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Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks

https://doi.org/10.24072/pcjournal.68
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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/s00239-003-0007-2openalex-snapshot
Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes
inferredcites →https://doi.org/10.1007/s00239-007-9028-6openalex-snapshot
Effect of Divergence Time and Recombination Rate on Molecular Evolution of Drosophila INE-1 Transposable Elements and Other Candidates for Neutrally Evolving Sites
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.molcel.2015.02.002openalex-snapshot
High-Resolution Chromatin Dynamics during a Yeast Stress Response
inferredcites →https://doi.org/10.1016/j.ygeno.2008.01.005openalex-snapshot
Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets
inferredcites →https://doi.org/10.1016/s0097-8485(96)80013-1openalex-snapshot
Censor—a program for identification and elimination of repetitive elements from DNA sequences
inferredcites →https://doi.org/10.1016/s0168-9525(00)02024-2openalex-snapshot
EMBOSS: The European Molecular Biology Open Software Suite
inferredcites →https://doi.org/10.1023/a:1005727132202openalex-snapshot
The promoter of the tobacco Tnt1 retrotransposon is induced by wounding and by abiotic stress
inferredcites →https://doi.org/10.1023/a:1016072014259openalex-snapshot
Transposable elements and the evolution of genome size in eukaryotes
inferredcites →https://doi.org/10.1038/nature03667openalex-snapshot
An Arabidopsis hAT-like transposase is essential for plant development
inferredcites →https://doi.org/10.1038/nature04696openalex-snapshot
A distal enhancer and an ultraconserved exon are derived from a novel retroposon
inferredcites →https://doi.org/10.1038/nature08479openalex-snapshot
Unexpected consequences of a sudden and massive transposon amplification on rice gene expression
inferredcites →https://doi.org/10.1038/nature09290openalex-snapshot
Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases
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/ncomms5104openalex-snapshot
Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana
inferredcites →https://doi.org/10.1038/ng.2684openalex-snapshot
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
inferredcites →https://doi.org/10.1038/nrg1272openalex-snapshot
Network biology: understanding the cell's functional organization
inferredcites →https://doi.org/10.1038/nrg3374openalex-snapshot
How important are transposons for plant evolution?
inferredcites →https://doi.org/10.1038/nrg793openalex-snapshot
Plant transposable elements: where genetics meets genomics
inferredcites →https://doi.org/10.1038/s41467-018-06772-3openalex-snapshot
Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana
inferredcites →https://doi.org/10.1073/pnas.0308127100openalex-snapshot
Darwin's abominable mystery: Insights from a supertree of the angiosperms
inferredcites →https://doi.org/10.1073/pnas.0601161103openalex-snapshot
Birth of a chimeric primate gene by capture of the transposase gene from a mobile element
inferredcites →https://doi.org/10.1073/pnas.0611223104openalex-snapshot
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
inferredcites →https://doi.org/10.1093/bioinformatics/btn322openalex-snapshot
Database indexing for production MegaBLAST searches
inferredcites →https://doi.org/10.1093/bioinformatics/btr189openalex-snapshot
MEME-ChIP: motif analysis of large DNA datasets
inferredcites →https://doi.org/10.1093/jxb/erw256openalex-snapshot
Cross species selection scans identify components of C 4 photosynthesis in the grasses
inferredcites →https://doi.org/10.1093/molbev/msv226openalex-snapshot
Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/gkp335openalex-snapshot
MEME SUITE: tools for motif discovery and searching
inferredcites →https://doi.org/10.1093/nar/gkv1463openalex-snapshot
Transcriptional regulatory networks inArabidopsis thalianaduring single and combined stresses
inferredcites →https://doi.org/10.1093/nar/gky995openalex-snapshot
The Pfam protein families database in 2019
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004145openalex-snapshot
Evolution of a Polymorphic Regulatory Element in Interferon-γ Through Transposition and Mutation
inferredcites →https://doi.org/10.1101/gad.1217304openalex-snapshot
siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis
inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
inferredcites →https://doi.org/10.1105/tpc.114.127001openalex-snapshot
Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis
inferredcites →https://doi.org/10.1105/tpc.114.130591openalex-snapshot
A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thaliana
inferredcites →https://doi.org/10.1105/tpc.15.00482openalex-snapshot
A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History
inferredcites →https://doi.org/10.1109/jproc.2016.2590833openalex-snapshot
De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue
inferredcites →https://doi.org/10.1111/j.1365-313x.2006.02936.xopenalex-snapshot
Control of FWA gene silencing in Arabidopsis thaliana by SINE‐related direct repeats
inferredcites →https://doi.org/10.1111/tpj.12017openalex-snapshot
Integrative analysis of chromatin states in A rabidopsis identified potential regulatory mechanisms for natural antisense transcript production
inferredcites →https://doi.org/10.1126/science.1178534openalex-snapshot
The B73 Maize Genome: Complexity, Diversity, and Dynamics
inferredcites →https://doi.org/10.1128/jvi.01771-08openalex-snapshot
Geminivirus AL2 and L2 Proteins Suppress Transcriptional Gene Silencing and Cause Genome-Wide Reductions in Cytosine Methylation
inferredcites →https://doi.org/10.1159/000084957openalex-snapshot
Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae
inferredcites →https://doi.org/10.1186/1471-2105-7-474openalex-snapshot
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
inferredcites →https://doi.org/10.1186/s13059-017-1265-4openalex-snapshot
Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding
inferredcites →https://doi.org/10.1186/s13059-018-1479-0openalex-snapshot
Impact of transposable elements on genome structure and evolution in bread wheat
inferredcites →https://doi.org/10.1186/s13100-015-0041-9openalex-snapshot
Repbase Update, a database of repetitive elements in eukaryotic genomes
inferredcites →https://doi.org/10.1371/journal.pbio.0050129openalex-snapshot
Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis
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.pcbi.1002195openalex-snapshot
Accelerated Profile HMM Searches
inferredcites →https://doi.org/10.1371/journal.pgen.0030086openalex-snapshot
Arabidopsis TFL2/LHP1 Specifically Associates with Genes Marked by Trimethylation of Histone H3 Lysine 27
inferredcites →https://doi.org/10.1371/journal.pgen.1000077openalex-snapshot
Genic and Global Functions for Paf1C in Chromatin Modification and Gene Expression in Arabidopsis
inferredcites →https://doi.org/10.1371/journal.pone.0016526openalex-snapshot
Considering Transposable Element Diversification in De Novo Annotation Approaches
inferredcites →https://doi.org/10.1371/journal.pone.0019949openalex-snapshot
Major-Effect Alleles at Relatively Few Loci Underlie Distinct Vernalization and Flowering Variation in Arabidopsis Accessions
inferredcites →https://doi.org/10.1371/journal.pone.0025988openalex-snapshot
S-MART, A Software Toolbox to Aid RNA-seq Data Analysis
inferredcites →https://doi.org/10.1371/journal.pone.0091929openalex-snapshot
PASTEC: An Automatic Transposable Element Classification Tool
inferredcites →https://doi.org/10.3732/ajb.0800060openalex-snapshot
Angiosperm diversification through time

