The conserved DNMT1-dependent methylation regions in human cells are vulnerable to neurotoxicant rotenone exposure

Table 2 Human DNMT1-dependent genes altered by rotenone

Gene	Log2FC	FDR	Region type	Function/process
MYH3	− 1.62	3.31E−09	Intragenic	Myosin protein; cell movement and transport
PPFIA4	− 1.37	2.59E−13	Intragenic	Neurotransmitter release synaptic function
COL9A2	− 0.79	1.53E−04	Intragenic	Collagen; extracellular matrix organization
DNAAF3	− 0.78	3.59E−02	Intragenic	Dynein protein assembly; cell movement
LRRC8D	− 0.78	8.42E−05	Intragenic	Ion channel protein; neurotransmission
PLEKHG4	− 0.65	2.74E−03	Intragenic	Guanine exchange factor; cell signaling
ADRA2C	0.59	2.93E−02	Intergenic	Neurotransmitter release synaptic function
EML2	0.62	5.99E−05	Promoter	Microtubule protein; synaptic function
HCN2	0.66	1.10E−03	Intragenic	Voltage gated ion channel; action potential
KDM7A	0.67	1.16E−04	Intergenic	Histone demethylase; neurodevelopment
PHLDB3	0.76	3.75E−04	Intragenic	Enzyme binding; cell growth and proliferation
GIPR	0.76	2.37E−02	Promoter	Gastric inhibitory peptide; insulin release
BCL3	0.78	2.00E−02	Intragenic	Proto-oncogene; cell growth and proliferation
NEFM	0.80	4.33E−07	Intragenic	Neurofilament; synaptic function

Log2FC is the log base twofold change of the fragments per kilobase of exon per million fragments mapped (FPKM) or “read counts” of the rotenone-treated HEK293 relative to the vehicle control. FDR is the adjusted p value using the false-discovery rate correction for multiple hypotheses

ISSN: 1756-8935