Predicting Lung Chromatin Access Profiling in an Animal Model

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PROJECT SUMMARY/ABSTRACT Chemical modifications to specific histones and DNA sequences within nucleosomes attract chromatin remodeling complexes. Remodeling complexes create regions of open and restricted chromatin access to control gene expression. Environmental factors disrupt assigning epigenetic marks to histones and/or DNA that alter chromatin access, altering gene expression and increasing disease risk. The recent development of the cutting-edge technology assay for transposase-accessible chromatin, using ATAC sequencing (ATAC-seq), makes identification possible of chromatin access with nucleotide resolution on ~5000 cells. ATAC-seq determines the genomic location of open chromatin, DNA binding proteins, individual nucleosomes, and chromatin compaction. Defining chromatin access provides information about the functional state of DNA regulatory regions that may be altered by preterm birth and mechanical ventilation (PTMV). We will use ATAC-seq to identify the impact of PTMV on chromatin remodeling in our unique preterm lamb model of bronchopulmonary dysplasia (BPD). Our revised R21’s new data show that 1) chromatin landscape patterns are different in lung and brain from PTMV lambs versus healthy control lambs, 2) these differences are reflected within CD4+ T cells from PTMV lambs versus healthy control lambs, and 3) housekeeping genes are conserved among lamb CD4+ T cells, lung, brain, and human B cells. We hypothesize that PTMV negatively impact assignment of epigenetic marks necessary to direct chromatin remodeling and establish proper chromatin access throughout the genome. We will test our hypothesis by doing the following 2 specific aims. Specific Aim 1. Determine alterations to chromatin landscape induced by PTMV. Tissue-specific differences in chromatin landscapes will be identified by comparing results between lung and brain. Specific Aim 2. Compare alterations in chromatin landscape in CD4+ T cells with those identified in the lung and brain obtained in Aim 1. Tissue-specific differences in chromatin landscapes will be identified by comparing results between CD4+ T cells and lung and brain from the same lamb. Results of our revised R21 application will be significant because they will identify CD4+ T cells as accessible biomarkers of epigenetic changes in chromatin landscape in the lung and brain, which become adversely affected in preterm infants with evolving BPD but are not readily accessible for molecular analysis. Innovative approaches combine ATAC-seq with our preterm lamb model of BPD. Our collaborative, multiple- PI members bring expertise in epigenetics, preterm lamb model of BPD, and leukocyte biology. Translational potential arises from defining epigenetic biomarkers in CD4+ lymphocytes that correlate with altered gene expression in lung and brain tissue. Impact of our R21 project will be a novel approach that may be applicable to human preterm infants at risk for BPD, in part because ATAC-seq analysis now is available for single cells.