Genomic maps of lincRNA occupancy reveal principles of RNA-chromatin interactions

By Ci Chu, Kun Qu, F. Zhong, S. Artandi, Howard Y. Chang. Molecules and Cells, 2011

1,211 citations recorded by the source corpus.

SUMMARY Long intergenic noncoding RNAs (lincRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retrieve specific lincRNAs with bound protein and DNA sequences, which are enumerated by deep sequencing. ChIRP-seq of three lincRNAs reveal that RNA occupancy sites in the genome are focal, sequence-specific, and numerous. Drosophila roX2 RNA occupies male X-linked gene bodies with increasing tendency toward the 3’ end, peaking at CES sites. Human telomerase RNA TERC occupies telomeres and Wnt pathway genes. HOTAIR lincRNA preferentially occupies a GA-rich DNA motif to nucleate broad domains of Polycomb occupancy and histone H3 lysine 27 trimethylation. HOTAIR occupancy occurs independently of EZH2, suggesting the order of RNA guidance of Polycomb occupancy. ChIRP-seq is generally applicable to illuminate the intersection of RNA and chromatin with newfound precision genome-wide.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c5d62a702aacc43bb377b573910412bf392cfea7

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Citations in the corpus

The Xist lncRNA exploits three-dimensional genome architecture to spread across the X-chromosome (2013, background): “This broad localization pattern contrasts sharply with the roX2 ncRNA in Drosophila, which, despite its similar function of regulating gene expression across an entire chromosome, binds at discrete sites (32, 33).”
Transcriptional and Post-transcriptional Gene Regulation by Long Non-coding RNA (2017, background): “HOX transcript antisense RNA (HOTAIR), one of these lncRNAs expressed from the HOX-C cluster, has been shown to recruit PRC2 and lysine (K)-specific demethylase 1A (LSD1) to the HOX-D cluster by recognising a specific GA-rich DNA motif [85], maintaining repression over a 40-kb region of the chromoso”
Long Noncoding RNAs in Cardiovascular Diseases (2015, positive): “This method is an improvement to the previously published method called chromatin isolation by RNA purification (ChIRP).(28) In principle, dChIRP works by mixing biotinylated antisense 20-mer oligonucleotides targeting several RNA domains (eg, species-conserved regions, devoid of low complexity) wit”
Long noncoding RNAs: Cellular address codes in development and disease (2013, positive): “For instance, human HOTAIR lncRNA binds to PRC2 and LSD1 complexes and couples H3K27methylation andH3K4 demethylation activity to hundreds of sites genome-wide (Chu et al., 2011; Tsai et al., 2010).”
MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures (2015, neutral): “Input signal [0-19]”