Analysis of Co-transcriptional RNA Processing by RNA-ChIP Assay (original) (raw)

Abstract

It was initially assumed that RNA biogenesis and processing were two independent processes with transcripts undergoing splicing only after being completely synthesized and released from the DNA template. However, transcription and splicing are tightly linked and increasing evidence shows that nascent transcripts can undergo splicing in the vicinity of chromatin while still attached to the RNA polymerase II (RNAPII) transcriptional machinery. These co-transcriptionally spliced RNA molecules are very labile due to dynamic processing and represent a minor subpopulation among total cellular RNA species. Thus, it is difficult to isolate these RNAs in order to study the dynamics and mechanisms of co-transcriptional RNA splicing. To overcome this problem, the RNA-chromatin immunoprecipitation (ChIP) assay, adapted from classical ChIP, allows to co-purify and isolate nascent RNAs after immunoprecipitation of RNAPII. Thanks to this technique, we have shown that co-transcriptional RNA splicing occurs with distinct efficiencies for different genes and different exons of a given transcript and can represent a rate-limiting step in the biological response of messenger RNA synthesis to extracellular stimuli and drug treatments.

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Acknowledgements

This work was supported by the EURASNET European Network of Excellence and ANR.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
    Danielle Bittencourt
  2. INSERM, Lyon, France
    Didier Auboeuf

Authors

  1. Danielle Bittencourt
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  2. Didier Auboeuf
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Correspondence toDidier Auboeuf .

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Editors and Affiliations

  1. , Department of Biological Sciences, St. John's University, Utopia Parkway 8000, Queens, 11439, New York, USA
    Ales Vancura

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Bittencourt, D., Auboeuf, D. (2012). Analysis of Co-transcriptional RNA Processing by RNA-ChIP Assay. In: Vancura, A. (eds) Transcriptional Regulation. Methods in Molecular Biology, vol 809. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-376-9\_36

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