Understanding the complexity of the transcriptomes in E. coli K12

了解大肠杆菌 K12 转录组的复杂性

基本信息

批准号：
9243267
负责人：
Zhengchang Su
金额：
$ 28.74万
依托单位：
UNIVERSITY OF NORTH CAROLINA CHARLOTTE
依托单位国家：
美国
项目类别：
财政年份：
2014
资助国家：
美国
起止时间：
2014-06-01 至 2019-03-31
项目状态：
已结题

项目摘要

DESCRIPTION (provided by applicant): Using high density tilling microarray and/or directional RNA-seq techniques, it was recently found that alternative and varying-level (dynamic) transcriptions within operons are highly prevalent and the non-coding RNA (ncRNA) and anti-sense RNA (asRNA) transcriptions are also highly pervasive. Thus prokaryotic transcriptomes seem to be more complex than previously thought. However, little is known about the patterns and rules of the transcriptomic complexity and its biological implications, as well as its underlying molecular mechanisms. Moreover, the generality of such transcriptomic complexity remains unknown because inconsistent and even contradictory results have been reported even in the same strains. Furthermore, the investigation of the transcriptomic complexity in prokaryotes has been hindered by the highly biased sequence reads of the current directional RNA-seq techniques that is further confounded in prokaryotes for the highly labile nature and extremely low concentrations of their RNAs in the cells, and the lack of an effective method for their enrichment, leading to highly non-uniform read coverage, and even numerous uncovered gaps in transcribed regions. Such highly non-uniform read coverage and prevalent uncovered gap make it very difficult to assembly full-length transcripts, let alone to detect dynamic transcriptions along operons. Consequently, little is known about the transcriptomic complexity in many medically important prokaryotes, and even in the most widely-studied model bacterium E. coli K12. This project plans to address these problems using E. coli K12 as the model system. The specific aims are: 1) to develop an algorithm and tool for sufficiently correcting the read biases in the current RNA-seq techniques; 2) to develop an accurate and efficient algorithm and tool for simultaneously assembling prokaryotic full-length transcripts and detecting possible dynamic transcriptions along the assembled transcripts using RNA-seq short reads; 3) to characterize the patterns and biological roles of alternative and dynamic operon utilizations as well as asRNA and ncRNA transcriptions in E. coli K12. Accomplishment of this project will not only further our understanding of the global architecture and complexity of the transcriptomes in E. coli K12, but also will provide the research community with computational tools and experimental methods to address the similar questions in other prokaryotes, thereby facilitating the community efforts to decipher gene regulatory networks in all sequenced prokaryotic genomes. A better understanding of the gene regulatory networks of medically, agriculturally and industriously important prokaryotes will enhance our ability to prevent and cure infectious diseases, and to produce foods and other important products.>

描述（由申请人提供）：使用高密度填充微阵列和/或定向RNA-seq技术，最近发现操纵子内的替代和变化水平（动态）转录非常普遍，并且非编码RNA（ncRNA）和反义 RNA (asRNA) 转录也非常普遍。因此，原核转录组似乎比以前想象的更复杂。然而，人们对转录组复杂性的模式和规则及其生物学意义及其潜在的分子机制知之甚少。此外，这种转录组复杂性的普遍性仍然未知，因为即使在相同菌株中也报道了不一致甚至矛盾的结果。此外，对原核生物转录组复杂性的研究受到当前定向 RNA-seq 技术的高度偏差序列读取的阻碍，而原核生物中的 RNA 的高度不稳定性质和细胞中 RNA 浓度极低，进一步混淆了原核生物的转录组复杂性。缺乏有效的富集方法，导致读数覆盖高度不均匀，甚至转录区域中存在大量未发现的空白。这种高度不均匀的读数覆盖和普遍存在的未覆盖间隙使得组装全长转录本非常困难，更不用说检测沿操纵子的动态转录了。因此，人们对许多医学上重要的原核生物，甚至是研究最广泛的模型细菌大肠杆菌 K12 的转录组复杂性知之甚少。该项目计划使用大肠杆菌 K12 作为模型系统来解决这些问题。具体目标是：1）开发一种算法和工具，以充分纠正当前RNA-seq技术中的read偏差； 2）开发准确高效的算法和工具，用于同时组装原核全长转录本并使用RNA-seq短读长检测组装转录本上可能的动态转录； 3) 表征大肠杆菌 K12 中替代和动态操纵子利用以及 asRNA 和 ncRNA 转录的模式和生物学作用。该项目的完成不仅将进一步加深我们对大肠杆菌K12转录组的整体结构和复杂性的理解，而且将为研究界提供计算工具和实验方法来解决其他原核生物中的类似问题，从而促进社区努力破译所有已测序的原核基因组中的基因调控网络。更好地了解医学、农业和工业上重要的原核生物的基因调控网络将增强我们预防和治疗传染病以及生产食品和其他重要产品的能力。>