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Biophysical proves that enhancer activity is independent of H3K27 acetylation modification
[ Instrument Network Instrument R & D ] On February 21, Genome Biology published a research paper "Histone H3K27 acetylation is dispensable for enhancer activity in mouse embryonic stem cells" by Zhu Bing's group at the Institute of Biophysics, Chinese Academy of Sciences. The acetylation of lysine at position 27 of histone H3 (H3K27ac) is an epigenetic marker known to active enhancers. However, relevance does not equal causality. The work found that when the enhancer almost completely lost histone H3K27ac modification, its transcriptional regulation activity remained essentially unchanged. Because the transcriptional regulatory activity of enhancers does not depend on acetylation at a single site, but is regulated by the synergistic effect of acetylation of multiple histone lysine sites.
Enhancers are important elements that regulate the spatiotemporal specific expression of genes, and play an important role in the process of cell differentiation and disease occurrence. How to accurately identify enhancer regions and sequences from the voluminous genomic sequences has always been the focus of research in the field. In the current post-genomic era, researchers have used the rapid development of high-throughput sequencing technology to systematically analyze the characteristics of chromatin throughout the genome, including DNA modifications, histone modifications, the degree of chromatin opening, and various Distribution of chromatin-like proteins on the genome. Histone H3K4me1, H3K27ac modification, and high enrichment of histone variant H3.3 and its high frequency replacement are specific epigenetic markers of widely recognized enhancers. Among them, the ability of H3K27ac to indicate active enhancers is irrefutable, but whether this modification can functionally affect enhancer activity has been controversial in the field.
In order to specifically study the biological function of H3K27ac in the enhancer region, the work was to mutate the lysine at position 27 of the histone variant H3.3 in mouse embryonic stem cells, and mutate it to a non-acetylated modification Arginine (H3.3K27R). Genome-wide analysis revealed that H3K27ac in the active enhancer region of H3.3K27R mutant cells disappeared completely, but the cell transcriptome was hardly affected. The recently developed "Activity-by-Contact" model can relatively well predict the correspondence between enhancers and the genes they regulate. Using this model, analysis of the work shows that gene transcription is not sensitive to the disappearance of the related enhancer region H3K27ac, and only a few genes show up- or down-regulation. Even for super-enhancers that are highly tissue-specific and highly enriched in H3K27ac modifications, there is no significant change in transcription levels in the genes they regulate.
Further research found that the acetylation distribution of H3K9, H3K18, H3K122, H4K5, and H4K8 in the genome did not change significantly. The acetylation modification can neutralize the positivity of lysine and weaken the ability of histone to bind to DNA. Therefore, this study shows that the activity of the enhancer does not depend on the acetylation modification at a single specific site, but requires the synergistic effect of acetylation modification at multiple sites to loosen the chromatin structure and thus maintain the activity of the enhancer. status.
Researchers Zhu Bing and Xiong Jun from the Institute of Biophysics are the corresponding authors of the dissertation. PhD student Zhang Tiantian and researcher Zhang Zhuqiang are the co-first authors of the dissertation. This project was supported by the Ministry of Science and Technology, the Chinese Academy of Sciences and the Natural Science Foundation of China.