Evidence for Active Maintenance of Inverted Repeat Structures Identified by a Comparative Genomic Approach

Zhao, Guoyan; Chang, Kuan Y.; Varley, Katherine E.; Stormo, Gary D.

doi:10.1371/journal.pone.0000262

Cited by 15 publications

(12 citation statements)

References 31 publications

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“…Such regulation in response to the environmental or physiological conditions suggests that the transport of sequence-specific silencing information is physiologically important. Notably, there are many sources of dsRNA in the genome of C. elegans (157), and endogenous siRNAs have been detected in vivo (5). However, it is currently unknown whether the silencing information from such endogenous RNAi is transported between cells.…”

Section: Transport Of Silencing Information Between Cellsmentioning

confidence: 99%

Transport of Sequence-Specific RNA Interference Information Between Cells

2007

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When eukaryotic cells encounter double-stranded RNA, genes of matching sequence are silenced through RNA interference. Surprisingly, in some animals and plants, the same gene is specifically silenced even in cells that did not encounter the double-stranded RNA, due to the transport of a gene-specific silencing signal between cells. This silencing signal likely has an RNA component that gives it sequence-specificity, however its precise identity remains unknown. Studies in the worm Caenorhabditis elegans and in plants have revealed parts of a complex protein machinery that transports this silencing signal. Some of these proteins are conserved in vertebrates, including mammals, raising the possibility that higher animals can communicate gene-specific silencing information between cells. Such communication provides antiviral immunity in plants and perhaps in C. elegans. Identifying the transported silencing signal and deciphering the evolutionarily selected role of the transport machinery are some of the key challenges for the future.

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Section: Transport Of Silencing Information Between Cellsmentioning

confidence: 99%

Transport of Sequence-Specific RNA Interference Information Between Cells

2007

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“…The identification of the long inverted repeat in the HS strain is a signature of a transposable element. The distance between the complementary LIR 'stem' regions, in this case 441 bp suggest that this is not an active transposon but more likely a fossil of a transposable element [384,385].…”

Section: Discussionmentioning

confidence: 96%

A genomic approach to understanding metabolic insecticide resistance to diamides in diamondback moth (Plutella xylostella)

Mallott¹

2016

2016 International Congress of Entomology

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“…Inverted repeats are significantly enriched in eukaryotic genomes, suggesting that they are functionally important. 43,62,63 The majority of human inverted repeats are derived from SINEs. 43 These elements should therefore provide the most attractive structural models of mammalian pre-mRNA splicing, alleviating uncertainties in accuracy of RNA secondary structure predictions encountered with typical pre-mRNAs.…”

Section: Discussionmentioning

confidence: 99%

The role of short RNA loops in recognition of a single-hairpin exon derived from a mammalian-wide interspersed repeat

et al. 2015

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Splice-site selection is controlled by secondary structure through sequestration or approximation of splicing signals in primary transcripts but the exact role of even the simplest and most prevalent structural motifs in exon recognition remains poorly understood. Here we took advantage of a single-hairpin exon that was activated in a mammalian-wide interspersed repeat (MIR) by a mutation stabilizing a terminal triloop, with splice sites positioned close to each other in a lower stem of the hairpin. We first show that the MIR exon inclusion in mRNA correlated inversely with hairpin stabilities. Employing a systematic manipulation of unpaired regions without altering splice-site configuration, we demonstrate a high correlation between exon inclusion of terminal tri-and tetraloop mutants and matching tri-/ tetramers in splicing silencers/enhancers. Loop-specific exon inclusion levels and enhancer/silencer associations were preserved across primate cell lines, in 4 hybrid transcripts and also in the context of a distinct stem, but only if its loopclosing base pairs were shared with the MIR hairpin. Unlike terminal loops, splicing activities of internal loop mutants were predicted by their intramolecular Watson-Crick interactions with the antiparallel strand of the MIR hairpin rather than by frequencies of corresponding trinucleotides in splicing silencers/enhancers. We also show that splicing outcome of oligonucleotides targeting the MIR exon depend on the identity of the triloop adjacent to their antisense target. Finally, we identify proteins regulating MIR exon recognition and reveal a distinct requirement of adjacent exons for C-terminal extensions of Tra2a and Tra2b RNA recognition motifs.

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Evidence for Active Maintenance of Inverted Repeat Structures Identified by a Comparative Genomic Approach

Cited by 15 publications

References 31 publications

Transport of Sequence-Specific RNA Interference Information Between Cells

Transport of Sequence-Specific RNA Interference Information Between Cells

A genomic approach to understanding metabolic insecticide resistance to diamides in diamondback moth (Plutella xylostella)

The role of short RNA loops in recognition of a single-hairpin exon derived from a mammalian-wide interspersed repeat

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