This study examined hypermethylated and downregulated genes specific to carbon tetrachloride (CCl
4
) by Methyl-Seq analysis combined with expression microarray analysis in the liver of rats treated with CCl
4
or
N-
nitrosodiethylamine (DEN) for 28 days, by excluding those with DEN. Among 52 genes,
Ldlrad4
,
Proc
,
Cdh17
, and
Nfia
were confirmed to show promoter-region hypermethylation by methylation-specific quantitative PCR analysis on day 28. The transcript levels of these 4 genes decreased by real-time reverse transcription-PCR analysis in the livers of rats treated with nongenotoxic hepatocarcinogens for up to 90 days compared with untreated controls and genotoxic hepatocarcinogens. Immunohistochemically, LDLRAD4 and PROC showed decreased immunoreactivity, forming negative foci, in glutathione
S
-transferase placental form (GST-P)
+
foci, and incidences of LDLRAD4
−
and PROC
−
foci in GST-P
+
foci induced by treatment with nongenotoxic hepatocarcinogens for 84 or 90 days were increased compared with those with genotoxic hepatocarcinogens. In contrast, CDH17 and NFIA responded to hepatocarcinogens without any relation to the genotoxic potential of carcinogens. All 4 genes did not respond to renal carcinogens after treatment for 28 days. Considering that
Ldlrad4
is a negative regulator of transforming growth factor-β signaling,
Proc
participating in p21
WAF1/CIP1
upregulation by activation,
Cdh17
inducing cell cycle arrest by gene knockdown, and
Nfia
playing a role in a tumor-suppressor, all these genes may be potential
in vivo
epigenetic markers of nongenotoxic hepatocarcinogens from the early stages of treatment in terms of gene expression changes. LDLRAD4 and PROC may have a role in the development of preneoplastic lesions produced by nongenotoxic hepatocarcinogens.