Poly(ADP-Ribose) Polymerase pp 211-228

Part of the Methods in Molecular Biology book series (MIMB, volume 1608) | Cite as

Methodology to Identify Poly-ADP-Ribose Polymerase 1 (PARP1)–mRNA Targets by PAR-CLiP

  • Manana Melikisvili
  • Elena Matveeva
  • Yvonne Fondufe-Mittendorf
Protocol

Abstract

There is a long list of important RNA-binding proteins (RBP) involved in different steps of gene expression through posttranscriptional modifications: pre-mRNA splicing, mRNA stabilization, polyadenylation, mRNA export from nucleus to the cytoplasm, and translation. The critical role of RNA–protein interaction necessitates a continuous identification of proteins involved in this process. Here we describe the identification of Poly-ADP-Ribose Polymerase 1 (PARP1) as an RNA binding protein involved in RNA splicing.

Key words

PARP1 Chromatin mRNA PAR-CliP RNA-binding proteins Splicing 

References

  1. 1.
    Ascano M, Hafner M, Cekan P, Gerstberger S, Tuschl T (2012) Identification of RNA–protein interaction networks using PAR-CLIP. Wiley Interdiscip Rev RNA 3(2):159–177. doi:10.1002/wrna.1103 CrossRefPubMedGoogle Scholar
  2. 2.
    Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T (2010) PAR-CliP – a method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp 41. doi:10.3791/2034
  3. 3.
    Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141(1):129–141. doi:10.1016/j.cell.2010.03.009 CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Spitzer J, Hafner M, Landthaler M, Ascano M, Farazi T, Wardle G, Nusbaum J, Khorshid M, Burger L, Zavolan M, Tuschl T (2014) PAR-CLIP (Photoactivatable Ribonucleoside-enhanced crosslinking and immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins. Methods Enzymol 539:113–161. doi:10.1016/B978-0-12-420120-0.00008-6 CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Elena Matveeva JM, Zhang Q, Eteleeb AM, Convertini P, Chen J, Infantino V, Stamm S, Wang J, Rouchka EC, Fondufe-Mittendorf YN (2015) Involvement of PARP1 in the regulation of alternative splicing. Cell Discov 2. doi:10.1038/celldisc.2015.46

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Manana Melikisvili
    • 1
  • Elena Matveeva
    • 1
  • Yvonne Fondufe-Mittendorf
    • 1
  1. 1.Department of Molecular and Cellular BiochemistryUniversity of KentuckyLexingtonUSA

Personalised recommendations