Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Alu elements”

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 1,279 records · Page 71Linked to original sources
PubMed2003

[Polymorphism analysis for DYS19 and DYS287 of three Li populations in Haina Island, China].

The distribution of Y-chromosome specific microsatellite DYS19, in 289 males of three ethnic populations in Hainan Island was studied with the method of PCR followed by denatured polyacrylamide gel electrophoresis and silver staining. The three ethnic populations are Bendi Li, Qi Li and Ha Li. The results showed that four alleles (190bp, 194bp, 198bp, 202bp designated as alleles B, C, D and E respectively), were observed in DYS19, the frequency ranged from 0.660-0.854, and was predominant in three Li subgroups. The pairwise comparison with Fisher's Exact test reveals that there exists significant difference (P<0.01) in DYS19 phenotype distribution between Qi Li and Ha Li populations. The polymorphism of the Y-chromosome specific Alu insert sequence DYS287 was investigated also in three Li populations. The results demonstrated that with 150 bp product in all Bendi-Li, Qi-li and Ha-li, YAP element is absent. The preliminary study provides reference populations for detecting male migration events and for reconstructing paternal history.

English Abstract↗
PubMed2000

LINE L1 retrotransposable element is targeted during the initial stages of apoptotic DNA fragmentation.

Using a directional cloning strategy, DNA sequence information was obtained corresponding to the site of early radiation-induced apoptotic DNA fragmentation within the human lymphoblastoid cell line TK6. Data were obtained from 88 distinct clones comprising approximately 65 kbp of sequenced material. Analysis of all cloned material showed that sequences in the 10 bp immediately adjacent to the cleavage sites were enriched in short oligoT tracts. The proportion of repetitive DNA within the entire cloned material was found to be within the normal range. However the distribution of Alu and LINE repetitive DNA were biased to positions at or adjacent to the apoptotic cleavage site. In particular, a non-random distribution of five cleavage sites was found clustered within the second ORF of the LINE L1 that partially overlapped with two binding sites for the nuclear matrix-associated protein SATB1. Three other clones, containing alpha satellite elements, were also linked to a DNA matrix binding function. These data indicate that the site of chromatin loop formation at the nuclear matrix may be a specific target for early DNA fragmentation events during apoptosis.

Apoptosis↗
PubMedDate not supplied

[Distribution of Alu repeats along the human genome: formation of clusters and features of insertion regions].

The contextual analysis of nucleotide sequences of 22 Alu repeats arrangement regions in the human genome has been carried out and some of their peculiarities have been revealed. In particular, the occurrence of marked and statistical non-random homology between the repeats and the regions of their integration has been shown. A mechanism of choosing the Alu repeats insertion regions in the genome has been suggested taking into account these peculiarities. Using a sample of the 80 human Alu repeats sequences peculiarities of these repeats location within the genome has been investigated. A tendency to the formation of Alu repeats clusters in various regions of the genome was revealed. A range of possible mechanisms on such Alu clusters emergence is considered. On the basis of the data obtained an "attraction" mechanism, according to which integration of Alu repeats into the definite region of the genome increases the insertion probability of other Alu repeats into the same region, are proposed.

Biological Evolution↗
PubMed1984

Mobile genetic elements in animal cells and their biological significance.

