Suppression of Enhancer Overactivation by a RACK7-Histone Demethylase Complex
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Regulation of enhancer activity is important for controlling gene expression programs. Here, we report that a biochemical complex containing a potential chromatin reader, RACK7, and the histone lysine 4 tri-methyl (H3K4me3)-specific demethylase KDM5C occupies many active enhancers, including almost all super-enhancers. Loss of RACK7 or KDM5C results in overactivation of enhancers, characterized by the deposition of H3K4me3 and H3K27Ac, together with increased transcription of eRNAs and nearby genes. Furthermore, loss of RACK7 or KDM5C leads to de-repression of S100A oncogenes and various cancer-related phenotypes. Our findings reveal a RACK7/KDM5C-regulated, dynamic interchange between histone H3K4me1 and H3K4me3 at active enhancers, representing an additional layer of regulation of enhancer activity. We propose that RACK7/KDM5C functions as an enhancer "brake" to ensure appropriate enhancer activity, which, when compromised, could contribute to tumorigenesis.
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ZMYND8 functions as a reader to recognize the acetylation of histone 3 at K14.
“ZMYND8 (also named PRKCBP1 or RACK7) functions as a reader to recognize the acetylation of histone 3 at K14.”
From HBO1 functions as an epigenetic barrier to hepatocyte plasticity and reprogramming during liver injury (2025) · cites this paper as [37]
The Results section ('RACK7 primarily binds active enhancers'; page unavailable) identifies RACK7 as ZMYND8 and reports its binding at active enhancers. It describes the related protein BS69/ZMYND11—not RACK7—as a histone-mark reader. Searches for H3K14, lysine-14 acetylation, and acetylated-histone recognition found no passage saying that ZMYND8 reads H3K14 acetylation. (LLM, conf=0.86)
Experimental — accuracy not yet measuredZMYND8 occupies many active enhancers and recruits KDM5C to super enhancer regions to maintain low H3K4me3 levels resulting in repression of enhancer activity.
“ZMYND8 occupies many active enhancers and recruits KDM5C to super enhancer regions to maintain low H3K4me3 levels resulting in the repression of enhancer activity 35–37.”
From HBO1 functions as an epigenetic barrier to hepatocyte plasticity and reprogramming during liver injury (2025) · cites this paper as [37]
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Self-citation
- Authors
- Shen, H., Xu, W., Guo, R., Rong, B., Gu, L., Wang, Z., He, C., Zheng, L., Hu, X., Hu, Z., Shao, Z.-M., Yang, P., Wu, F., Shi, Y. G., Shi, Y., & Lan, F.
- Affiliations
- Shanghai Medical College of Fudan University (CN)
- Boston Children's Hospital (US)
- Fudan University (CN)
- Brigham and Women's Hospital (US)
- Corresponding author
- Shi, Yang
- Lan, Fei
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2016-04
- Volume
- 165
- Issue
- 2
- Pages
- 331-342
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC4826479
- OpenAlex
- W2313634983
- Cited by
- 184
- References
- 61
- Citations by year
- 2026: 12 · 2025: 21 · 2024: 13 · 2023: 17 · 2022: 17 · 2021: 26 · 2020: 13 · 2019: 13 · 2018: 22 · 2017: 21 · 2016: 9
- FWCI
- 11.26
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 371 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- American Cancer Society
- Constellation Pharmaceuticals
- National Cancer Institute (R01CA118487, CA118487)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (U54HD090255)
- Topics
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- KDM5C, enhancer regulation, super-enhancers, H3K4 demethylation, H3K4me3, H3K4me1, histone demethylase, chromatin reader, carcinogenesis, H3K27 acetylation
- MeSH terms
- Receptors for Activated C Kinase, Animals, Enhancer Elements, Genetic, Gene Expression Regulation, Humans, Neoplasm Transplantation, S100 Proteins, Receptors, Cell Surface, Transcription, Genetic, Mice, Gene Knockout Techniques, Histone Demethylases, Carcinogenesis, Heterografts
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