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Genome-wide views of long non-coding RNAs

Nature Reviews Genetics volume 12, pages 742–743 (2011)Cite this article

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Several lncRNAs are known to act in trans but, until now, methods to identify their genomic targets have been locus-specific. Chu et al. demonstrate that a method called chromatin isolation by RNA purification (ChIRP) provides high-resolution genome-wide maps of lncRNA occupancy. In ChIRP, chromatin is crosslinked and then extracted and fragmented. These samples are then hybridized to biotinylated oligonucleotide probes that have sequences that tile across the lncRNA of interest; researchers can then pull out fragments of DNA that are bound by the lncRNA and identify them by deep sequencing.

The authors tested ChIRP on three lncRNAs from two species (humans and flies), including human HOX transcript antisense RNA (HOTAIR), an lncRNA that influences the DNA binding of the Polycomb complex PRC2. The ChIRP results suggest that lncRNAs tend to have numerous, focal binding sites that are characterized by particular DNA sequence motifs — characteristics that resemble transcription factor occupancy patterns. They also provide insights into specific functions of the individual lncRNAs, such as showing that HOTAIR directs PRC2 binding and has a preference for GA-rich motifs.

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ORIGINAL RESEARCH PAPERS

  1. Chu, C. et al. Genomic maps of long noncoding RNA occupancy reveal principles of RNA–chromatin interactions. Mol. Cell 29 Sept 2011 (doi: 10.1016/j.molcel.2011.08.027)

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  2. Cabili, M. N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915–1927 (2011)

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  1. Mary Muers
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Muers, M. Genome-wide views of long non-coding RNAs. Nat Rev Genet 12, 742–743 (2011). https://doi.org/10.1038/nrg3088

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