In our publication (Oh KS et al. 2019 Epigenetics and Chromatin), we presented an improved a genomic TF footprinting protocol which addresses the difficulty of capturing highly dynamic interactions of some TFs with target DNA elements in chromatin. The additional crosslinking step which we introduced in the protocol can be easily incorporated by any laboratory. We have performed the modified assays and generated a panel of sequencing libraries to systematically assess how the various protocols affect the genomic footprints of dynamic proteins. The enrichment, complexity, and quality of each library was confirmed, and all the libraries were subject to ultra-deep Illumina paired-end read sequencing. The resulting dataset represents an unprecedented-scale resource data for the epigenetics and immunology communities, in addition to providing an insight on the effects of various crosslinking protocols. In another publication (Pacholewska A et al. 2019 Epigenomics), we reported a strong linkage between expression of lncRNAs and their putative target mRNAs in primary macrophages. A global computational analysis revealed that the pairwise relationship between the non-coding and coding transcripts is preserved in a genetically distinct cellular context. Tissue-resident macrophages play a major role in tissue homeostasis. They have also been associated with age-related pathological inflammation. It is important to understand how macrophages are epigenetically and functionally altered during aging and in age-dependent chronic inflammation. To address this, we expanded our efforts to tissue-resident macrophages including peritoneal, Kupffer, and brain-resident macrophages. We performed ATAC-seq and RNA-seq using tissue-resident macrophages from young and aged mice (NIA aged colony at Charles River Lab) treated with lipopolysaccharide (LPS) for 0, 3, 8 hours. The analysis of these data is ongoing and so far has revealed intriguing age-related differential basal gene expression and responses to an inflammatory stimulus.
