위암 세포주에서 DNA double strand break sites 전장 분석 연구
Identification of genome-wide DNA double strand break sites in gastric cancer cell lines
임채현 (chae hyun lim, 포항공과대학교)
- 주제(키워드) DNA double-strand break , DSB , gastric cancer cell lines
- 발행기관 포항공과대학교 일반대학원
- 학위수여년월2013. 8
- 학과 및 전공일반대학원 융합생명공학부
- 세부전공시스템 유전체학
- 저작권포항공과대학교 논문은 저작권에 의해 보호받습니다.
- 초록 moremore
- A DNA double-strand break (DSB) is the most dangerous DNA lesions with serious consequences for cell survival. The non-homologous end joining (NHEJ) repair pathway is the main repair mechanism in mammals. To identify the DNA double-strand break sites which associated with NHEJ in human gastric cance...
- A DNA double-strand break (DSB) is the most dangerous DNA lesions with serious consequences for cell survival. The non-homologous end joining (NHEJ) repair pathway is the main repair mechanism in mammals. To identify the DNA double-strand break sites which associated with NHEJ in human gastric cancer cells, we performed ChIP-Seq using antibodies against Ku 70/80, DNA-PKcs, XRCC4 and γH2AX. The NHEJ pathway-associated proteins were enriched at 253 sites in SNU484 and 202 sites in KATOIII cell lines. In order to identify whether the NHEJ pathway associated protein binding regions are potential DSB sites, we investigated DNase I digestion efficiency and analyzed the features of the single-nucleotide polymorphism (SNP) frequency. The potential DSB sites showed increased DNase I digestion efficiency and SNP frequency. The Gene Ontology (GO) analysis revealed that the “cell cycle” related term in the biological pathway was enriched at the potential DSB sites. The most enriched motif from sequence analysis of the potential DSB sites was the STAT5 binding sequence. For validation of the potential DSB sites, we performed ChIP-PCR and detected positive enrichment at selected potential DSB sites. The increased level of specificity protein 1 (SP1) was reported in the diffuse type of gastric cancer cells such as SNU484 and KATOIII and our potential DSB site was further examined to see their overlap with SP1 binding sites. Relatively high enrichment of SP1 at potential DSB sites was detected in diffuse types rather than intestinal types. We could conclude that the DSBs spontaneously occurred without any external stimuli and the NHEJ pathway related proteins were bound to the DSB sites. From the genome-wide mapping and sequence analysis in gastric cancer cells, the true spontaneous DSB sites were identified and increased the possibility of developing new cancer diagnostic markers using the DSB sites.