Population Genomics of Transposable Elements in Drosophila melanogaster

Petrov, Dmitri A.; Fiston-Lavier, Anna-Sophie; Lipatov, Mikhail; Kapa, Lenkov; González, Josefa

doi:10.1093/molbev/msq337

Cited by 165 publications

(235 citation statements)

References 73 publications

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“…To explore the evolutionary implications of our observations, we used existing data (Petrov et al 2011) on the population frequencies of many transposons, including 56 of the TSCbearing insertions we identified (Methods; Supplemental Table S6). Of those insertions, 45 are estimated to be rare or very rare variants in the wild North-American (NA) populations studied.…”

Section: Population Genetics Of Transposon-derived Genic Tscsmentioning

confidence: 99%

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High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

et al. 2012

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Many eukaryotic genes possess multiple alternative promoters with distinct expression specificities. Therefore, comprehensively annotating promoters and deciphering their individual regulatory dynamics is critical for gene expression profiling applications and for our understanding of regulatory complexity. We introduce RAMPAGE, a novel promoter activity profiling approach that combines extremely specific 59-complete cDNA sequencing with an integrated data analysis workflow, to address the limitations of current techniques. RAMPAGE features a streamlined protocol for fast and easy generation of highly multiplexed sequencing libraries, offers very high transcription start site specificity, generates accurate and reproducible promoter expression measurements, and yields extensive transcript connectivity information through paired-end cDNA sequencing. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive data set that represents the first available developmental time-course of promoter usage. We found that >40% of developmentally expressed genes have at least two promoters and that alternative promoters generally implement distinct regulatory programs. Transposable elements, long proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, contribute at least 1300 promoters shaping the developmental transcriptome of D. melanogaster. Hundreds of these promoters drive the expression of annotated genes, and transposons often impart their own expression specificity upon the genes they regulate. These observations provide support for the theory that transposons may drive regulatory innovation through the distribution of stereotyped cis-regulatory modules throughout their host genomes.

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Section: Population Genetics Of Transposon-derived Genic Tscsmentioning

confidence: 99%

“…We used the genotyping data for FlyBase-annotated transposon insertions from Petrov et al (2011). Each transposon-contained TSC was attributed to a FlyBase transposon annotation if it fully overlapped one of them (108 insertions).…”

Section: Population Genetics Data Analysismentioning

confidence: 99%

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

et al. 2012

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“…These lower estimates, however, do not include the possible presence in natural populations of genotypes with high mutation rates or the deleterious consequences of transposable element (TE) insertions. In fact, TEs are very abundant in natural populations of D. melanogaster [51][52][53][54][55][56][57][58][59][60] and have been proposed to be an important source of BGS in this species [30]. Therefore, U,0.6 represents a lower boundary for the deleterious mutation rate when inferring the consequences of BGS.…”

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confidence: 99%

“…TEs are pervasive across the D. melanogaster genome [51][52][53][54][55][56][57][58][59][60]. Cridland et al (2013) recently reported a detailed analysis of TE abundance and distribution in D. melanogaster based on deepcoverage, whole-genome sequencing [60].…”

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confidence: 99%

Background selection as baseline for nucleotide variation across theDrosophilagenome

Comeron

2014

Preprint

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The constant removal of deleterious mutations by natural selection causes a reduction in neutral diversity and efficacy of selection at genetically linked sites (a process called Background Selection, BGS). Population genetic studies, however, often ignore BGS effects when investigating demographic events or the presence of other types of selection. To obtain a more realistic evolutionary expectation that incorporates the unavoidable consequences of deleterious mutations, we generated high-resolution landscapes of variation across the Drosophila melanogaster genome under a BGS scenario independent of polymorphism data. We find that BGS plays a significant role in shaping levels of variation across the entire genome, including long introns and intergenic regions distant from annotated genes. We also find that a very large percentage of the observed variation in diversity across autosomes can be explained by BGS alone, up to 70% across individual chromosome arms at 100-kb scale, thus indicating that BGS predictions can be used as baseline to infer additional types of selection and demographic events. This approach allows detecting several outlier regions with signal of recent adaptive events and selective sweeps. The use of a BGS baseline, however, is particularly appropriate to investigate the presence of balancing selection and our study exposes numerous genomic regions with the predicted signature of higher polymorphism than expected when a BGS context is taken into account. Importantly, we show that these conclusions are robust to the mutation and selection parameters of the BGS model. Finally, analyses of protein evolution together with previous comparisons of genetic maps between Drosophila species, suggest temporally variable recombination landscapes and, thus, local BGS effects that may differ between extant and past phases. Because genome-wide BGS and temporal changes in linkage effects can skew approaches to estimate demographic and selective events, future analyses should incorporate BGS predictions and capture local recombination variation across genomes and along lineages.

