Abstract
Recent studies on enzymes and reader proteins for histone crotonylation support a function of histone crotonylation in transcription. However, the enzyme(s) responsible for histone decrotonylation (HDCR) remains poorly defined. Moreover, it remains to be determined if histone crotonylation is physiologically significant and functionally distinct from or redundant to histone acetylation. Here we present evidence that class I histone deacetylases (HDACs) rather than sirtuin family deacetylases (SIRTs) are the major histone decrotonylases, and that histone crotonylation is as dynamic as histone acetylation in mammalian cells. Notably, we have generated novel HDAC1 and HDAC3 mutants with impaired HDAC but intact HDCR activity. Using these mutants we demonstrate that selective HDCR in mammalian cells correlates with a broad transcriptional repression and diminished promoter association of crotonylation but not acetylation reader proteins. Furthermore, we show that histone crotonylation is enriched in and required for self-renewal of mouse embryonic stem cells.
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Acknowledgements
We thank members of Wong's laboratory for valuable discussion. We thank Dr Cheng-Ming Chiang (UT Southwestern) for critical reading of the manuscript. This study is supported by grants from the National Science and Technology Major Project “Key New Drug Creation and Manufacturing Program” of China (2014ZX09507002-005 to JW), the Ministry of Science and Technology of China (2015CB910402 to JW), the National Natural Science Foundation of China (81530078 and 31571325 to JW), the Science and Technology Commission of Shanghai Municipality (14XD1401700 and 11DZ2260300 to JW).
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( Supplementary information is linked to the online version of the paper on the Cell Research website.)
Supplementary information
Supplementary information, Figure S1
Characterization of pan-Kcr antibodies. (PDF 631 kb)
Supplementary information, Figure S2
The class II HDACs and multiple SIRTs are inactive in histone decrotonylation. (PDF 1458 kb)
Supplementary information, Figure S3
The SIRT2 and SIRT3 are inactive in histone decrotonylation. (PDF 1169 kb)
Supplementary information, Figure S4
Knockdown of SIRT1, SIRT3 or SIRT1/3/5 in combination has no obvious effect on global histone acetylation and crotonylation. (PDF 534 kb)
Supplementary information, Figure S5
TSA treatment results in a similar kinetic increase of histone acetylation and crotonylation in mammalian cells. (PDF 598 kb)
Supplementary information, Figure S6
The same enzymatic center catalyzes histone deacetylation and decrotonylation for SIRT1 and HDCA1. (PDF 819 kb)
Supplementary information, Figure S7
Various HDAC1 mutations result in loss of both HDAC and HDCR activities. (PDF 1253 kb)
Supplementary information, Figure S8
The HDAC1-VRPP mutantis active in decrotonylation of multiple sites of his tone crotonylation. (PDF 611 kb)
Supplementary information, Figure S9
The HDAC1-VRPP mutant is active in transcriptional repression. (PDF 506 kb)
Supplementary Table S1
Sequences for qRT-PCR primers (PDF 111 kb)
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Wei, W., Liu, X., Chen, J. et al. Class I histone deacetylases are major histone decrotonylases: evidence for critical and broad function of histone crotonylation in transcription. Cell Res 27, 898–915 (2017). https://doi.org/10.1038/cr.2017.68
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DOI: https://doi.org/10.1038/cr.2017.68
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