ChIRP-Seq
ChIRP-Seq
Chromatin isolation by RNA purification (ChIRP-Seq) is a protocol that detects the locations on the genome where non-coding RNAs (ncRNAs), such as long non-coding RNAs (lncRNAs), and their proteins are bound . In this method, samples are first crosslinked and sonicated. Biotinylated tiling oligos are hybridized to the RNAs of interest, and the complexes are captured with streptavidin magnetic beads. After treatment with RNase H the DNA is extracted and sequenced. With deep sequencing the lncRNA/protein interaction site can be determined at single-base resolution.
- ChIRP-Seq: Chu C., Qu K., Zhong F. L., Artandi S. E. and Chang H. Y. (2011) Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell 44: 667-678
- Leveille N., Melo C. A., Rooijers K., Diaz-Lagares A., Melo S. A., et al. (2015) Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA. Nat Commun 6: 6520
- Li Z., Huang C., Bao C., Chen L., Lin M., et al. (2015) Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol 22: 256-264
- Luo M., Jeong M., Sun D., Park H. J., Rodriguez B. A., et al. (2015) Long Non-Coding RNAs Control Hematopoietic Stem Cell Function. Cell Stem Cell 16: 426-438
- Montes M., Nielsen M. M., Maglieri G., Jacobsen A., Hojfeldt J., et al. (2015) The lncRNA MIR31HG regulates p16(INK4A) expression to modulate senescence. Nat Commun 6: 6967
- Yin Y., Yan P., Lu J., Song G., Zhu Y., et al. (2015) Opposing Roles for the lncRNA Haunt and Its Genomic Locus in Regulating HOXA Gene Activation during Embryonic Stem Cell Differentiation. Cell Stem Cell 16: 504-516
- Quinn J. J., Ilik I. A., Qu K., Georgiev P., Chu C., et al. (2014) Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Nat Biotechnol 32: 933-940
- Li Z., Chao T. C., Chang K. Y., Lin N., Patil V. S., et al. (2014) The long noncoding RNA THRIL regulates TNFalpha expression through its interaction with hnRNPL. Proc Natl Acad Sci U S A 111: 1002-1007
- Trimarchi T., Bilal E., Ntziachristos P., Fabbri G., Dalla-Favera R., et al. (2014) Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia. Cell 158: 593-606