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Plant Small RNA

Plant Small RNA
Biogenesis, Regulation and Application

by Praveen Guleria,Vineet Kumar

  • Publisher : Academic Press
  • Release : 2020-02
  • Pages : 660
  • ISBN : 9780128171127
  • Language : En, Es, Fr & De
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Plant Small RNA: Biogenesis, Regulation and Application describes the biosynthesis of small RNA in plant systems. With an emphasis on the various molecular mechanisms affected by small RNA and their applications in supporting plant growth and survival, this books presents the basics and most recent advancements in small RNA mediated plant genomics, metabolomics, proteomics and physiology. In addition, it emphasizes the various molecular mechanisms affected by small RNA and their applications in supporting plant growth and survival. Final sections cover the most recent advancements in small RNA mediated plant genomics, metabolomics, proteomics and physiology. Presents foundational information about small RNA biology and regulation in plants Includes small RNA pathway advances Describes the application and scope of small RNA technology for agricultural stability

Discovery of Endogenous Plant Small RNAs and Their Role in Trans-species Gene Regulation

Discovery of Endogenous Plant Small RNAs and Their Role in Trans-species Gene Regulation
A Book

by Saima Shahid

  • Publisher : Unknown Publisher
  • Release : 2017
  • Pages : 129
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Endogenous small RNAs (20 - 24 nt) engage in complex regulation of gene expression and thus shape and direct plant development, defense, stress response and the epigenome. Based on their biogenesis and functions, endogenous small RNAs can be divided into many categories and subcategories. MicroRNAs (miRNAs) represent the most well-annotated type of small RNAs that regulate gene expression via transcript cleavage or translational repression. However, MIRNAs only contribute to a minor fraction of all the expressed small RNAs in plants. Small RNA genes other than MIRNAs remain poorly annotated, which limits complete elucidation of their regulatory roles. Furthermore, inconsistent MIRNA discovery methodologies in published studies have resulted in widespread discrepancies among existing annotations. To address these issues, and to improve current understanding of small RNA gene functions, we developed robust methodologies for de novo annotation of plant small RNA genes. Our comprehensive small RNA loci discovery based on deep sequencing data and small RNA biogenesis patterns provided refinement of existing MIRNA annotations and their functions in the basal land plant Physcomitrella patens. We also identified numerous P. patens siRNA loci producing almost equal mixture of 23-24 nt small RNAs, confirming that the heterochromatic siRNA pathway is present in the bryophyte lineage. Our de novo annotation of small RNA genes in Amborella trichopoda, the basal-most lineage of flowering plants, revealed a striking predominance of lineage-specific, intronic 23-24 nt MIRNAs and hairpin RNAs that has not been reported in any plants so far. Most of these non-canonical MIRNAs lacked easily identifiable targets in the transcriptome, suggesting these may have functions other than sequence-dependent targeting. In the monocot rice, 24 nt long intronic miRNAs function in RNA dependent DNA methylation. It is possible that A. trichopoda 23-24 nt MIRNAs function in a similar way, and such non-canonical miRNA pathways may have been retained in specific lineages of flowering plants. At least 19 A. trichopoda miRNA families were broadly conserved across land plants, and most of these also had conserved targets. These findings confirmed the presence of all major small RNA gene classes in the basal lineage of flowering plants, as well as the existence of species-specific diversities in small RNA populations expressed in non-model plants. Finally, we explored the potential exchange of endogenous small RNAs between parasitic plants and their hosts. Parasitic plants intimately connect to their hosts through a specialized feeding organ called haustoria. Bidirectional exchange of thousands of mRNAs between the stem parasite C. campestris and its hosts have been previously reported. Host-induced gene silencing has also been shown in several parasitic species including Cuscuta and Triphysaria versicolor (root parasite). De novo annotation of small RNA genes from C. campestris - A. thaliana associations revealed an unprecedented abundance of 22 nt parasite miRNAs in the haustorial interface. Several of these interface-induced C. campestris miRNAs directed slicing of six host mRNAs and triggered secondary siRNA production specifically in interface. Among these targets, Botrytis Induced Kinase 1 (BIK1) encodes a receptor-like cytoplasmic kinase and functions in in plant immunity. Another target, Sieve-Element-Occlusion-Related 1 (SEOR1) encodes a protein thought to be involved in sealing phloem sieve elements after wounding. Additionally, mRNAs encoding three auxin receptors, TIR1, AFB2, and AFB3 were targeted by a C. campestris miRNA and showed a unique pattern of secondary siRNA production in parasite-host interface. Such secondary siRNA production depended on host machinery for RNA interference. Growth of C. campestris on seor1 mutant significantly increased parasite biomass accumulation compared to wild type. Furthermore, interface-induced parasite miRNA-directed cleavage of host TIR1/AFB was also detected in C. campestris -N. benthamiana. Our findings thus confirm conserved trans-species targeting by C. campestris miRNAs across the haustorial interface, and the potential roles of these miRNAs as virulence factors in plant parasitism.

