Publications by authors named "Qili Fei"

16 Publications

  • Page 1 of 1

Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution.

Sci Rep 2021 May 4;11(1):9471. Epub 2021 May 4.

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.

The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.
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http://dx.doi.org/10.1038/s41598-021-88160-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8096831PMC
May 2021

Stabilization of ERK-Phosphorylated METTL3 by USP5 Increases mA Methylation.

Mol Cell 2020 11;80(4):633-647.e7

Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA. Electronic address:

N-methyladenosine (mA) is the most abundant mRNA modification and is installed by the METTL3-METTL14-WTAP methyltransferase complex. Although the importance of mA methylation in mRNA metabolism has been well documented recently, regulation of the mA machinery remains obscure. Through a genome-wide CRISPR screen, we identify the ERK pathway and USP5 as positive regulators of the mA deposition. We find that ERK phosphorylates METTL3 at S43/S50/S525 and WTAP at S306/S341, followed by deubiquitination by USP5, resulting in stabilization of the mA methyltransferase complex. Lack of METTL3/WTAP phosphorylation reduces decay of mA-labeled pluripotent factor transcripts and traps mouse embryonic stem cells in the pluripotent state. The same phosphorylation can also be found in ERK-activated human cancer cells and contribute to tumorigenesis. Our study reveals an unrecognized function of ERK in regulating mA methylation.
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http://dx.doi.org/10.1016/j.molcel.2020.10.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7720844PMC
November 2020

YTHDF2 promotes mitotic entry and is regulated by cell cycle mediators.

PLoS Biol 2020 04 8;18(4):e3000664. Epub 2020 Apr 8.

Department of Chemistry, The University of Chicago, Chicago, Illinois, United States of America.

The N6-methyladenosine (m6A) modification regulates mRNA stability and translation. Here, we show that transcriptomic m6A modification can be dynamic and the m6A reader protein YTH N6-methyladenosine RNA binding protein 2 (YTHDF2) promotes mRNA decay during cell cycle. Depletion of YTHDF2 in HeLa cells leads to the delay of mitotic entry due to overaccumulation of negative regulators of cell cycle such as Wee1-like protein kinase (WEE1). We demonstrate that WEE1 transcripts contain m6A modification, which promotes their decay through YTHDF2. Moreover, we found that YTHDF2 protein stability is dependent on cyclin-dependent kinase 1 (CDK1) activity. Thus, CDK1, YTHDF2, and WEE1 form a feedforward regulatory loop to promote mitotic entry. We further identified Cullin 1 (CUL1), Cullin 4A (CUL4A), damaged DNA-binding protein 1 (DDB1), and S-phase kinase-associated protein 2 (SKP2) as components of E3 ubiquitin ligase complexes that mediate YTHDF2 proteolysis. Our study provides insights into how cell cycle mediators modulate transcriptomic m6A modification, which in turn regulates the cell cycle.
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http://dx.doi.org/10.1371/journal.pbio.3000664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7170294PMC
April 2020

mA mRNA Methylation Is Essential for Oligodendrocyte Maturation and CNS Myelination.

Neuron 2020 01 31;105(2):293-309.e5. Epub 2019 Dec 31.

Center for Peripheral Neuropathy and Department of Neurology, University of Chicago, Chicago, IL 60637, USA. Electronic address:

The molecular mechanisms that govern the maturation of oligodendrocyte lineage cells remain unclear. Emerging studies have shown that N-methyladenosine (mA), the most common internal RNA modification of mammalian mRNA, plays a critical role in various developmental processes. Here, we demonstrate that oligodendrocyte lineage progression is accompanied by dynamic changes in mA modification on numerous transcripts. In vivo conditional inactivation of an essential mA writer component, METTL14, results in decreased oligodendrocyte numbers and CNS hypomyelination, although oligodendrocyte precursor cell (OPC) numbers are normal. In vitro Mettl14 ablation disrupts postmitotic oligodendrocyte maturation and has distinct effects on OPC and oligodendrocyte transcriptomes. Moreover, the loss of Mettl14 in oligodendrocyte lineage cells causes aberrant splicing of myriad RNA transcripts, including those that encode the essential paranodal component neurofascin 155 (NF155). Together, our findings indicate that dynamic RNA methylation plays an important regulatory role in oligodendrocyte development and CNS myelination.
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http://dx.doi.org/10.1016/j.neuron.2019.12.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7137581PMC
January 2020

Disruption of miRNA sequences by TALENs and CRISPR/Cas9 induces varied lengths of miRNA production.

