Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in <i>Arabidopsis</i>

Wang, Huan; Chung, Phil Hyun; Li, Jun; Jang, In‐Cheol; Kean, Michelle J.; Xu, Jun; Chua, Nam‐Hai

doi:10.1101/gr.165555.113

Cited by 330 publications

(319 citation statements)

References 55 publications

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“…A variety of lncRNA-mediated regulation mechanisms have been unraveled, including target mimicry, transcription interference, PRC2-associated histone methylation, and DNA methylation (26). However, although the number of known plant lncRNAs is expanding, the great majority have no known function (60)(61)(62)(63)(64)(65). In wheat, the lncRNA landscape has been profiled during fungal responses and heat stress, but the characterization of function is deficient (66,67).…”

Section: Discussionmentioning

confidence: 99%

Long noncoding miRNA gene represses wheat β-diketone waxes

Huang

Feurtado

Smith

et al. 2017

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

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The cuticle of terrestrial plants functions as a protective barrier against many biotic and abiotic stresses. In wheat and other Triticeae, β-diketone waxes are major components of the epicuticular layer leading to the bluish-white glaucous trait in reproductive-age plants. Glaucousness in durum wheat is controlled by a metabolic gene cluster at the WAX1 (W1) locus and a dominant suppressor INHIBITOR of WAX1 (Iw1) on chromosome 2B. The wheat D subgenome from progenitor Aegilops tauschii contains W2 and Iw2 paralogs on chromosome 2D. Here we identify the Iw1 gene from durum wheat and demonstrate the unique regulatory mechanism by which Iw1 acts to suppress a carboxylesterase-like protein gene, W1-COE, within the W1 multigene locus. Iw1 is a long noncoding RNA (lncRNA) containing an inverted repeat (IR) with >80% identity to W1-COE. The Iw1 transcript forms a miRNA precursor-like long hairpin producing a 21-nt predominant miRNA, miRW1, and smaller numbers of related sRNAs associated with the nonglaucous phenotype. When Iw1 was introduced into glaucous bread wheat, miRW1 accumulated, W1-COE and its paralog W2-COE were down-regulated, and the phenotype was nonglaucous and β-diketone-depleted. The IR region of Iw1 has >94% identity to an IR region on chromosome 2 in Ae. tauschii that also produces miRW1 and lies within the marker-based location of Iw2. We propose the Iw loci arose from an inverted duplication of W1-COE and/or W2-COE in ancestral wheat to form evolutionarily young miRNA genes that act to repress the glaucous trait.glaucous | inhibitor of wax | small RNA | long noncoding RNA | WAX1 P lant epicuticular waxes deposited on the outer surface of the plant cuticle produce a water-resistant layer that serves to reduce nonstomatal water loss and mitigate the effects of heat and UV radiation as well as pathogen and insect attacks (1). Grasses in the Triticeae tribe, subfamily Pooideae, which include the cultivated species barley (Hordeum vulgare; 2n = 2x = 14), rye (Secale cereale, 2n = 2x = 14), durum wheat (Triticum durum; 2n = 4x = 28, AABB), and bread wheat (Triticum aestivum; 2n = 6x = 42, AABBDD), have two predominant pathways for wax production: (i) an alcohol-and alkane-rich wax pathway and (ii) a pathway leading to β-diketones and derivatives including hydroxy-β-diketones (2). The alcohol and alkane waxes are prevalent in earlier development and on leaves, whereas β-diketones dominate during the reproductive phase, particularly on leaf sheaths and flower heads (3, 4). β-Diketone wax is predominantly hentriacontane-14, 16-dione, which consists of a 31-carbon chain with carbonyl groups at C 14 and C 16 . In durum wheat, about 20% of the β-diketone is hydroxylated to form 25-hydroxy-β-diketone, whereas in bread wheat hydroxylation is at C 8 or C 9 (5). β-Diketone wax deposition manifests visibly as glaucousness, a bluish-white coloration on stems, leaves, and flower heads. However, the relationship between a glaucous appearance and the total amount of cuticular wax can be inconsistent, especially during t...

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Section: Discussionmentioning

confidence: 99%

Long noncoding miRNA gene represses wheat β-diketone waxes

Huang

Feurtado

Smith

et al. 2017

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

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“…They are transcribed with the opposite orientation to the sense DNA strand of their mRNA/lncRNA counterparts at the same or separate genomic loci and form perfect/imperfect pairs. 20,21 They are prevalent in eukaryotes, including humans, mice, yeast, Drosophila, and Aragidopsis.…”

Section: Classification Of Distinct Lncrnas Based On Their Genomic Comentioning

confidence: 99%

“…21,22 For example, Kcnq1ot1 antisense silences its flanking genes via deposition of inactive chromatin-specific histone modifications. 23 Currently, the highest estimated number of human NATs is around 6,000.…”

Section: Classification Of Distinct Lncrnas Based On Their Genomic Comentioning

confidence: 99%

LncRNA BCAR4 wires up signaling transduction in breast cancer

et al. 2015

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“…Large numbers of lncRNAs have been identified in Arabidopsis thaliana [25][26][27], rice [28,29], wheat [30,31], maize [32], cotton [33,34], Brassica napus [35], and Populus [36,37], and have been found to play important roles in growth, development, differentiation, and stress responses. LncRNAs involved in the responses of plants to biotic stresses have also been identified.…”

Section: Introductionmentioning

confidence: 99%

Long Non-Coding RNAs Responsive to Witches’ Broom Disease in Paulownia tomentosa

Wang

Zhai

Cao

et al. 2017

Forests

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Paulownia witches' broom (PaWB) disease caused by phytoplasmas is a fatal disease that leads to considerable economic losses. Long non-coding RNAs (lncRNAs) have been demonstrated to play critical regulatory roles in posttranscriptional and transcriptional regulation. However, lncRNAs and their functional roles remain poorly characterized in Paulownia. To identify lncRNAs and investigate their roles in the response to PaWB phytoplasmas, RNA sequencing was performed for healthy Paulownia tomentosa, PaWB-infected P. tomentosa, and for healthy and PaWB-infected P. tomentosa treated with 100 mg L −1 rifampicin. A total of 28,614 unique mRNAs and 3693 potential lncRNAs were identified. Comparisons between lncRNAs and coding genes indicated that lncRNAs tended to have shorter transcripts and fewer exon numbers, and displayed significant expression specificity. Based on our comparison scheme, 1063 PaWB-related mRNAs and 110 PaWB-related lncRNAs were identified; among them, 12 PaWB-related candidate target genes that were regulated by nine PaWB-related lncRNAs were characterized. This study provides the first catalog of lncRNAs expressed in Paulownia and gives a revealing insight into the molecular mechanism responsible for PaWB.

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Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis

Cited by 330 publications

References 55 publications

Long noncoding miRNA gene represses wheat β-diketone waxes

Long noncoding miRNA gene represses wheat β-diketone waxes

LncRNA BCAR4 wires up signaling transduction in breast cancer

Long Non-Coding RNAs Responsive to Witches’ Broom Disease in Paulownia tomentosa

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