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

https://doi.org/10.1101/547877
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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/s00239-007-9028-6openalex-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/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
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/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.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/10.1007/s00412-019-00718-4openalex-snapshot
Heterogeneous transposable elements as silencers, enhancers and targets of meiotic recombination
inferred← citeshttps://doi.org/10.1042/bst20190937openalex-snapshot
Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs
inferred← citeshttps://doi.org/10.1080/07352689.2021.1920731openalex-snapshot
On the Role of Transposable Elements in the Regulation of Gene Expression and Subgenomic Interactions in Crop Genomes
inferred← citeshttps://doi.org/10.1080/21541264.2020.1803031openalex-snapshot
The contribution of transposable elements to transcriptional novelty in plants: theFLCaffair
inferred← citeshttps://doi.org/10.1101/2022.10.24.513474openalex-snapshot
Transposons Repressed by H3K27me3 Were Co-Opted as Cis-Regulatory Elements of H3K27me3 Controlled Protein Coding Genes During Evolution of Plants
inferred← citeshttps://doi.org/10.1186/s12864-021-08215-8openalex-snapshot
Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum
inferred← citeshttps://doi.org/10.24072/pci.genomics.100004openalex-snapshot
Using small fragments to discover old TE remnants: the Duster approach empowers the TE detection
inferred← citeshttps://doi.org/10.3390/genes12060859openalex-snapshot
A Global Landscape of Miniature Inverted-Repeat Transposable Elements in the Carrot Genome
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