Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila

Genome Biology and Evolution
Manee M ManeeC M Bergman

Abstract

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 ...Continue Reading

References

Jun 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·L C WatersL Y Ch'ang
Jan 1, 1989·Annual Review of Genetics·B Charlesworth, C H Langley
Nov 21, 1995·Proceedings of the National Academy of Sciences of the United States of America·A C SpradlingG M Rubin
Jun 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·J M DelpuechR T Roush
May 29, 2002·Molecular Biology and Evolution·Carolina BartoloméBrian Charlesworth
Sep 28, 2002·Science·P J DabornR H ffrench-Constant
Jan 23, 2003·Genome Biology·Joshua S KaminkerSusan E Celniker
Nov 25, 2003·BMC Bioinformatics·Eldon EmberlyEric D Siggia
Dec 3, 2004·Molecular Biology and Evolution·Daniel N Lerman, Martin E Feder
Jul 19, 2005·Genome Research·Adam SiepelDavid Haussler
Sep 20, 2005·Current Biology : CB·Daven C Presgraves
Dec 13, 2005·Genome Research·Michael Ashburner, Casey M Bergman
Dec 29, 2005·Nature Genetics·Jared A DrakeJoel N Hirschhorn
Feb 8, 2007·Genome Biology·Penelope R HaddrillBrian Charlesworth
Jun 27, 2007·Proceedings of the National Academy of Sciences of the United States of America·Casey M Bergman, Douda Bensasson
Jul 25, 2007·Molecular Biology and Evolution·Sònia CasillasCasey M Bergman
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Mar 24, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Yuh Chwen G Lee, Charles H Langley
Dec 22, 2010·Molecular Biology and Evolution·Dmitri A PetrovJosefa González
Mar 25, 2011·Nature·Nicolas NègreKevin P White
May 17, 2011·PLoS Computational Biology·Ying ZhangDixie L Mager
Dec 17, 2011·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Thomas BrodyWard F Odenwald
Feb 10, 2012·Nature·Trudy F C MackayRichard A Gibbs
Aug 22, 2012·Briefings in Bioinformatics·Robert M KuhnW James Kent
Jan 19, 2013·Science·Cosmas D ArnoldAlexander Stark
Jul 26, 2013·Molecular Biology and Evolution·Julie M CridlandKevin R Thornton
Dec 18, 2013·Genetics·Justin P BlumenstielCasey M Bergman
Dec 19, 2013·PloS One·Igor V MakuninStepan N Belyakin
Apr 23, 2014·Nucleic Acids Research·Jiali ZhuangZhiping Weng
Oct 9, 2014·Annual Review of Genetics·Maite G BarrónJosefa González

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Citations

Apr 28, 2019·Molecular Biology and Evolution·Jasmina UzunovićStephen I Wright
Feb 11, 2021·Genome Research·Mahul ChakrabortyJ J Emerson

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Methods Mentioned

BETA
pool-seq

Software Mentioned

ngs
BEDtools
dm3
UCSC Genome Browser
mapper
overlapSelect
TEMP
te
_ mapper
R

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