Miniature inverted-repeat transposable elements: discovery, distribution, and activity

Genome ◽  
2013 ◽  
Vol 56 (9) ◽  
pp. 475-486 ◽  
Author(s):  
Isam Fattash ◽  
Rebecca Rooke ◽  
Amy Wong ◽  
Caleb Hui ◽  
Tina Luu ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Copy Number ◽  
Copy Numbers ◽  
Number Increase ◽  
Eukaryotic Organisms ◽  
Eukaryotic Genomes ◽  
Copy Number Increase

Eukaryotic organisms have dynamic genomes, with transposable elements (TEs) as a major contributing factor. Although the large autonomous TEs can significantly shape genomic structures during evolution, genomes often harbor more miniature nonautonomous TEs that can infest genomic niches where large TEs are rare. In spite of their cut-and-paste transposition mechanisms that do not inherently favor copy number increase, miniature inverted-repeat transposable elements (MITEs) are abundant in eukaryotic genomes and exist in high copy numbers. Based on the large number of MITE families revealed in previous studies, accurate annotation of MITEs, particularly in newly sequenced genomes, will identify more genomes highly rich in these elements. Novel families identified from these analyses, together with the currently known families, will further deepen our understanding of the origins, transposase sources, and dramatic amplification of these elements.

scholarly journals Transposable element numbers in cosmopolitan inversions from a natural population of Drosophila melanogaster.

Genetics ◽  
1994 ◽  
Vol 137 (3) ◽  
pp. 815-827 ◽  
Author(s):  
P D Sniegowski ◽  
B Charlesworth
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Population ◽  
Copy Number ◽  
Population Studies ◽  
Low Frequency ◽  
Chromosomal Inversions ◽  
Copy Numbers ◽  
Number Increase ◽  
Natural Selection Theory ◽  
Copy Number Increase

Abstract Population studies of the distribution of transposable elements (TEs) on the chromosomes of Drosophila melanogaster have suggested that their copy number increase due to transposition is balanced by some form of natural selection. Theory suggests that, as a consequence of deleterious ectopic meiotic exchange between TEs, selection can favor genomes with lower TE copy numbers. This predicts that TEs should be less deleterious, and hence more abundant, in chromosomal regions in which recombination is reduced. To test this, we surveyed the abundance and locations of 10 families of TEs in recombination-suppressing chromosomal inversions from a natural population. The sample of 49 chromosomes included multiple independent isolates of seven different inversions and a corresponding set of standard chromosomes. For all 10 TE families pooled, copy numbers were significantly higher overall within low frequency inversions than within corresponding regions of standard chromosomes. TEs occupied chromosomal sites at significantly higher frequencies within the In(3R)Mo and In(3R)K inversions than within the corresponding regions of standard 3R chromosomes. These results are consistent with the predictions of the ectopic exchange model.

Alternative pathways of MYCN gene copy number increase in primary neuroblastoma tumors

2004 ◽  
Vol 153 (1) ◽  
pp. 10-15 ◽  
Author(s):  
Alexander Valent ◽  
Marine Guillaud-Bataille ◽  
Chantal Farra ◽  
François Lozach ◽  
Barbara Spengler ◽  
...  
Keyword(s):  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Alternative Pathways ◽  
Mycn Gene ◽  
Number Increase ◽  
Copy Number Increase

scholarly journals PVT1 dependence in cancer with MYC copy-number increase

Nature ◽  
2014 ◽  
Vol 512 (7512) ◽  
pp. 82-86 ◽  
Author(s):  
Yuen-Yi Tseng ◽  
Branden S. Moriarity ◽  
Wuming Gong ◽  
Ryutaro Akiyama ◽  
Ashutosh Tiwari ◽  
...  
Keyword(s):  
Copy Number ◽  
Number Increase ◽  
Copy Number Increase

scholarly journals The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. I. Element frequencies and distribution

1992 ◽  
Vol 60 (2) ◽  
pp. 103-114 ◽  
Author(s):  
Brian Charlesworth ◽  
Angela Lapid ◽  
Darlene Canada
Keyword(s):  
Population Dynamics ◽  
Drosophila Melanogaster ◽  
Linkage Disequilibrium ◽  
Transposable Elements ◽  
Copy Number ◽  
Polytene Chromosomes ◽  
Chromosome Band ◽  
High Frequencies ◽  
Copy Numbers

