{"title":"转座因子和外显子之间的融合转录本能否在小鼠(小家鼠)中产生pirna ?","authors":"Bairon Hernández, Gonzalo Riadi","doi":"10.3390/MOL2NET-04-06118","DOIUrl":null,"url":null,"abstract":"A Fusion Transcript (FT) is a RNA molecule product of cis/trans-splicing of two differently annotated elements, either genes or Transposable Elements (TE). It may be coding or non-coding. There are many examples of gene-gene FTs in cancer. Lately, FTs have been also reported in control conditions in different organisms. Moreover, other authors argue that a FT might be a product of artifacts, either experimental or computational. In a recent work, we have developed a pipeline to predict FTs between an exon and a TE. In it, we have found 813 exon-TE FTs from 438 different genes. This prediction was made starting with RNA-seq data from Nucleus Accumbens in mouse (M. musculus) treated with cocaine vs. control. From that group, 20 candidates were taken and all were validated experimentally through PCR. However, the depth of sequencing is low. We can further gather supporting evidence of their expression by filtering the candidates, which could be regulated by small RNAs, the same way piRNAs regulate TEs. We aligned around 5 million mouse piRNAs against the 813 mouse exon-TE Fts, identifying 112 piRNAs that map only across the juction point of exon-TE FTs, in 56 genes. These piRNAs do not map on the reference genome or on the transcriptome sequences. These results suggest that either: 1) piRNAs might regulate the expression of exon-TE FTs, or 2) the exon-TE Fts may be the origin of piRNAs. In either case, they suggest that exon-TE FTs may express in germline. Grant Fondecyt #11140869.","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2019-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Can Fusion Transcripts between a transposable element and an exon generate piRNAs in mouse (Mus musculus)?\",\"authors\":\"Bairon Hernández, Gonzalo Riadi\",\"doi\":\"10.3390/MOL2NET-04-06118\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"A Fusion Transcript (FT) is a RNA molecule product of cis/trans-splicing of two differently annotated elements, either genes or Transposable Elements (TE). It may be coding or non-coding. There are many examples of gene-gene FTs in cancer. Lately, FTs have been also reported in control conditions in different organisms. Moreover, other authors argue that a FT might be a product of artifacts, either experimental or computational. In a recent work, we have developed a pipeline to predict FTs between an exon and a TE. In it, we have found 813 exon-TE FTs from 438 different genes. This prediction was made starting with RNA-seq data from Nucleus Accumbens in mouse (M. musculus) treated with cocaine vs. control. From that group, 20 candidates were taken and all were validated experimentally through PCR. However, the depth of sequencing is low. We can further gather supporting evidence of their expression by filtering the candidates, which could be regulated by small RNAs, the same way piRNAs regulate TEs. We aligned around 5 million mouse piRNAs against the 813 mouse exon-TE Fts, identifying 112 piRNAs that map only across the juction point of exon-TE FTs, in 56 genes. These piRNAs do not map on the reference genome or on the transcriptome sequences. These results suggest that either: 1) piRNAs might regulate the expression of exon-TE FTs, or 2) the exon-TE Fts may be the origin of piRNAs. In either case, they suggest that exon-TE FTs may express in germline. Grant Fondecyt #11140869.\",\"PeriodicalId\":20475,\"journal\":{\"name\":\"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2019-01-05\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.3390/MOL2NET-04-06118\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3390/MOL2NET-04-06118","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
摘要
融合转录物(FT)是两种不同注释元件顺式/反式剪接的RNA分子产物,可以是基因或转座元件(TE)。它可能是编码的,也可能是非编码的。癌症中有很多基因-基因FTs的例子。最近,在不同生物的对照条件下也报道了FTs。此外,其他作者认为,金融时报可能是人工产物,要么是实验性的,要么是计算性的。在最近的一项工作中,我们开发了一个管道来预测外显子和TE之间的ft。在其中,我们发现了来自438个不同基因的813个外显子te ft。这一预测是从可卡因治疗小鼠伏隔核与对照组的RNA-seq数据开始的。从该组中选取20个候选样本,全部通过PCR进行实验验证。但测序深度较低。通过筛选候选基因,我们可以进一步收集支持它们表达的证据,这些候选基因可能受到小rna的调节,就像pirna调节TEs一样。我们将大约500万个小鼠pirna与813个小鼠外显子- te ft进行比对,鉴定出56个基因中112个pirna仅在外显子- te ft的连接点上定位。这些pirna不映射到参考基因组或转录组序列上。这些结果表明:1)pirna可能调节外显子- te ft的表达,或2)外显子- te ft可能是pirna的起源。在这两种情况下,他们认为外显子- te ft可能在种系中表达。Grant Fondecyt #11140869。
Can Fusion Transcripts between a transposable element and an exon generate piRNAs in mouse (Mus musculus)?
A Fusion Transcript (FT) is a RNA molecule product of cis/trans-splicing of two differently annotated elements, either genes or Transposable Elements (TE). It may be coding or non-coding. There are many examples of gene-gene FTs in cancer. Lately, FTs have been also reported in control conditions in different organisms. Moreover, other authors argue that a FT might be a product of artifacts, either experimental or computational. In a recent work, we have developed a pipeline to predict FTs between an exon and a TE. In it, we have found 813 exon-TE FTs from 438 different genes. This prediction was made starting with RNA-seq data from Nucleus Accumbens in mouse (M. musculus) treated with cocaine vs. control. From that group, 20 candidates were taken and all were validated experimentally through PCR. However, the depth of sequencing is low. We can further gather supporting evidence of their expression by filtering the candidates, which could be regulated by small RNAs, the same way piRNAs regulate TEs. We aligned around 5 million mouse piRNAs against the 813 mouse exon-TE Fts, identifying 112 piRNAs that map only across the juction point of exon-TE FTs, in 56 genes. These piRNAs do not map on the reference genome or on the transcriptome sequences. These results suggest that either: 1) piRNAs might regulate the expression of exon-TE FTs, or 2) the exon-TE Fts may be the origin of piRNAs. In either case, they suggest that exon-TE FTs may express in germline. Grant Fondecyt #11140869.