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The composition of piRNA clusters in Drosophila melanogaster deviates from expectations under the trap model

https://doi.org/10.1101/2023.02.14.528490

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.cell.2007.01.043openalex-snapshot

Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila

inferredcites →https://doi.org/10.1016/j.cell.2009.03.040openalex-snapshot

Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary

inferredcites →https://doi.org/10.1016/j.cell.2012.10.040openalex-snapshot

Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression

inferredcites →https://doi.org/10.1016/j.cell.2014.04.031openalex-snapshot

The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

inferredcites →https://doi.org/10.1016/j.cell.2018.06.040openalex-snapshot

Hijacking Oogenesis Enables Massive Propagation of LINE and Retroviral Transposons

inferredcites →https://doi.org/10.1016/j.devcel.2018.10.011openalex-snapshot

A Robust Transposon-Endogenizing Response from Germline Stem Cells

inferredcites →https://doi.org/10.1016/j.molcel.2021.04.022openalex-snapshot

The SARS-CoV-2 RNA interactome

inferredcites →https://doi.org/10.1016/j.molcel.2021.09.017openalex-snapshot

Transposon-taming piRNAs in the germline: Where do they come from?

inferredcites →https://doi.org/10.1016/j.tpb.2023.02.001openalex-snapshot

A Population Genetics Theory for piRNA-regulated Transposable Elements

inferredcites →https://doi.org/10.1017/s0016672300021455openalex-snapshot

The population dynamics of transposable elements

inferredcites →https://doi.org/10.1017/s0016672303006505openalex-snapshot

Mutation accumulation and the effect of copia insertions in Drosophila melanogaster

inferredcites →https://doi.org/10.1023/a:1018310418744openalex-snapshot

Population genetics models of transposable elements

inferredcites →https://doi.org/10.1038/284601a0openalex-snapshot

Selfish genes, the phenotype paradigm and genome evolution

inferredcites →https://doi.org/10.1038/284604a0openalex-snapshot

Selfish DNA: the ultimate parasite

inferredcites →https://doi.org/10.1038/hdy.1979.92openalex-snapshot

The I-R system of hybrid dysgenesis in Drosophila melanogaster: influence on SF females sterility of their inducer and reactive paternal chromosomes

inferredcites →https://doi.org/10.1038/nature10811openalex-snapshot

The Drosophila melanogaster Genetic Reference Panel

inferredcites →https://doi.org/10.1038/nature11416openalex-snapshot

Paramutation in Drosophila linked to emergence of a piRNA-producing locus

inferredcites →https://doi.org/10.1038/nrg.2017.7openalex-snapshot

Integration site selection by retroviruses and transposable elements in eukaryotes

inferredcites →https://doi.org/10.1038/nrg2165openalex-snapshot

A unified classification system for eukaryotic transposable elements

inferredcites →https://doi.org/10.1038/s41467-019-12884-1openalex-snapshot

Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits

inferredcites →https://doi.org/10.1038/s41467-022-29518-8openalex-snapshot

Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila

inferredcites →https://doi.org/10.1038/s41576-018-0073-3openalex-snapshot

PIWI-interacting RNAs: small RNAs with big functions

inferredcites →https://doi.org/10.1038/s41588-017-0010-yopenalex-snapshot

Hidden genetic variation shapes the structure of functional elements in Drosophila

inferredcites →https://doi.org/10.1073/pnas.0702552104openalex-snapshot

Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster

inferredcites →https://doi.org/10.1073/pnas.1313677110openalex-snapshot

Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters

inferredcites →https://doi.org/10.1073/pnas.1524143113openalex-snapshot

Experimental evolution reveals hyperparasitic interactions among transposable elements

inferredcites →https://doi.org/10.1073/pnas.80.6.1655openalex-snapshot

Evolution of hybrid dysgenesis determinants in Drosophila melanogaster

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot

Minimap2: pairwise alignment for nucleotide sequences

inferredcites →https://doi.org/10.1093/dnares/dsx017openalex-snapshot

Short and long-term evolutionary dynamics of subtelomeric piRNA clusters in Drosophila

inferredcites →https://doi.org/10.1093/gbe/evaa064openalex-snapshot

piRNA Clusters Need a Minimum Size to Control Transposable Element Invasions

inferredcites →https://doi.org/10.1093/gbe/evu217openalex-snapshot

Variation in piRNA and Transposable Element Content in Strains of Drosophila melanogaster

