Fuller Cassandra N, Mansoor Sabrina, Jeanne Dit Fouque Kevin, Tose Lilian Valadares, Rodriguez-Casariego Javier, Kosmopoulou Mariangela, Suckau Detlev, de Luna Vitorino Francisca N, Garcia Benjamin A, Eirin-Lopez Jose M, Fernandez-Lima Francisco
Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States.
Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, FL 33199, United States.
Nucleic Acids Res. 2025 Jul 19;53(14). doi: 10.1093/nar/gkaf740.
Epigenetic modifications directly regulate the patterns of gene expression by altering DNA accessibility and chromatin structure. A knowledge gap is presented by the need to directly measure these modifications, especially for unannotated organisms with unknown primary histone sequences. In the present work, we developed and applied a novel workflow for identifying and annotating histone proteoforms directly from mass spectrometry-based measurements for the endangered Caribbean coral Acropora cervicornis. Combining high-accuracy de novo top-down and bottom-up analysis based on tandem liquid chromatography, trapped ion mobility spectrometry, non-ergodic electron-based fragmentation, and high-resolution mass spectrometry, near complete primary sequence (up to 99%) and over 86 post-translational modification annotations were obtained from pull-down histone fractions. In the absence of reliable genome annotations, H2A, H2B, and H4 histone sequences and the annotation of the post-translational modifications of the stressed A. cervicornis coral allow for a better understanding of chromatin remodeling and new strategies for targeting intervention and restoration of endangered reef corals.
表观遗传修饰通过改变DNA可及性和染色质结构直接调控基因表达模式。直接测量这些修饰存在知识空白，尤其是对于那些主要组蛋白序列未知的未注释生物。在本研究中，我们开发并应用了一种新颖的工作流程，用于直接从基于质谱的测量中识别和注释濒危加勒比珊瑚鹿角珊瑚（Acropora cervicornis）的组蛋白蛋白变体。结合基于串联液相色谱、捕集离子淌度质谱、非遍历电子碎片化和高分辨率质谱的高精度从头测序的自上而下和自下而上分析，从下拉的组蛋白组分中获得了近完整的一级序列（高达99%）和超过86个翻译后修饰注释。在缺乏可靠基因组注释的情况下，应激的鹿角珊瑚的H2A、H2B和H4组蛋白序列以及翻译后修饰注释有助于更好地理解染色质重塑以及针对濒危珊瑚礁珊瑚进行靶向干预和恢复的新策略。
