Transposable element polymorphisms recapitulate human evolution

Rishishwar, Lavanya; Villa, Cristiano; Jordan, I. King

doi:10.1186/s13100-015-0052-6

Cited by 63 publications

(76 citation statements)

References 46 publications

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“…ACE gene is one of the insertional polymorphisms of Alu elements [44][45]. Many reports studied the Alu polymorphisms in the context of human genetics and evolution [46][47][48][49][50][51][52][53] . Recently, various studies reported the relationship between ACE gene polymorphism and Type 2 Diabetes.…”

Section: Discussionmentioning

confidence: 99%

Association of ACE <i>DD</i> Genotype with Hypertension among the Tribal Populations of South India

Paramasivam

Nandakumar

Arumugam

et al. 2016

ILNS

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The Renin-Angiotensin System (RAS) is an important regulator of the blood pressure(BP). The level of the vasoactive peptide Angiotensin-II, is mainly determined by the RAS enzyme, angiotensin converting enzyme-1 (ACE-1). Polymorphisms in ACE gene is reported to be associated with hypertension in various populations worldwide. We investigated the association of ACE I/D polymorphisms with hypertension among the tribal populations of South India. Samples were collected from hypertensive patients (n = 33) and healthy controls (n = 37). Genotyping was performed using Polymerase chain reaction (PCR) with allele specific primers. The DD genotype is significantly observed among the cases (OR = 1.0) . Specifically, the DD genotype is more evident among the females (OR = 0.705) than males (OR = 1.22) and is analysed to be associated with hypertension among the tribal populations of South India.

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Section: Discussionmentioning

confidence: 99%

Association of ACE <i>DD</i> Genotype with Hypertension among the Tribal Populations of South India

Paramasivam

Nandakumar

Arumugam

et al. 2016

ILNS

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“…The population allele frequencies of the predicted TE insertions were computed from the Phase 3 release of the 1KGP (Sudmant et al, 2015) as previously described (Rishishwar et al, 2015). …”

Section: Methodsmentioning

confidence: 99%

Patterns of Transposable Element Expression and Insertion in Cancer

Clayton

Wang

Rishishwar

et al. 2016

Front. Mol. Biosci.

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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.

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“…For example, they describe a greater genetic diversity in African human populations [30] and that a small population of common ancestors of all toothed whales diverged to launch the lineages of sperm whales and dolphins [34]. Furthermore, it was shown that human polymorphic TEs are substantial geographically differentiated with many population-specific TE insertions [41].…”

Section: Alu Duplex Pcrsmentioning

confidence: 99%

“…Large-scale analyses have already shown contributions to human genomic diversity [38][39][40]. For example, a recent bioinformatic study illustrated human evolution by analyzing TE polymorphisms based on the data of the 1000 genome project [41]. Thus, with next generation sequencing (NGS), whole genome sequencing (WGS) analyses can be accomplished, saving both money and time.…”

Section: Introductionmentioning

confidence: 99%

Duplex Alu Screening for Degraded DNA of Skeletal Human Remains

Haß¹,

Hummel²,

Piskurek³

2017

Diversity

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Abstract:The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs), have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. We developed duplex Alu screening PCRs with flanking primers for two Alu elements, each combined with a single internal Alu primer. By adding an internal primer, the approximately 400-500 bp presence signals of Alu elements can be detected within a range of less than 200 bp. Thus, our PCR approach is suited for highly fragmented ancient DNA samples, whereas NGS analyses frequently are unable to handle repetitive elements. With this analysis system, we examined remains of 12 individuals from the Lichtenstein cave with different degrees of DNA degradation. The duplex PCRs showed fully informative amplification results for all of the chosen Alu loci in eight of the 12 samples. Our analysis system showed that Alu presence/absence analysis is possible in samples with different degrees of DNA degradation and it reduces the amount of valuable skeletal material needed by a factor of four, as compared with a singleplex approach.

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Transposable element polymorphisms recapitulate human evolution

Cited by 63 publications

References 46 publications

Association of ACE <i>DD</i> Genotype with Hypertension among the Tribal Populations of South India

Association of ACE <i>DD</i> Genotype with Hypertension among the Tribal Populations of South India

Patterns of Transposable Element Expression and Insertion in Cancer

Duplex Alu Screening for Degraded DNA of Skeletal Human Remains

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