Diverse ncRNAs Research Articles

RNA-Based Technologies for Engineering Plant Virus Resistance.

In recent years, non-coding RNAs (ncRNAs) have gained unprecedented attention as new and crucial players in the regulation of numerous cellular processes and disease responses. In this review, we describe how diverse ncRNAs, including both small RNAs and long ncRNAs, may be used to engineer resistance against plant viruses. We discuss how double-stranded RNAs and small RNAs, such as artificial microRNAs and trans-acting small interfering RNAs, either produced in transgenic plants or delivered exogenously to non-transgenic plants, may constitute powerful RNA interference (RNAi)-based technology that can be exploited to control plant viruses. Additionally, we describe how RNA guided CRISPR-CAS gene-editing systems have been deployed to inhibit plant virus infections, and we provide a comparative analysis of RNAi approaches and CRISPR-Cas technology. The two main strategies for engineering virus resistance are also discussed, including direct targeting of viral DNA or RNA, or inactivation of plant host susceptibility genes. We also elaborate on the challenges that need to be overcome before such technologies can be broadly exploited for crop protection against viruses.

Plant Noncoding RNAs: Hidden Players in Development and Stress Responses.

A large and significant portion of eukaryotic transcriptomes consists of noncoding RNAs (ncRNAs) that have minimal or no protein-coding capacity but are functional. Diverse ncRNAs, including both small RNAs and long ncRNAs (lncRNAs), play essential regulatory roles in almost all biological processes by modulating gene expression at the transcriptional and posttranscriptional levels. In this review, we summarize the current knowledge of plant small RNAs and lncRNAs, with a focus on their biogenesis, modes of action, local and systemic movement, and functions at the nexus of plant development and environmental responses. The complex connections among small RNAs, lncRNAs, and small peptides in plants are also discussed, along with the challenges of identifying and investigating new classes of ncRNAs.

MNDR v2.0: an updated resource of ncRNA-disease associations in mammals.

Accumulating evidence suggests that diverse non-coding RNAs (ncRNAs) are involved in the progression of a wide variety of diseases. In recent years, abundant ncRNA–disease associations have been found and predicted according to experiments and prediction algorithms. Diverse ncRNA–disease associations are scattered over many resources and mammals, whereas a global view of diverse ncRNA–disease associations is not available for any mammals. Hence, we have updated the MNDR v2.0 database (www.rna-society.org/mndr/) by integrating experimental and prediction associations from manual literature curation and other resources under one common framework. The new developments in MNDR v2.0 include (i) an over 220-fold increase in ncRNA–disease associations enhancement compared with the previous version (including lncRNA, miRNA, piRNA, snoRNA and more than 1400 diseases); (ii) integrating experimental and prediction evidence from 14 resources and prediction algorithms for each ncRNA–disease association; (iii) mapping disease names to the Disease Ontology and Medical Subject Headings (MeSH); (iv) providing a confidence score for each ncRNA–disease association and (v) an increase of species coverage to six mammals. Finally, MNDR v2.0 intends to provide the scientific community with a resource for efficient browsing and extraction of the associations between diverse ncRNAs and diseases, including >260 000 ncRNA–disease associations.

Mammalian ncRNA-disease repository: a global view of ncRNA-mediated disease network

