ChIRP-Seq

ChIRP-Seq

ChIRP, also commonly referred to as ChIRP-seq, is a protocol to detect the locations on the genome where ncRNAs, such as 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. Deep sequencing can determine the lncRNA/protein interaction site at single-base resolution.

Pros:

• Identifies binding sites anywhere on the genome
• Enables discovery of new binding sites
• Allows selection of specific RNAs of interest

Cons:

• Nonspecific oligonucleotide interactions can lead to misinterpretation of binding sites
• Chromatin can be disrupted during the preparation stage
• The sequence of the RNA of interest must be known

• 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

1. Tomita S., Abdalla M. O., Fujiwara S., et al. Roles of long noncoding RNAs in chromosome domains. Wiley Interdiscip Rev RNA. 2017;8:n/a-n/a
2. Schmitt A. M. and Chang H. Y. Long Noncoding RNAs in Cancer Pathways. Cancer Cell. 2016;29:452-463
3. Simon M. D. Insight into lncRNA biology using hybridization capture analyses. Biochim Biophys Acta. 2016;1859:121-127
4. Yang Y., Wen L. and Zhu H. Unveiling the hidden function of long non-coding RNA by identifying its major partner-protein. Cell Biosci. 2015;5:59
5. Chu C., Spitale R. C. and Chang H. Y. Technologies to probe functions and mechanisms of long noncoding RNAs. Nat Struct Mol Biol. 2015;22:29-35

1. 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
2. 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
3. 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
4. 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
5. 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
6. 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
7. 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
8. 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