Mobile genetic elements were discovered by McClintock while analysing unstable mutations in maize. The structural and functional studies of such elements became possible after their cloning, first from the genome of Drosophila melanogaster. In particular, Ilyin et al. demonstrated the varying location of the described elements in D. melanogaster chromosomes, thus providing the first evidence of their mobility. Mobile elements comprise a significant part of the genetic material in D. melanogaster (not less than 10%). Several classes of mobile elements do exist. Mobile dispersed genetic elements (mdg elements) are among the best characterized ones. Mdg elements are represented in the genome by dozens of families, each consisting of 10-150 copies. They are very similar structurally to proviruses of endogenous retroviruses. In particular, the both contain long terminal repeats (LTRs). The nucleotide sequences of LTRs and their flanking sequences of several mdg elements were determined. Their analysis suggested that RNA reverse transcription should be involved in the mdg amplification. It has been found that putative transposition intermediates, i.e. extrachromosomal DNA copies of mdg elements, are synthesized by reverse transcriptase in D. melanogaster culture cells. Another type of mobile genes is represented by P factor and similar elements. P factor seems to encode 'transposase' participating in direct excision and insertion of P elements themselves as well as of other mobile genes (mdg and fold-back elements). Besides these 'active transposons' which encode the enzyme machinery for transposition, a number of other sequences which may be transposed are present in the genome. RNAs synthesized on such elements can serve as a template for reverse transcriptase, and the DNA formed can then be inserted at new sites of the genome. Among such sequences are the so-called short ubiquitous repeats: B1 and B2 in mouse genome and Alu in human genome. We found that, at least in several cases, B-type sequences were located at the 3' end of mRNA. Short repetitive sequences were also detected at the 3' end of certain mRNAs of D. melanogaster. Usually the transpositions of mobile genes occur very rarely. However, under certain conditions, for example, in hybrid dysgenesis, they become more frequent. The strain with a mutation in cut locus was obtained in hybrid dysgenesis. This mutation depends on an insertion of mdg4 at the cut locus. Genetic instability in this strain is maintained for a long time. 'Transposition bursts' were found to occur in some germ cells.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1992

Characterization of the translocation breakpoint sequences of two DEK-CAN fusion genes present in t(6;9) acute myeloid leukemia and a SET-CAN fusion gene found in a case of acute undifferentiated leukemia.

The t(6;9) associated with a subtype of acute myeloid leukemia (AML) was shown to generate a fusion between the 3' part of the CAN gene on chromosome 9 and the 5' part of the DEK gene on chromosome 6. The same part of the CAN gene appeared to be involved in a case of acute undifferentiated leukemia (AUL) as well, where it was fused to the SET gene. Genomic sequences around the translocation breakpoint were determined in two t(6;9) samples and in the case of the SET-CAN fusion. Although coexpression of myeloid markers and terminal deoxynucleotidyl transferase was shown to be one of the characteristics of t(6;9) AML, no addition of random nucleotides at the translocation breakpoint could be found. In addition, the breakpoint regions did not reveal heptamer-nonamer sequences, purine-pyrimidine tracts, a chi-octamer motif, or Alu repeats. The sequence in which the translocation breakpoints occurred was enriched in A/T. Notably, the specific introns in which clustering of breakpoints occurs in DEK and CAN both contain a LINE-I element. As LINE-I elements occur with a moderate frequency in the human genome, the presence of such an element in both breakpoint regions may be more than coincidental and may play a role in the translocation process.

Acute Disease↗
PubMed1994

The human calbindin-D9k gene. Complete structure and implications on steroid hormone regulation.

The gene encoding the human calbindin-D9k has been cloned and the complete sequence established. The gene spans about 5.5 kilobases and is localized on the X-chromosome, consists of three exons and carries four Alu repeats. The promoter and 1300 base-pairs of 5' flanking region have been characterized. Besides a TATA box and two CAAT-like motifs a sequence related to a vitamin D response element was detected about 1.1 kilobases upstream from the promoter. A sequence positioned 50 nucleotides downstream from the promoter showed extensive homology to the estrogen response element at the same location within the rat calbindin-D9k gene. Two essential nucleotides within this region are changed when the rat and human sequences are compared. The human element failed to bind the estrogen receptor as determined by gel retardation assay. It is proposed that a two-nucleotide change within this region causes the gene to lack expression in human uterus and possibly placenta.

Animals↗
PubMed1994

Laser micromanipulators for biotechnology and genome research.

The use of lasers for complete micromanipulation of metaphase chromosomes, cells and subcellular structures is reviewed. DNA probes from single microdissected chromosome segments can be prepared using Alu or Adaptor PCR. In plant biotechnology, laser microsurgery can be used to prepare non-enzymatically protoplasts from Medicago sativa. Microgravity can be simulated in the alga Chara by lifting intracellular gravity transmitting elements with the optical tweezers.

Base Sequence↗
PubMed1982

A monkey Alu sequence is flanked by 13-base pair direct repeats by an interrupted alpha-satellite DNA sequence.

A member of the Alu family, the dominant family of short interspersed repeated DNA sequences in primates, interrupts a cloned repeat unit of African green monkey alpha-satellite DNA. The Alu is immediately flanked by 13-base-pair duplications of the known sequence of the satellite at the site of insertion. These observations support the idea that Ala family members may be moveable elements.

Animals↗
PubMed1993

Identification of a functional role for the 3' region of the human oestrogen receptor gene.

A well-conserved feature of the steroid receptor gene family is the presence of an exceptionally long 3' untranslated region (UTR). Analysis of this sequence from the human oestrogen receptor (hER) gene showed the presence of a number of AT-rich regions that included thirteen repeats of the ATTTA motif, an element known to have a destabilizing effect in other systems. In the region 3' of the gene there were a further eight copies of this pentamer. Also located in this sequence were two members of the Alu repetitive family in inverse orientation and in a tandem arrangement. Transfection experiments in which the 3' UTR and 3' flanking sequence were included in chloramphenicol acetyltransferase expression vectors revealed a large destabilization effect with several different fragments. This inherent instability appears to be determined by the primary nucleotide sequence but may act in conjunction with other factors. This post-transcriptional regulatory mechanism may contribute to the control of the level of the hER mRNA.

Base Sequence↗
PubMed1991

Analysis of complex mutations induced in cells by herpes simplex virus type-1.

The shuttle vector plasmid pZ189 was used as a target for mutagenesis in COS-1 cells. Complex mutations were analyzed in 5 plasmids that were recovered from noninfected cells and 15 plasmids that were recovered from cells that were infected with herpes simplex virus type-1 (HSV-1). Complex mutations in noninfected cells consisted of duplications and rearrangements of plasmid DNA, while those from cells that were infected with HSV-1 included 8 that were enlarged due to insertion of other DNA sequences. Plasmids that contained inserted DNA showed an increase in size of from 118 bp up to around 4500 bp. Maps were constructed based on restriction enzyme digestion, and some or all of each plasmid was examined by DNA sequencing. The inserted DNA was not derived from HSV-1 in any case, since it did not hybridize to DNA from HSV-1 and showed no sequence similarities to the virus. Instead, inserted DNA was found to hybridize to HindIII-digested cellular DNA as a single or double band in 5 plasmids and contained multiple repeat sequences such as alpha satellite, Alu or Kpn repeats in 4 plasmids. In four enlarged plasmids the identity of the inserted sequences could not be determined. The junctions between the shuttle vector and the inserted DNA did not show features of transposable elements and no homology was detected between inserted sequences and the sequence at the insertion site. No preferred site for recombination was detected. Although no similarities were found among the inserted sequences, it is possible that the cellular sequences represent cellular targets for virus-mediated rearrangement. It appears that HSV-1 stimulates nonhomologous recombination between DNA sequences in virus-infected cells.

Animals↗
PubMed1998

Further characterization of thyroid hormone response elements in the human type 1 iodothyronine deiodinase gene.

The increased type 1 iodothyronine deiodinase expression in hyperthyroid patients increases the fraction of plasma T3 generated from T4 by the propylthiouracil-sensitive pathway. In this study, we extend our analysis of the thyroid hormone response elements (TREs) in the 5' flanking region of the human dio1 gene. The 5' TRE (TRE2), a direct repeat separated by 4 bp (DR+4) at -660 bp, arises from an A to G substitution in an Alu sequence, the first example of this phenomenon. An SP1 binding site immediately 5' to TRE2 increases basal expression of a 430-bp dio1 promoter-chloramphenicol acetyltransferase construct in the presence of unliganded thyroid hormone receptor, thus decreasing T3 responsiveness, but does not do so when this complex is placed in its more 5' wild-type location. The two octameric binding sites of TRE1, a retinoid X-receptor independent DR+10 structure at -90, can be exchanged or inverted without loss of T3 response potency, despite significant changes in thyroid hormone receptor binding, as assessed by gel shift assays. However, the retinoic acid response of the 716-bp dio1 5' flanking region is unaffected by elimination of TRE2 but is lost with mutations in TRE1. These findings indicate the importance of functional analyses of potential ligand-responsive transcription factors, as well as the influence of position, on TRE function and interaction with basal transcription factors. The unusual features of these TREs emphasize the need to consider alternatives to canonical half-site arrangements of receptor binding sites and contexts in the evaluation of T3- and retinoic acid-responsive genes.

