Non-coding RNAs in marine Synechococcus and their regulation under environmentally relevant stress conditions

Regulatory small RNAs (sRNAs) have crucial roles in the adaptive responses of bacteria to changes in the environment. Thus far, potential regulatory RNAs have been studied mainly in marine picocyanobacteria in genetically intractable Prochlorococcus, rendering their molecular analysis difficult. Synechococcus sp. WH7803 is a model cyanobacterium, representative of the picocyanobacteria from the mesotrophic areas of the ocean. Similar to the closely related Prochlorococcus it possesses a relatively streamlined genome and a small number of genes, but is genetically tractable. Here, a comparative genome analysis was performed for this and four additional marine Synechococcus to identify the suite of possible sRNAs and other RNA elements. Based on the prediction and on complementary microarray profiling, we have identified several known as well as 32 novel sRNAs. Some sRNAs overlap adjacent coding regions, for instance for the central photosynthetic gene psbA. Several of these novel sRNAs responded specifically to environmentally relevant stress conditions. Among them are six sRNAs changing their accumulation level under cold stress, six responding to high light and two to iron limitation. Target predictions suggested genes encoding components of the light-harvesting apparatus as targets of sRNAs originating from genomic islands and that one of the iron-regulated sRNAs might be a functional homolog of RyhB. These data suggest that marine Synechococcus mount adaptive responses to these different stresses involving regulatory sRNAs.     

Review of Non-coding RNAs and the epigenetic regulation of gene expression

Advances in sequencing and detection technology over the past two decades, highlighted by the data explosion brought about by the human genome project, have transformed what was previously assumed to be a relatively simple genetic landscape into a new picture where the so-called “dark matter” of the genome has stolen the spotlight from the not so hip protein-coding genes. The simplified central dogma of molecular biology, in which a gene encodes for a protein via a messenger RNA (mRNA), is still at the core of genetics but is now caught in a much more complex web of regulation by the genomic region previously known as “junk” DNA. Books such as Non-coding RNAs and epigenetic regulation of gene expression, published by Caister Academic Press, become essential guidelines to help us understand the current status of the very fast paced field of RNA research, which has only just started to uncover the roles of non-coding RNAs (ncRNAs) in the regulation of gene expression.     

Functional roles of non-coding Y RNAs

Non-coding RNAs are involved in a multitude of cellular processes but the biochemical function of many small non-coding RNAs remains unclear. The family of small non-coding Y RNAs is conserved in vertebrates and related RNAs are present in some prokaryotic species. Y RNAs are also homologous to the newly identified family of non-coding stem-bulge RNAs (sbRNAs) in nematodes, for which potential physiological functions are only now emerging. Y RNAs are essential for the initiation of chromosomal DNA replication in vertebrates and, when bound to the Ro60 protein, they are involved in RNA stability and cellular responses to stress in several eukaryotic and prokaryotic species. Additionally, short fragments of Y RNAs have recently been identified as abundant components in the blood and tissues of humans and other mammals, with potential diagnostic value. While the number of functional roles of Y RNAs is growing, it is becoming increasingly clear that the conserved structural domains of Y RNAs are essential for distinct cellular functions. Here, we review the biochemical functions associated with these structural RNA domains, as well as the functional conservation of Y RNAs in different species. The existing biochemical and structural evidence supports a domain model for these small non-coding RNAs that has direct implications for the modular evolution of functional non-coding RNAs.     

Long Non-coding RNAs in the Cytoplasm

An enormous amount of long non-coding RNAs (lncRNAs) transcribed from eukaryotic genome are important regulators in different aspects of cellular events. Cytoplasm is the residence and the site of action for many lncRNAs. The cytoplasmic lncRNAs play indispensable roles with multiple molecular mechanisms in animal and human cells. In this review, we mainly talk about functions and the underlying mechanisms of lncRNAs in the cytoplasm. We highlight relatively well-studied examples of cytoplasmic lncRNAs for their roles in modulating mRNA stability, regulating mRNA translation, serving as competing endogenous RNAs, functioning as precursors of microRNAs, and mediating protein modifications. We also elaborate the perspectives of cytoplasmic lncRNA studies.     

非编码RNA与细胞自噬调控

细胞自噬是真核生物细胞中高度保守的重要代谢途径。该途径是将细胞内有害或不需要的大分子分解并回收,从而使细胞在生长或环境改变导致的应激和压力条件下获得生存优势。近年越来越多的证据表明,非编码RNA,包括微RNA(microRNA,miRNA)和长非编码RNA(long non-coding RNA,lncRNA),在自噬过程中发挥了重要的作用。本文综述了miRNA和lncRNA在多种细胞环境中对细胞自噬的调控机制,并讨论了这些自噬相关的非编码RNA在疾病分子诊断、分类和预后中的作用,及其作为疾病治疗靶标的可能性。     

Non-coding RNAs in human disease

The relevance of the non-coding genome to human disease has mainly been studied in the context of the widespread disruption of microRNA (miRNA) expression and function that is seen in human cancer. However, we are only beginning to understand the nature and extent of the involvement of non-coding RNAs (ncRNAs) in disease. Other ncRNAs, such as PIWI-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), transcribed ultraconserved regions (T-UCRs) and large intergenic non-coding RNAs (lincRNAs) are emerging as key elements of cellular homeostasis. Along with microRNAs, dysregulation of these ncRNAs is being found to have relevance not only to tumorigenesis, but also to neurological, cardiovascular, developmental and other diseases. There is great interest in therapeutic strategies to counteract these perturbations of ncRNAs.     

非编码RNA与病毒性心肌炎

病毒性心肌炎(Viral myocarditis,VMC)是一种由病毒感染所引起的以心肌细胞炎症为特征的疾病。由于病毒性心肌炎的发病机制尚未完全研究清楚,因此该病的诊断及治疗对于临床医生来说仍具有极大的挑战性。非编码RNAs (Non-coding RNAs,ncRNAs)是一类不具有编码蛋白质功能的RNA,越来越多的研究表明ncRNAs参与到调控VMC的发生和发展过程中,这可能成为VMC的治疗或诊断的新研究靶点。文中对近3年来关于ncRNAs在VMC的发病机制及诊断中可能发挥的作用进行了综述。     

Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs

Recent advances have fuelled rapid growth in our appreciation of the tremendous number, diversity and biological importance of non-coding (nc)RNAs. Because ncRNAs typically function as ribonucleoprotein (RNP) complexes and not as naked RNAs, understanding their biogenesis is crucial to comprehending their regulation and function. The small nuclear and small nucleolar RNPs are two well studied classes of ncRNPs with elaborate assembly and trafficking pathways that provide paradigms for understanding the biogenesis of other ncRNPs.     

生物信息学在长非编码RNA研究中的应用

长非编码RNA(lncRNA)是一类转录本长度大于200个核苷酸的非编码RNA分子,它们在细胞生命活动中的许多关键过程中起到重要调控作用。近年来关于lncRNA的研究发展迅速,涌现出一批用于lncRNA的鉴定、定量、结构分析以及功能预测的生物信息学工具和数据库,本文将对这些lncRNA研究的资源进行综述。