Global Profiling of the Lysine Crotonylome in Different Pluripotent States

• 作者: Yuan Lv Chen Bu Jin Meng Carl Ward Giacomo Volpe Jieyi Hu Mengling Jiang Lin Guo Jiekai Chen Miguel A.Esteban Xichen Bao Zhongyi Cheng
• 来源期刊: 基因组蛋白质组与生物信息学报（英文版）
• 年，卷（期）: 2021,（1）
• 所属期刊栏目: ORIGINAL RESEARCH
• 页码范围: 80-93
• 页数: 14页
• 语种: 英文

摘要

Pluripotent stem cells (PSCs) can be expanded in vitro in different culture conditions, resulting in a spectrum of cell states with distinct properties. Understanding how PSCs transition from one state to another, ultimately leading to lineage-specific differentiation, is important for devel-opmental biology and regenerative medicine. Although there is significant information regarding gene expression changes controlling these transitions, less is known about post-translational modifi-cations of proteins. Protein crotonylation is a newly discovered post-translational modification where lysine residues are modified with a crotonyl group. Here, we employed affinity purification of crotonylated peptides and liquid chromatography–tandem mass spectrometry (LC–MS/MS) to systematically profile protein crotonylation in mouse PSCs in different states includ-ing ground, metastable, and primed states, as well as metastable PSCs undergoing early pluripotency exit. We successfully identified 3628 high-confidence crotonylated sites in 1426 proteins. These crotonylated proteins are enriched for factors involved in functions/processes related to pluripotency such as RNA biogenesis, central carbon metabolism, and proteasome function. Moreover, we found that increasing the cellular levels of crotonyl-coenzyme A (crotonyl-CoA) through crotonic acid treatment promotes proteasome activity in metastable PSCs and delays their differentiation, consis-tent with previous observations showing that enhanced proteasome activity helps to sustain pluripo-tency. Our atlas of protein crotonylation will be valuable for further studies of pluripotency regulation and may also provide insights into the role of metabolism in other cell fate transitions.