microRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants

Allen, Edwards; Xie, Zhixin; Gustafson, Adam M.; Carrington, James C.

doi:10.1016/j.cell.2005.04.004

Cited by 2,020 publications

(2,148 citation statements)

References 66 publications

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“…These proteins were found to be targeted by miRNA families miR-164, -397, -408, -2936, -3434, and -8051, respectively. Such findings were reported by various researchers (Allen et al, 2005;Wang et al, 2012;Ghani et al, 2013). Phytochrome c is an important chromoprotein that is involved in auxin signaling for plant elongation (Favero et al, 2016) targeted by miR-164.…”

Section: Potential Targets Of the Genus Coffeamentioning

confidence: 55%

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

Bibi¹,

Barozai²,

Din³

2017

Turk J Agric For

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IntroductionMicroRNAs (miRNAs) are an extensive class of noncoding small endogenous RNAs of 18 to 26 nt in length that are derived from self-complementary fold-back structures of longer precursor sequences (pre-miRNAs) and are generated by Dicer-like 1 (DCL1) in plants (Bartel, 2004). Mature miRNAs inhibit gene expression at posttranscriptional levels by either targeting mRNAs for degradation or inhibiting protein translation. Both processes are accomplished by the complementary base pairing of miRNAs to their target mRNA sequences (Ambros, 2004). In plants, for a majority of cases, miRNAs interact with their targets through perfect or near-perfect base pairing and lead to target mRNA degradation (Jones-Rhoades et al., 2006). Increasing evidence has revealed that miRNAs play an important role in a wide range of development processes in plants, including cell proliferation, stress response, metabolism, inflammation, and signal transduction (Ambros, 2004;Jones-Rhoades et al., 2006;Zhang et al., 2007a;Ali et al., 2016) and crosskingdom gene regulation (Barozai and Din, 2017). To date, more than 28,645 miRNAs have been identified from 223 species of plants and animals and deposited in the publicly available database miRBase (Release 21) (Griffiths-Jones et al., 2008). The majority of plant miRNAs have been found in species with fully sequenced genomes including 713 from Oryza sativa, 401 from Populus trichocarpa, 384 from Arabidopsis thaliana, 343 from Solanum tuberosum, 321 from Zea mays, and 241 from Sorghum bicolor (Griffiths-Jones et al., 2008). miRNA-related research is continuously growing and miRNAs, along with their functions, are being identified and elucidated using a wide variety of computational tools and experimental methods including direct cloning, deep sequencing, and other approaches. Comparison of miRNAs across multiple plant species has demonstrated that some miRNAs are highly evolutionary conserved from species to species, such as from mosses to higher flowering eudicots in the plant kingdom (Floyd and Bowman, 2004;Zhang et al., 2006aZhang et al., , 2006b. Conservation of miRNA sequences has provided a powerful strategy for identifying miRNAs in other species. Currently, comparative genome-based homolog searches have been used to identify conserved miRNAs in many plant species, including cotton (

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Section: Potential Targets Of the Genus Coffeamentioning

confidence: 55%

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

Bibi¹,

Barozai²,

Din³

2017

Turk J Agric For

View full text Add to dashboard Cite

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“…Arabidopsis PHO2 encodes an ubiquitinconjugating E2 enzyme that plays a role in the maintenance of Pi homeostasis (Bari et al, 2006). The Arabidopsis PHO2 mRNA is targeted by miR399 in multiple sites in its 59-untranslated region (59-UTR; Allen et al, 2005). cDNA sequencing demonstrated that the GRMZM2G381709 59-UTR encompassed the putative miR399 target sites ( Fig.…”