Plant Biotechnol J 2020 07 20;18(7):1526-1536. Epub 2019 Dec 20.

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.

MicroRNAs (miRNAs) are 20-24 nucleotides (nt) small RNAs functioning in eukaryotes. The length and sequence of miRNAs are not only related to the biogenesis of miRNAs but are also important for downstream physiological processes like ta-siRNA production. To investigate these roles, it is informative to create small mutations within mature miRNA sequences. We used both TALENs (transcription activator-like effector nucleases) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) to introduce heritable base pair mutations in mature miRNA sequences. For rice, TALEN constructs were built targeting five different mature miRNA sequences and yielding heritable mutations. Among the resulting mutants, mir390 mutant showed a severe defect in the shoot apical meristem (SAM), a shootless phenotype, which could be rescued by the wild-type MIR390. Small RNA sequencing showed the two base pair deletion in mir390 substantially interfered with miR390 biogenesis. In Arabidopsis, CRISPR/Cas9-mediated editing of the miR160* strand confirmed that the asymmetric structure of miRNA is not a necessary determinant for secondary siRNA production. CRISPR/Cas9 with double-guide RNAs successfully generated mir160a null mutants with fragment deletions, at a higher efficiency than a single-guide RNA. The difference between the phenotypic severity of miR160a mutants in Col-0 versus Ler backgrounds highlights a diverged role for miR160a in different ecotypes. Overall, we demonstrated that TALENs and CRISPR/Cas9 are both effective in modifying miRNA precursor structure, disrupting miRNA processing and generating miRNA null mutant plants.
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http://dx.doi.org/10.1111/pbi.13315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7292542PMC
July 2020

Single base resolution mapping of 2'-O-methylation sites in human mRNA and in 3' terminal ends of small RNAs.

Methods 2019 03 22;156:85-90. Epub 2018 Nov 22.

Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA. Electronic address:

The post-transcriptional modification 2'-O-Methyl (2'OMe) could be present on the ribose of all four ribonucleosides, and is highly prevalent in a wide variety of RNA species, including the 5' RNA cap of viruses and higher eukaryotes, as well as internally in transfer RNA and ribosomal RNA. Recent studies have suggested that 2'OMe is also located internally in low-abundance RNA species such as viral RNA and mRNA. To profile 2'OMe on different RNA species, we have developed Nm-seq, which could identify 2'OMe sites at single base resolution. Nm-seq is particularly useful for identifying 2'OMe sites located at the 3' terminal ends of small RNAs. Here, we present an optimized protocol for Nm-seq and a protocol for applying Nm-seq to identify 2'OMe sites on small RNA 3' terminal ends.
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http://dx.doi.org/10.1016/j.ymeth.2018.11.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6397781PMC
March 2019

Differential mA, mA, and mA Demethylation Mediated by FTO in the Cell Nucleus and Cytoplasm.

Mol Cell 2018 09 6;71(6):973-985.e5. Epub 2018 Sep 6.

Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA. Electronic address:

FTO, the first RNA demethylase discovered, mediates the demethylation of internal N-methyladenosine (mA) and N, 2-O-dimethyladenosine (mA) at the +1 position from the 5' cap in mRNA. Here we demonstrate that the cellular distribution of FTO is distinct among different cell lines, affecting the access of FTO to different RNA substrates. We find that FTO binds multiple RNA species, including mRNA, snRNA, and tRNA, and can demethylate internal mA and cap mA in mRNA, internal mA in U6 RNA, internal and cap mA in snRNAs, and N-methyladenosine (mA) in tRNA. FTO-mediated demethylation has a greater effect on the transcript levels of mRNAs possessing internal mA than the ones with cap mA in the tested cells. We also show that FTO can directly repress translation by catalyzing mA tRNA demethylation. Collectively, FTO-mediated RNA demethylation occurs to mA and mA in mRNA and snRNA as well as mA in tRNA.
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http://dx.doi.org/10.1016/j.molcel.2018.08.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6151148PMC
September 2018

Biogenesis of a 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation.

Proc Natl Acad Sci U S A 2018 07 16;115(31):8037-8042. Epub 2018 Jul 16.

