Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila.

Manee, Manee M; Jackson, John; Bergman, Casey M

Manee, Manee M; Jackson, John; Bergman, Casey M.

Afiliación

Manee MM; Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
Jackson J; National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
Bergman CM; Center of Excellence for Genomics (CEG), King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.

Genome Biol Evol ; 10(6): 1533-1545, 2018 06 01.

Article en En | MEDLINE | ID: mdl-29850787

RESUMEN

Highly conserved noncoding elements (CNEs) constitute a significant proportion of the genomes of multicellular eukaryotes. The function of most CNEs remains elusive, but growing evidence indicates they are under some form of purifying selection. Noncoding regions in many species also harbor large numbers of transposable element (TE) insertions, which are typically lineage specific and depleted in exons because of their deleterious effects on gene function or expression. However, it is currently unknown whether the landscape of TE insertions in noncoding regions is random or influenced by purifying selection on CNEs. Here, we combine comparative and population genomic data in Drosophila melanogaster to show that the abundance of TE insertions in intronic and intergenic CNEs is reduced relative to random expectation, supporting the idea that selective constraints on CNEs eliminate a proportion of TE insertions in noncoding regions. However, we find no evidence for differences in the allele frequency spectra for polymorphic TE insertions in CNEs versus those in unconstrained spacer regions, suggesting that the distribution of fitness effects acting on observable TE insertions is similar across different functional compartments in noncoding DNA. Our results provide evidence that selective constraints on CNEs contribute to shaping the landscape of TE insertion in eukaryotic genomes, and provide further evidence that CNEs are indeed functionally constrained and not simply mutational cold spots.

Asunto(s)

Secuencia Conservada/genética; Elementos Transponibles de ADN/genética; Drosophila melanogaster/genética; Drosophila/genética; Genoma de los Insectos/genética; ARN no Traducido/genética; Animales; Eucariontes/genética; Exones/genética; Frecuencia de los Genes/genética; Mutación/genética; Selección Genética/genética

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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Elementos Transponibles de ADN / Secuencia Conservada / ARN no Traducido / Drosophila / Drosophila melanogaster / Genoma de los Insectos Límite: Animals Idioma: En Revista: Genome Biol Evol Asunto de la revista: BIOLOGIA / BIOLOGIA MOLECULAR Año: 2018 Tipo del documento: Article País de afiliación: Reino Unido Pais de publicación: Reino Unido

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