Location: Animal Disease ResearchTitle: Genome-wide histone modifications and CTCF enrichment predict gene expression in sheep macrophages
|MASSA, ALISHA - Washington State University|
|HERNDON, MARIA - Washington State University|
|MURDOCH, BRENDA - University Of Idaho|
Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/30/2020
Publication Date: 1/7/2021
Citation: Massa, A.T., Mousel, M.R., Herndon, M.K., Herndon, D.R., Murdoch, B.M., White, S.N. 2021. Genome-wide histone modifications and CTCF enrichment predict gene expression in sheep macrophages. Frontiers in Genetics. 11. Article 612031. https://doi.org/10.3389/fgene.2020.612031.
Interpretive Summary: Macrophages are an important cell type of the immune system that respond to foreign invaders like infectious viruses, bacteria, and parasites. Within the lung, there are many macrophages that help to prevent diseases by consuming foreign invaders and perform the first steps in activating an immune response in the rest of the body. Small changes in DNA can affect how macrophages respond to invaders. We worked to determine how the DNA of sheep macrophages is organized and identify DNA "on/off" switches that will improve our ability to define DNA changes that control macrophage response to foreign invaders. This is the first study of sheep immune cells with a core FAANG assay, called chromatin immunoprecipitation with DNA sequencing (ChIP-Seq). Over 248,000 regions of the genome were identified as regulatory elements (DNA "on/off" switches). Approximately 12% of the unclassified sheep macrophage genome was assigned putative biological function. Active regions identified in this study compared well with previously published gene expression data (Sheep Gene Expression Atlas). These data will improve the ability of scientists to identify causal mutations that affect disease outcome variability.
Technical Abstract: Immune cells have the most diverse gene expression and epigenetic regulation of any cell types; macrophages function in both innate immunity, establishment of adaptive immunity, and serve to highlight tissue-specific gene regulation. Increasing evidence supports subtle genetic changes alter macrophage response to key production and zoonotic pathogens including viruses like small ruminant lentiviruses and bacteria like Coxiella burnetii. Tissue-specific gene regulation in macrophages also affects their role in homeostasis and wound healing. Here we report the first genome-wide survey of regulatory elements in any sheep immune cell. We assayed histone modifications and CTCF enrichment by chromatin immunoprecipitation with deep sequencing (ChIP-seq) in alveolar macrophages from two sheep to determine regulatory elements and insulator anchors at topologically activating domains important for immunity-related gene expression. Histone modifications included H3K4me3 (active promoters), H3K27ac (active enhancers), H3K4me1 (primed enhancers), and H3K27me3 (broadly repressed silencers) elements. Physical boundaries of chromatin domains that constrain regulatory element activity were assessed with CTCF. Overall, we identified 248,674 reproducible regulatory element peaks. All datasets exceeded the FAANG and ENCODE standards of 20 million to 45 million useable fragments for narrow and broad marks, respectively. These five marks assigned a putative biological function to nearly 12% of the genome of macrophages. Active elements showed high consensus with RNA-seq gene expression data and are predictive of immunity-related gene expression from the publicly available Sheep Gene Expression Atlas. Silencer elements were not enriched for expressed genes, but rather for repressed developmental genes. CTCF enrichment enabled putative determination of 11,000 chromatin domains with mean size of 258 kilobases. This is the first time molecular CTCF enrichment has been used to determine putative topological domains and the first ChIP-seq dataset in any sheep immune cell, to our knowledge. Furthermore, these data will empower phenotype-associated mutation discovery since most causal variants are within regulatory elements.