Base Sequence↗
PubMed1993

Hereditary overexpression of adenosine deaminase in erythrocytes: evidence for a cis-acting mutation.

Overexpression of adenosine deaminase (ADA) in red blood cells is inherited as an autosomal dominant trait and causes hemolytic anemia. The increased ADA activity in erythrocytes is due to an increase in steady-state levels of ADA mRNA of normal sequence. Increased ADA mRNA may be due to a cis-acting mutation which results in increased transcription or a loss of down-regulation during erythroid differentiation. Alternatively, it is possible that the mutation is in a trans-acting factor which interacts with normal ADA transcriptional elements to cause overexpression in red blood cells. To discriminate between a cis-acting and a trans-acting mutation, we took advantage of a highly polymorphic TAAA repeat located at the tail end of an Alu repeat approximately 1.1 kb upstream of the ADA gene. Using PCR to amplify this region, we identified five different alleles in 19 members of the family. All 11 affected individuals had an ADA allele with 12 TAAA repeats, whereas none of the 8 normal individuals did. We conclude that this disorder results from a cis-acting mutation in the vicinity of the ADA gene.

Adenosine Deaminase↗
PubMed1993

Duplication in the hypoxanthine phosphoribosyl-transferase gene caused by Alu-Alu recombination in a patient with Lesch Nyhan syndrome.

We have determined the structure, at the nucleotide sequence level, of a duplication in the hprt gene in a patient with Lesch-Nyhan syndrome (LN). The duplication extends over exons 7 and 8 and approximately 1.8 kb of the surrounding hprt sequence. The duplication junction is localized within two Alu sequences and has apparently been generated by unequal homologous recombination. This is the second reported case of a partial duplication of the hprt gene in an LN patient, and the first that involves an Alu-Alu recombination.

Base Sequence↗
PubMed2002

Pstl repeat: a family of short interspersed nucleotide element (SINE)-like sequences in the genomes of cattle, goat, and buffalo.

The PstI family of elements are short, highly repetitive DNA sequences interspersed throughout the genome of the Bovidae. We have cloned and sequenced some members of the PstI family from cattle, goat, and buffalo. These elements are approximately 500 bp, have a copy number of 2 x 10(5) - 4 x 10(5), and comprise about 4% of the haploid genome. Studies of nucleotide sequence homology indicate that the buffalo and goat PstI repeats (type II) are similar types of short interspersed nucleotide element (SINE) sequences, but the cattle PstI repeat (type I) is considerably more divergent. Additionally, the goat PstI sequence showed significant sequence homology with bovine serine tRNA, and is therefore likely derived from serine tRNA. Interestingly, Southern hybridization suggests that both types of SINEs (I and II) are present in all the species of Bovidae. Dendrogram analysis indicates that cattle PstI SINE is similar to bovine Alu-like SINEs. Goat and buffalo SINEs formed a separate cluster, suggesting that these two types of SINEs evolved separately in the genome of the Bovidae.

Animals↗
PubMed2001

Genomic and phylogenetic analysis of the human CD1 and HLA class I multicopy genes.

The human CD1 proteins belong to a lipid-glycolipid antigen-presenting gene family and are related in structure and function to the MHC class I molecules. Previous mapping and DNA hybridization studies have shown that five linked genes located within a cluster on human chromosome 1q22-23 encode the CD1 protein family. We have analyzed the complete genomic sequence of the human CD1 gene cluster and found that the five active genes are distributed over 175,600 nucleotides and separated by four expanded intervening genomic regions (IGRs) ranging in length between 20 and 68 kb. The IGRs are composed mostly of retroelements including five full-length L1 PA sequences and various pseudogenes. Some L1 sequences have acted as receptors for other subtypes or families of retroelements. Alu molecular clocks that have evolved during primate history are found distributed within the HLA class I duplicated segments (duplicons) but not within the duplicons of CD1. Phylogeny of the alpha3 domain of the class I-like superfamily of proteins shows that the CD1 cluster is well separated from HLA class I by a number of superfamily members including MIC (PERB11), HFE, Zn-alpha2-GP, FcRn, and MR1. Phylogenetically, the human CD1 sequences are interspersed by CD1 sequences from other mammalian species, whereas the human HLA class I sequences cluster together and are separated from the other mammalian sequences. Genomic and phylogenetic analyses support the view that the human CD1 gene copies were duplicated prior to the evolution of primates and the bulk of the HLA class I genes found in humans. In contrast to the HLA class I genomic structure, the human CD1 duplicons are smaller in size, they lack Alu clocks, and they are interrupted by IGRs at least 4 to 14 times longer than the CD1 genes themselves. The IGRs seem to have been created as "buffer zones" to protect the CD1 genes from disruption by transposable elements.

