Long non-coding RNA-mediated mechanisms independent of the RNAi pathway in animals and plants

Au, Phil Chi Khang; Zhu, Qian; Dennis, E. S.; Wang, Ming-Bo

doi:10.4161/rna.8.3.14382

Cited by 41 publications

(23 citation statements)

References 122 publications

(154 reference statements)

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“…Although only a limited number of long ncRNAs have been characterized in some detail in plants, fungi, and metazoans, the majority have been shown to affect mRNA transcript levels (Au et al, 2011;Kim and Sung, 2012;Rinn and Chang, 2012). Long ncRNAs involved in the repression of transcription are predominant and implicate diverse mechanisms, Quantitative RT-PCR was performed on root RNAs purified from six Suc gradient fractions to quantify transcripts from PHO1;2 and PHO1;3 in wild-type (WT) plants grown in Pi-sufficient or Pi-deficient media (A), PHO1;2 in the wild type, in the cis-NAT PHO1;2 RNAi lines Ri1 and Ri2, and in the lines OX8 and OX32 overexpressing a modified NAT PHO1;2 , with all plants grown in Pi-sufficient medium (B), and the endogenous cis-NAT PHO1;2 in wild-type plants grown on Pi-sufficient or Pi-deficient media, and both the endogenous and transgenic NAT PHO1;2 in the OX8 and OX32 lines grown on Pi-sufficient conditions (C).…”

Section: Discussionmentioning

confidence: 99%

“…Studies performed mainly in yeast and animals have revealed that NATs can participate in a broad range of regulatory events, including transcriptional interference, RNA masking-induced alternative splicing, X chromosome inactivation, genomic imprinting, RNA editing, DNA methylation, and siRNA-induced gene silencing (Faghihi and Wahlestedt, 2009;Au et al, 2011;Rinn and Chang, 2012). While the expression of some NATs has been associated with transcriptional activation, NAT expression primarily results in the suppression of gene expression and involves pathways leading to transcriptional downregulation, such as histone modification and the recruitment of chromatin modifiers, or posttranscriptional downregulation, such as the generation of siRNAs (Ponting et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

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A Rice cis-Natural Antisense RNA Acts as a Translational Enhancer for Its Cognate mRNA and Contributes to Phosphate Homeostasis and Plant Fitness

et al. 2013

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ORCID ID: 0000-0002-9562-1226 (M.J.).cis-natural antisense transcripts (cis-NATs) are widespread in plants and are often associated with downregulation of their associated sense genes. We found that a cis-NAT positively regulates the level of a protein critical for phosphate homeostasis in rice (Oryza sativa). PHOSPHATE1;2 (PHO1;2), a gene involved in phosphate loading into the xylem in rice, and its associated cis-NAT PHO1;2 are both controlled by promoters active in the vascular cylinder of roots and leaves. While the PHO1;2 promoter is unresponsive to the plant phosphate status, the cis-NAT PHO1;2 promoter is strongly upregulated under phosphate deficiency. Expression of both cis-NAT PHO1;2 and the PHO1;2 protein increased in phosphate-deficient plants, while the PHO1;2 mRNA level remained stable. Downregulation of cis-NAT PHO1;2 expression by RNA interference resulted in a decrease in PHO1;2 protein, impaired the transfer of phosphate from root to shoot, and decreased seed yield. Constitutive overexpression of NAT PHO1;2 in trans led to a strong increase of PHO1;2, even under phosphate-sufficient conditions. Under all conditions, no changes occurred in the level of expression, sequence, or nuclear export of PHO1;2 mRNA. However, expression of cis-NAT PHO1;2 was associated with a shift of both PHO1;2 and cis-NAT PHO1;2 toward the polysomes. These findings reveal an unexpected role for cis-NAT PHO1;2 in promoting PHO1;2 translation and affecting phosphate homeostasis and plant fitness.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Rice cis-Natural Antisense RNA Acts as a Translational Enhancer for Its Cognate mRNA and Contributes to Phosphate Homeostasis and Plant Fitness

et al. 2013

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“…LncRNA can function as scaffolds to affect complex assembly and chromatin remodeling, or as enhancers and decoys for promoting and inhibiting target gene transcriptions. [9][10][11] The dysregulated expression of lncRNAs has been implicated in many diseases, including cancers. 8 well-documented lncRNAs, and the high expression level of HOTAIR has become a powerful predictor of metastasis and death in breast cancer.…”

