顺式天然反义转录本（cis-NATs）组学筛查及功能诠释初探

发布时间：2018-01-13 01:31

本文关键词：顺式天然反义转录本（cis-NATs）组学筛查及功能诠释初探　出处：《南昌大学》2012年硕士论文　论文类型：学位论文

【摘要】：目的：顺式天然反义转录本（cis-NAT）是指自然状态下源于基因相同区域的反义RNA,可与正义转录本形成正义反义转录本对（SA pair）。这种转录方式在真核生物的转录及转录后调控过程中发挥重要作用，，可影响多种生理或病理过程（如肿瘤）。近来测序数据的累积和高通量芯片技术的出现使利用组学方法系统研究cis-NATs成为可能。然而，目前这类研究仅限于少数模式生物的编码基因，而基于非编码序列的次代转录组测序数据分析方案尚缺乏。方法：本研究首先设计了基于Ensembl基因诠释信息的非编码cis-NATs的筛查流程，在灵长目和啮齿目18个物种中进行搜索。考虑到次代测序能够提供更为丰富的组织转录信息，本研究同时研发了一套基于次代测序的新cis-NATs发现流程（Gene2DGE），并使用该流程在human143B细胞的ssRNA-seq（strand-specific RNA-seq）数据集中进行搜索。最后基于候选的cis-NATs进行验证和功能学实验。结果：以人类为例，本研究在基因组中发现18,510个SA基因对，并鉴定出11,493个为非编码cis-NATs，占所有cis-NATs的62.1%，提示非编码基因是cis-NATs的重要来源。而在其他物种中，所发现的非编码相关的数据均明显低于人类。同时我们的筛查还发现一定数目的非编码Cis-NATs具备物种间的保守性，提示非人物种中的非编cis-NATs尚待深入研究。鉴定出73个新的与cis-NATs相关的转录活性区域；其中43个位于线粒体染色体上，而基于大鼠的组织mRNA-seq以及相应的细胞学实验提示：新的线粒体cis-NATs具有保守性，可能在线粒体中发挥重要功能。结论：1.基于Ensembl基因诠释系统和本实验室研发程序筛查出高覆盖度的cis-NATs，并筛查同源性和保守型高SA基因。2.新的高通量核酸测序技术在已有诠释信息的基础上提供了新的cis-NATs，RNA-seq的结果极大提高对于非编码cis-NATs的发现。3.验证实验和功能实验提示线粒体中的新cis-NATs确实存在并可能具有重要的生物功能。
[Abstract]:Objective: cis-natural antisense transcripts (cis-NATs) are antisense RNA derived from the same region of gene in natural state. Sense antisense transcripts can be formed with sense transcripts on SA pairs.This transcription mode plays an important role in the transcriptional and post-transcriptional regulation of eukaryotes. The recent accumulation of sequencing data and the advent of high-throughput microarray techniques have made it possible to systematically study cis-NATs using a genomics approach. At present, this kind of research is limited to the coding genes of a few model organisms, but the non-coding sequence based secondary generation transposed sequence analysis scheme is still lacking. Methods: in this study, we first designed the screening process of non-coding cis-NATs based on Ensembl gene interpretation information. Search in 18 species of primates and rodents. Considering that secondary generation sequencing can provide richer tissue transcription information. In this study, we also developed a new cis-NATs discovery process based on the next generation sequencing, Gene2DGE). And use this process in human143B cell ssRNA-seq(strand-specific RNA-seq). Finally, based on candidate cis-NATs for verification and functional experiments. Results: in this study, 18,510 pairs of SA genes were found in human genome, and 11,493 pairs were identified as non-coding cis-NATs. It accounts for 62.1% of all cis-NATs, suggesting that non-coding genes are an important source of cis-NATs, while in other species. The uncoded data found were significantly lower than those in humans. At the same time, we also found that a certain number of non-coding Cis-NATs have inter-species conservation. It is suggested that the non-coding cis-NATs in non-human species needs further study and 73 new transcriptional active regions related to cis-NATs have been identified. 43 of them were located on mitochondria chromosomes, and the tissue mRNA-seq based on rat and corresponding cytological experiments indicated that the new mitochondrial cis-NATs was conserved. It may play an important role in mitochondria. Conclusion 1. Cis-NATs with high coverage was screened based on Ensembl gene interpretation system and our laboratory development program. And screening homologous and conserved high SA gene. 2. The new high-throughput nucleic acid sequencing technology provides a new cis-NATs based on the existing interpretation information. The results of RNA-seq greatly improve the discovery of non-coding cis-NATs. 3. Validation and functional experiments suggest that new cis-NATs in mitochondria exists and may be important. Biological function.
【学位授予单位】：南昌大学
【学位级别】：硕士
【学位授予年份】：2012
【分类号】：R346

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