Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

• Published in: Molecular cell Vol. 44; no. 4; pp. 667 - 678
• Main Authors: Chu, Ci, Qu, Kun, Zhong, Franklin L., Artandi, Steven E., Chang, Howard Y.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 18.11.2011
• Subjects: Animals; Base Sequence; Breast Neoplasms - genetics; Breast Neoplasms - metabolism; Cell Line, Tumor; Chromatin; Chromatin - chemistry; Chromatin - genetics; Chromatin - metabolism; Chromatin Assembly and Disassembly - genetics; Chromosome Mapping - methods; DNA; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Drosophila; Drosophila melanogaster - genetics; Drosophila melanogaster - metabolism; Drosophila Proteins - genetics; Drosophila Proteins - metabolism; Enhancer of Zeste Homolog 2 Protein; Female; Gene mapping; genes; Genome-Wide Association Study; Genomes; Genomics; high-throughput nucleotide sequencing; High-Throughput Screening Assays; Histone H3; histones; Histones - genetics; Histones - metabolism; Humans; Lysine; Male; males; Methylation; Molecular Sequence Data; non-coding RNA; Nucleotide Motifs - genetics; Nucleotide sequence; nucleotide sequences; occupancy; Oligonucleotides; polycomb group proteins; Polycomb Repressive Complex 2; protein purification; RNA; RNA - genetics; RNA - metabolism; RNA, Long Noncoding; RNA, Untranslated - chemistry; RNA, Untranslated - genetics; RNA, Untranslated - metabolism; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Telomerase; Telomerase - genetics; Telomerase - metabolism; Telomeres; Transcription Factors - genetics; Transcription Factors - metabolism; Wnt protein; Wnt Signaling Pathway - genetics; X chromosome
• ISSN: 1097-2765; 1097-4164; 1097-4164
• DOI: 10.1016/j.molcel.2011.08.027

Long noncoding RNAs (lncRNAs) 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 lncRNAs with bound protein and DNA sequences, which are enumerated by deep sequencing. ChIRP-seq of three lncRNAs 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 lncRNA 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. ► ChIRP-seq maps the binding sites of specific RNAs on chromatin genome wide ► RNA-genome interactions are numerous, focal, and sequence-specific ► Telomerase RNA TERC binds telomeres and Wnt pathway genes ► HOTAIR lncRNA nucleates broader domains of Polycomb and H3K27me3 occupancy