Dataset Information

Contrasting patterns of transposable-element insertion polymorphism and nucleotide diversity in autotetraploid and allotetraploid Arabidopsis species.

ABSTRACT: It has been hypothesized that polyploidy permits the proliferation of transposable elements, due to both the masking of deleterious recessive mutations and the breakdown of host silencing mechanisms. We investigated the patterns of insertion polymorphism of an Ac-like transposable element and nucleotide diversity at 18 gene fragments in the allotetraploid Arabidopsis suecica and the autotetraploid A. arenosa. All identified insertions were fixed in A. suecica, and many were clearly inherited from the parental species A. thaliana or A. arenosa. These results are inconsistent with a rapid increase in transposition associated with hybrid breakdown but support the evidence from nucleotide polymorphism patterns of a recent single origin of this species leading to genomewide fixations of transposable elements. In contrast, most insertions were segregating at very low frequencies in A. arenosa samples, showing a significant departure from neutrality in favor of purifying selection, even when we account for population subdivision inferred from sequence variation. Patterns of nucleotide variation at reference genes are consistent with the TE results, showing evidence for higher effective population sizes in A. arenosa than in related diploid taxa but a near complete population bottleneck associated with the origins of A. suecica.

SUBMITTER: Hazzouri KM

PROVIDER: S-EPMC2390634 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature

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Contrasting patterns of transposable-element insertion polymorphism and nucleotide diversity in autotetraploid and allotetraploid Arabidopsis species.

Hazzouri Khaled M KM Mohajer Arezou A Dejak Steven I SI Otto Sarah P SP Wright Stephen I SI

Genetics 20080501 1

It has been hypothesized that polyploidy permits the proliferation of transposable elements, due to both the masking of deleterious recessive mutations and the breakdown of host silencing mechanisms. We investigated the patterns of insertion polymorphism of an Ac-like transposable element and nucleotide diversity at 18 gene fragments in the allotetraploid Arabidopsis suecica and the autotetraploid A. arenosa. All identified insertions were fixed in A. suecica, and many were clearly inherited fro ...[more]

PMID: 18493073

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Project description:Human transposable element (TE) activity in somatic tissues causes mutations that can contribute to tumorigenesis. Indeed, TE insertion mutations have been implicated in the etiology of a number of different cancer types. Nevertheless, the full extent of somatic TE activity, along with its relationship to tumorigenesis, have yet to be fully explored. Recent developments in bioinformatics software make it possible to analyze TE expression levels and TE insertional activity directly from transcriptome (RNA-seq) and whole genome (DNA-seq) next-generation sequence data. We applied these new sequence analysis techniques to matched normal and primary tumor patient samples from the Cancer Genome Atlas (TCGA) in order to analyze the patterns of TE expression and insertion for three cancer types: breast invasive carcinoma, head and neck squamous cell carcinoma, and lung adenocarcinoma. Our analysis focused on the three most abundant families of active human TEs: Alu, SVA, and L1. We found evidence for high levels of somatic TE activity for these three families in normal and cancer samples across diverse tissue types. Abundant transcripts for all three TE families were detected in both normal and cancer tissues along with an average of ~80 unique TE insertions per individual patient/tissue. We observed an increase in L1 transcript expression and L1 insertional activity in primary tumor samples for all three cancer types. Tumor-specific TE insertions are enriched for private mutations, consistent with a potentially causal role in tumorigenesis. We used genome feature analysis to investigate two specific cases of putative cancer-causing TE mutations in further detail. An Alu insertion in an upstream enhancer of the CBL tumor suppressor gene is associated with down-regulation of the gene in a single breast cancer patient, and an L1 insertion in the first exon of the BAALC gene also disrupts its expression in head and neck squamous cell carcinoma. Our results are consistent with widespread somatic activity of human TEs leading to numerous insertion mutations that can contribute to tumorigenesis in a variety of tissues.

Dataset Information

Contrasting patterns of transposable-element insertion polymorphism and nucleotide diversity in autotetraploid and allotetraploid Arabidopsis species.

Publications

Contrasting patterns of transposable-element insertion polymorphism and nucleotide diversity in autotetraploid and allotetraploid Arabidopsis species.

Similar Datasets

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