Ribosomes Meet Epigenetics

Chen et al. link chromatin modifying machinery with ribosome biogenesis. The Plant Cell (2018). https://doi.org/10.1105/tpc.17.00626

by Xiangsong Chen and Xuehua Zhong

Background: All cells need to make proteins to function properly. Ribosomes are the protein production factories consisting of ribosomal RNA (rRNA) and ribosomal proteins. Much like a large cake needs to be sliced into small pieces to serve many people, long precursor rRNA molecules in cells must be cut into smaller mature rRNAs to make functional proteins. If rRNA processing is altered, it can lead to the production of proteins that do not function properly and this can cause diseases and developmental defects. Epigenetics refers to modifications of DNA, RNA, and associated histone proteins that can affect gene expression – and therefore protein production. For example, the enzyme histone deacetylase (HDAC), is an epigenetic modifier that remove chemical tags on histones. HDACs regulate many basic cellular activities influencing plant growth and development by switching genes “off” so they are not expressed and proteins they encode are not produced.

Question: We want to know how exactly HDAC regulates ribosome biogenesis, which is required for protein production in the cell.

Findings: We found a previously undiscovered way in which rRNA processing and protein production is controlled, involving the plant-specific HDACs, HD2C and HD2B. Both of these enzymes are important for normal leaf and root development in the flowering plant Arabidopsis. Mutations in genes encoding HD2B and HD2C cause abnormal rRNA processing and also change the production of message RNAs required for making ribosomal proteins. Interestingly, we found two ways in which HD2C can regulate rRNA processing. Much like other HDACs function to regulate gene expression, HD2C turns down the expression of many genes critical for rRNA processing. We further identified a novel mechanism by which HD2C directly binds to the rRNA itself to prevent rRNA methylation, necessary for proper rRNA processing.

Next Steps: Plants are subjected to many environmental stresses, and it is critical for them to balance development and stress tolerance. An imbalance in protein production caused by ribosome deficiency changes how plant cells responds to various stresses. A next step is to investigate how HD2C and other epigenetic modifying enzymes control rRNA processing to balance development and stress tolerance.

Chen, X., Lu, L., Qian, S., calf, M., Smith, L.M., and Zhong, X. (2018). Canonical and Non-canonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing. Plant Cell January 2018, DOI: https://doi.org/10.1105/tpc.17.00626