Class I histone deacetylases are major histone decrotonylases: evidence for critical and broad function of histone crotonylation in transcription
Open accessAbstract
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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HDACs regulate several other lysine acylations-including depropionylation, demyristoylation, and desuccinylation-which contribute to transcriptional control, metabolic regulation, and cellular stress responses.
“In addition to removing acetyl groups, HDACs regulate several other lysine acylations—including depropionylation, demyristoylation, and desuccinylation—which contribute to transcriptional control, metabolic regulation, and cellular stress responses (Wei et al., 2017).”
From Histone modifications and depression: epigenetic mechanisms, therapeutic targets, and translational outlook (2026) · cites this paper as Wei et al., 2017
The Introduction (page not provided) reports depropionylase activity in several SIRTs and desuccinylase activity in SIRT5, and the paper links histone decrotonylation to transcriptional regulation. It does not substantiate demyristoylation or cellular stress responses, and its findings on transcription concern crotonylation rather than all the acylations listed in the claim. (LLM, conf=0.86)
Experimental — accuracy not yet measuredHistone crotonylation is catalyzed by HATs, which add a crotonyl group from crotonyl-CoA to histone amino acid residues, while HDACs 1/2/3 and sirtuin 1/2/3 act as decrotonylases.
“histone crotonylation is catalyzed by HATs, which add a crotonyl group from crotonyl-coenzyme A (CoA) to amino acid residues of histones,111 while HDACs 1/2/3 and sirtuin 1/2/3, act as decrotonylases.180–182”
From Epigenetic regulation in major depression and other stress-related disorders: molecular mechanisms, clinical relevance and therapeutic potential (2023) · cites this paper as [182]
The Results section ('Class I HDACs possess HDCR activity'; page unavailable) supports decrotonylase activity for HDAC1/2/3 and SIRT1. The Discussion reports prior in-vitro activity for SIRT2 and SIRT3, but says this study detected no significant activity for either in cells. Thus, the unqualified inclusion of SIRT2/3 is not fully supported. The HAT clause carries a different citation and is not assessed here. (LLM, conf=0.88)
Experimental — accuracy not yet measuredHDAC1/2 have been implicated in the regulation of histone crotonylation levels in cells.
“Recently, HDAC1/2 have been implicated in the regulation of histone crotonylation levels in cells21,22.”
From Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo (2018) · cites this paper as [21]
siRNA knockdown of HDAC1/2 or HDAC inhibitor treatment causes increased levels of histone crotonylation.
“siRNA knockdown of HDAC1/221 or treatment with HDAC inhibitors22 caused increased levels of histone crotonylation; although counterintuitively, the average level of H3K18cr at transcriptional start sites (TSS) was reduced following HDAC inhibitor treatment22.”
From Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo (2018) · cites this paper as [21]
Total decrotonylase activity correlates with the total amount of HDAC1/2.
“This difference in activity suggests that HDAC2 acts as a histone decrotonylase, consistent with data from Wei et al.21 and that total decrotonylase activity (similar to deacetylase) correlates with the total amount of HDAC1/2.”
From Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo (2018) · cites this paper as [21]
Overexpression of class I HDACs (HDAC1, 2, 3 and 8) in HeLa cells decreases global histone crotonylation levels, whereas knockdown or HDAC inhibitor treatment produces the opposite effect.
“Wei et al.21 demonstrated that overexpression of class I HDACs (HDAC1, 2, 3 and 8) in HeLa cells were able to decrease global histone crotonylation levels, while knock-down or HDAC inhibitor treatment produced the opposite effect21.”
From Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo (2018) · cites this paper as [21]
The difference in activity between HDAC1-KO; HDAC2-Het and DKO cells suggests HDAC2 acts as a histone decrotonylase.
“This difference in activity suggests that HDAC2 acts as a histone decrotonylase, consistent with data from Wei et al.21 and that total decrotonylase activity (similar to deacetylase) correlates with the total amount of HDAC1/2.”
From Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo (2018) · cites this paper as [21]
Decrotonylase activity has been described for HDAC1-3 and Sirtuins 1-3.
“To date, decrotonylase activity has been described for HDAC1-3 and Sirtuins 1-316–18,21,22.”
From Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo (2018) · cites this paper as [21]
For zinc-dependent HDACs, only few examples of deacylation activities other than deacetylation have been reported and these have been weaker than their potencies against Kac.
“For the zinc-dependent HDACs, on the other hand, only few examples of deacylation activities other than deacetylation have been reported and these have been weaker than their potencies against Kac (Madsen and Olsen, 2012a; Aramsangtienchai et al., 2016; Wei et al., 2017).”
From Histone deacetylase 11 is an ε-N-Myristoyllysine hydrolase (2018) · cites this paper as Wei et al., 2017
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“In addition to removing acetyl groups, HDACs regulate several other lysine acylations—including depropionylation, demyristoylation, and desuccinylation—which contribute to transcriptional control, metabolic regulation, and cellular stress responses (Wei et al., 2017).”
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- Authors
- Wei, W., Liu, X., Chen, J., Gao, S., Lu, L., Zhang, H., Ding, G., Wang, Z., Chen, Z., Shi, T., Li, J., Yu, J., & Wong, J.
- Affiliations
- East China Normal University (CN)
- Beijing Advanced Innovation Center for Food Nutrition and Human Health (CN)
- Shanghai Jiao Tong University (CN)
- Corresponding author
- Yu, Jianjun
- Wong, Jiemin
- ORCID
- Venue
- Cell Research
- Published
- 2017-05-12
- Volume
- 27
- Issue
- 7
- Pages
- 898-915
- ISSN
- 1001-0602 (ISSN-L)
- 1748-7838
- PMC
- PMC5518989
- OpenAlex
- W2613130271
- Cited by
- 304
- References
- 54
- Citations by year
- 2026: 37 · 2025: 38 · 2024: 44 · 2023: 39 · 2022: 38 · 2021: 45 · 2020: 26 · 2019: 18 · 2018: 16 · 2017: 3
- FWCI
- 7.04
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Cell Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- University of Texas Southwestern Medical Center
- National Natural Science Foundation of China (31571325, 11DZ2260300, 81530078)
- Science and Technology Commission of Shanghai Municipality (14XD1401700, 11DZ2260300)
- National Science and Technology Major Project
- National Key New Drug Creation and Manufacturing Program, Ministry of Science and Technology
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Histone Deacetylase Inhibitors Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- histone crotonylation, class I histone deacetylases, HDAC1, HDAC3, histone acetylation, transcriptional repression, embryonic stem cell self-renewal, sirtuin deacetylase
- MeSH terms
- Acetylation, Animals, Cell Line, Histone Deacetylases, Histones, Humans, Hydroxamic Acids, Lysine, Niacinamide, Transcription Factors, Transcription, Genetic, Gene Expression, Sirtuins, Mutant Proteins, Mice, Histone Deacetylase Inhibitors
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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