Donald Danforth Plant Science Center, St. Louis, MO 63132;

Phased, secondary siRNAs (phasiRNAs) represent a class of small RNAs in plants generated via distinct biogenesis pathways, predominantly dependent on the activity of 22-nt miRNAs. Most 22-nt miRNAs are processed by DCL1 from miRNA precursors containing an asymmetric bulge, yielding a 22/21-nt miRNA/miRNA* duplex. Here we show that miR1510, a soybean miRNA capable of triggering phasiRNA production from numerous (s), previously described as 21 nt in its mature form, primarily accumulates as a 22-nt isoform via monouridylation. We demonstrate that, in , this uridylation is performed by HESO1. Biochemical experiments showed that the 3' terminus of miR1510 is only partially 2'--methylated because of the terminal mispairing in the miR1510/miR1510* duplex that inhibits HEN1 activity in soybean. miR1510 emerged in the Phaseoleae ∼41-42 million years ago with a conserved precursor structure yielding a 22-nt monouridylated form, yet a variant in mung bean is processed directly in a 22-nt mature form. This analysis of miR1510 yields two observations: () plants can utilize postprocessing modification to generate abundant 22-nt miRNA isoforms to more efficiently regulate target mRNA abundances; and () comparative analysis demonstrates an example of selective optimization of precursor processing of a young plant miRNA.
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http://dx.doi.org/10.1073/pnas.1807403115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6077734PMC
July 2018

CRISPR/Cas9-mediated resistance to cauliflower mosaic virus.

Plant Direct 2018 Mar 7;2(3):e00047. Epub 2018 Mar 7.

Department of Plant Pathology, Physiology and Weed Science Virginia Tech Blacksburg VA USA.

Viral diseases are a leading cause of worldwide yield losses in crop production. Breeding of resistance genes ( gene) into elite crop cultivars has been the standard and most cost-effective practice. However, gene-mediated resistance is limited by the available genes within genetic resources and in many cases, by strain specificity. Therefore, it is important to generate new and broad-spectrum antiviral strategies. The CRISPR-Cas9 (clustered regularly interspaced palindromic repeat, CRISPR-associated) editing system has been employed to confer resistance to human viruses and several plant single-stranded DNA geminiviruses, pointing out the possible application of the CRISPR-Cas9 system for virus control. Here, we demonstrate that strong viral resistance to cauliflower mosaic virus (CaMV), a pararetrovirus with a double-stranded DNA genome, can be achieved through Cas9-mediated multiplex targeting of the viral coat protein sequence. We further show that small interfering RNAs (siRNA) are produced and mostly map to the 3' end of single-guide RNAs (sgRNA), although very low levels of siRNAs map to the spacer region as well. However, these siRNAs are not responsible for the inhibited CaMV infection because there is no resistance if Cas9 is not present. We have also observed edited viruses in systematically infected leaves in some transgenic plants, with short deletions or insertions consistent with Cas9-induced DNA breaks at the sgRNA target sites in coat protein coding sequence. These edited coat proteins, in most cases, led to earlier translation stop and thus, nonfunctional coat proteins. We also recovered wild-type CP sequence in these infected transgenic plants, suggesting these edited viral genomes were packaged by wild-type coat proteins. Our data demonstrate that the CRISPR-Cas9 system can be used for virus control against plant pararetroviruses with further modifications.
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http://dx.doi.org/10.1002/pld3.47DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508564PMC
March 2018

N-Allyladenosine: A New Small Molecule for RNA Labeling Identified by Mutation Assay.

J Am Chem Soc 2017 12 15;139(48):17213-17216. Epub 2017 Nov 15.

MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University , Zheda Road 38, Hangzhou 310027, China.

RNA labeling is crucial for the study of RNA structure and metabolism. Herein we report N-allyladenosine (aA) as a new small molecule for RNA labeling through both metabolic and enzyme-assisted manners. aA behaves like A and can be metabolically incorporated into newly synthesized RNAs inside mammalian cells. We also show that human RNA N-methyladenosine (mA) methyltransferases METTL3/METTL14 can work with a synthetic cofactor, namely allyl-SAM (S-adenosyl methionine with methyl replaced by allyl) in order to site-specifically install an allyl group to the N-position of A within specific sequence to generate aA-labeled RNAs. The iodination of N-allyl group of aA under mild buffer conditions spontaneously induces the formation of N,N-cyclized adenosine and creates mutations at its opposite site during complementary DNA synthesis of reverse transcription. The existing mA in RNA is inert to methyltransferase-assisted allyl labeling, which offers a chance to differentiate mA from A at individual RNA sites. Our work demonstrates a new method for RNA labeling, which could find applications in developing sequencing methods for nascent RNAs and RNA modifications.
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http://dx.doi.org/10.1021/jacs.7b06837DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813804PMC
December 2017

Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways.

J Exp Bot 2016 11 4;67(21):6037-6049. Epub 2016 Oct 4.

Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA

Dissection of the genetic pathways and mechanisms by which anther development occurs in grasses is crucial for both a basic understanding of plant development and for examining traits of agronomic importance such as male sterility. In rice, MULTIPLE SPOROCYTES1 (MSP1), a leucine-rich-repeat receptor kinase, plays an important role in anther development by limiting the number of sporocytes. OsTDL1a (a TPD1-like gene in rice) encodes a small protein that acts as a cofactor of MSP1 in the same regulatory pathway. In this study, we analyzed small RNA and mRNA changes in different stages of spikelets from wild-type rice, and from msp1 and ostdl1a mutants. Analysis of the small RNA data identified miRNAs demonstrating differential abundances. miR2275 was depleted in the two rice mutants; this miRNA is specifically enriched in anthers and functions to trigger the production of 24-nt phased secondary siRNAs (phasiRNAs) from PHAS loci. We observed that the 24-nt phasiRNAs as well as their precursor PHAS mRNAs were also depleted in the two mutants. An analysis of co-expression identified three Argonaute-encoding genes (OsAGO1d, OsAGO2b, and OsAGO18) that accumulate transcripts coordinately with phasiRNAs, suggesting a functional relationship. By mRNA in situ analysis, we demonstrated a strong correlation between the spatiotemporal pattern of these OsAGO transcripts and phasiRNA accumulations.
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http://dx.doi.org/10.1093/jxb/erw361DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100018PMC
November 2016

Regulatory Role of a Receptor-Like Kinase in Specifying Anther Cell Identity.

Plant Physiol 2016 07 20;171(3):2085-100. Epub 2016 May 20.

State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University and University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China (L.Y., X.Q., M.C., W.L., D.Z.); Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711 (Q.F., B.C.M.); Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (B.C.M.); Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian 223300, China (W.L., D.Z.); and School of Agriculture, Food, and Wine, University of Adelaide, South Australia 5064, Australia (D.Z.)

In flowering plants, sequential formation of anther cell types is a highly ordered process that is essential for successful meiosis and sexual reproduction. Differentiation of meristematic cells and cell-cell communication are proposed to coordinate anther development. Among the proposed mechanisms of cell fate specification are cell surface-localized Leu-rich repeat receptor-like kinases (LRR-RLKs) and their putative ligands. Here, we present the genetic and biochemical evidence that a rice (Oryza sativa) LRR-RLK, MSP1 (MULTIPLE SPOROCYTE1), interacts with its ligand OsTDL1A (TPD1-like 1A), specifying the cell identity of anther wall layers and microsporocytes. An in vitro assay indicates that the 21-amino acid peptide of OsTDL1A has a physical interaction with the LRR domain of MSP1. The ostdl1a msp1 double mutant showed the defect in lacking middle layers and tapetal cells and having an increased number of microsporocytes similar to the ostdl1a or msp1 single mutant, indicating the same pathway of OsTDL1A-MSP1 in regulating anther development. Genome-wide expression profiles showed the altered expression of genes encoding transcription factors, particularly basic helix-loop-helix and basic leucine zipper domain transcription factors in ostdl1a and msp1 Among these reduced expressed genes, one putatively encodes a TGA (TGACGTCA cis-element-binding protein) factor OsTGA10, and another one encodes a plant-specific CC-type glutaredoxin OsGrx_I1. OsTGA10 was shown to interact with OsGrx_I1, suggesting that OsTDL1A-MSP1 signaling specifies anther cell fate directly or indirectly affecting redox status. Collectively, these data point to a central role of the OsTDL1A-MSP1 signaling pathway in specifying somatic cell identity and suppressing overproliferation of archesporial cells in rice.
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http://dx.doi.org/10.1104/pp.16.00016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936546PMC
July 2016

Small RNAs Add Zing to the Zig-Zag-Zig Model of Plant Defenses.

Mol Plant Microbe Interact 2016 Mar 11;29(3):165-9. Epub 2016 Feb 11.

Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, U.S.A.

Plant small RNAs play important roles in transcriptional and posttranscriptional regulation, with ongoing work demonstrating their functions in diverse pathways. Their roles in defense responses are a topic of active investigation, particularly the rich set of micro (mi)RNAs that target disease resistance genes such as nucleotide binding/leucine-rich repeat (NB-LRR) genes. The miRNA-NB-LRR interactions result in the production of phased, secondary small interfering (phasi)RNAs, and phasiRNAs function in both cis and trans to propagate negative regulatory effects across additional members of the target gene family. Yet, while phasiRNAs have the capacity to trigger targeted decay of specific targets, both in cis and trans, their functional relevance in NB-LRR regulation remains largely a matter of speculation.
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http://dx.doi.org/10.1094/MPMI-09-15-0212-FIDOI Listing
March 2016

Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactions and their abundances.

