title: Filtrating colorectal cancer associated genes by integrated analyses of global DNA methylation and hydroxymethylation in cancer and normal tissue.
abstract: Recently, 5-hydroxymethylcytosine patterning across the tumor genome was considered as a hallmark of cancer development and progression. However, locus-specific difference of hydroxymethylation between colorectal cancer and normal tissue is unknown. In this study, we performed a newly developed method, HMST-seq, to profile 726 aberrant methylated loci and 689 aberrant hydroxymethylated loci synchronously in genome wide of colorectal cancers, majority of which presented higher methylation or lower hydroxymethylationin than in normal group. Besides, abnormal hydroxymethylated modification was more frequently occur at proximal regions close to TSSs and TSSs regions than abnormal methylation. Subsequently, we screened four genes (ALOX15, GHRHR, TFPI2 and TKTL1) with aberrant methylation and aberrant hydroxymethylation at some genome position by functional enrichment analysis as candidate genes associated with colorectal cancer. Our results may allow us to select differentially epigenetically modified target genes implicated in colorectal cancer tumorigenesis.
authors.affiliation: Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Build 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.|Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng New District, ShenZhen 518118, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Gao
authors.affiliation: BGI-Shenzhen, Build 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.|E-GENE Technologies, Co., Ltd., 16 West Jinniu Road, Pingshan New District, Shenzhen, 518118, China.
authors.forename: Yudong
authors.initials: Y
authors.lastname: Xia
authors.affiliation: Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Tang
authors.affiliation: Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhao
authors.affiliation: Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China.
authors.forename: Congcong
authors.initials: C
authors.lastname: Jin
authors.affiliation: BGI-Shenzhen, Build 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors.forename: Huijuan
authors.initials: H
authors.lastname: Luo
authors.affiliation: BGI-Shenzhen, Build 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors.forename: Junwen
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China.
authors.forename: Qingshu
authors.initials: Q
authors.lastname: Li
authors.affiliation: Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China.
authors.forename: Yalan
authors.initials: Y
authors.lastname: Wang
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives* / Q000737:chemistry; D001093:Arachidonate 15-Lipoxygenase / Q000235:genetics; D015179:Colorectal Neoplasms / Q000235:genetics*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006023:Glycoproteins / Q000235:genetics; D006801:Humans; D017422:Sequence Analysis, DNA; D014174:Transketolase / Q000235:genetics
chemical_list: D006023:Glycoproteins; C021240:tissue-factor-pathway inhibitor 2; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; C515716:ALOX15 protein, human; D001093:Arachidonate 15-Lipoxygenase; C505431:TKTL1 protein, human; D014174:Transketolase