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.