Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation

Bryan A. Gibson, Yajie Zhang, Hong Jiang, Kristine M. Hussey, Jonathan H. Shrimp, Hening Lin, Frank Schwede, Yonghao Yu, W. Lee Kraus

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Abstract

Poly[adenosine diphosphate (ADP)-ribose] polymerases (PARPs) are a family of enzymes that modulate diverse biological processes through covalent transfer of ADP-ribose from the oxidized form of nicotinamide adenine dinucleotide (NAD+ ) onto substrate proteins. Here we report a robust NAD+ analog-sensitive approach for PARPs, which allows PARP-specific ADP-ribosylation of substrates that is suitable for subsequent coppercatalyzed azide-alkyne cycloaddition reactions. Using this approach, we mapped hundreds of sites of ADP-ribosylation for PARPs 1, 2, and 3 across the proteome, as well as thousands of PARP-1-mediated ADP-ribosylation sites across the genome. We found that PARP-1 ADP-ribosylates and inhibits negative elongation factor (NELF), a protein complex that regulates promoter-proximal pausing by RNA polymerase II (Pol II). Depletion or inhibition of PARP-1 or mutation of the ADP-ribosylation sites on NELF-E promotes Pol II pausing, providing a clear functional link between PARP-1, ADP-ribosylation, and NELF. This analog-sensitive approach should be broadly applicable across the PARP family and has the potential to illuminate the ADP-ribosylated proteome and the molecular mechanisms used by individual PARPs to mediate their responses to cellular signals.

Original languageEnglish (US)
Pages (from-to)45-50
Number of pages6
JournalScience
Volume353
Issue number6294
DOIs
StatePublished - Jul 1 2016

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Cite this

Gibson, B. A., Zhang, Y., Jiang, H., Hussey, K. M., Shrimp, J. H., Lin, H., Schwede, F., Yu, Y., & Kraus, W. L. (2016). Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation. Science, 353(6294), 45-50. https://doi.org/10.1126/science.aaf7865