Section: Introductionmentioning

confidence: 99%

Long non-coding RNA Linc00152 is involved in cell cycle arrest, apoptosis, epithelial to mesenchymal transition, cell migration and invasion in gastric cancer

et al. 2015

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Gastric cancer remains a serious threat to public health with high incidence and mortality worldwide. Accumulating evidence demonstrates that long non-coding RNAs (lncRNAs) play important roles in regulating gene expression and are involved in various pathological processes, including gastric cancer. To investigate the possible role of dysregulated lncRNAs in gastric cancer development, we performed lncRNA microarray and identified 3141 significantly differentially expressed lncRNAs in gastric cancer tissues. Next, some of deregulated lncRNAs were validated among about 60 paired gastric cancer specimens such as Linc00261, DKFZP434K028, RPL34-AS1, H19, HOTAIR and Linc00152. Our results found that the decline of DKFZP434K028 and RPL34-AS1, and the increased expression of Linc00152 positively correlated with larger tumor size. The high expression levels of HOTAIR were associated with lymphatic metastasis and poor differentiation. Since the biological roles of Linc00152 are largely unknown in gastric cancer pathogenesis, we assessed its functions by silencing its up-regulation in gastric cancer cells. We found that Linc00152 knockdown could inhibit cell proliferation and colony formation, promote cell cycle arrest at G1 phase, trigger late apoptosis, reduce the epithelial to mesenchymal transition (EMT) program, and suppress cell migration and invasion. Taken together, we delineate the gastric cancer lncRNA signature and demonstrate the oncogenic functions of Linc00152. These findings may have implications for developing lncRNA-based biomarkers for diagnosis and therapeutics for gastric cancer.

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“…We refer readers to the many excellent recent reviews on these topics (Peculis 2000;Xiao et al 2002;Henras et al 2004;Okamura and Lai 2008;Kim et al 2009;Feuerhahn et al 2010;Blackburn and Collins 2011;Czech and Hannon 2011;Siomi et al 2011). Although lncRNAs are found across many taxa, and many crucial discoveries have been made in plants, fungi, and invertebrates (Gelbart and Kuroda 2009;Au et al 2011), we largely limit our discussion to mammalian examples, with occasional reference to lncRNAs of other taxa. chauvinistic toward our own species, we like to think that man is surely one of the most complicated species on earth and thus needs just about the maximum number of genes" (Comings 1972, p. 313).…”

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confidence: 99%

Long Noncoding RNAs: Past, Present, and Future

2013

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Long noncoding RNAs (lncRNAs) have gained widespread attention in recent years as a potentially new and crucial layer of biological regulation. lncRNAs of all kinds have been implicated in a range of developmental processes and diseases, but knowledge of the mechanisms by which they act is still surprisingly limited, and claims that almost the entirety of the mammalian genome is transcribed into functional noncoding transcripts remain controversial. At the same time, a small number of well-studied lncRNAs have given us important clues about the biology of these molecules, and a few key functional and mechanistic themes have begun to emerge, although the robustness of these models and classification schemes remains to be seen. Here, we review the current state of knowledge of the lncRNA field, discussing what is known about the genomic contexts, biological functions, and mechanisms of action of lncRNAs. We also reflect on how the recent interest in lncRNAs is deeply rooted in biology's longstanding concern with the evolution and function of genomes.T HE past several years have witnessed a steep rise of interest in the study of lncRNAs. Almost on a weekly basis, it seems that a new lncRNA is found to be up-or downregulated in a particular disease, or a new class of noncoding transcripts is uncovered by a transcriptomic study, or a new article heralds a paradigm shift that lncRNAs will bring to our understanding of biology. Without a doubt, the advent of sensitive, high-throughput genomic technologies such as microarrays and next-generation sequencing (NGS) has resulted in an unprecedented ability to detect novel transcripts, the vast majority of which seem not to be derived from annotated protein-coding genes. Despite this explosion of data, however, surprisingly little is known about how lncRNAs function, how many different types of lncRNAs exist, or even whether most of them carry biological significance.In this review, we focus on recently discovered lncRNAs of .200 nt, place these new discoveries in historical context, and outline areas where additional work is needed. The review does not cover "classic" ncRNAs such as ribosomal (r) RNAs, ribozymes, transfer (t)RNAs, small nuclear (sn)RNAs, small nucleolar (sno)RNAs, and telomere-associated RNAs (TERC, TERRA); nor does it cover small ncRNAs such as microRNAs (miRNAs), endogenous small interfering (endo-si)RNAs that participate in RNA interference (RNAi), and Piwi-associated (pi)RNAs. We refer readers to the many

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Long non-coding RNA-mediated mechanisms independent of the RNAi pathway in animals and plants

Cited by 41 publications

References 122 publications

A Rice cis-Natural Antisense RNA Acts as a Translational Enhancer for Its Cognate mRNA and Contributes to Phosphate Homeostasis and Plant Fitness

A Rice cis-Natural Antisense RNA Acts as a Translational Enhancer for Its Cognate mRNA and Contributes to Phosphate Homeostasis and Plant Fitness

Long non-coding RNA Linc00152 is involved in cell cycle arrest, apoptosis, epithelial to mesenchymal transition, cell migration and invasion in gastric cancer

Long Noncoding RNAs: Past, Present, and Future

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