Identity by descent and DNA sequence variation of human SINE and LINE elements

Salem, Abdel Halim; Ray, David A.; Batzer, Mark A.

doi:10.1159/000080803

Cited by 32 publications

(28 citation statements)

References 121 publications

(90 reference statements)

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“…First, the presence of a SINE element represents identity by descent, since the probability that two different young SINE repeats would integrate independently at the same chromosomal location is small. Although there have been a few reports of parallel insertion events (Kass et al 2000;Cantrell et al 2001), these are considered to be very rare, at least for primate Alus (Roy-Engel et al 2002;Salem et al 2005). Second, the ancestral state of each SINE insertion polymorphism is known to be the absence of the Table S1.…”

Section: Resultsmentioning

confidence: 99%

Short interspersed elements (SINEs) are a major source of canine genomic diversity

Wang¹,

Kirkness²

2005

Genome Res.

114

116

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SINEs are retrotransposons that have enjoyed remarkable reproductive success during the course of mammalian evolution, and have played a major role in shaping mammalian genomes. Previously, an analysis of survey-sequence data from an individual dog (a poodle) indicated that canine genomes harbor a high frequency of alleles that differ only by the absence or presence of a SINEC_Cf repeat. Comparison of this survey-sequence data with a draft genome sequence of a distinct dog (a boxer) has confirmed this prediction, and revealed the chromosomal coordinates for >10,000 loci that are bimorphic for SINEC_Cf insertions. Analysis of SINE insertion sites from the genomes of nine additional dogs indicates that 3%-5% are absent from either the poodle or boxer genome sequences—suggesting that an additional 10,000 bimorphic loci could be readily identified in the general dog population. We describe a methodology that can be used to identify these loci, and could be adapted to exploit these bimorphic loci for genotyping purposes. Approximately half of all annotated canine genes contain SINEC_Cf repeats, and these elements are occasionally transcribed. When transcribed in the antisense orientation, they provide splice acceptor sites that can result in incorporation of novel exons. The high frequency of bimorphic SINE insertions in the dog population is predicted to provide numerous examples of allele-specific transcription patterns that will be valuable for the study of differential gene expression among multiple dog breeds.

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Section: Resultsmentioning

confidence: 99%

Short interspersed elements (SINEs) are a major source of canine genomic diversity

Wang¹,

Kirkness²

2005

Genome Res.

114

116

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“…identical by descent (Salem et al 2005;Ray et al 2011) and reveals extensive, lineage-specific retrotransposition. As expected, they are conserved at higher frequencies at orthologous loci in the related classical lines (B6, A/J, and WSB).…”

Section: à16mentioning

confidence: 99%

Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance

Li¹,

Akagi²,

Hu³

et al. 2012

Genome Res.

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Endogenous retrotransposons have caused extensive genomic variation within mammalian species, but the functional implications of such mobilization are mostly unknown. We mapped thousands of endogenous retrovirus (ERV) germline integrants in highly divergent, previously unsequenced mouse lineages, facilitating a comparison of gene expression in the presence or absence of local insertions. Polymorphic ERVs occur relatively infrequently in gene introns and are particularly depleted from genes involved in embryogenesis or that are highly expressed in embryonic stem cells. Their genomic distribution implies ongoing negative selection due to deleterious effects on gene expression and function. A polymorphic, intronic ERV at Slc15a2 triggers up to 49-fold increases in premature transcriptional termination and up to 39-fold reductions in full-length transcripts in adult mouse tissues, thereby disrupting protein expression and functional activity. Prematurely truncated transcripts also occur at Polr1a, Spon1, and up to~5% of other genes when intronic ERV polymorphisms are present. Analysis of expression quantitative trait loci (eQTLs) in recombinant BxD mouse strains demonstrated very strong genetic associations between the polymorphic ERV in cis and disrupted transcript levels. Premature polyadenylation is triggered at genomic distances up to >12.5 kb upstream of the ERV, both in cis and between alleles. The parent of origin of the ERV is associated with variable expression of nonterminated transcripts and differential DNA methylation at its 59-long terminal repeat. This study defines an unexpectedly strong functional impact of ERVs in disrupting gene transcription at a distance and demonstrates that ongoing retrotransposition can contribute significantly to natural phenotypic diversity.

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“…Because Alu insertions are unique events that are identical-by-descent or free of homoplasy, they have been useful in genetic mapping and population genetics studies (Batzer et al, 1994;Batzer and Deininger, 1991;Perna et al, 1992;Roy-Engel et al, 2001;Salem et al, 2003Salem et al, , 2005aStoneking et al, 1997;Tishkoff et al, 2000). In addition, Alu elements are known to impact several aspects of the genome.…”

Section: Introductionmentioning

confidence: 99%

Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms

Wang

Song

Gonder

et al. 2006

Gene

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Alu elements are the most active and predominant type of short interspersed elements (SINEs) in the human genome. Recently inserted polymorphic (for presence/absence) Alu elements contribute to genome diversity among different human populations, and they are useful genetic markers for population genetic studies. The objective of this study is to identify polymorphic Alu insertions through an in silico comparative genomics approach and to analyze their distribution pattern throughout the human genome. By computationally comparing the public and Celera sequence assemblies of the human genome, we identified a total of 800 polymorphic Alu elements. We used polymerase chain reaction-based assays to screen a randomly selected set of 16 of these 800 Alu insertion polymorphisms using a human diversity panel to demonstrate the efficiency of our approach. Based on sequence analysis of the 800 Alu polymorphisms, we report three new Alu subfamilies, Ya3, Ya4b, and Yb11, with Yb11 being the smallest known Alu subfamily. Analysis of retrotransposition activity revealed Yb11, Ya8, Ya5, Yb9, and Yb8 as the most active Alu subfamilies and the maintenance of a very low level of retrotransposition activity or recent gene conversion events involving S subfamilies. The 800 polymorphic Alu insertions are characterized by the presence of target site duplications (TSDs) and longer than average polyA-tail length. Their pre-integration sites largely follow an extended "NT-AARA" motif. Among chromosomes, the density of Alu insertion polymorphisms is positively correlated with the Alu-site availability and is inversely correlated with the densities of older Alu elements and genes.

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Identity by descent and DNA sequence variation of human SINE and LINE elements

Cited by 32 publications

References 121 publications

Short interspersed elements (SINEs) are a major source of canine genomic diversity

Short interspersed elements (SINEs) are a major source of canine genomic diversity

Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance

Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms

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