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

Research output: Contribution to journalArticle

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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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Adenosine Diphosphate Ribose
Poly Adenosine Diphosphate Ribose
Adenosine Diphosphate
NAD
Proteome
Biological Phenomena
Alkynes
Azides
RNA Polymerase II
Cycloaddition Reaction
Proteins
Genome

ASJC Scopus subject areas

  • General

Cite this

Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation. / Gibson, Bryan A.; Zhang, Yajie; Jiang, Hong; Hussey, Kristine M.; Shrimp, Jonathan H.; Lin, Hening; Schwede, Frank; Yu, Yonghao; Kraus, W. Lee.

In: Science, Vol. 353, No. 6294, 01.07.2016, p. 45-50.

Research output: Contribution to journalArticle

Gibson, BA, Zhang, Y, Jiang, H, Hussey, KM, Shrimp, JH, Lin, H, Schwede, F, Yu, Y & Kraus, WL 2016, 'Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation', Science, vol. 353, no. 6294, pp. 45-50. https://doi.org/10.1126/science.aaf7865
Gibson BA, Zhang Y, Jiang H, Hussey KM, Shrimp JH, Lin H et al. Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation. Science. 2016 Jul 1;353(6294):45-50. https://doi.org/10.1126/science.aaf7865
Gibson, Bryan A. ; Zhang, Yajie ; Jiang, Hong ; Hussey, Kristine M. ; Shrimp, Jonathan H. ; Lin, Hening ; Schwede, Frank ; Yu, Yonghao ; Kraus, W. Lee. / Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation. In: Science. 2016 ; Vol. 353, No. 6294. pp. 45-50.
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