Rise of the RNA Machines: Exploring the Structure of Long Non-Coding RNAs

Novikova, Irina; Hennelly, Scott P.; Tung, Chang‐Shung; Sanbonmatsu, Karissa Y.

doi:10.1016/j.jmb.2013.02.030

Cited by 125 publications

(105 citation statements)

References 133 publications

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“…However, a significant portion of the poly(A) RNA pool are non-coding RNAs, such as pri-miRNA and long non-coding antisense RNAs that do not leave the cell nucleus. 32,33 Thus, the selective storage of mRNA in the cell nucleus, which can then be quickly used after the end of stressful conditions, may be a strategy of plants to survive in hypoxic conditions and recover in normal conditions after stress.…”

Section: Discussionmentioning

confidence: 99%

Regulation of poly(A) RNA retention in the nucleus as a survival strategy of plants during hypoxia

2016

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Last finding indicates that post-transcriptional processes are significant in low-oxygen conditions, but their nature is poorly understood. Here, we localized poly(A) RNA and mRNA coding proteins involved and not involved with resistance to hypoxia in Lupinus luteus and Arabidopsis thaliana during submergence and after recovery of aerobic conditions. We showed a strong nuclear accumulation of poly(A) RNA and 6 of 7 studied mRNAs with a concurrent strong reduction in RNA polymerase II transcription during hypoxia. In this study, the nucleus did not accumulate mRNA of the ADH1 (alcohol dehydrogenase 1) gene, which is a core hypoxia gene. The RNA accumulation in the nucleus is among the mechanisms of post-transcriptional gene regulation that prevents translation. However re-aeration was accompanied by a strong increase in the amount of the mRNAs in the cytoplasm and a simultaneous decrease in nuclear mRNAs. This finding indicates that the nucleus is a storage site for those of mRNAs which are not involved in the response to hypoxia for use by the plants after the hypoxic stress. In this study, the highest intensity of RNA accumulation occurred in Cajal bodies (CBs); the intensity of accumulation was inversely correlated with transcription. Under hypoxia, ncb-1 mutants of Arabidopsis thaliana with a complete absence of CBs died sooner than wild type (WT), accompanied by a strong reduction in the level of poly(A) RNA in the nucleus. These results suggest that the CBs not only participate in the storage of the nuclear RNA, but they also could take part in its stabilization under low-oxygen conditions.

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Section: Discussionmentioning

confidence: 99%

Regulation of poly(A) RNA retention in the nucleus as a survival strategy of plants during hypoxia

2016

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“…RNA molecules that are not templates for protein synthesis are designated noncoding RNAs (ncRNAs) (Ernst and Morton, 2013;Novikova et al, 2013), and ncRNAs larger than 200 bases are defined as lncRNAs (Cesana et al, 2011). A number of in vivo and in vitro experiments have demonstrated important biological roles for lncRNAs (Eddy, 2001;Mattick, 2004;Mattick and Makunin, 2006), but a comparatively small number of lncRNAs have been characterized in plants (Swiezewski et al, 2009).…”

Section: Rna-seq Identifies O2-regulated Protein-coding and Noncodingmentioning

confidence: 99%

Genome-Wide Characterization ofcis-Acting DNA Targets Reveals the Transcriptional Regulatory Framework ofOpaque2in Maize

et al. 2015

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Opaque2 (O2) is a transcription factor that plays important roles during maize endosperm development. Mutation of the O2 gene improves the nutritional value of maize seeds but also confers pleiotropic effects that result in reduced agronomic quality. To reveal the transcriptional regulatory framework of O2, we studied the transcriptome of o2 mutants using RNA sequencing (RNA-Seq) and determined O2 DNA binding targets using chromatin immunoprecipitation coupled to highthroughput sequencing (ChIP-Seq). The RNA-Seq analysis revealed 1605 differentially expressed genes (DEGs) and 383 differentially expressed long, noncoding RNAs. The DEGs cover a wide range of functions related to nutrient reservoir activity, nitrogen metabolism, stress resistance, etc. ChIP-Seq analysis detected 1686 O2 DNA binding sites distributed over 1143 genes. Overlay of the RNA-Seq and ChIP-Seq results revealed 35 O2-modulated target genes. We identified four O2 binding motifs; among them, TGACGTGG appears to be the most conserved and strongest. We confirmed that, except for the 16-and 18-kD zeins, O2 directly regulates expression of all other zeins. O2 directly regulates two transcription factors, genes linked to carbon and amino acid metabolism and abiotic stress resistance. We built a hierarchical regulatory model for O2 that provides an understanding of its pleiotropic biological effects.