What points at this work

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

inferred← citeshttps://doi.org/10.2139/ssrn.4837262openalex-extracted
How Does Adaptive Radiation Impact Repeatome Evolution? Comparative Genomic Analysis of Acacia Subg. Phyllodineae (Dc.) Ser. (Leguminosae Juss.)
inferred← citeshttps://doi.org/10.1016/j.cub.2023.08.073openalex-snapshot
The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes
inferred← citeshttps://doi.org/10.1016/j.pbi.2025.102818openalex-snapshot
The natural history of transposons in plant pangenomes and panepigenomes
inferred← citeshttps://doi.org/10.1016/j.semcdb.2024.05.001openalex-snapshot
From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements
inferred← citeshttps://doi.org/10.1101/2024.06.17.598857openalex-snapshot
panREPET: a reference-free pipeline for detecting shared Transposable Elements from pan-genomes to retrace their dynamics in a species
inferred← citeshttps://doi.org/10.1111/plb.70057openalex-snapshot
Factors determining chromosomal localization of transposable elements in plants
inferred← citeshttps://doi.org/10.1111/tpj.70685openalex-snapshot
Nuclear DNA of plastid origin (NUPTs), neglected driver of genome variation and evolutionary innovation
inferred← citeshttps://doi.org/10.1186/s13059-026-03984-5openalex-snapshot
A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species
inferred← citeshttps://doi.org/10.1186/s13100-026-00403-1openalex-snapshot
Stones in genomic storms: transposable element-driven variation in Prunus fruit trees
inferred← citeshttps://doi.org/10.3390/agronomy13020292openalex-snapshot
Long-Read cDNA Sequencing Revealed Novel Expressed Genes and Dynamic Transcriptome Landscape of Triticale (x Triticosecale Wittmack) Seed at Different Developing Stages
inferred← citeshttps://doi.org/10.3390/cells10112952openalex-snapshot
The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation
inferred← citeshttps://doi.org/10.3390/plants12112159openalex-snapshot
The Role of Chromatin Modifications in the Evolution of Giant Plant Genomes
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