Section: Analysis Of Mirnas and Their Targetsmentioning

confidence: 99%

Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses

et al. 2016

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(A.L., M.J.A.) Endogenous small RNAs (sRNAs) contribute to gene regulation and genome homeostasis, but their activities and functions are incompletely known. The maize genome has a high number of transposable elements (TEs; almost 85%), some of which spawn abundant sRNAs. We performed sRNA and total RNA sequencing from control and abiotically stressed B73 wild-type plants and rmr6-1 mutants. RMR6 encodes the largest subunit of the RNA polymerase IV complex and is responsible for accumulation of most 24-nucleotide (nt) small interfering RNAs (siRNAs). We identified novel MIRNA loci and verified miR399 target conservation in maize. RMR6-dependent 23-24 nt siRNA loci were specifically enriched in the upstream region of the most highly expressed genes. Most genes misregulated in rmr6-1 did not show a significant correlation with loss of flanking siRNAs, but we identified one gene supporting existing models of direct gene regulation by TE-derived siRNAs. Long-term drought correlated with changes of miRNA and sRNA accumulation, in particular inducing down-regulation of a set of sRNA loci in the wild-typeleaf.

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“…(100) siRNAs are produced mainly from transposons, heterochromatic repeats and viral sequences and serve as negative regulators or chromatin modulators of their own sources, whereas miRNAs are encoded in intergenic regions and regulate other loci important for animal and plant development. In addition to functioning as translational repressors as do animal miRNAs, plant miRNAs behave as siRNAs that exert negative cis-and trans-acting effects (101) on cleavage of the target loci through imperfect matches. Moreover, RNAi pathways operate at the genome-wide scale, which may directly affect epigenetic modification of homologous sequences that induces gene silencing and DNA elimination.…”

Section: Transcriptional Regulation In Allopolyploidsmentioning

confidence: 99%

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

2006

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SummaryPolyploidy is produced by multiplication of a single genome (autopolyploid) or combination of two or more divergent genomes (allopolyploid). The available data obtained from the study of synthetic (newly created or human-made) plant allopolyploids have documented dynamic and stochastic changes in genomic organization and gene expression, including sequence elimination, inter-chromosomal exchanges, cytosine methylation, gene repression, novel activation, genetic dominance, subfunctionalization and transposon activation. The underlying mechanisms for these alterations are poorly understood. To promote a better understanding of genomic and gene expression changes in polyploidy, we briefly review origins and forms of polyploidy and summarize what has been learned from genome-wide gene expression analyses in newly synthesized autoand allopolyploids. We show transcriptome divergence between the progenitors and in the newly formed allopolyploids. We propose models for transcriptional regulation, chromatin modification and RNA-mediated pathways in establishing locus-specific expression of orthologous and homoeologous genes during allopolyploid formation and evolution. Polyploidy and its formsPolyploidy occurs throughout the evolutionary history of all eukaryotes, (1,2) predominately in flowering plants (3,4) including many important agricultural crops. (5) Compared to plants, polyploidy occurs rarely in animals, but clearly exists in some invertebrates (e.g. insects) and vertebrates (e.g. fish, amphibians and reptiles). (4,6) The relative paucity of polyploidy in animals is attributed to the delicate schemes of sex determination and animal development, which are disrupted by polyploidization. (7,8) Therefore, polyploid animals rarely exist. (9) Moreover, aneuploid and polyploid cells in animals and human are often associated with malignant cell proliferation or carcinogenesis. (10) However, endopolyploidy (somatic polyploid cells within a diploid individual) appears to be a physiological response to developmental changes in plants and some animals, (11,12) indicating plasticity of plant and animal genomes. In the post-sequencing era, polyploidy is proving to be a fascinating and challenging field of plant biology, stimulating many research advances and insightful reviews. (2,13 -24) Here we attempt to update the views using genomic-scale results and provide new mechanistic insights.Historically, Winkler (1916) introduced the term polyploidy, (25) and Winge (1917) called attention to the general importance of polyploidy in the evolution of angiosperms. (26) At that time, research in polyploidy was somewhat limited by the plant and animal materials that were available in nature. In 1937, Blakeslee and Avery induced polyploidy in plants using colchicine, a chemical inhibitor of mitotic cell divisions. (27) The technique has been successfully used to induce chromosome doubling in meristemic cells of diploids and interspecific hybrids. Doubling a single 'diploid' genome results in an autotetraploid, while doubling c...

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microRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants

Cited by 2,020 publications

References 66 publications

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

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