3.3 Chromatin conformation and gene expression changes
We next explore the functional effects of 3D genome changes between LDC liver cells and WCC liver cells, we performed KEGG pathway analysis with genes located in the 5% genomic regions that switched between compartment B and compartment A in either direction (A=>B or B=>A) in both LDC and WCC liver cells. The pathway enrichment analysis showed these genes were strongly associated with extreme environment adaption-related pathways, including Tight junction (Bethany et al., 2018; Ying et al., 2015), Notch signaling pathway (Ishida et al., 2013; Kim et al., 2019; Wang et al., 2012), Vascular smooth muscle contraction (Cardona et al., 2014), RIG-I-like receptor signaling pathway (Liu et al., 2017; Zhang et al., 2018a) (Fig. 6 and Table 1). Within the consistent A/B compartment-switching regions, we found a series of genes related to cell proliferation and differentiation in Tight junction, Notch signaling pathway and RIG-I-like receptor signaling pathway which were upregulated in A-type compartment in LDC cells comparing with WCC cells. Likewise, it should be noted that serine – threonine kinases, ie, rho-associated coiled-coil kinase isoform 2 (ROCK2), myosin light chain kinase (MYLK) in the Vascular smooth muscle contraction pathway were upregulated in A-type compartment in WCC cells.