Changes in H3K27ac at gene regulatory regions in porcine alveolar macrophages following LPS or PolyIC exposure

Authors: URIBE, JUBER - Iowa State University; LIU, HAIBO - Iowa State University; Byrne, Kristen; Bond, Zahra; Loving, Crystal; TUGGLE, CHRISTOPHER - Iowa State University

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/8/2020
Publication Date: 8/20/2020
Citation: Uribe, J.H., Liu, H., Byrne, K.A., Bond, Z.F., Loving, C.L., Tuggle, C. 2020. Changes in H3K27ac at gene regulatory regions in porcine alveolar macrophages following LPS or PolyIC exposure. Frontiers in Genetics. 11. https://doi.org/10.3389/fgene.2020.00817.
DOI: https://doi.org/10.3389/fgene.2020.00817

Interpretive Summary: Changes in DNA structure play a large role in immune responses to infectious diseases. All cells have the same DNA, but differences in the structure of the DNA allow each individual cell to respond differently according to its role in the body. Our goal was to identify and map changes in DNA structure in an important immune cell in response to microbial compounds. Macrophages, an immune cell required for responding to and preventing respiratory disease, were isolated from the lung and exposed to bacterial and viral particles to mimic disease. By analyzing DNA and RNA collected from the stimulated cells, we were able to create the first DNA map of the porcine macrophage response. Overall, DNA in the macrophages was already in a state that allowed the cells to immediately respond to both bacterial and viral diseases. DNA changes after stimulation were minimal, though the macrophages produced important immune proteins after stimulation. The information gathered in this study will provide a useful tool to further study responses to porcine diseases and identify methods to reduce disease and improve the health of swine.

Technical Abstract: Changes in chromatin structure, especially in histone modifications (HMs), linked with chromatin 23 accessibility for transcription machinery, are considered to play significant roles in transcriptional 24 regulation. Alveolar macrophages (AM) are important immune cells for protection against pulmonary 25 pathogens, and must readily respond to bacteria and viruses that enter the airways. Mechanism(s) 26 controlling AM innate response to different pathogen-associated molecular patterns (PAMPs) are not 27 well defined in pigs. By combining RNA sequencing with chromatin immunoprecipitation and 28 sequencing (ChIP-seq) for four histone marks (H3K4me3, H3K4me1, H3K27ac and H3K27me3), we 29 established a chromatin state map for AM, and investigated the potential regulatory effect of 30 identified histone modifications on RNA abundance changes in AM stimulated with two different 31 PAMPs, lipopolysaccharide (LPS) and Poly(I:C). The integrative analysis suggests that the 32 differential gene expression between non-stimulated and stimulated AM is significantly associated 33 with changes in the H3K27ac level at active regulatory regions. Although global changes in 34 chromatin states were minor after stimulation, detected chromatin state changes for selected 35 differentially expressed genes involved TLR4, TLR3 and RIG-I signaling pathways. Given that the 36 dramatic transcriptomic changes and minor chromatin state changes occurred in response to both 37 stimuli, we conclude that regulatory elements (i.e. active promoters) were already active/poised in 38 AM for immediate inflammatory response to PAMPs. In summary, our data provides the first 39 chromatin state map of porcine AM in response to bacterial and viral PAMPs, contributing to the 40 Functional Annotation of Animal Genomes (FAANG) project. and demonstrates the role of HMs, 41 especially H3K27ac, in regulating transcription in AM in response to LPS and Poly(I:C).