Convergence in LINE-1 nucleotide variations can benefit redundantly forming triplexes with lncRNA in mammalian X-chromosome inactivation

Mobile DNA
Yoko MatsunoHajime Yamakage

Abstract

Associations between X-inactive transcript (Xist)-long noncoding RNA (lncRNA) and chromatin are critical intermolecular interactions in the X-chromosome inactivation (XCI) process. Despite high-resolution analyses of the Xist RNA-binding sites, specific interaction sequences are yet to be identified. Based on elusive features of the association between Xist RNA and chromatin and the possible existence of multiple low-affinity binding sites in Xist RNA, we defined short motifs (≥5 nucleotides), termed as redundant UC/TC (r-UC/TC) or AG (r-AG) motifs, which may help in the mediation of triplex formation between the lncRNAs and duplex DNA. The study showed that r-UC motifs are densely dispersed throughout mouse and human Xist/XIST RNAs, whereas r-AG motifs are even more densely dispersed along opossum RNA-on-the-silent X (Rsx) RNA, and also along both full-length and truncated long interspersed nuclear elements (LINE-1s, L1s) of the three species. Predicted secondary structures of the lncRNAs showed that the length range of these sequence motifs available for forming triplexes was even shorter, mainly 5- to 9-nucleotides long. Quartz crystal microbalance (QCM) measurements and Monte Carlo (MC) simulations indicated that minimum-le...Continue Reading

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Citations

Oct 11, 2019·Nature Reviews. Rheumatology·Nathalie C Lambert
Mar 9, 2020·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Rachel J O'Neill
Feb 2, 2020·Biotechnology Letters·Daigo InaokaHiroyuki Kugoh
Apr 20, 2021·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Aline MuyleJames M A Turner

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Methods Mentioned

BETA
circular
quartz crystal microbalance
SHAPE-MaP

Software Mentioned

DNAMotifFinder
SHAPE
BLAST
RepeatMasker
Mfold
MaP
AQUA
Basic Local Alignment Search Tool ( BLAST )

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