Data_Sheet_11_Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure.xlsx

Changes in chromatin structure, especially in histone modifications (HMs), linked with chromatin accessibility for transcription machinery, are considered to play significant roles in transcriptional regulation. Alveolar macrophages (AM) are important immune cells for protection against pulmonary pathogens, and must readily respond to bacteria and viruses that enter the airways. Mechanism(s) controlling AM innate response to different pathogen-associated molecular patterns (PAMPs) are not well defined in pigs. By combining RNA sequencing (RNA-seq) with chromatin immunoprecipitation and sequencing (ChIP-seq) for four histone marks (H3K4me3, H3K4me1, H3K27ac and H3K27me3), we established a chromatin state map for AM stimulated with two different PAMPs, lipopolysaccharide (LPS) and Poly(I:C), and investigated the potential effect of identified histone modifications on transcription factor binding motif (TFBM) prediction and RNA abundance changes in these AM. The integrative analysis suggests that the differential gene expression between non-stimulated and stimulated AM is significantly associated with changes in the H3K27ac level at active regulatory regions. Although global changes in chromatin states were minor after stimulation, we detected chromatin state changes for differentially expressed genes involved in the TLR4, TLR3 and RIG-I signaling pathways. We found that regions marked by H3K27ac genome-wide were enriched for TFBMs of TF that are involved in the inflammatory response. We further documented that TF whose expression was induced by these stimuli had TFBMs enriched within H3K27ac-marked regions whose chromatin state changed by these same stimuli. Given that the dramatic transcriptomic changes and minor chromatin state changes occurred in response to both stimuli, we conclude that regulatory elements (i.e. active promoters) that contain transcription factor binding motifs were already active/poised in AM for immediate inflammatory response to PAMPs. In summary, our data provides the first chromatin state map of porcine AM in response to bacterial and viral PAMPs, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the role of HMs, especially H3K27ac, in regulating transcription in AM in response to LPS and Poly(I:C).

染色质结构的改变，尤其是与转录机器可及的染色质区域相关的组蛋白修饰（histone modifications, HMs）变化，被认为在转录调控中发挥重要作用。肺泡巨噬细胞（alveolar macrophages, AM）是抵御肺部病原体的重要免疫细胞，需快速响应侵入气道的细菌与病毒。调控肺泡巨噬细胞对不同病原体相关分子模式（pathogen-associated molecular patterns, PAMPs）的先天免疫应答的机制，在猪中尚未得到明确阐释。本研究将RNA测序（RNA sequencing, RNA-seq）与针对四种组蛋白标记（H3K4me3、H3K4me1、H3K27ac及H3K27me3）的染色质免疫共沉淀测序（chromatin immunoprecipitation and sequencing, ChIP-seq）相结合，为经两种不同病原体相关分子模式——脂多糖（lipopolysaccharide, LPS）与聚肌胞苷酸（Poly(I:C)）——刺激的肺泡巨噬细胞构建了染色质状态图谱，并探究了所鉴定的组蛋白修饰对这些肺泡巨噬细胞中转录因子结合基序（transcription factor binding motif, TFBM）预测及RNA丰度变化的潜在影响。整合分析结果显示，未刺激与刺激后的肺泡巨噬细胞之间的差异基因表达，与活性调控区域内H3K27ac的水平变化显著相关。尽管刺激后染色质状态的全局变化较为微弱，但本研究仍检测到了参与TLR4、TLR3及RIG-I信号通路的差异表达基因的染色质状态改变。本研究发现，全基因组范围内被H3K27ac标记的区域，富集了参与炎症应答的转录因子（transcription factor, TF）的结合基序。本研究进一步证实，经上述刺激诱导表达的转录因子，其结合基序富集于经相同刺激发生染色质状态改变的H3K27ac标记区域内。鉴于两种刺激均可引发显著的转录组变化，但染色质状态变化微弱，本研究得出结论：包含转录因子结合基序的调控元件（即活性启动子）在肺泡巨噬细胞中已处于激活或待命状态，以便快速对病原体相关分子模式产生炎症应答。综上，本研究的数据首次构建了猪源肺泡巨噬细胞在响应细菌与病毒源性病原体相关分子模式时的染色质状态图谱，为动物基因组功能注释（Functional Annotation of Animal Genomes, FAANG）项目提供了支撑，并阐明了组蛋白修饰（尤其是H3K27ac）在肺泡巨噬细胞响应脂多糖与聚肌胞苷酸过程中调控转录的作用。