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Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

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What this work says

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

inferredcites →https://doi.org/10.1002/j.1460-2075.1991.tb07718.xopenalex-snapshot

The origin of footprints of the Tc1 transposon of Caenorhabditis elegans.

inferredcites →https://doi.org/10.1016/0092-8674(82)90463-9openalex-snapshot

The molecular basis of P-M hybrid dysgenesis: The role of the P element, a P-strain-specific transposon family

inferredcites →https://doi.org/10.1016/j.ajhg.2015.12.023openalex-snapshot

A Burden of Rare Variants Associated with Extremes of Gene Expression in Human Peripheral Blood

inferredcites →https://doi.org/10.1016/j.cell.2006.08.003openalex-snapshot

Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis

inferredcites →https://doi.org/10.1016/j.cell.2008.03.029openalex-snapshot

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

inferredcites →https://doi.org/10.1016/j.cell.2008.12.038openalex-snapshot

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

inferredcites →https://doi.org/10.1016/j.cell.2012.09.001openalex-snapshot

Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA

inferredcites →https://doi.org/10.1016/j.cell.2012.10.054openalex-snapshot

Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome

inferredcites →https://doi.org/10.1016/j.cell.2013.02.033openalex-snapshot

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

inferredcites →https://doi.org/10.1016/j.celrep.2014.08.019openalex-snapshot

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana

inferredcites →https://doi.org/10.1016/j.cub.2006.05.045openalex-snapshot

Parent-Dependent Loss of Gene Silencing during Interspecies Hybridization

inferredcites →https://doi.org/10.1016/j.cub.2012.07.061openalex-snapshot

DNA Methylation Dynamics during Sexual Reproduction in Arabidopsis thaliana

inferredcites →https://doi.org/10.1016/j.molcel.2014.07.009openalex-snapshot

Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila

inferredcites →https://doi.org/10.1038/35075612openalex-snapshot

Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis

inferredcites →https://doi.org/10.1038/8803openalex-snapshot

Maintenance of genomic methylation requires a SWI2/SNF2-like protein

inferredcites →https://doi.org/10.1038/nature02651openalex-snapshot

Role of transposable elements in heterochromatin and epigenetic control

inferredcites →https://doi.org/10.1038/nature03667openalex-snapshot

An Arabidopsis hAT-like transposase is essential for plant development

inferredcites →https://doi.org/10.1038/nature06745openalex-snapshot

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

inferredcites →https://doi.org/10.1038/nature08084openalex-snapshot

Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis

inferredcites →https://doi.org/10.1038/nature08328openalex-snapshot

Selective epigenetic control of retrotransposition in Arabidopsis

inferredcites →https://doi.org/10.1038/nature09861openalex-snapshot

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

inferredcites →https://doi.org/10.1038/nature11968openalex-snapshot

Patterns of population epigenomic diversity

inferredcites →https://doi.org/10.1038/ng.1042openalex-snapshot

Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel

inferredcites →https://doi.org/10.1038/ng.3046openalex-snapshot

The genome of the stress-tolerant wild tomato species Solanum pennellii

inferredcites →https://doi.org/10.1038/ng.911openalex-snapshot

Whole-genome sequencing of multiple Arabidopsis thaliana populations

inferredcites →https://doi.org/10.1038/ng1138openalex-snapshot

Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis

inferredcites →https://doi.org/10.1038/ng1929openalex-snapshot

Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.2474openalex-snapshot

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

inferredcites →https://doi.org/10.1038/nrg1834openalex-snapshot

Inherited epigenetic variation — revisiting soft inheritance

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

A unified classification system for eukaryotic transposable elements

inferredcites →https://doi.org/10.1038/nrg3683openalex-snapshot

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

inferredcites →https://doi.org/10.1038/nrg3685openalex-snapshot

Epigenetic reprogramming in plant sexual reproduction

inferredcites →https://doi.org/10.1073/pnas.0508192102openalex-snapshot

Evidence for maternally transmitted small interfering RNA in the repression of transposition in Drosophila virilis

inferredcites →https://doi.org/10.1073/pnas.1107739108openalex-snapshot

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

inferredcites →https://doi.org/10.1073/pnas.1530509100openalex-snapshot

Statistical significance for genomewide studies

inferredcites →https://doi.org/10.1093/bfgp/elu002openalex-snapshot

The bright side of transposons in crop evolution

inferredcites →https://doi.org/10.1093/bioinformatics/btp163openalex-snapshot

Biopython: freely available Python tools for computational molecular biology and bioinformatics

