Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

An in situ method for tagging chromatin-associated RNAs

RNA comprises a substantial fraction of eukaryotic chromatin, but techniques to identify and map RNAs are cumbersome. We adapted existing tagmentation-based profiling techniques to enable chromatin-associated RNAs to be profiled in a simple workflow, enhancing the capability to identify regulatory RNAs.

This is a preview of subscription content, access via your institution

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: RT&Tag procedure.


  1. Quinodoz, S. A. & Guttman, M. Essential roles for RNA in shaping nuclear organization. Cold Spring Harb. Perspect. Biol. (2022). A review article that presents current thinking about how noncoding nuclear RNAs functionally interact with chromatin.

    Article  PubMed  Google Scholar 

  2. Di, L. et al. RNA sequencing by direct tagmentation of RNA/DNA hybrids. Proc. Natl Acad. Sci. USA 117, 2886–2893 (2020). Demonstrates that Tn5 transposase tagments RNA:DNA hybrids generated by reverse transcription.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Kaya-Okur, H. S. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Commun. 10, 1930 (2019). Introduces the CUT&Tag method for in situ chromatin profiling by antibody-targeted tagmentation.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Conrad, T. & Akhtar, A. Dosage compensation in Drosophila melanogaster: epigenetic fine-tuning of chromosome-wide transcription. Nat. Rev. Genet. 13, 123–134 (2012). A review that describes Drosophila melanogaster dosage compensation by twofold upregulation of X-chromosome genes.

    Article  CAS  PubMed  Google Scholar 

  5. He, P. C. & He, C. m6A RNA methylation: from mechanisms to therapeutic potential. EMBO J. 40, e105977 (2021). A review that describes known mechanisms and roles of mRNA m6A modification in gene regulation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This is a summary of: Khyzha, N., Henikoff, S. & Ahmad, K. Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation. Nat. Methods (2022)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

An in situ method for tagging chromatin-associated RNAs. Nat Methods 19, 1351–1352 (2022).

Download citation

  • Published:

  • Issue Date:

  • DOI:


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing