Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in <i>Arabidopsis</i>

Li, Jun; Jung, Chan-Sik; Xu, Jun; Wang, Huan; Deng, Shulin; Bernad, Lucía; Arenas-Huertero, Catalina; Chua, Nam‐Hai

doi:10.1105/tpc.112.102855

Cited by 641 publications

(763 citation statements)

References 75 publications

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“…Furthermore, we demonstrated that AtGUT15 is capped and undergoes alternative splicing. The same mRNA-like features have also been observed in mammalian and other plant lncRNAs [4, 6, 24]. …”

Section: Discussionsupporting

confidence: 62%

A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis

et al. 2018

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The Arabidopsis GUT15 RNA belongs to a class of noncoding RNAs that are expressed from the intergenic regions of protein-coding genes. We show that the RNA polymerase II transcribed GUT15 transcript serves as a precursor for two stable RNA species, a tRNA-like molecule and GUT15-tRF-F5, which are both encoded by the final intron in the GUT15 gene. The GUT15-encoded tRNA-like molecule cannot be autonomously transcribed by RNA polymerase III. However, this molecule contains a CCA motif, suggesting that it may enter the tRNA maturation pathway. The GUT15-encoded tRNA-like sequence has an inhibiting effect on the splicing of its host intron. Moreover, we demonstrate that the canonical tRNA genes nested within introns do not affect the splicing patterns of their host protein-coding transcripts.

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Section: Discussionsupporting

confidence: 62%

A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis

et al. 2018

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“…Some of these molecules function in chromatin modification or as miRNA mimics, whereas others are involved in ribosome biogenesis [i.e., small nucleolar RNAs (snoRNAs)]. Here, we used existing compendia of ncRNAs (49,50) to seek ones that may be ribosome-associated. First, we identified ncRNAs with mRNA-seq reads (>5 rpkM) in both normoxic and hypoxic samples.…”

Section: Hypoxia Reduces Ribosome Protection Associated With Initiatimentioning

confidence: 99%

“…Plants produce over 30,000 putative noncoding RNAs (ncRNAs) that are 5′-capped and 3′-polyadenylated (48,49). These include natural antisense transcripts (NATs), long intergenic/intronic ncRNAs (lincRNAs), and RNAs encoding ORFs of only 30-100 amino acids [small ORFs (sORFs)] (50).…”

Section: Hypoxia Reduces Ribosome Protection Associated With Initiatimentioning

confidence: 99%

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

Juntawong

Girke

Bazin

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

343

392

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Translational regulation contributes to plasticity in metabolism and growth that enables plants to survive in a dynamic environment. Here, we used the precise mapping of ribosome footprints (RFs) on mRNAs to investigate translational regulation under control and sublethal hypoxia stress conditions in seedlings of Arabidopsis thaliana. Ribosomes were obtained by differential centrifugation or immunopurification and were digested with RNase I to generate footprint fragments that were deep-sequenced. Comparison of RF number and position on genic regions with fragmented total and polysomal mRNA illuminated numerous aspects of posttranscriptional and translational control under both growth conditions. When seedlings were oxygen-deprived, the frequency of ribosomes at the start codon was reduced, consistent with a global decline in initiation of translation. Hypoxia-up-regulated gene transcripts increased in polysome complexes during the stress, but the number of ribosomes per transcript relative to normoxic conditions was not enhanced. On the other hand, many mRNAs with limited change in steady-state abundance had significantly fewer ribosomes but with an overall similar distribution under hypoxia, consistent with restriction of initiation rather than elongation of translation. RF profiling also exposed the inhibitory effect of upstream ORFs on the translation of downstream protein-coding regions under normoxia, which was further modulated by hypoxia. The data document translation of alternatively spliced mRNAs and expose ribosome association with some noncoding RNAs. Altogether, we present an experimental approach that illuminates prevalent and nuanced regulation of protein synthesis under optimal and energy-limiting conditions. ribosome profiling | uORF | alternative splicing | long intergenic noncoding RNA | translational efficiency

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“…Thousands of lincRNAs are found in mouse (Guttman et al, 2009(Guttman et al, , 2010Liu et al, 2011;Luo et al, 2013;Sigova et al, 2013), human (Cabili et al, 2011;Hangauer et al, 2013;Sigova et al, 2013), chimpanzee (Wetterbom et al, 2010), zebrafish (Pauli et al, 2012;Ulitsky et al, 2011), frog (Tan et al, 2013), nematode (Nam and Bartel, 2012) and Arabidopsis (Liu et al, 2012). Some newly identified lincRNAs have well-validated functions.…”

Section: Introductionmentioning

confidence: 99%

Identification and analysis of mouse non-coding RNA using transcriptome data

Zhao

Liu

Zeng

et al. 2016

Sci. China Life Sci.

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Transcripts are expressed spatially and temporally and they are very complicated, precise and specific; however, most studies are focused on protein-coding related genes. Recently, massively parallel cDNA sequencing (RNA-seq) has emerged to be a new and promising tool for transcriptome research, and numbers of non-coding RNAs, especially lincRNAs, have been widely identified and well characterized as important regulators of diverse biological processes. In this study, we used ultra-deep RNA-seq data from 15 mouse tissues to study the diversity and dynamic of non-coding RNAs in mouse. Using our own criteria, we identified totally 16,249 non-coding genes (21,569 non-coding RNAs) in mouse. We annotated these non-coding RNAs by diverse properties and found non-coding RNAs are generally shorter, have fewer exons, express in lower level and are more strikingly tissue-specific compared with protein-coding genes. Moreover, these non-coding RNAs show significant enrichment with transcriptional initiation and elongation signals including histone modifications (H3K4me3, H3K27me3 and H3K36me3), RNAPII binding sites and CAGE tags. The gene set enrichment analysis (GSEA) result revealed several sets of lincRNAs associated with diverse biological processes such as immune effector process, muscle development and sexual reproduction. Taken together, this study provides a more comprehensive annotation of mouse non-coding RNAs and gives an opportunity for future functional and evolutionary study of mouse non-coding RNAs.non-coding RNA, RNA-seq, transcriptome, lincRNA, mouse Citation:

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Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

Cited by 641 publications

References 75 publications

A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis

A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

Identification and analysis of mouse non-coding RNA using transcriptome data

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