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Chromatin Isolation via RNA Precipitation (ChIRP) Probe Sets

ChIRP is a rapid technique to discover RNA-associated DNA sequences and map genomic binding sites of chromatin associated long noncoding RNAs (lncRNAs) with high sensitivity and low background. This method allows you to map which chromatin regions come together for coordinated expression, determine which genes are expressed together, and learn the role of lncRNA in chromatin regulation. Target lncRNAs are affinity captured using antisense-oligos, designed by our ChIRP probe designer, and the lncRNA-associated DNA chromatin is sequenced to create a sequencing library. With the DNA sequence data, it is possible to generate a genomic binding site map at a resolution of several hundred bases.

ChIRP Probe Designer


ChIRP oligo sets can be designed at LGC, Biosearch Technologies' dedicated web-based designer and ordered directly. The oligos are delivered in plates with 5 nmol of each individual oligo per well, so that they may be combined into suitable sets.  We recommend using between 8 and 48 oligos per set. The linker we use is C3(Biotin); 3’ modification which is different than the one used originally, but has been approved by the originators of this technology. Buffers and other reagents for the complete ChIRP method are provided by EMD/Millipore. Biosearch Technologies and EMD/Millipore are exclusively licensed to provide ChIRP probe sets.

A protocol from the inventors of ChIRP, practical considerations, and a video demonstrating the protocol can be found here. Specific experimental questions should be directed to the authors. More literature references can be found under the Literature Reference tab of this page.

ChIRP Technology

Chromatin Isolation by RNA Purification (ChIRP) as first described by Chu et al. (1), reviewed by Chu et al. (2), and shown by Chu et al. (3), is covered under US Patent (4). Results from the successful practice of the method also has been published here (5, 6) and elsewhere.

We do not, however, offer technical support for the use of ChIRP probes.  The user is referred to practical considerations well explained and shown by Chu et al. in reference 3.  Specific experimental questions should be directed to the authors.

References

  1. Chu C, Qu K, Zhong FL, Artandi SE, Chang HY (2011) Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions Mol. Cell 44(4), 667-78. doi: 10.1016/j.molcel.2011.08.027
  2. Chu C, Spitale RC, Chang HY (2015) Technologies for illuminating long noncoding RNA function and mechanism. Nat. Struct. Mol. Biol. 22(1), 29-35 doi: 10.1038/nsmb.2921.
  3. Chu C, Quinn J, Chang HY (2012) Chromatin isolation by RNA purification (ChIRP). J. Vis. Exp. (61), e3912. doi: 10.3791/3912
  4. Chang HY, Chu C (2014) RNA interactome analysis. US Patent 8,748,354
  5. Prensner JR, Iyer MK, Sahu A, Asangani IA, Cao Q, Patel L, Vergara IA, Davicioni E, Erho N, Ghadessi M, Jenkins RB, Triche TJ, Malik R, Bedenis R, McGregor N, Ma T, Chen W, Han S, Jing X, Cao X, Wang X, Chandler B, Yan W, Siddiqui J, Kunju LP, Dhanasekaran SM, Pienta KJ, Feng FY, Chinnaiyan AM (2013) The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat. Genetics 45(11), 1392-8. doi: 10.1038/ng.277
  6. Quinn JJ, Ilik IA, Qu K, Georgiev P, Chu C, Akhtar A, Chang HY (2014) Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification.Nat. Biotechnol. 32(9), 933-40. doi: 10.1038/nbt.2943

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