逆转座子LINE1在Hela细胞中的表达及转录组分析
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摘要
为研究逆转座子LINE1(简称为L1)在Hela细胞内的作用机制,对转染L1的Hela细胞和正常细胞进行转录组测序,通过对转录组数据进行拼接组装,对差异表达基因进行了生物信息学分析。结果表明:试验共筛选出391个差异表达基因,其中45.6%的差异表达基因显著性上调,这些基因通过GO分类注释,可分为14类;通过KEGG对差异基因进行通路富集,表明差异基因主要富集在破骨细胞分化、色氨酸代谢、乙型肝炎、病毒致癌作用和可卡因成瘾等信号通路,发现了一些与细胞黏着连接、表皮相关的基因有差异性表达。研究表明,通过转录组测序,获得了丰富的关于L1在Hela细胞中表达的信息,为进一步研究L1在细胞中的作用机制供了思路和理论依据。
Transcriptional sequencing and bioinformatics analysis of retrotransposon LINE1(L1) as a reverse transcriptase-mediated replicative nucleotide element was performed on Hela cells transfected with L1 and wide-type cells to investigate the molecular mechanism of L1 in Hela cells. Bioinformatics analysis showed that a total of 391 differentially expressed genes were screened by splicing and assembling the transcription data, 45.6% of which were significantly increased. These genes can be classified into 14 categories through the GO classification annotation. KEGG pathway enrichment indicated that differentially expressed genes mainly enriched in osteoclast differentiation, tryptophan metabolism, hepatitis B, viral carcinogenic and cocaine addiction and some of genes were found to be related to the adhesion and epidermis of the cells. Abundant transcriptome information on the expression of L1 in Hela cells by RNA-seq will provide insight and theoretical basis for further study of L1 mechanism in cells.
Transcriptional sequencing and bioinformatics analysis of retrotransposon LINE1(L1) as a reverse transcriptase-mediated replicative nucleotide element was performed on Hela cells transfected with L1 and wide-type cells to investigate the molecular mechanism of L1 in Hela cells. Bioinformatics analysis showed that a total of 391 differentially expressed genes were screened by splicing and assembling the transcription data, 45.6% of which were significantly increased. These genes can be classified into 14 categories through the GO classification annotation. KEGG pathway enrichment indicated that differentially expressed genes mainly enriched in osteoclast differentiation, tryptophan metabolism, hepatitis B, viral carcinogenic and cocaine addiction and some of genes were found to be related to the adhesion and epidermis of the cells. Abundant transcriptome information on the expression of L1 in Hela cells by RNA-seq will provide insight and theoretical basis for further study of L1 mechanism in cells.
引文
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[3] Denli A M,Narvaiza I,Kerman B E,et al.Primate-specific ORF0 contributes to retrotransposon-mediated diversity[J].Cell,2015,163(3):583-593.
[4] Baba Y,Yagi T,Sawayama H,et al.Long interspersed element-1 methylation level as a prognostic biomarker in gastrointestinal cancers[J].Digestion,2018,97(1):26-30.
[5] Zhao K,Du J,Peng Y F,et al.LINE1 contributes to autoimmunity through both RIG-I- and MDA5-mediated RNA sensing pathways[J].Journal of Autoimmunity,2018,90:105-115.
[6] Beck C R,Garcia-Perez J L,Badge R M,et al.LINE-1 elements in structural variation and disease[J].Annual Review of Genomics and Human Genetics,2011,12:187-215.
[7] Fiano V,Zugna D,Grasso C,et al.LINE-1 methylation status in prostate cancer and non-neoplastic tissue adjacent to tumor in association with mortality[J].Epigenetics,2017,12(1):11-18.
[8] Tahara T,Tahara S,Horiguchi N,et al.Methylation status of IGF2 DMR and LINE1 in leukocyte DNA provides distinct clinicopathological features of gastric cancer patients[J].Clinical and Experimental Medicine,2018,18(2):215-220.
[9] Roman-Gomez J,Jimenez-Velasco A,Agirre X,et al.Promoter hypomethylation of the LINE-1 retrotransposable elements activates sense/antisense transcription and marks the progression of chronic myeloid leukemia[J].Oncogene,2005,24(48):7213-7223.
[10] Saito K,Kawakami K,Matsumoto I,et al.Long interspersed nuclear element 1 hypomethylation is a marker of poor prognosis in stage IA non-small cell lung cancer[J].Clinical Cancer Research,2010,16(8):2418-2426.
[11] Svensson V,Vento-Tormo R,Teichmann S A.Exponential scaling of single-cell RNA-seq in the past decade[J].Nature Protocols,2018,13(4):599-604.
[12] Cordaux R,Batzer M A.The impact of retrotransposons on human genome evolution[J].Nature Reviews Genetics,2009,10(10):691-703.
[13] Huang C R L,Schneider A M,Lu Yunqi,et al.Mobile interspersed repeats are major structural variants in the human genome[J].Cell,2010,141(7):1171-1182.
[14] Hancks D C,Kazazian Jr H H.Active human retrotransposons:variation and disease[J].Current Opinion in Genetics & Development,2012,22(3):191-203.
[15] Yang Fan,Deng Xinxian,Ma Wenxiu,et al.The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation[J].Genome Biology,2015,16:52.
[16] Chen A,Beetham H,Black M A,et al.E-cadherin loss alters cytoskeletal organization and adhesion in non-malignant breast cells but is insufficient to induce an epithelial-mesenchymal transition[J].BMC Cancer,2014,14:552.
[17] Kazazian Jr H H,Moran J V.Mobile DNA in health and disease[J].New England Journal of Medicine,2017,377(4):361-370.
[18] Chen Shue,Yu Mengchao,Chu Xu,et al.Cold-induced retrotransposition of fish LINEs[J].Journal of Genetics and Genomics,2017,44(8):385-394.
[19] Iskow R C,Mccabe M T,Mills R E,et al.Natural mutagenesis of human genomes by endogenous retrotransposons[J].Cell,2010,141(7):1253-1261.
[20] Shukla R,Upton K R,Muňoz-Lopez M,et al.Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma[J].Cell,2013,153(1):101-111.
[21] Solyom S,Ewing A D,Rahrmann E P,et al.Extensive somatic L1 retrotransposition in colorectal tumors[J].Genome Research,2012,22(12):2328-2338.
[22] Liu Xinneng,Jin Yongtang,Xu Peiwei,et al.Relationship between Line 1 methylation and clinical data of non-small cell lung cancer[J].Chinese Journal of Medical Genetics,2014,31(3):307-311.
[23] Zelic R,Fiano V,Zugna D,et al.Global hypomethylation (LINE-1) and gene-specific hypermethylation (GSTP1) on initial negative prostate biopsy as markers of prostate cancer on a rebiopsy[J].Clinical Cancer Research,2016,22(4):984-992.
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