Plant J 2015 Aug 30;83(3):451-65. Epub 2015 Jun 30.

Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA.

Small RNAs are a class of non-coding RNAs that are of great importance in gene expression regulatory networks. Different families of small RNAs are generated via distinct biogenesis pathways. One such family specific to plants is that of phased, secondary siRNAs (phasiRNAs); these require RDR6, DCL4, and (typically) a microRNA (miRNA) trigger for their biogenesis. Protein-encoding genes are an important source of phasi-RNAs. The model legume Medicago truncatula generates phasiRNAs from many PHAS loci, and we aimed to investigate their biogenesis and mechanism by which miRNAs trigger these molecules. We modulated miRNA abundances in transgenic tissues showing that the abundance of phasiRNAs correlates with the levels of both miRNA triggers and the target, precursor transcripts. We identified sets of phasiRNAs or PHAS loci that predominantly and substantially increase in response to miRNA overexpression. In the process of validating targets from miRNA overexpression tissues, we found that in the miRNA-mRNA target pairing, the 3' terminal nucleotide (the 22nd position), but not the 10th position, is important for phasiRNA production. Mutating the single 3' terminal nucleotide dramatically diminishes phasiRNA production. Ectopic expression of Medicago NB-LRR-targeting miRNAs in Arabidopsis showed that only a few NB-LRRs are capable of phasiRNA production; our data indicate that this might be due to target inaccessibility determined by sequences flanking target sites. Our results suggest that target accessibility is an important component in miRNA-target interactions that could be utilized in target prediction, and the evolution of mRNA sequences flanking miRNA-target sites may be impacted.
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http://dx.doi.org/10.1111/tpj.12900DOI Listing
August 2015

Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks.

Plant Cell 2013 Jul 23;25(7):2400-15. Epub 2013 Jul 23.

Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.

Plant genomes are the source of large numbers of small RNAs, generated via a variety of genetically separable pathways. Several of these pathways converge in the production of phased, secondary, small interfering RNAs (phasiRNAs), originally designated as trans-acting small interfering RNAs or tasiRNAs. PhasiRNA biogenesis requires the involvement of microRNAs as well as the cellular machinery for the production of siRNAs. PhasiRNAs in Arabidopsis thaliana have been well described for their ability to function in trans to suppress target transcript levels. Plant genomic data from an expanding set of species have demonstrated that Arabidopsis is relatively sparing in its use of phasiRNAs, while other genomes contain hundreds or even thousands of phasiRNA-generating loci. In the dicots, targets of those phasiRNAs include several large or conserved families of genes, such as those encoding disease resistance proteins or transcription factors. Suppression of nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance genes by small RNAs is particularly unusual because of a high level of redundancy. In this review, we discuss plant phasiRNAs and the possible mechanistic significance of phasiRNA-based regulation of the NB-LRRs.
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http://dx.doi.org/10.1105/tpc.113.114652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753373PMC
July 2013

[Evaluation of reconstruction of extensor pollicis function by transfer of extensor indicis].

Zhongguo Xiu Fu Chong Jian Wai Ke Za Zhi 2004 Jul;18(4):301-3

Department of Hand Surgery, Tianjin Hospital, PR China.

Objective: To assess the long-time results of reconstruction of the extensor pollicis longus (EPL) function by transfer of the extensor indicis (EI).

Methods: From August 1978 to March 2003, 46 cases of loss of the EPL function were treated by transfer of the extensor indicis. Of 46 cases, there were 32 males and 14 females, aged 16-51 years with an average of 36 years; there were 24 cases of old traumatic rupture and 22 cases of secondary rupture. The disease course was 2 days to 5 months, averaged 74 days. A specific EI-EPL evaluation method (SEEM) was used to measure the EPL function after transfer.

Results: Forty-one cases were followed up 9 years and 3 months on average (7 months to 23 years). Based on the SEEM, the results were excellent and good in 39 of 41 patients. The elevation deficit and combined flexion deficit were 0-2.2 cm (1.8 cm on average) and 0-3 cm (1.6 cm on average); the independent extension deficit was 0 degrees-8 degrees (5 degrees on average).

Conclusion: Restoration of the extensor pollicis function by transfer of the extensor indicis is an effective and safe treatment option and the SEEM is a valid method for assessing EPL function.
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July 2004