inferredcites →https://doi.org/10.1093/genetics/143.4.1663openalex-snapshot

The Regulatory Properties of Autonomous Subtelomeric P Elements Are Sensitive to a Suppressor of variegation in Drosophila melanogaster

inferredcites →https://doi.org/10.1093/genetics/155.4.1841openalex-snapshot

P-Element Repression in Drosophila melanogaster by a Naturally Occurring Defective Telomeric P Copy

inferredcites →https://doi.org/10.1093/genetics/86.4.813openalex-snapshot

HYBRID DYSGENESIS IN DROSOPHILA MELANOGASTER: A SYNDROME OF ABERRANT TRAITS INCLUDING MUTATION, STERILITY AND MALE RECOMBINATION

inferredcites →https://doi.org/10.1093/jhered/esh050openalex-snapshot

Accumulation of Transposable Elements in the Genome of Drosophila melanogaster is Associated with a Decrease in Fitness

inferredcites →https://doi.org/10.1093/molbev/msaa308openalex-snapshot

Tirant Stealthily Invaded Natural Drosophila melanogaster Populations during the Last Century

inferredcites →https://doi.org/10.1093/molbev/msab199openalex-snapshot

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

inferredcites →https://doi.org/10.1093/molbev/msac141openalex-snapshot

The Transposition Rate Has Little Influence on the Plateauing Level of the P-element

inferredcites →https://doi.org/10.1093/molbev/msg102openalex-snapshot

Size Matters: Non-LTR Retrotransposable Elements and Ectopic Recombination in Drosophila

inferredcites →https://doi.org/10.1093/molbev/msw137openalex-snapshot

PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq

inferredcites →https://doi.org/10.1093/molbev/msy083openalex-snapshot

Neutral Theory, Transposable Elements, and Eukaryotic Genome Evolution

inferredcites →https://doi.org/10.1093/molbev/msz079openalex-snapshot

Dynamics of Transposable Element Invasions with piRNA Clusters

inferredcites →https://doi.org/10.1093/nar/gku1099openalex-snapshot

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

inferredcites →https://doi.org/10.1093/nar/gkz1080openalex-snapshot

Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004150openalex-snapshot

On the Abundance and Distribution of Transposable Elements in the Genome of Drosophila melanogaster

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040188openalex-snapshot

The genomic rate of transposable element movement in Drosophila melanogaster.

inferredcites →https://doi.org/10.1101/2022.02.08.479612openalex-snapshot

Maternally inherited siRNAs initiate piRNA cluster formation

inferredcites →https://doi.org/10.1101/2022.08.29.505639openalex-snapshot

Reactivation of an errantivirus in Drosophila ovarian somatic tissue: from germline invasion to taming

inferredcites →https://doi.org/10.1101/gad.209841.112openalex-snapshot

Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state

inferredcites →https://doi.org/10.1101/gad.245514.114openalex-snapshot

Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing

inferredcites →https://doi.org/10.1101/gr.185579.114openalex-snapshot

The Release 6 reference sequence of the Drosophila melanogaster genome

inferredcites →https://doi.org/10.1101/gr.213512.116openalex-snapshot

Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster

inferredcites →https://doi.org/10.1101/gr.228627.117openalex-snapshot

Molecular dissection of a natural transposable element invasion

inferredcites →https://doi.org/10.1111/1755-0998.13455openalex-snapshot

Novel quality metrics allow identifying and generating high‐quality assemblies of piRNA clusters

inferredcites →https://doi.org/10.1111/mec.12170openalex-snapshot

The impact of transposable elements in environmental adaptation

inferredcites →https://doi.org/10.1111/mec.16052openalex-snapshot

Prevalence and polymorphism of a mussel transmissible cancer in Europe

inferredcites →https://doi.org/10.1126/science.1139816openalex-snapshot

Sequence Finishing and Mapping of Drosophila melanogaster Heterochromatin

inferredcites →https://doi.org/10.1126/science.1140494openalex-snapshot

A Slicer-Mediated Mechanism for Repeat-Associated siRNA 5' End Formation in Drosophila

inferredcites →https://doi.org/10.1126/science.1165171openalex-snapshot

An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing

inferredcites →https://doi.org/10.1126/science.1198374openalex-snapshot

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

inferredcites →https://doi.org/10.1126/science.abj6987openalex-snapshot

The complete sequence of a human genome

inferredcites →https://doi.org/10.1146/annurev-genet-120213-092359openalex-snapshot

