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

Carlevaro-Fita, Joana; Das, Monalisa; Polidori, Taisia; Navarro, Carmen; Johnson, Rory

doi:10.1101/189753

Cited by 28 publications

(36 citation statements)

References 77 publications

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“…Localization of lncRNAs and their interactions with other molecules are considered to be very important clues to their function [ 8 ]. Several studies have suggested that TEs also have important roles in localization and intermolecular interactions with lncRNAs, by acting as the recognition domain within lncRNAs [ 40 , 41 , 42 ].…”

Section: Discussionmentioning

confidence: 99%

Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs

Chishima

Iwakiri

Hamada

2018

Genes

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It has been recently suggested that transposable elements (TEs) are re-used as functional elements of long non-coding RNAs (lncRNAs). This is supported by some examples such as the human endogenous retrovirus subfamily H (HERVH) elements contained within lncRNAs and expressed specifically in human embryonic stem cells (hESCs), as required to maintain hESC identity. There are at least two unanswered questions about all lncRNAs. How many TEs are re-used within lncRNAs? Are there any other TEs that affect tissue specificity of lncRNA expression? To answer these questions, we comprehensively identify TEs that are significantly related to tissue-specific expression levels of lncRNAs. We downloaded lncRNA expression data corresponding to normal human tissue from the Expression Atlas and transformed the data into tissue specificity estimates. Then, Fisher’s exact tests were performed to verify whether the presence or absence of TE-derived sequences influences the tissue specificity of lncRNA expression. Many TE–tissue pairs associated with tissue-specific expression of lncRNAs were detected, indicating that multiple TE families can be re-used as functional domains or regulatory sequences of lncRNAs. In particular, we found that the antisense promoter region of L1PA2, a LINE-1 subfamily, appears to act as a promoter for lncRNAs with placenta-specific expression.

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Section: Discussionmentioning

confidence: 99%

Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs

Chishima

Iwakiri

Hamada

2018

Genes

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“…Transposable element-associated lncRNAs (TE-lncRNAs) overlap with transposons that provide lncRNAs with distinct characteristics and chromatin environment. Transposons such as ALU elements promote nuclear localization of human lncRNAs (Lubelsky and Ulitsky 2018 ; Carlevaro-Fita et al 2019 ). The evolutionary origins and functional diversification of lncRNAs are also influenced by transposable elements (Kapusta et al 2013 ).…”

Section: Discovery and Classification Of Lncrnasmentioning

confidence: 99%

Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses

Chen

Zhu

Kaufmann

2020

Planta

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Main conclusion Long non-coding RNAs modulate gene activity in plant development and stress responses by various molecular mechanisms. Abstract Long non-coding RNAs (lncRNAs) are transcripts larger than 200 nucleotides without protein coding potential. Computational approaches have identified numerous lncRNAs in different plant species. Research in the past decade has unveiled that plant lncRNAs participate in a wide range of biological processes, including regulation of flowering time and morphogenesis of reproductive organs, as well as abiotic and biotic stress responses. LncRNAs execute their functions by interacting with DNA, RNA and protein molecules, and by modulating the expression level of their targets through epigenetic, transcriptional, post-transcriptional or translational regulation. In this review, we summarize characteristics of plant lncRNAs, discuss recent progress on understanding of lncRNA functions, and propose an experimental framework for functional characterization.

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“…For example, LTRs were detected in ~250 exons of human protein-coding genes [15,60,61] and can also act as transcriptional promoters and enhancers, often in a tissue-specific manner [78]. A number of exons of long non-coding RNAs originated from LTRs [79]. The exonized LTRs employ diverse sets of splice sites and their exonization levels are relatively high, yet significantly lower than those exhibited by Alus [15].…”

Section: Te Clusters As Exonization Targetsmentioning

confidence: 99%

Transposon clusters as substrates for aberrant splice-site activation

et al. 2020

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Transposed elements (TEs) have dramatically shaped evolution of the exon-intron structure and significantly contributed to morbidity, but how recent TE invasions into older TEs cooperate in generating new coding sequences is poorly understood. Employing an updated repository of new exon-intron boundaries induced by pathogenic mutations, termed DBASS, here we identify novel TE clusters that facilitated exon selection. To explore the extent to which such TE exons maintain RNA secondary structure of their progenitors, we carried out structural studies with a composite exon that was derived from a long terminal repeat (LTR78) and AluJ and was activated by a C > T mutation optimizing the 5ʹ splice site. Using a combination of SHAPE, DMS and enzymatic probing, we show that the diseasecausing mutation disrupted a conserved AluJ stem that evolved from helix 3.3 (or 5b) of 7SL RNA, liberating a primordial GC 5ʹ splice site from the paired conformation for interactions with the spliceosome. The mutation also reduced flexibility of conserved residues in adjacent exon-derived loops of the central Alu hairpin, revealing a cross-talk between traditional and auxilliary splicing motifs that evolved from opposite termini of 7SL RNA and were approximated by Watson-Crick base-pairing already in organisms without spliceosomal introns. We also identify existing Alu exons activated by the same RNA rearrangement. Collectively, these results provide valuable TE exon models for studying formation and kinetics of pre-mRNA building blocks required for splice-site selection and will be useful for fine-tuning auxilliary splicing motifs and exon and intron size constraints that govern aberrant splice-site activation.

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

Cited by 28 publications

References 77 publications

Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs

Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs

Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses

Transposon clusters as substrates for aberrant splice-site activation

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