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Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements

https://doi.org/10.1101/185694
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What this work says

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

inferredcites →https://doi.org/10.1007/978-1-4939-0931-5_12openalex-snapshot
Computing siRNA and piRNA Overlap Signatures
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.2009.04.027openalex-snapshot
Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies
inferredcites →https://doi.org/10.1016/j.cell.2012.02.057openalex-snapshot
A Role for Neuronal piRNAs in the Epigenetic Control of Memory-Related Synaptic Plasticity
inferredcites →https://doi.org/10.1016/j.cub.2009.11.064openalex-snapshot
A Broadly Conserved Pathway Generates 3′UTR-Directed Primary piRNAs
inferredcites →https://doi.org/10.1016/j.gene.2009.07.004openalex-snapshot
Evolution of the RNA-dependent RNA polymerase (RdRP) genes: Duplications and possible losses before and after the divergence of major eukaryotic groups
inferredcites →https://doi.org/10.1016/j.molcel.2011.10.011openalex-snapshot
Heterotypic piRNA Ping-Pong Requires Qin, a Protein with Both E3 Ligase and Tudor Domains
inferredcites →https://doi.org/10.1016/j.pt.2014.01.001openalex-snapshot
How might flukes and tapeworms maintain genome integrity without a canonical piRNA pathway?
inferredcites →https://doi.org/10.1016/j.tibs.2015.12.008openalex-snapshot
One Loop to Rule Them All: The Ping-Pong Cycle and piRNA-Guided Silencing
inferredcites →https://doi.org/10.1016/s0960-9822(01)00299-8openalex-snapshot
Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline
inferredcites →https://doi.org/10.1016/s1534-5807(03)00228-4openalex-snapshot
The Small RNA Profile during Drosophila melanogaster Development
inferredcites →https://doi.org/10.1038/hdy.1979.88openalex-snapshot
An advantage for the evolution of male haploidy and systems with similar genetic transmission
inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot
Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/ncomms13856openalex-snapshot
A somatic piRNA pathway in the Drosophila fat body ensures metabolic homeostasis and normal lifespan
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1042/bst20130086openalex-snapshot
Functional diversification of Argonautes in nematodes: an expanding universe
inferredcites →https://doi.org/10.1093/bioinformatics/btg180openalex-snapshot
MrBayes 3: Bayesian phylogenetic inference under mixed models
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/btu031openalex-snapshot
InterProScan 5: genome-scale protein function classification
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/gbe/evw018openalex-snapshot
Duplication and Diversification of Dipteran Argonaute Genes, and the Evolutionary Divergence of Piwi and Aubergine
inferredcites →https://doi.org/10.1093/gbe/evw281openalex-snapshot
Phylogenetic Origin and Diversification of RNAi Pathway Genes in Insects
inferredcites →https://doi.org/10.1093/molbev/msq284openalex-snapshot
Recurrent Adaptation in RNA Interference Genes Across the Drosophila Phylogeny
inferredcites →https://doi.org/10.1093/molbev/mss075openalex-snapshot
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
inferredcites →https://doi.org/10.1093/molbev/msv093openalex-snapshot
Comparative Genomics Reveals the Origins and Diversity of Arthropod Immune Systems
inferredcites →https://doi.org/10.1093/nar/26.21.4983openalex-snapshot
Incorporation of terminal phosphorothioates into oligonucleotides
inferredcites →https://doi.org/10.1093/nar/gkf436openalex-snapshot
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
inferredcites →https://doi.org/10.1093/nar/gkv590openalex-snapshot
Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs inAedes aegyptimosquito cells
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
inferredcites →https://doi.org/10.1096/fj.201600637rropenalex-snapshot
piRNAs and their diverse roles: a transposable element‐driven tactic for gene regulation?
inferredcites →https://doi.org/10.1098/rstb.2008.0168openalex-snapshot
The evolution of RNAi as a defence against viruses and transposable elements
inferredcites →https://doi.org/10.1105/tpc.10.12.2087openalex-snapshot
Isolation of an RNA-Directed RNA Polymerase–Specific cDNA Clone from Tomato
inferredcites →https://doi.org/10.1111/j.1467-9868.2005.00503.xopenalex-snapshot
Regularization and Variable Selection Via the Elastic Net
inferredcites →https://doi.org/10.1126/science.1116110openalex-snapshot
SMEDWI-2 Is a PIWI-Like Protein That Regulates Planarian Stem Cells
inferredcites →https://doi.org/10.1126/science.1157396openalex-snapshot
Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells
inferredcites →https://doi.org/10.1126/science.1231965openalex-snapshot
Transposition-Driven Genomic Heterogeneity in the Drosophila Brain
inferredcites →https://doi.org/10.1126/science.1257570openalex-snapshot
Phylogenomics resolves the timing and pattern of insect evolution
inferredcites →https://doi.org/10.1126/science.aaa1264openalex-snapshot
piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production
inferredcites →https://doi.org/10.1146/annurev-ento-120710-100659openalex-snapshot
Reevaluating the Arthropod Tree of Life
inferredcites →https://doi.org/10.1186/1471-2164-9-425openalex-snapshot
Comparative genomics of small RNA regulatory pathway components in vector mosquitoes
inferredcites →https://doi.org/10.1186/1758-907x-3-9openalex-snapshot
Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection
inferredcites →https://doi.org/10.1186/gb-2008-9-1-r10openalex-snapshot
Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium
inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
inferredcites →https://doi.org/10.1186/s12864-017-3903-3openalex-snapshot
Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1261/rna.1085008openalex-snapshot
The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians
inferredcites →https://doi.org/10.1371/journal.pbio.1002061openalex-snapshot
Ancient and Novel Small RNA Pathways Compensate for the Loss of piRNAs in Multiple Independent Nematode Lineages
inferredcites →https://doi.org/10.1371/journal.ppat.1002470openalex-snapshot
Production of Virus-Derived Ping-Pong-Dependent piRNA-like Small RNAs in the Mosquito Soma
inferredcites →https://doi.org/10.2144/000114102openalex-snapshot
Terminator Oligo Blocking Efficiently Eliminates rRNA from Drosophila Small RNA Sequencing Libraries

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.molcel.2018.08.007openalex-snapshot
A Single Mechanism of Biogenesis, Initiated and Directed by PIWI Proteins, Explains piRNA Production in Most Animals
inferred← citeshttps://doi.org/10.1016/j.ydbio.2017.10.010openalex-snapshot
EvoRegen in animals: Time to uncover deep conservation or convergence of adult stem cell evolution and regenerative processes
inferred← citeshttps://doi.org/10.3390/genes9050254openalex-snapshot
The Role of Transposable Elements in Speciation
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