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“…53 Strong evidences describe that human genome has more than 14000 lncRNA genes units, associated with the regulation of distinct mechanisms and harboring expression patterns depending on the cell type, developmental stage, or disease situation, such as cancer. [54][55][56][57] lncRNAs can regulate several processes in eukaryotic organisms, although most of their functions and biochemical properties are still unknown. They can be classified according to their genomic location and biogenesis: being expressed from intergenic regions (lincRNA) such as lincRNA-p21 58 and Pint lncRNA; 59 from vestigial genes that lost their coding potential (pseudogene-encoded lncRNAs) as BRAFP1, 60 INTS6P1, 61 and HMGA1P6; 62 from the opposite strand of mRNA (antisense lncRNA) as PCNA-AS1 63 and MDC1-AS; 64 or can be generated by the splicing machinery, 54,65,66 constituting long intronic ncRNA as ci-ankrd52.…”

Section: Long Noncoding Rnasmentioning

confidence: 99%

“…[54][55][56][57] lncRNAs can regulate several processes in eukaryotic organisms, although most of their functions and biochemical properties are still unknown. They can be classified according to their genomic location and biogenesis: being expressed from intergenic regions (lincRNA) such as lincRNA-p21 58 and Pint lncRNA; 59 from vestigial genes that lost their coding potential (pseudogene-encoded lncRNAs) as BRAFP1, 60 INTS6P1, 61 and HMGA1P6; 62 from the opposite strand of mRNA (antisense lncRNA) as PCNA-AS1 63 and MDC1-AS; 64 or can be generated by the splicing machinery, 54,65,66 constituting long intronic ncRNA as ci-ankrd52. 67 lncRNAs influence gene expression by several pathways and are often associated with epigenetic regulation by silencing specific genes 68 and acting as chromatin modulators 69,70 and histone modificators.…”

Section: Long Noncoding Rnasmentioning

confidence: 99%

Long Noncoding RNAs in HPV-Induced Oncogenesis

Goedert¹,

Plaça²,

Nunes³

et al. 2016

Advances in Tumor Virology

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Long noncoding RNAs (lncRNAs) play important roles in a wide range of oncogenic processes, including malignant transformation, epigenetic reprogramming, epithelial-to-mesenchymal transition, and metastasis development. LncRNAs induced by oncogenic viral proteins were shown to play critical roles in tumor initiation and progression. Despite this, little is known about Human papillomavirus (HPV)-induced modulation of host's lncRNAs. In this review, we gathered published information about altered lncRNAs upon HPV status (infection/protein activity), making use of descriptive research works and published gene expression microarray experiments. A diversity of lncRNAs demonstrated to be altered, including metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), H19, and maternally expressed gene 3 (MEG3). Their functions in several cancers were reviewed, indicating that they may represent potential candidates for future research on HPV-induced oncogenesis.KEY WORDS: human papillomavirus, lncRNA, cancer, ncRNA, virus CITATION: goedert et al. long noncoding rnAs in HPv-induced oncogenesis.

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Rise of the RNA Machines: Exploring the Structure of Long Non-Coding RNAs

Cited by 125 publications

References 133 publications

Regulation of poly(A) RNA retention in the nucleus as a survival strategy of plants during hypoxia

Regulation of poly(A) RNA retention in the nucleus as a survival strategy of plants during hypoxia

Genome-Wide Characterization ofcis-Acting DNA Targets Reveals the Transcriptional Regulatory Framework ofOpaque2in Maize

Long Noncoding RNAs in HPV-Induced Oncogenesis

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