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Non-coding RNA

Zooming in on lncRNA functions

Nature Reviews Genetics volume 15, pages 574–575 (2014)Cite this article

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Quinn et al. developed a method called domain-specific chromatin isolation by RNA purification (dChIRP), in which several antisense oligonucleotide pools are used to target specific domains of lncRNAs. In this method, cells are subjected to fixation, crosslinking and sonication, and the resultant sheared chromatin is hybridized to the biotinylated oligonucleotide pools to recover chromatin fragments containing specific lncRNA domains of interest. The RNA, DNA and protein components associated with the lncRNA domains can then be analysed separately.

The authors successfully applied dChIRP to study putative functional domains in the roX1 lncRNA of Drosophila melanogaster. roX1 is essential for dosage compensation, in which expression from the single X chromosome in male flies is upregulated by twofold to match expression from the pairs of autosomal chromosomes. They also showed that the three D domains of roX1 bind directly to male-specific lethal (MSL) proteins to mediate X chromosome upregulation and that the three intervening U domains exhibit minimal binding to MSL proteins but instead associate with each other.

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References

  1. Quinn, J. J. et al. Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Nature Biotech. http://dx.doi.org/10.1038/nbt.2943 (2014)

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  1. Esther Lau
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Lau, E. Zooming in on lncRNA functions. Nat Rev Genet 15, 574–575 (2014). https://doi.org/10.1038/nrg3795

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