AIM:To identify the novel methylation-silenced gene pentraxin 3(PTX3) in esophageal squamous cell carcinoma(ESCC).METHODS:PTX3 mRNA expression was examined in six human ESCC cell lines,one human immortalized normal es...AIM:To identify the novel methylation-silenced gene pentraxin 3(PTX3) in esophageal squamous cell carcinoma(ESCC).METHODS:PTX3 mRNA expression was examined in six human ESCC cell lines,one human immortalized normal esophageal epithelial cell line,primary ESCC tumor tissue,and paired adjacent nontumor tissue using reverse transcription polymerase chain reaction(RTPCR).Semi-quantitative immunohistochemistry was used to examine cellular localisation and protein levels.Methylation specific PCR and bisulphite genomic sequencing were employed to investigate the methylation of the candidate gene.RESULTS:In the majority of ESCC cell lines,we found that PTX3 expression was down-regulated due to gene promoter hypermethylation,which was further confirmed by bisulphite genomic sequencing.Demethylation treatment with 5-aza-2'-deoxycytidine restored PTX3 mRNA expression in ESCC cell lines.Methylation was more common in tumor tissues(85%) than in adjacent nontumor tissues(25%)(P < 0.01).CONCLUSION:PTX3 is down-regulated through promoter hypermethylation in ESCC,and could potentially serve as a biomarker of ESCC.展开更多
Sequence assembling is an important step for bioinformatics study.With the help of next generation sequencing(NGS)technology,high throughput DNA fragment(reads)can be randomly sampled from DNA or RNA molecular sequenc...Sequence assembling is an important step for bioinformatics study.With the help of next generation sequencing(NGS)technology,high throughput DNA fragment(reads)can be randomly sampled from DNA or RNA molecular sequence.However,as the positions of reads being sampled are unknown,assembling process is required for combining overlapped reads to reconstruct the original DNA or RNA sequence.Compared with traditional Sanger sequencing methods,although the throughput of NGS reads increases,the read length is shorter and the error rate is higher.It introduces several problems in assembling.Moreover,paired-end reads instead of single-end reads can be sampled which contain more information.The existing assemblers cannot fully utilize this information and fails to assemble longer contigs.In this article,we will revisit the major problems of assembling NGS reads on genomic,transcriptomic,metagenomic and metatranscriptomic data.We will also describe our IDBA package for solving these problems.IDBA package has adopted several novel ideas in assembling,including using multiple k,local assembling and progressive depth removal.Compared with existence assemblers,IDBA has better performance on many simulated and real sequencing datasets.展开更多
基金Supported by National High Technology Research and Development Program of China (863 Program),No. 2007AA02Z4Z4China Postdoctoral Science Foundation,No. 20090460394Beijing Municipal Natural Science Foundation,No. 7072022
文摘AIM:To identify the novel methylation-silenced gene pentraxin 3(PTX3) in esophageal squamous cell carcinoma(ESCC).METHODS:PTX3 mRNA expression was examined in six human ESCC cell lines,one human immortalized normal esophageal epithelial cell line,primary ESCC tumor tissue,and paired adjacent nontumor tissue using reverse transcription polymerase chain reaction(RTPCR).Semi-quantitative immunohistochemistry was used to examine cellular localisation and protein levels.Methylation specific PCR and bisulphite genomic sequencing were employed to investigate the methylation of the candidate gene.RESULTS:In the majority of ESCC cell lines,we found that PTX3 expression was down-regulated due to gene promoter hypermethylation,which was further confirmed by bisulphite genomic sequencing.Demethylation treatment with 5-aza-2'-deoxycytidine restored PTX3 mRNA expression in ESCC cell lines.Methylation was more common in tumor tissues(85%) than in adjacent nontumor tissues(25%)(P < 0.01).CONCLUSION:PTX3 is down-regulated through promoter hypermethylation in ESCC,and could potentially serve as a biomarker of ESCC.
基金supported in part by Hong Kong GRF HKU 7111/12E, 719611EShenzhen Basic Research Project JCYJ20120618143038947 (SIRI/04/04/2012/05)Outstanding Researcher Award (102009124).
文摘Sequence assembling is an important step for bioinformatics study.With the help of next generation sequencing(NGS)technology,high throughput DNA fragment(reads)can be randomly sampled from DNA or RNA molecular sequence.However,as the positions of reads being sampled are unknown,assembling process is required for combining overlapped reads to reconstruct the original DNA or RNA sequence.Compared with traditional Sanger sequencing methods,although the throughput of NGS reads increases,the read length is shorter and the error rate is higher.It introduces several problems in assembling.Moreover,paired-end reads instead of single-end reads can be sampled which contain more information.The existing assemblers cannot fully utilize this information and fails to assemble longer contigs.In this article,we will revisit the major problems of assembling NGS reads on genomic,transcriptomic,metagenomic and metatranscriptomic data.We will also describe our IDBA package for solving these problems.IDBA package has adopted several novel ideas in assembling,including using multiple k,local assembling and progressive depth removal.Compared with existence assemblers,IDBA has better performance on many simulated and real sequencing datasets.