Dear Editor Recently, substantial studies have begun to explore the functional diversity and mechanistic roles of ncRNAs in mammals.1 Now, it has become increasingly apparent that ncRNAs are involved in multiple major biological processes, such as developmental timing, fat metabolism and cell death.2 Furthermore, the epigenetic and genetic defects in ncRNAs and their processing machinery have been implicated in the etiology of many forms of diseases.3 Several databases that documented the relevance of the microRNAs(miRNAs) to diseases have been constructed and provided useful results.4, 5 However, miRNAs are just the tip of the iceberg, other ncRNAs such as long non-coding RNAs (lncRNAs), PIWI-interacting RNAs (piRNAs) and small nucleolar RNAs (snoRNAs) have also been demonstrated to contribute to diseases.3, 6 Accumulated evidence suggest the diverse non-coding RNAs (ncRNAs) involved in a wide variety of diseases progression.3, 6, 7 It is a key challenge for understanding the precise behavior of diverse ncRNAs in mammalian diseases and deciphering the cross-regulations among disease-associated ncRNAs. Because there was no repository focused on diverse ncRNA-disease relationships in mammals, we have developed a manually curated diverse ncRNA-disease repository (MNDR, www.rna-society.org/mndr/) by integrating evidence in three mammals. Totally, 807 lncRNA-associated, 229 miRNA-associated, 13 piRNA-associated and 100 snoRNA-associated entries for 1149 curated entries were documented for three mammals (866 Homo sapiens-associated, 251 Mus musculus-associated and 32 Rattus norvegicus-associated entries) (Table 1). Table 1 The statistics of the ncRNA-disease entries in MNDR database Recent investigations indicated there are complex regulations among diverse ncRNAs and protein-coding genes. Such as, PTEN gene and the PTEN pseudogenes (ptenp1, one of lncRNAs) share a high degree of sequence homology, changes in ptenp1 expression levels indirectly affect PTEN expression by sequestering PTEN-targeting miRNAs.8 Thus understanding the mutual regulating pattern among diverse ncRNAs and protein-coding genes, particularly in disease conditions, is a key challenge. Thus, MNDR is not only a knowledge depository but providing us a good opportunity to view the ncRNA-mediated disease network globally (in visualization page: www.rna-society.org/mndr/visualization.html). Diverse ncRNAs and interaction genes were represented as nodes and the regulations were denoted as edges. Based on such a simplified ncRNA-mediated disease network, interesting observations have been achieved. The result showed that snoRNA htr, as a hub node, has intensively linked to 21 interaction genes in the network. More important, through BCL2, BCL2L1 and BAX, the snoRNA htr can communicate with the lncRNA malat1 (Supplementary Figure 1). Another example is snoRNA htr and lncRNA h19 are linked by E2F1 and MYC. When combined with human disease-associated miRNA evidence from mir2disease database, lncRNAs, miRNAs and snoRNAs, together with their interaction/target genes, can be integrated into bigger expanding ncRNA-mediated disease network. The biggest sub-network has 129 nodes and 149 edges, involving 33 lncRNAs, 1 snoRNA, 19 miRNAs and 76 interaction protein-coding genes(Supplementary Figure 2). In this network, more regulations among diverse ncRNAs directly or indirectly via intermediate genes, lncRNA dgcr5, har1a and har1b, were connected with hsa-mir-21 via intermediate gene REST. Interestingly, hsa-mir-21 and snoRNA htr were linked by key anti-apoptosis gene BCL2. Similar results were observed that lncRNA dgcr5, har1a and har1b can also communicate with snoRNA htr through alternative route NFKB1-hsa-mir-9-REST. Hence, according to current data, the two pivot protein-coding genes (BCL2 and NFKB1) and several ncRNAs (lncRNA malat1, snoRNA htr and miRNA hsa-mir-21, has-mir-9) collectively play an important role in the ncRNA-mediated disease network (Supplementary Figure 2). Importantly, the crosstalk between lncRNA malat1 and miRNA hsa-mir-21 can be found conserved in mouse ncRNA-mediated disease network. Above observations indicated diverse ncRNAs could communicate with each other in disease state through some disease-associated genes in mammals, highlighting the complexity, conservative and plasticity of the regulatory relationships between diverse ncRNAs and protein-coding genes in diseases.

Animal snoRNAs and scaRNAs with exceptional structures

The overwhelming majority of small nucleolar RNAs (snoRNAs) fall into two clearly defined classes characterized by distinctive secondary structures and sequence motifs. A small group of diverse ncRNAs, however, shares the hallmarks of one or both classes of snoRNAs but differs substantially from the norm in some respects. Here, we compile the available information on these exceptional cases, conduct a thorough homology search throughout the available metazoan genomes, provide improved and expanded alignments, and investigate the evolutionary histories of these ncRNA families as well as their mutual relationships.