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Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs

https://doi.org/10.1101/189753
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What this work says

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

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LINEs and SINEs of primate evolution
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Colon cancer associated transcript‐1: A novel RNA expressed in malignant and pre‐malignant human tissues
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RNA Pulldown Protocol for In Vitro Detection and Identification of RNA-Associated Proteins
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Long Noncoding RNAs in Cancer Pathways
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mRNA Localization: Gene Expression in the Spatial Dimension
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lincRNAs: Genomics, Evolution, and Mechanisms
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Evolution of Alu Elements toward Enhancers
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Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species
inferredcites →https://doi.org/10.1016/j.celrep.2015.11.036openalex-snapshot
Nuclear Retention of mRNA in Mammalian Tissues
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cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture
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Transposable elements in gene regulation and in the evolution of vertebrate genomes
inferredcites →https://doi.org/10.1016/j.gene.2010.12.010openalex-snapshot
Epigenetic regulation of transposable element derived human gene promoters
inferredcites →https://doi.org/10.1016/j.gene.2014.06.043openalex-snapshot
The ways of action of long non-coding RNAs in cytoplasm and nucleus
inferredcites →https://doi.org/10.1016/j.tibs.2016.07.003openalex-snapshot
Linking Long Noncoding RNA Localization and Function
inferredcites →https://doi.org/10.1016/j.tig.2014.08.004openalex-snapshot
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications
inferredcites →https://doi.org/10.1038/nature09701openalex-snapshot
lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements
inferredcites →https://doi.org/10.1038/nature10887openalex-snapshot
Modular regulatory principles of large non-coding RNAs
inferredcites →https://doi.org/10.1038/nature11233openalex-snapshot
Landscape of transcription in human cells
inferredcites →https://doi.org/10.1038/nature11508openalex-snapshot
Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat
inferredcites →https://doi.org/10.1038/nature12943openalex-snapshot
The evolution of lncRNA repertoires and expression patterns in tetrapods
inferredcites →https://doi.org/10.1038/nature15393openalex-snapshot
A global reference for human genetic variation
inferredcites →https://doi.org/10.1038/nature25757openalex-snapshot
Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells
inferredcites →https://doi.org/10.1038/ncomms11021openalex-snapshot
Function and evolution of local repeats in the Firre locus
inferredcites →https://doi.org/10.1038/ng.368openalex-snapshot
The regulated retrotransposon transcriptome of mammalian cells
inferredcites →https://doi.org/10.1038/ng.3988openalex-snapshot
High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
inferredcites →https://doi.org/10.1038/ng1269openalex-snapshot
RNA truncation by premature polyadenylation attenuates human mobile element activity
inferredcites →https://doi.org/10.1038/nmeth.3810openalex-snapshot
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)
inferredcites →https://doi.org/10.1038/nrg.2016.139openalex-snapshot
Regulatory activities of transposable elements: from conflicts to benefits
inferredcites →https://doi.org/10.1038/nrg2337openalex-snapshot
Transposable elements and the evolution of regulatory networks
inferredcites →https://doi.org/10.1038/nrg2640openalex-snapshot
The impact of retrotransposons on human genome evolution
inferredcites →https://doi.org/10.1038/nsmb.2480openalex-snapshot
Structure and function of long noncoding RNAs in epigenetic regulation
inferredcites →https://doi.org/10.1038/nsmb.2764openalex-snapshot
Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
inferredcites →https://doi.org/10.1038/nsmb.3325openalex-snapshot
Integrative classification of human coding and noncoding genes through RNA metabolism profiles
inferredcites →https://doi.org/10.1073/pnas.0903103106openalex-snapshot
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
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/nar/23.1.170openalex-snapshot
Ubiquitous mammalian-wide interspersed repeats (MIRs) are molecular fossils from the mesozoic era
inferredcites →https://doi.org/10.1093/nar/29.1.308openalex-snapshot
dbSNP: the NCBI database of genetic variation
inferredcites →https://doi.org/10.1093/nar/gkl525openalex-snapshot
Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication
inferredcites →https://doi.org/10.1093/nar/gks1099openalex-snapshot
LncRNADisease: a database for long-non-coding RNA-associated diseases
inferredcites →https://doi.org/10.1093/nar/gkt1229openalex-snapshot
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
inferredcites →https://doi.org/10.1093/nar/gkt1248openalex-snapshot
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data
inferredcites →https://doi.org/10.1093/nar/gkt596openalex-snapshot
Widespread purifying selection on RNA structure in mammals
inferredcites →https://doi.org/10.1093/nar/gku988openalex-snapshot