SummaryData were collected on the distribution of nine families of transposable elements among second and third chromosomes isolated from a natural population of Drosophila melanogaster, by means of in situ hybridization of element probes to polytene chromosomes. It was found that the copy numbers per chromosome in the distal sections of the chromosome arms followed a Poisson distribution. Elements appeared to be distributed randomly along the distal sections of the chromosome arms. There was no evidence for linkage disequilibrium in the distal sections of the chromosomes, but some significant disequilibrium was detected in proximal regions. There were many significant correlations between different element families with respect to the identity of the sites that were occupied in the sample. There were also significant correlations between families with respect to sites at which elements achieved relatively high frequencies. Element frequencies per chromosome band were generally low in the distal sections, but were higher proximally. These results are discussed in the light of models of the population dynamics of transposable elements. It is concluded that they provide strong evidence for the operation of a force or forces opposing transpositional increase in copy number. The data suggest that the rate of transposition perelement per generation is of the order of 10−4, for the elements included in this study.

DNA sequence copy number increase at 8q: A potential new prognostic marker in high-grade osteosarcoma

1999 ◽  
Vol 84 (2) ◽  
pp. 114-121 ◽  
Author(s):  
Maija Tarkkanen ◽  
Inkeri Elomaa ◽  
Carl Blomqvist ◽  
Aarne H. Kivioja ◽  
Pirkko Kellokumpu-Lehtinen ◽  
...  
Keyword(s):  
Prognostic Marker ◽  
Dna Sequence ◽  
Copy Number ◽  
High Grade ◽  
Number Increase ◽  
High Grade Osteosarcoma ◽  
Copy Number Increase

scholarly journals Copy number increase of ACTN4 is a prognostic indicator in salivary gland carcinoma

2014 ◽  
Vol 3 (3) ◽  
pp. 613-622 ◽  
Author(s):  
Yukio Watabe ◽  
Taisuke Mori ◽  
Seiichi Yoshimoto ◽  
Takeshi Nomura ◽  
Takahiko Shibahara ◽  
...  
Keyword(s):  
Salivary Gland ◽  
Copy Number ◽  
Prognostic Indicator ◽  
Salivary Gland Carcinoma ◽  
Number Increase ◽  
Gland Carcinoma ◽  
Copy Number Increase

19q13-ERCC1 Gene Copy Number Increase in Non–Small-Cell Lung Cancer

2013 ◽  
Vol 14 (5) ◽  
pp. 549-557 ◽  
Author(s):  
Elsa Vanhecke ◽  
Alexander Valent ◽  
Ximing Tang ◽  
Philippe Vielh ◽  
Luc Friboulet ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Copy Number ◽  
Gene Copy Number ◽  
Small Cell ◽  
Gene Copy ◽  
Small Cell Lung ◽  
Number Increase ◽  
Copy Number Increase

scholarly journals Mechanisms of Topoisomerase I (TOP1) Gene Copy Number Increase in a Stage III Colorectal Cancer Patient Cohort

PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e60613 ◽  
Author(s):  
David Hersi Smith ◽  
Ib Jarle Christensen ◽  
Niels Frank Jensen ◽  
Bo Markussen ◽  
Maria Unni Rømer ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Patient ◽  
Copy Number ◽  
Topoisomerase I ◽  
Colorectal Cancer Patient ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Patient Cohort ◽  
Number Increase ◽  
Copy Number Increase

Copy number variation of glyoxalase I

2014 ◽  
Vol 42 (2) ◽  
pp. 500-503 ◽  
Author(s):  
Alaa Shafie ◽  
Mingzhan Xue ◽  
Paul J. Thornalley ◽  
Naila Rabbani
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Mouse Genome ◽  
Glyoxalase I ◽  
Number Increase ◽  
Number Variation ◽  
Tumour Cell Lines ◽  
Human Tumour Cell Lines ◽  
Human And Mouse ◽  
Copy Number Increase

The glyoxalase I gene GLO1 is a hotspot for copy number variation in the human and mouse genomes. The additional copies are often functional, giving rise to 2–4-fold increased glyoxalase I expression and activity. The prevalence of GLO1 copy number increase in the human population appears to be approximately 2% and may be linked to a risk of obesity, diabetes and aging. Increased GLO1 copy number has been found in human tumour cell lines and primary human tumours. The minimum common copy number increase region was approximately 1 Mb and it contained GLO1 and seven other genes. The increased copy number was generally functional, being associated with increased glyoxalase I protein and multidrug resistance in cancer chemotherapy. Glo1 duplication in the mouse genome is found within approximately 0.5 Mb of duplicated DNA. It was claimed to be linked to anxiety phenotypes, but other related discordant findings have doubted the association with glyoxalase I and further investigation is required.

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