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/btr539openalex-snapshot

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

inferredcites →https://doi.org/10.1093/bioinformatics/bts456openalex-snapshot

YAHA: fast and flexible long-read alignment with optimal breakpoint detection

inferredcites →https://doi.org/10.1093/bioinformatics/btt198openalex-snapshot

RSVSim: an R/Bioconductor package for the simulation of structural variations

inferredcites →https://doi.org/10.1093/bioinformatics/btu314openalex-snapshot

SAMBLASTER : fast duplicate marking and structural variant read extraction

inferredcites →https://doi.org/10.1093/nar/19.6.1349openalex-snapshot

A simple and rapid method for the preparation of plant genomic DNA for PCR analysis

inferredcites →https://doi.org/10.1101/gr.177659.114openalex-snapshot

Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations

inferredcites →https://doi.org/10.1104/pp.106.081091openalex-snapshot

Early Steps in the Biosynthesis of NAD in Arabidopsis Start with Aspartate and Occur in the Plastid

inferredcites →https://doi.org/10.1104/pp.108.119487openalex-snapshot

A Genome-Wide Functional Investigation into the Roles of Receptor-Like Proteins in Arabidopsis

inferredcites →https://doi.org/10.1105/tpc.12.3.357openalex-snapshot

Silencing of Retrotransposons in Arabidopsis and Reactivation by the ddm1 Mutation

inferredcites →https://doi.org/10.1111/j.1469-8137.2010.03193.xopenalex-snapshot

Heterochromatin, small RNA and post‐fertilization dysgenesis in allopolyploid and interploid hybrids of Arabidopsis

inferredcites →https://doi.org/10.1111/tpj.12434openalex-snapshot

Extensive amplification of the E2F transcription factor binding sites by transposons during evolution of Brassica species

inferredcites →https://doi.org/10.1126/science.1074950openalex-snapshot

Dependence of Heterochromatic Histone H3 Methylation Patterns on the Arabidopsis Gene DDM1

inferredcites →https://doi.org/10.1126/science.1172417openalex-snapshot

Genome-Wide Demethylation of Arabidopsis Endosperm

inferredcites →https://doi.org/10.1126/science.1224839openalex-snapshot

Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot

BLAST+: architecture and applications

inferredcites →https://doi.org/10.1186/1471-2164-16-1openalex-snapshot

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing

inferredcites →https://doi.org/10.1186/gb-2014-15-6-r84openalex-snapshot

LUMPY: a probabilistic framework for structural variant discovery

inferredcites →https://doi.org/10.1186/preaccept-2240693321179140openalex-snapshot

Mobster: accurate detection of mobile element insertions in next generation sequencing data

inferredcites →https://doi.org/10.1186/s12864-015-1975-5openalex-snapshot

Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution

inferredcites →https://doi.org/10.1371/journal.pgen.0010060openalex-snapshot

Genome-Wide Association Mapping in Arabidopsis Identifies Previously Known Flowering Time and Pathogen Resistance Genes

inferredcites →https://doi.org/10.1371/journal.pgen.1004915openalex-snapshot

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

inferredcites →https://doi.org/10.1534/g3.112.005348openalex-snapshot

The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice

inferredcites →https://doi.org/10.7554/elife.03198openalex-snapshot

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

inferredcites →https://doi.org/10.7554/elife.15716openalex-snapshot

The Arabidopsis thaliana mobilome and its impact at the species level

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.gde.2018.02.006openalex-snapshot

Transposable element activity, genome regulation and human health

inferred← citeshttps://doi.org/10.1093/gbe/evaa180openalex-snapshot

Impact of Transposable Elements on Methylation and Gene Expression across Natural Accessions of Brachypodium distachyon

inferred← citeshttps://doi.org/10.1093/gbe/evx276openalex-snapshot

Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon

inferred← citeshttps://doi.org/10.1093/jxb/erx377openalex-snapshot

Natural genetic variation and hybridization in plants

inferred← citeshttps://doi.org/10.1101/2023.04.04.535574openalex-snapshot

Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen

inferred← citeshttps://doi.org/10.1101/753814openalex-snapshot

Hybrid incompatibility between D. virilis and D. lumei is stronger in the presence of transposable elements

inferred← citeshttps://doi.org/10.1101/gr.205468.116openalex-snapshot

DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

inferred← citeshttps://doi.org/10.1111/brv.12453openalex-snapshot

Epigenetically facilitated mutational assimilation: epigenetics as a hub within the inclusive evolutionary synthesis

inferred← citeshttps://doi.org/10.11648/j.ajbio.20221002.15openalex-snapshot

Review on Role of Mobile Element in Crop Genetic Variability

inferred← citeshttps://doi.org/10.1186/s13059-016-1127-5openalex-snapshot

Methylome evolution in plants

inferred← citeshttps://doi.org/10.1371/journal.pgen.1010087openalex-snapshot

Meiotic, genomic and evolutionary properties of crossover distribution in Drosophila yakuba

inferred← citeshttps://doi.org/10.21203/rs.3.rs-6266511/v1openalex-snapshot

Naturally occurring variation in gene-associated transposable elements impacts gene expression and phenotypic diversity in woodland strawberry

inferred← citeshttps://doi.org/10.3390/books978-3-03928-367-5openalex-snapshot

Repetitive DNA Sequences

inferred← citeshttps://doi.org/10.70675/e8c61c9ezb3e5z4b52zb2d5z82fe029de9bbopenalex-snapshot

Réponse du méthylome suite à l'exposition au froid chez une espèce à génome complexe : le maïs (Zea mays ssp. mays)

inferred← citeshttps://doi.org/10.7554/elife.15716openalex-snapshot

The Arabidopsis thaliana mobilome and its impact at the species level

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