Population Genomics of Transposable Elements in Drosophila

inferredcites →https://doi.org/10.1146/annurev.ge.23.120189.001343openalex-snapshot

THE POPULATION GENETICS OF DROSOPHILA TRANSPOSABLE ELEMENTS

inferredcites →https://doi.org/10.1186/1471-2105-13-5openalex-snapshot

proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis

inferredcites →https://doi.org/10.1186/1759-8753-5-13openalex-snapshot

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

inferredcites →https://doi.org/10.1186/1759-8753-5-22openalex-snapshot

piRNA clusters and open chromatin structure

inferredcites →https://doi.org/10.1186/gb-2006-7-11-r112openalex-snapshot

Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome

inferredcites →https://doi.org/10.1186/s13059-019-1736-xopenalex-snapshot

Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion

inferredcites →https://doi.org/10.1242/dev.124.14.2789openalex-snapshot

Infection of the germ line by retroviral particles produced in the follicle cells: a possible mechanism for the mobilization of the gypsy retroelement of Drosophila

inferredcites →https://doi.org/10.1261/rna.029769.111openalex-snapshot

Production of artificial piRNAs in flies and mice

inferredcites →https://doi.org/10.1261/rna.061119.117openalex-snapshot

Temperature-responsive miRNAs in Drosophila orchestrate adaptation to different ambient temperatures

inferredcites →https://doi.org/10.1371/journal.pcbi.0010022openalex-snapshot

Combined Evidence Annotation of Transposable Elements in Genome Sequences

inferredcites →https://doi.org/10.1371/journal.pgen.0030158openalex-snapshot

Telomeric Trans-Silencing: An Epigenetic Repression Combining RNA Silencing and Heterochromatin Formation

inferredcites →https://doi.org/10.1371/journal.pgen.1002487openalex-snapshot

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

inferredcites →https://doi.org/10.1371/journal.pgen.1004138openalex-snapshot

Euchromatic Transposon Insertions Trigger Production of Novel Pi- and Endo-siRNAs at the Target Sites in the Drosophila Germline

inferredcites →https://doi.org/10.1371/journal.pgen.1005406openalex-snapshot

Tempo and Mode of Transposable Element Activity in Drosophila

inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot

Cutadapt removes adapter sequences from high-throughput sequencing reads

inferredcites →https://doi.org/10.1515/9781400840915openalex-snapshot

A Biologist's Guide to Mathematical Modeling in Ecology and Evolution

inferredcites →https://doi.org/10.1534/genetics.104.031211openalex-snapshot

The First Steps of Transposable Elements Invasion

inferredcites →https://doi.org/10.1534/genetics.115.180307openalex-snapshot

Paramutation inDrosophilaRequires Both Nuclear and Cytoplasmic Actors of the piRNA Pathway and InducesCis-spreading of piRNA Production

inferredcites →https://doi.org/10.3389/fgene.2014.00257openalex-snapshot

History of the discovery of a master locus producing piRNAs: the flamenco/COM locus in Drosophila melanogaster

inferredcites →https://doi.org/10.7554/elife.80067openalex-snapshot

The Drosophila ZAD zinc finger protein Kipferl guides Rhino to piRNA clusters

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1073/pnas.2313866121openalex-snapshot

Genomes of historical specimens reveal multiple invasions of LTR retrotransposons in Drosophila melanogaster during the 19th century

inferred← citeshttps://doi.org/10.1093/genetics/iyad181openalex-snapshot

The impact of paramutations on the invasion dynamics of transposable elements

inferred← citeshttps://doi.org/10.1101/2023.06.06.543830openalex-snapshot

Genomes of historical specimens reveal multiple invasions of LTR retrotransposons in Drosophila melanogaster populations during the 19 th century

inferred← citeshttps://doi.org/10.1101/2023.10.30.564725openalex-snapshot

Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s

inferred← citeshttps://doi.org/10.1186/s12915-025-02370-0openalex-snapshot

The impact of insertion bias into piRNA clusters on the invasion of transposable elements

inferred← citeshttps://doi.org/10.64898/2026.01.19.700409openalex-snapshot

Rapid evolution and comparative analysis of piRNA clusters in D. simulans

inferred← citeshttps://doi.org/10.70675/107f1badz2604z41b8z8fbfz190bb4221fe3openalex-snapshot

Dynamics of Transposable Elements Under Regulation By piRNA

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