Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome

Sela, Noa; Mersch, Britta; Gal-Mark, Nurit; Lev-Maor, Galit; Hotz‐Wagenblatt, Agnes; Ast, Gil

doi:10.1186/gb-2007-8-6-r127

Cited by 207 publications

(318 citation statements)

References 57 publications

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“…Most of the identified TE insertions were within non-coding regions (introns and flanking sequences), and such insertions were virtually absent from the CDSs, as previously reported in Drosophila (Fontanillas et al, 2007;Kaminker et al, 2002;Miller et al, 2000), reinforcing the view that insertions in non-coding regions are tolerated, whereas TE insertions within or close to coding regions can have deleterious effects and are removed through purifying selection (Lipatov et al, 2005;Sela et al, 2007;Yang and Barbash, 2008). Considering all of the genes in each category studied here, the highest percentage of genes harboring TEs in their flanking regions were found among Cyps associated with insecticide resistance and their neighboring non-Cyp genes in both D. melanogaster and D. simulans.…”

Section: Discussionsupporting

confidence: 67%

Genomic regions harboring insecticide resistance-associated Cyp genes are enriched by transposable element fragments carrying putative transcription factor binding sites in two sibling Drosophila species

Carareto

Hernandez

Vieira

2014

Gene

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a b s t r a c tIn the present study, an in silico analysis was performed to identify transposable element (TE) fragments inserted in Cyps with functions associated with resistance to insecticides and developmental regulation as well as in neighboring genes in two sibling species , Drosophila melanogaster and Drosophila simulans . The Cyps associated with insecticide resistance and their neighboring non-Cyp genes have accumulated a greater number of TE fragments than the other Cyps or a random sample of genes, predominantly in the 5′-flanking regions. Most of the insertions were due to DNA transposons, with DNAREP1 fragments being the most common. These fragments carry putative binding sites for transcription factors, which reinforces the hypothesis that DNAREP1 may influence gene regulation and play a role in the adaptation of the Drosophila species.

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Section: Discussionsupporting

confidence: 67%

Genomic regions harboring insecticide resistance-associated Cyp genes are enriched by transposable element fragments carrying putative transcription factor binding sites in two sibling Drosophila species

Carareto

Hernandez

Vieira

2014

Gene

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“…The preferential insertion of SINEs into introns, rather than exons, reflects selection against the deleterious effects of SINE insertions in protein-coding regions [43]. There are numerous examples of disease-causing SINE insertions in exons [44 -46].…”

Section: Resultsmentioning

confidence: 99%

Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales

et al. 2010

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Whales in the suborder Mysticeti are filter feeders that use baleen to sift zooplankton and small fish from ocean waters. Adult mysticetes lack teeth, although tooth buds are present in foetal stages. Cladistic analyses suggest that functional teeth were lost in the common ancestor of crown-group Mysticeti. DNA sequences for the tooth-specific genes, ameloblastin (AMBN), enamelin (ENAM) and amelogenin (AMEL), have frameshift mutations and/or stop codons in this taxon, but none of these molecular cavities are shared by all extant mysticetes. Here, we provide the first evidence for pseudogenization of a tooth gene, enamelysin (MMP20), in the common ancestor of living baleen whales. Specifically, pseudogenization resulted from the insertion of a CHR-2 SINE retroposon in exon 2 of MMP20. Genomic and palaeontological data now provide congruent support for the loss of enamel-capped teeth on the common ancestral branch of crown-group mysticetes. The new data for MMP20 also document a polymorphic stop codon in exon 2 of the pygmy sperm whale (Kogia breviceps), which has enamel-less teeth. These results, in conjunction with the evidence for pseudogenization of MMP20 in Hoffmann's two-toed sloth (Choloepus hoffmanni), another enamel-less species, support the hypothesis that the only unique, non-overlapping function of the MMP20 gene is in enamel formation.

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“…Yet, retrotransposons contain promoters and enhancers (1) and can serve relevant host function in promoting mRNA synthesis of the immediately downstream host genes (6,7). The majority of retrotransposons, however, are located in the intergenic or intronic regions up to hundreds of kilobases from the promoters of linked genes (2,8). Whether these distant retrotransposons serve a beneficial host function is not known.…”

mentioning

confidence: 99%

Long-range function of an intergenic retrotransposon

Pi¹,

Zhu²,

Wu³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Retrotransposons including endogenous retroviruses and their solitary long terminal repeats (LTRs) compose >40% of the human genome. Many of them are located in intergenic regions far from genes. Whether these intergenic retrotransposons serve beneficial host functions is not known. Here we show that an LTR retrotransposon of ERV-9 human endogenous retrovirus located 40-70 kb upstream of the human fetal γ-and adult β-globin genes serves a long-range, host function. The ERV-9 LTR contains multiple CCAAT and GATA motifs and competitively recruits a high concentration of NF-Y and GATA-2 present in low abundance in adult erythroid cells to assemble an LTR/RNA polymerase II complex. The LTR complex transcribes intergenic RNAs unidirectionally through the intervening DNA to loop with and modulate transcription factor occupancies at the far downstream globin promoters, thereby modulating globin gene switching by a competitive mechanism.

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Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome

Cited by 207 publications

References 57 publications

Genomic regions harboring insecticide resistance-associated Cyp genes are enriched by transposable element fragments carrying putative transcription factor binding sites in two sibling Drosophila species

Genomic regions harboring insecticide resistance-associated Cyp genes are enriched by transposable element fragments carrying putative transcription factor binding sites in two sibling Drosophila species

Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales

Long-range function of an intergenic retrotransposon

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