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“…TE propagation rates can be inferred from comparative phylogenetic analyses of related organisms (14)(15)(16)(17)(18)(19)(20) or endpoint analyses of TE abundance within populations (11,(21)(22)(23). By making assumptions about the mechanisms of TE proliferation, models can be constructed to describe the distribution of TEs within genomes over evolutionary time scales, and sequenced genomes can be analyzed and fit to TE proliferation models to infer phylogeny of TE copies and estimate their rates of propagation (24).…”

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confidence: 99%

Real-time transposable element activity in individual live cells

Kim

Lee

Sherer

et al. 2016

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

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The excision and reintegration of transposable elements (TEs) restructure their host genomes, generating cellular diversity involved in evolution, development, and the etiology of human diseases. Our current knowledge of TE behavior primarily results from bulk techniques that generate time and cell ensemble averages, but cannot capture cell-to-cell variation or local environmental and temporal variability. We have developed an experimental system based on the bacterial TE IS608 that uses fluorescent reporters to directly observe single TE excision events in individual cells in real time. We find that TE activity depends upon the TE's orientation in the genome and the amount of transposase protein in the cell. We also find that TE activity is highly variable throughout the lifetime of the cell. Upon entering stationary phase, TE activity increases in cells hereditarily predisposed to TE activity. These direct observations demonstrate that real-time live-cell imaging of evolution at the molecular and individual event level is a powerful tool for the exploration of genome plasticity in stressed cells.transposable elements | evolution | quantitative biology A transposable element (TE) is a mobile genetic element that propagates within its host genome by self-catalyzed copying or excision followed by genomic reintegration (1). TEs exist in all domains of life, and the activity of TEs necessarily generates mutations in the host genome. Consequently, TEs are major contributors to disease (2-8), development (9, 10), and evolution (11, 12); they are also used as molecular tools in synthetic biology and bioengineering (13).Despite their ubiquity and importance, surprisingly little is known about the behavior and dynamics of TE activity in living cells. TE propagation rates can be inferred from comparative phylogenetic analyses of related organisms (14-20) or endpoint analyses of TE abundance within populations (11,(21)(22)(23). By making assumptions about the mechanisms of TE proliferation, models can be constructed to describe the distribution of TEs within genomes over evolutionary time scales, and sequenced genomes can be analyzed and fit to TE proliferation models to infer phylogeny of TE copies and estimate their rates of propagation (24). However, most sequencing techniques require bulk sampling of cells to provide genetic material, and sequencing is therefore generally an average over many cells. As a result, without extremely deep or single-cell sequencing techniques, most current methods are sufficient to detect only those TE events that have occurred in the germ line and therefore appear in every somatic cell in the body (25).TE rates can also be estimated by measuring relative abundances in populations that have been allowed to mutate over laboratory time scales. One of the first examples of this approach was that by Paquin and Williamson (23) to study the effects of temperature on the rate of integration of Ty retrotransposons in Saccharomyces cerevisiae after growth for 6-8 generations, resulting in yeast re...

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Population Genomics of Transposable Elements in Drosophila melanogaster

Cited by 165 publications

References 73 publications

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

Background selection as baseline for nucleotide variation across theDrosophilagenome

Real-time transposable element activity in individual live cells

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