Apple miRNAs and tasiRNAs with novel regulatory networks

Xia, Rui; Zhu, Hong; An, Yong-qiang; Beers, Eric P.; Liu, Zongrang

doi:10.1186/gb-2012-13-6-r47

Cited by 278 publications

(340 citation statements)

References 77 publications

(139 reference statements)

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“…In addition, unlike conserved miRNAs that often targeted multiple members of a gene family, most novel miRNAs targeted genes from different gene families. Similar observations were made in other plant species, reflecting the properties of young miRNAs (Pantaleo et al, 2010;Xia et al, 2012;Zhu et al, 2012).…”

Section: Two Clusters Of Novel Fve-mirnas Targeting Fbx Genessupporting

confidence: 85%

“…miRNA Identification miRNA identification was based on previously well-established criteria (Meyers et al, 2008;Xia et al, 2012) and is summarized in Supplemental Figure S1. The raw reads were processed by first discarding low-quality reads, then removing adaptors, and finally collapsing identical small RNA reads into one using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.…”

Section: Rna Extraction and Sequencingmentioning

confidence: 99%

“…Two parameters, the alignment score and the category, were used to evaluate the reliability of target genes (Supplemental Tables S4 and S5). An alignment score up to 5 was used in target prediction Xia et al, 2012); a lower score indicates a better alignment between miRNA and its target. The category score (between 0 and 4), on the other hand, considers the ratio of the PARE tag reads mapped to the corresponding miRNA-mediated cleavage site to the total number of PARE tags in a given target mRNA (Addo-Quaye et al, 2009).…”

Section: Mirna-target Analysismentioning

confidence: 99%

“…Recently, genome-wide small RNA sequencing and analyses of an ever-expanding number of plant species have revealed the production of 21-nucleotide secondary small interfering RNAs (siRNAs) from hundreds of genes through a mechanism like tasiRNAs. These siRNAs may function in trans (tasiRNAs) or in cis (cis-acting siRNAs) to cleave their target genes (Johnson et al, 2009;Zhai et al, 2011;Xia et al, 2012Xia et al, , 2013Fei et al, 2013). Collectively, these tasiRNAs and cis-acting siRNAs, which are produced via progressive 21-nucleotide cleavage from the trigger miRNA cleavage site, are termed phased small interfering RNAs (phasiRNAs).…”

mentioning

confidence: 99%

“…Accordingly, phasiRNA-producing loci are termed PHAS loci (Zhai et al, 2011). In dicots, phasiRNAs have been found to be generated from and presumably to regulate large and conserved gene families such as those coding for the NUCLEOTIDE-BINDING AND LEUCINE-RICH REPEAT (NB-LRR) proteins, MYB transcription factors, and PENTATRICOPEPTIDE REPEAT (PPR) proteins (Zhai et al, 2011;Xia et al, 2012Xia et al, , 2013. The vast phasiRNA networks in higher plant genomes are just beginning to be recognized and discovered, and the functional roles of these phasiRNA networks are yet to be illuminated.…”

mentioning

confidence: 99%

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Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry

Xia

Ye²,

Liu³

et al. 2015

Plant Physiol.

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The wild strawberry (Fragaria vesca) has recently emerged as an excellent model for cultivated strawberry (Fragaria 3 ananassa) as well as other Rosaceae fruit crops due to its short seed-to-fruit cycle, diploidy, and sequenced genome. Deep sequencing and parallel analysis of RNA ends were used to identify F. vesca microRNAs (miRNAs) and their target genes, respectively. Thirtyeight novel and 31 known miRNAs were identified. Many known miRNAs targeted not only conserved mRNA targets but also developed new target genes in F. vesca. Significantly, two new clusters of miRNAs were found to collectively target 94 F-BOX (FBX) genes. One of the miRNAs in the new cluster is 22 nucleotides and triggers phased small interfering RNA production from six FBX genes, which amplifies the silencing to additional FBX genes. Comparative genomics revealed that the main novel miRNA cluster evolved from duplications of FBX genes. Finally, conserved trans-acting siRNA pathways were characterized and confirmed with distinct features. Our work identified novel miRNA-FBX networks in F. vesca and shed light on the evolution of miRNAs/phased small interfering RNA networks that regulate large gene families in higher plants.

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Section: Two Clusters Of Novel Fve-mirnas Targeting Fbx Genessupporting

confidence: 85%

Section: Rna Extraction and Sequencingmentioning

confidence: 99%

Section: Mirna-target Analysismentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry

Xia

Ye²,

Liu³

et al. 2015

Plant Physiol.