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs
inferredcites →https://doi.org/10.1093/nar/gkv1094openalex-snapshot
Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers
inferredcites →https://doi.org/10.1093/nar/gkw599openalex-snapshot
Inverted repeatAluelements in the human lincRNA-p21 adopt a conserved secondary structure that regulates RNA function
inferredcites →https://doi.org/10.1093/nar/gkw888openalex-snapshot
POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins
inferredcites →https://doi.org/10.1101/gr.080663.108openalex-snapshot
Evolution of the mammalian transcription factor binding repertoire via transposable elements
inferredcites →https://doi.org/10.1101/gr.091678.109openalex-snapshot
Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression
inferredcites →https://doi.org/10.1101/gr.131037.111openalex-snapshot
Genome-wide analysis of long noncoding RNA stability
inferredcites →https://doi.org/10.1101/gr.132159.111openalex-snapshot
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
inferredcites →https://doi.org/10.1101/gr.135350.111openalex-snapshot
GENCODE: The reference human genome annotation for The ENCODE Project
inferredcites →https://doi.org/10.1101/gr.165035.113openalex-snapshot
Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
inferredcites →https://doi.org/10.1101/gr.181974.114openalex-snapshot
Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells
inferredcites →https://doi.org/10.1101/gr.208652.116openalex-snapshot
The identification and functional annotation of RNA structures conserved in vertebrates
inferredcites →https://doi.org/10.1101/gr.3715005openalex-snapshot
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
inferredcites →https://doi.org/10.1126/science.1082588openalex-snapshot
The Birth of an Alternatively Spliced Exon: 3' Splice-Site Selection in Alu Exons
inferredcites →https://doi.org/10.1128/mcb.01673-13openalex-snapshot
A Novel RNA Motif Mediates the Strict Nuclear Localization of a Long Noncoding RNA
inferredcites →https://doi.org/10.1186/1756-0500-3-294openalex-snapshot
REAP: A two minute cell fractionation method
inferredcites →https://doi.org/10.1186/1759-8753-5-14openalex-snapshot
Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression
inferredcites →https://doi.org/10.1186/gb-2007-8-6-r127openalex-snapshot
Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome
inferredcites →https://doi.org/10.1186/gb-2012-13-11-r107openalex-snapshot
Transposable elements reveal a stem cell-specific class of long noncoding RNAs
inferredcites →https://doi.org/10.1186/gb-2013-14-5-r49openalex-snapshot
Mutations within lncRNAs are effectively selected against in fruitfly but not in human
inferredcites →https://doi.org/10.1186/s12915-016-0283-0openalex-snapshot
Secondary structure impacts patterns of selection in human lncRNAs
inferredcites →https://doi.org/10.1186/s13059-014-0537-5openalex-snapshot
Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions
inferredcites →https://doi.org/10.1186/s13059-015-0586-4openalex-snapshot
Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution
inferredcites →https://doi.org/10.1186/s13059-017-1293-0openalex-snapshot
A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes
inferredcites →https://doi.org/10.1186/s13059-017-1331-yopenalex-snapshot
The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element
inferredcites →https://doi.org/10.1261/rna.044560.114openalex-snapshot
The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs
inferredcites →https://doi.org/10.1261/rna.053561.115openalex-snapshot
Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells
inferredcites →https://doi.org/10.1261/rna.060814.117openalex-snapshot
LncATLAS database for subcellular localization of long noncoding RNAs
inferredcites →https://doi.org/10.1261/rna.063172.117openalex-snapshot
CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells
inferredcites →https://doi.org/10.1371/journal.pgen.1003470openalex-snapshot
Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs
inferredcites →https://doi.org/10.1371/journal.pgen.1003588openalex-snapshot
Alu Elements in ANRIL Non-Coding RNA at Chromosome 9p21 Modulate Atherogenic Cell Functions through Trans-Regulation of Gene Networks
inferredcites →https://doi.org/10.4161/mge.19032openalex-snapshot
Protein interactions withpiALURNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly
inferredcites →https://doi.org/10.4161/mge.29255openalex-snapshot
Burgeoning evidence indicates that microRNAs were initially formed from transposable element sequences
inferredcites →https://doi.org/10.7554/elife.03058openalex-snapshot
Considerations when investigating lncRNA function in vivo

What points at this work

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

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Atlas of Subcellular RNA Localization Revealed by APEX-Seq
inferred← citeshttps://doi.org/10.1016/j.cell.2020.09.047openalex-snapshot
Functional Long Non-coding RNAs Evolve from Junk Transcripts
inferred← citeshttps://doi.org/10.1038/s41576-018-0017-yopenalex-snapshot
Towards a complete map of the human long non-coding RNA transcriptome
inferred← citeshttps://doi.org/10.1186/s13059-019-1757-5openalex-snapshot
Multilayered control of exon acquisition permits the emergence of novel forms of regulatory control
inferred← citeshttps://doi.org/10.3390/genes9010023openalex-snapshot
Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs
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