Epigenetic regulation by long noncoding RNAs in plants

Heo, Jae Bok; Lee, Yong Suk; Sung, Sibum

doi:10.1007/s10577-013-9392-6

Cited by 104 publications

(64 citation statements)

References 68 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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“…lncRNAs function through diverse mechanisms such as forming modular scaffolds for polycomb-mediated repression, activating chromatin-remodeling complexes, and attenuating miRNAmediated repression as miRNA target mimics [35]. Among these regulatory mechanisms, lncRNAs regulate some developmental processes by associating with sncRNAs in different ways.…”

Section: The Cross Talk Between Lncrnas and Sncrnasmentioning

confidence: 99%

miRNAs and lncRNAs in reproductive development

Zhang

Chen

2015

Plant Science

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“…A growing body of evidence indicates that plant lncRNAs have critical biological roles (e.g., cell differentiation, epigenetic modification, genomic imprinting, and stress tolerance) in different physiological and environmental conditions (Charon et al, 1997;Pignatta and Gehring, 2012;Heo et al, 2013;Zhang et al, 2014). However, detailed information for specific plant lncRNA(s) are widely dispersed in current scientific publications.…”

Section: Discussionmentioning

confidence: 99%

“…Another finding is that twenty lncRNAs from 159 intergenic regions in Arabidopsis thaliana were discovered to be responsive to Fusarium oxysporum using a strand-specific RNA-sequencing method (Zhu et al, 2014). Also, several other potential biological roles for plant lncRNAs have been reported, including cell differentiation (Charon et al, 1997), epigenetic splicing (Heo et al, 2013), and gene regulation (Kornienko et al, 2013).…”

Section: Introductionmentioning

confidence: 99%