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Soobok Joe,Jinyong Kim,Jinyoung Lee,Jongbum Jeon,Iksu Byeon,Sae-Won Han,Seung-Bum Ryoo,Kyu-Joo Park,Sang-Hyun Song,Sheehyun Cho,Hyeran Shim,Hoang Bao Khanh Chu,Jisun Kang,Hong Seok Lee,DongWoo Kim,You 생화학분자생물학회 2023 BMB Reports Vol.56 No.10
DNA methylation regulates gene expression and contributes totumorigenesis in the early stages of cancer. In colorectal cancer(CRC), CpG island methylator phenotype (CIMP) is recognizedas a distinct subset that is associated with specific molecularand clinical features. In this study, we investigated the genomewideDNA methylation patterns among patients with CRC. The methylation data of 1 unmatched normal, 142 adjacentnormal, and 294 tumor samples were analyzed. We identified40,003 differentially methylated positions with 6,933 (79.8%)hypermethylated and 16,145 (51.6%) hypomethylated probesin the genic region. Hypermethylated probes were predominantlyfound in promoter-like regions, CpG islands, and N shore sites;hypomethylated probes were enriched in open-sea regions. CRC tumors were categorized into three CIMP subgroups, with90 (30.6%) in the CIMP-high (CIMP-H), 115 (39.1%) in theCIMP-low (CIMP-L), and 89 (30.3%) in the non-CIMP group. The CIMP-H group was associated with microsatellite instabilityhightumors, hypermethylation of MLH1, older age, and rightsidedtumors. Our results showed that genome-wide methylationanalyses classified patients with CRC into three subgroupsaccording to CIMP levels, with clinical and molecular featuresconsistent with previous data.
Kim, Yong-Min,Kim, Seungill,Koo, Namjin,Shin, Ah-Young,Yeom, Seon-In,Seo, Eunyoung,Park, Seong-Jin,Kang, Won-Hee,Kim, Myung-Shin,Park, Jieun,Jang, Insu,Kim, Pan-Gyu,Byeon, Iksu,Kim, Min-Seo,Choi, JinH Oxford University Press 2017 DNA research Vol.24 No.1
<P><B>Abstract</B></P><P><I>Hibiscus syriacus</I> (L.) (rose of Sharon) is one of the most widespread garden shrubs in the world. We report a draft of the <I>H. syriacus</I> genome comprised of a 1.75 Gb assembly that covers 92% of the genome with only 1.7% (33 Mb) gap sequences. Predicted gene modeling detected 87,603 genes, mostly supported by deep RNA sequencing data. To define gene family distribution among relatives of <I>H. syriacus</I>, orthologous gene sets containing 164,660 genes in 21,472 clusters were identified by OrthoMCL analysis of five plant species, including <I>H. syriacus</I>, <I>Arabidopsis thaliana, Gossypium raimondii, Theobroma cacao</I> and <I>Amborella trichopoda.</I> We inferred their evolutionary relationships based on divergence times among Malvaceae plant genes and found that gene families involved in flowering regulation and disease resistance were more highly divergent and expanded in <I>H. syriacus</I> than in its close relatives, <I>G. raimondii</I> (DD) and <I>T. cacao</I>. Clustered gene families and gene collinearity analysis revealed that two recent rounds of whole-genome duplication were followed by diploidization of the <I>H. syriacus</I> genome after speciation. Copy number variation and phylogenetic divergence indicates that WGDs and subsequent diploidization led to unequal duplication and deletion of flowering-related genes in <I>H. syriacus</I> and may affect its unique floral morphology.</P>