Asthma and chronic obstructive pulmonary disease are inflammatory airway diseases for which alternative therapeutic strategies are urgently needed. Interestingly, HDAC inhibitors show anti-inflammatory effects in mouse models for these diseases. Here we explore underlying mechanisms that may explain these effects. In previous studies, effects of HDAC inhibitors on histone acetylation are often correlated with their effects on gene expression. However, effects of HDAC inhibitors on transcription factors and their acetylation status may be particularly important in explaining these effects. These effects are also cell type-specific. Recent developments (including chemoproteomics and acetylomics) allow for a more detailed understanding of the selectivity of HDAC inhibitors, which will drive their further development into applications in inflammatory airway diseases. Asthma and chronic obstructive pulmonary disease (COPD) are common inflammatory airway diseases. These diseases affect millions of people world-wide, and globally, the incidence is increasing. For asthma, the clinical symptoms include among others wheezing and shortness of breath. COPD is characterized by shortness of breath upon exercise and a largely irreversible and progressive airflow limitation [1][2][3][4]. In asthma the larger airways are mainly affected, whereas in COPD, the lung parenchyma and peripheral airways are mainly affected [3]. The immunopathology of asthma and COPD is characterized by different types of inflammatory cells that are at play. For example, asthma is driven by T helper 2 (T h 2) cells, dendritic cells and is characterized by eosinophilic inflammation. In asthma there is mast-cell sensitization by immunoglobulin E (IgE), and multiple bronchoconstrictors are released [1,2]. On the other hand, COPD is characterized by T helper 1 (T h 1) cells, cytotoxic T cells and neutrophilic inflammation [5,3]. The inflammation in COPD is also characterized by increased numbers of macrophages, neutrophils and innate lymphoid cells recruited from the circulation. A variety of pro-inflammatory mediators, including cytokines, chemokines, growth factors and lipid mediators are secreted by these cell types [5]. Currently, glucocorticoids are the cornerstone in the treatment of asthma and COPD, however, this is not effective in all patients. Severe asthmatics display glucocorticoid resistance [6], and the effectivity of glucocorticoids in COPD patients is subject to debate [7,8]. Alternative therapeutic strategies are needed for these patients, which currently form a major health burden for society due to high socioeconomic costs [1][2][3][4]9]. Studying the underlying molecular mechanisms may enable the identification of new therapeutic targets. These underlying processes may include epigenetic regulation, such as lysine acetylation. Lysine acetylation is a post-translational modification of proteins, which is crucial in the regulation of cellular processes such as signal transduction and gene expression [10,11]. Lysine acetylation was initiall...