alu-derived exons. The analysis suggests that modification of repetitive elements is a predominant activity for RNA editing with significant implications for cellular gene expression.

5' Untranslated Regions↗
PubMed1985

A gene encoding rat cholecystokinin. Isolation, nucleotide sequence, and promoter activity.

The gene for rat cholecystokinin (CCK) was isolated from a rat genomic DNA library. The transcription unit spans 7 kilobases and is interrupted by two introns. The initiator methionine codon lies 2 bases into exon 2; therefore, exon 1 is a noncoding exon. The transcription initiation site was determined using avian myeloblastosis reverse transcriptase, a cDNA primer, and mRNA isolated from a rat medullary thyroid carcinoma. A "TATA"-like sequence precedes the transcription initiation site at position -34. The polyadenylation site for the gene was mapped by a nuclease protection assay using a cRNA generated by transcription of the exon 3 region of the CCK gene with SP6 bacteriophage RNA polymerase. The sequence AT-TAAA is found 22 bases 5' to the site determined to be the polyadenylation addition site. Two regions of simple repetitive DNA occur within the CCK lambda clone, one within intron 2 and the other 4 kilobases 3' to the gene. Sequence analysis of the repetitive element 3' distal to the gene revealed two copies of the sequence 5'-(AC)n-3', where n is 22 and 25. A 114-base pair sequence of predominantly repeating purine-pyrimidine nucleotides separates these two d(AC) repeats. Transcriptional control elements were investigated by fusing regions of the CCK gene to the structural gene encoding chloramphenicol acetyltransferase. Promoter activity was determined by transfecting COS-7 cells with plasmids containing the gene fusions, followed by determining chloramphenicol acetyltransferase activity in cellular extracts. The region necessary for expression of the CCK gene fusions in COS-7 cells is within 144 bases 5' to the initiation of transcription.

Animals↗