Antigens, CD1↗
PubMed2006

Recently mobilized transposons in the human and chimpanzee genomes.

Transposable genetic elements are abundant in the genomes of most organisms, including humans. These endogenous mutagens can alter genes, promote genomic rearrangements, and may help to drive the speciation of organisms. In this study, we identified almost 11,000 transposon copies that are differentially present in the human and chimpanzee genomes. Most of these transposon copies were mobilized after the existence of a common ancestor of humans and chimpanzees, approximately 6 million years ago. Alu, L1, and SVA insertions accounted for >95% of the insertions in both species. Our data indicate that humans have supported higher levels of transposition than have chimpanzees during the past several million years and have amplified different transposon subfamilies. In both species, approximately 34% of the insertions were located within known genes. These insertions represent a form of species-specific genetic variation that may have contributed to the differential evolution of humans and chimpanzees. In addition to providing an initial overview of recently mobilized elements, our collections will be useful for assessing the impact of these insertions on their hosts and for studying the transposition mechanisms of these elements.

Animals↗
PubMed2002

Induction of human liver X receptor alpha gene expression via an autoregulatory loop mechanism.

The liver X receptors (LXRs), members of the nuclear receptor superfamily, play an important role in controlling lipid homeostasis by activating several genes involved in reverse cholesterol transport. These include members of the ATP binding cassette (ABC) superfamily of transporter proteins ABCA1 and ABCG1, surface constituents of plasma lipoproteins like apolipoprotein E, and cholesterol ester transport protein. They also play an important role in fatty acid metabolism by activating the sterol regulatory element-binding protein 1c gene. Here, we identify human LXRalpha (hLXRalpha) as an autoinducible gene. Induction in response to LXR ligands is observed in multiple human cell types including macrophages and occurs within 2--4 h. Analysis of the hLXRalpha promoter revealed three LXR response elements (LXREs); one exhibits strong affinity for both LXRalpha:RXR and LXRbeta:RXR (a type I LXRE), and deletion and mutational studies indicate it plays a critical role in LXR-mediated induction. The other two LXREs are identical to each other, exist within highly conserved Alu repeats, and exhibit selective binding to LXRalpha:RXR (type II LXREs). In transfections, the type I LXRE acts as a strong mediator of both LXRalpha and LXRbeta activity, whereas the type II LXRE acts as a weaker and selective mediator of LXRalpha activity. Our data suggest a model in which LXR ligands trigger an autoregulatory loop leading to selective induction of hLXRalpha gene expression. This would lead to increased hLXRalpha levels and transcription of its downstream target genes such as ABCA1, providing a simple yet exquisite mechanism for cells to respond to LXR ligands and cholesterol loading.

ATP Binding Cassette Transporter 1↗
PubMed1994

A rapid and simple method to isolate and characterize highly polymorphic markers from the centromeric regions of the human chromosomes.

Using oligonucleotide primers complementary to the 3' ends of either the Alu or the L1Hs consensus sequences in conjunction with a primer complementary to alpha satellite subsets specific to different human chromosomes, it was possible to detect and characterize polymorphisms originating from the microsatellites which are often present downstream these repetitive elements. The methodology does not require cloning, sequencing or synthesis of specific primers. Centromeric location was confirmed by linkage analysis, in situ hybridization and sequencing. The method is proposed for the generation of polymorphic markers from all centromeric regions.

Base Sequence↗