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Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications
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review article
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Europe PubMed Central
title
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications
(English)
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PubMed
author
Cédric Feschotte
series ordinal
2
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Aurélie Kapusta
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1
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language of work or name
English
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PubMed
publication date
October 2014
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published in
Trends in Genetics
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PubMed
volume
30
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PubMed
issue
10
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PubMed
page(s)
439-52
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PubMed
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28 September 2017
A new lncRNA, APTR, associates with and represses the CDKN1A/p21 promoter by recruiting polycomb proteins
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28 September 2017
A novel RNA motif mediates the strict nuclear localization of a long noncoding RNA
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28 September 2017
Elements and machinery of non-coding RNAs: toward their taxonomy
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28 September 2017
The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity
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28 September 2017
An atlas of active enhancers across human cell types and tissues
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28 September 2017
Diversity and dynamics of the Drosophila transcriptome
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28 September 2017
The four dimensions of noncoding RNA conservation.
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28 September 2017
Evolution of transcription factor binding in metazoans - mechanisms and functional implications
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28 September 2017
Genome-wide discovery and characterization of maize long non-coding RNAs.
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28 September 2017
Long noncoding RNAs in innate and adaptive immunity
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28 September 2017
Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development
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28 September 2017
The evolution of lncRNA repertoires and expression patterns in tetrapods
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28 September 2017
Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
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28 September 2017
The locust genome provides insight into swarm formation and long-distance flight
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28 September 2017
Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster
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28 September 2017
Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Identification of expressed and conserved human noncoding RNAs
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Binding interactions between long noncoding RNA HOTAIR and PRC2 proteins
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28 September 2017
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs
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28 September 2017
Genetic and epigenetic regulation of human lincRNA gene expression
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28 September 2017
Divergent transcription: a driving force for new gene origination?
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28 September 2017
Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells
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28 September 2017
Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Transcriptome surveillance by selective termination of noncoding RNA synthesis.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Targeted disruption of Hotair leads to homeotic transformation and gene derepression
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
New gene evolution: little did we know
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Comprehensive characterization of 10,571 mouse large intergenic noncoding RNAs from whole transcriptome sequencing
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Cell cycle regulation by long non-coding RNAs
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
lincRNAs: genomics, evolution, and mechanisms
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Promoter directionality is controlled by U1 snRNP and polyadenylation signals
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
A meta-analysis of the genomic and transcriptomic composition of complex life
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28 September 2017
Senescence-associated lncRNAs: senescence-associated long noncoding RNAs
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28 September 2017
Gene regulation by the act of long non-coding RNA transcription
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Mutations within lncRNAs are effectively selected against in fruitfly but not in human
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs
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28 September 2017
Long noncoding RNAs in development and disease of the central nervous system
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28 September 2017
Bidirectional promoters as important drivers for the emergence of species-specific transcripts
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation.
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28 September 2017
Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Identification and comparative analysis of ncRNAs in human, mouse and zebrafish indicate a conserved role in regulation of genes expressed in brain
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Transposable elements reveal a stem cell-specific class of long noncoding RNAs
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
LncRNADisease: a database for long-non-coding RNA-associated diseases.
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28 September 2017
Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
A misplaced lncRNA causes brachydactyly in humans
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Computational identification and functional predictions of long noncoding RNA in Zea mays
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Circadian changes in long noncoding RNAs in the pineal gland.
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28 September 2017
Genome sequence of the model medicinal mushroom Ganoderma lucidum
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Long noncoding RNAs in C. elegans
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Long non-coding RNAs: versatile master regulators of gene expression and crucial players in cancer.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Mutation in a primate-conserved retrotransposon reveals a noncoding RNA as a mediator of infantile encephalopathy
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Genome-wide analysis of long noncoding RNA stability
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Intragenic enhancers act as alternative promoters
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Dynamic interactions between transposable elements and their hosts
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Exonization of transposed elements: A challenge and opportunity for evolution
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters.
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28 September 2017
A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs
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28 September 2017
Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters
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28 September 2017
Structural and functional differences in the long non-coding RNA hotair in mouse and human
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28 September 2017
Functional consequences of bidirectional promoters
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28 September 2017
The sequence, structure and evolutionary features of HOTAIR in mammals
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28 September 2017
Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells
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28 September 2017
Enrichment of mRNA-like noncoding RNAs in the divergence of Drosophila males.
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28 September 2017
Origins, evolution, and phenotypic impact of new genes.
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28 September 2017
Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
siRNA-mediated methylation of Arabidopsis telomeres
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28 September 2017
Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells
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28 September 2017
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
The origins and impact of primate segmental duplications
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28 September 2017
Molecular mechanisms of gene regulation during Drosophila spermatogenesis
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28 September 2017
Endogenous retroviral LTRs as promoters for human genes: a critical assessment.
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28 September 2017
Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs
1 reference
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Comparative analyses of bidirectional promoters in vertebrates
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 September 2017
Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II.
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28 September 2017
InParanoid 6: eukaryotic ortholog clusters with inparalogs
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28 September 2017
Transcriptional noise and the fidelity of initiation by RNA polymerase II.
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28 September 2017
The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene
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28 September 2017
Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function
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28 September 2017
Comparative genomics of bidirectional gene pairs and its implications for the evolution of a transcriptional regulation system
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28 September 2017
Small regulatory RNAs in mammals
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28 September 2017
Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice.
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28 September 2017
How prevalent is functional alternative splicing in the human genome?
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28 September 2017
Comparative analysis of processed pseudogenes in the mouse and human genomes
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28 September 2017
An abundance of bidirectional promoters in the human genome
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28 September 2017
Neuronal untranslated BC1 RNA: targeted gene elimination in mice.
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28 September 2017
Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster
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28 September 2017
Sense-antisense gene pairs: sequence, transcription, and structure are not conserved between human and mouse
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31 May 2018
A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs
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31 May 2018
lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
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31 May 2018
Epigenetic interplay between mouse endogenous retroviruses and host genes
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31 May 2018
Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance
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28 November 2018
Distinct patterns of genetic variations in potential functional elements in long noncoding RNAs
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28 November 2018
Noncoding RNAs prevent spreading of a repressive histone mark
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28 November 2018
Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality.
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28 November 2018
Evidence of abundant purifying selection in humans for recently acquired regulatory functions
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28 November 2018
Transposable elements have rewired the core regulatory network of human embryonic stem cells
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4464757
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28 November 2018
Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila.
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28 November 2018
Bidirectional gene organization: a common architectural feature of the human genome.
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28 November 2018
Qualifying the relationship between sequence conservation and molecular function
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12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Functional analysis of the highly conserved exon IV of XIST RNA
1 reference
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12 December 2020
based on heuristic
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inferred from DOI database lookup
Identifiers
DOI
10.1016/J.TIG.2014.08.004
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
839581
Fatcat ID
release_pxiiusjcvnc6riv6mkxbz7h5li
0 references
OpenCitations bibliographic resource ID
839581
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
839581
PMC publication ID
4464757
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
839581
PubMed publication ID
25218058
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
839581
ResearchGate publication ID
265608047
0 references
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