Search results for "Repetitive Sequences"
showing 10 items of 72 documents
Basic issues in forensic DNA typing
1997
DNA analysis has become the standard method in forensic stain typing (termed DNA profiling). In contrast to conventional serological methods, any human tissue or body fluid can be analysed by DNA profiling as long as it contains nucleated cells. The majority of genetic systems studied at the DNA level are derived from "non-coding" portions from the human genome, and are located either in the vicinity of expressed (coding) genes or in stretches of DNA sequences interspersing with the genes. The typing results are usually recorded as DNA fragment lengths or "alleles" indicating the number of core repeat elements for short tandem repeat systems. These typing results do not contain any useful i…
New Foldback transposable element TFB1 found in histone genes of the midge Chironomus thummi
1990
A new Foldback transposable element (TFB1) has been found in the histone H1-H3 intergenic region in the midge Chironomus thummi thummi. TFB1 has long terminal inverted repeats, composed of short, degenerate subrepeats and is flanked by nine or ten base-pair “target site” duplications. TFB1 is present in at least two adjacent histone gene units in Ch. th. thummi, indicating a homogenization of histone gene repeats. The copy number and chromosomal distribution of TFB1 are different in the closely related subspecies Ch. th. thummi and Ch. th. piger, showing that amplification, elimination and transposition of TFB1 have occurred recently during evolution.
Massive LINE-1 retrotransposon enrichment in tamarins of the Cebidae family (Platyrrhini, Primates) and its significance for genome evolution
2021
To study heterochromatin distribution differences among tamarins, we applied LINE-1 probes using fluorescence in situ hybridization onto chromosomes of Saguinus mystax, Leontocebus fuscicollis, and Leontopithecus rosalia with the aim to investigate possible evolutionary implications. LINE-1 repeats were shown to be involved in genome architecture and in the occurrence of chromosomal rearrangements in many vertebrates. We found bright LINE-1 probe signals at centromeric or pericentromeric areas, GC rich, on almost all chromosomes in three tamarin species. We also found non-centromeric signals along chromosome arms. In a phylogenetic perspective, we analyzed the pattern of LINE-1 distribution…
Variations in Substitution Rate in Human and Mouse Genomes
2003
We present a method to quantify spatial fluctuations of the substitution rate on different length scales throughout genomes of eukaryotes. The fluctuations on large length scales are found to be predominantly a consequence of a coarse-graining effect of fluctuations on shorter length scales. This is verified for both the mouse and the human genome. We also found that both species show similar standard deviation of fluctuations even though their mean substitution rate differs by a factor of two. Our method furthermore allows to determine time-resolved substitution rate maps from which we can compute auto-correlation functions in order to quantify how fast the spatial fluctuations in substitu…
Inverted and mirror repeats in model nucleotide sequences.
2007
We analytically and numerically study the probabilistic properties of inverted and mirror repeats in model sequences of nucleic acids. We consider both perfect and non-perfect repeats, i.e. repeats with mismatches and gaps. The considered sequence models are independent identically distributed (i.i.d.) sequences, Markov processes and long range sequences. We show that the number of repeats in correlated sequences is significantly larger than in i.i.d. sequences and that this discrepancy increases exponentially with the repeat length for long range sequences.
The Gypsy Database (GyDB) of mobile genetic elements.
2007
In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses. Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by t…
Structure and evolution of the leucine plasmids carried by the endosymbiont (Buchnera aphidicola) from aphids of the family Aphididae.
1998
In all examined species of the family Aphididae, the bacterial endosymbiont Buchnera aphidicola carries a plasmid encoding the genes leuABCD (involved in leucine biosynthesis) along with repA1, repA2 and ORF1. The gene organisation of the leucine plasmids was conserved, except in Buchnera isolated from Pterocomma populeum, where ORF1 was located in a different position. An inverted repeat (LIR1) located between repA2 and leuA is found in all of the Buchnera leucine plasmids examined. The predicted secondary structure of the LIR1 transcript conforms to a long hairpin loop, suggesting an involvement in transcription termination or messenger stability. Phylogenetic reconstruction based on repA…
Incomplete sequence homogenization in 45S rDNA multigene families: intermixed IGS heterogeneity within the single NOR locus of the polyploid species …
2014
† Background and Aims Ribosomal sequences have become the classical example of the genomic homogenization of nuclear multigene families. Despite theoretical advantages and modelling predictions that support concerted evolution of the 45S rDNA, several reports have found intragenomic polymorphisms. However, the origins and causes of these rDNA polymorphisms are difficult to assess because seed plants show a wide range of 45S rDNA loci number variation, especially in polyploids. Medicago arborea is a tetraploid species that has a single 45S rDNA locus. This feature makes this species a suitable case study to assess the fate of ribosomal IGS homogenization in polyploid species showing nucleolu…
C9ORF72 hexanucleotide repeat expansions in the Italian sporadic ALS population.
2012
It has been recently reported that a large proportion of patients with familial amyotrophic lateral sclerosis (familial ALS) and frontotemporal dementia (FTD) are associated with a hexanucleotide (GGGGCC) repeat expansion in the first intron of C9ORF72. We have assessed 1,757 Italian sporadic ALS cases, 133 from Sardinia, 101 from Sicily, and 1,523 from mainland Italy. Sixty (3.7%) of 1,624 mainland Italians and Sicilians and 9 (6.8%) of the 133 Sardinian sporadic ALS cases carried the pathogenic repeat expansion. None of the 619 regionally-matched control samples (1,238 chromosomes) carried the expansion. Twenty-five cases (36.2%) had behavioral FTD in addition to ALS. FTD or unspecified d…
Genetic analysis of the short tandem repeat system D12S391 in the German and three Asian populations
1998
Abstract Genomic DNA samples from 222 individuals from Southern China, 154 individuals from Thailand, 100 individuals from Japan as well as from 124 German individuals were analysed for the short tandem repeat (STR) locus D12S391. Typing was carried out by polymerase chain reaction (PCR) amplification and subsequent polyacryramide gel electrophoresis and silver staining. In total, 12 alleles could be distinguished in two of the populations. Among Chinese, allele 19 is the most common with a frequency of 0.225, and among Germans, allele 18 with a frequency of 0.186. In the Thai population only 11 alleles could be distinguished and allele 19 is the most common with a frequency of 0.198. In Ja…