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Identification of phasiRNAs and their drought‐ responsiveness in Populus trichocarpa

Peng

Liang

et al. 2016

FEBS Letters

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Phased, secondary, small interfering RNA (phasiRNA) perform essential biological functions in plants. However, limited information is available on the role of phasiRNA genes in Populus (poplar), especially during drought stress. In this study, we identified 20 PHAS loci generating 91 phasiRNA in the genome of the model forest tree Populus trichocarpa (P. trichocarpa; western balsam-poplar) using the control and drought libraries. Our analysis indicated that six PHAS (PtPHA14-20) initiated by two Populus-specific miRNAs (miR6445 and miR6427) were specific to Populus. In addition, a total of 47 phasiRNA were found to be drought responsive, and five of them were confirmed by RT-qPCR. The phase cleavage of three PHAS loci by miRNA, and degradation of nine transcript targets by phasiRNA were experimentally confirmed based on degradome data. The identification of these Populus phasiRNA will contribute to a better understanding of their function and regulation during drought stress.

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Phenylpropanoid Metabolism

Rock

2017

Encyclopedia of Life Sciences

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Phenylpropanoid compounds encompass a wide range of structural classes with diverse biological functions in defence, survival and structural support associated with normal plant development (belying the term 'secondary metabolite'). The biosynthesis of phenylpropanoids is regulated by diverse environmental stimuli. Phenylpropanoid metabolism (other than flavonoids, not covered here) occupies a central place in the general aromatic metabolism of plants from shikimate to phenylalanine to lignin polymers and also to coumarins, phenolic volatiles and hydrolysable tannins. In recent years, genetics and biochemistry, along with methodology‐driven, computational, transgenic and comparative transcriptomic approaches, have led to significant advances in the identification of the families of genes encoding enzymes, transporters, regulatory factors involved in phenylpropanoid metabolism and a clearer picture of their functions in biotic and abiotic stress responses, plant development and enzyme/pathway evolution driven by interactions of species with their environment. Key Concepts Having one phenyl aromatic ring with one or more hydroxyl groups attached gives phenylpropanoids amphiphilic and reducing properties, underlying their ability to physically interact with other biomolecules. Plants invest a large percentage of their fixed carbon into synthesising phenylpropanoids, from simple volatile phenolic acids such as the defence hormone salicylic acid to complex polyphenolic flavonoids encompassing thousands of compounds with myriad physiological and adaptive functions. The shikimate pathway is the starting point for phenylpropanoid biosynthesis from shikimate product phenylalanine ( l ‐Phe), via the intermediate chorismate, which also serves as substrate for the synthesis of quinones and tocopherols important as electron acceptors in photosynthesis and aerobic respiration. Phenylpropanoid biosynthesis proceeds from deamination of Phe to cinnamate by the rate‐limiting and environmentally regulated enzyme PAL, followed by oxidation of the ring to p ‐coumarate, its activation with coenzymeA and a series of hydroxylation, methylation and reduction reactions to give cinnamic acids, ‐aldehydes and ‐alcohols that serve as substrates to generate a wide range of complex structures, notably polymers of coumaroyl, conferyl and sinapyl alcohols comprising lignin. Recent studies have established the major pathway in plants which proceeds from p ‐coumaroyl‐CoA → p ‐coumaryl‐shikimate → caffeoyl‐shikimate → caffeoyl‐CoA → feruloyl CoA → coniferaldehyde → 5‐OH coniferaldehyde → sinapaldehyde → sinapate/sinapyl alcohol (oxidation versus reduction, respectively), instead of the original model of a grid/matrix of parallel ring oxidation and side‐chain redox pathways from hydroxycinnamic acids to alcohols. Synthesis involves three subcellular compartments: chloroplast for Phe, cytosol for sinapoyl‐esters and the vacuole for trans‐esterifications. The identity of specific transporters, temporal‐ or organ‐specific regulatory factors for phenylpropanoid flux to (in)soluble polymers in the apoplast in response to biotic and abiotic stressors and whether lignin formation proceeds via precise channeling of individual precursors through metabolons (temporary structural–functional complexes formed between sequential enzymes) are key questions of practical significance that remain to be answered.

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Apple miRNAs and tasiRNAs with novel regulatory networks

Cited by 278 publications

References 77 publications

Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry

Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry

Identification of phasiRNAs and their drought‐ responsiveness in Populus trichocarpa

Phenylpropanoid Metabolism

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