Non Coding RNAs in Plants

Non Coding RNAs in Plants
A Book

by Volker A. Erdmann,Jan Barciszewski

  • Publisher : Springer Science & Business Media
  • Release : 2011-07-20
  • Pages : 510
  • ISBN : 9783642194542
  • Language : En, Es, Fr & De
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In the most recent years, each of the RNA silencing pathways of plants have appeared to generate ncRNAs with dedicated functions, specialized biological activities and specific functional scopes. RNA silencing plays a crucial role in coordinating the expression, stability, protection and inheritance of eukaryotic genomes. It compromises several mechanisms, that invariably depend on core small non coding RNAs and that achieve dedicated sequence-specific functions. RNA silencing has been recognized to carry critical developmental, stress-response and bodyguard functions be coordinating the expression, protection, stability and inheritance of virtually all eukaryotic genomes. Thus, the ncRNAs encompass a wide set of mechanisms that achieve specialized functions.

Genome-wide Analysis of Plant Heterochromatic Short-interfering RNAs

Genome-wide Analysis of Plant Heterochromatic Short-interfering RNAs
A Book

by Feng Wang

  • Publisher : Unknown Publisher
  • Release : 2016
  • Pages : 129
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Small RNAs, usually 20-24 nt in length, are critical regulators of plant transcriptomes. They are loaded into ARGONAUTE (AGO) proteins, and mediate gene silencing by interacting with target transcripts through sequence-specific base pairing. In plants, small RNAs are classified into various different groups based on their biogenesis and function; microRNAs (miRNAs) and heterochromatic short-interfering RNAs (het-siRNAs) are the two most important types of small RNAs in flowering plants. Plant small RNAs are subject to various forms of modification. Despite intensive studies about miRNA modification, knowledge about het-siRNA modification is lacking. I systematically studied non-templated nucleotide patterns in plant small RNAs by analyzing small RNA sequencing (sRNA-seq) libraries from Arabidopsis, tomato, Medicago, rice, maize and Physcomitrella. Elevated rates of non-templated nucleotides were observed at the 3' end of plant small RNAs from wild-type specimens of all analyzed species. In all species I analyzed, 'off-sized' small RNAs, such as 25 nt and 23 nt siRNAs arising from het-siRNA loci, often had higher rates of non-templated nucleotides at the 3' end. In Arabidopsis, 23 nt siRNAs arising from het-siRNA clusters display a distinct pattern of 3'-non-templated nucleotides. This pattern of 3'-non-templated nucleotides in 23 nt siRNAs is not dependent on known terminal nucleotidyl transferases, and may result from modifications added to longer het-siRNA precursors.Het-siRNAs negatively regulate gene expression through the RNA-directed DNA methylation (RdDM) pathway. Biogenesis of most het-siRNAs depends on the plant-specific RNA polymerase IV (Pol IV), and AGO4 is the major effector protein of het-siRNAs. Through genome-wide analysis of sRNA-seq data sets, I found that AGO4 is required for the accumulation of a small subset of het-siRNAs in Arabidopsis thaliana. The accumulation of AGO4-dependent het-siRNAs also requires several other RdDM components, including RNA POLYMERASE V (Pol V), DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1). I also demonstrated that het-siRNA accumulation could not be fully recovered by a slicing-defective AGO4 from ago4 mutant plants. These data suggest that AGO4-dependent het-siRNAs are secondary het-siRNAs, whose biogenesis requires prior activities of RdDM at certain loci.In the current RdDM model, AGO4-bound het-siRNAs target Pol V transcripts through sequence-specific base pairing. However, the details of such interactions are largely unknown. Through crosslinking immunoprecipitation by an Arabidopsis AGO4 antibody and subsequent high-throughput sequencing, I identified a handful of het-siRNA:target interactions in Arabidopsis thaliana. These de novo identified het-siRNA:target interactions suggest that het-siRNAs act on both cis and trans loci. Successful interaction between a het-siRNA and its target(s) requires extensive base-pairing, and induces target cleavage between the 10th to 11th nucleotide counting from the 5' end of het-siRNAs.

Plant Small RNA

Plant Small RNA
Biogenesis, Regulation and Application

by Praveen Guleria,Vineet Kumar

  • Publisher : Academic Press
  • Release : 2020-02-19
  • Pages : 635
  • ISBN : 012817336X
  • Language : En, Es, Fr & De
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Plant Small RNA: Biogenesis, Regulation and Application describes the biosynthesis of small RNA in plant systems. With an emphasis on the various molecular mechanisms affected by small RNA and their applications in supporting plant growth and survival, this books presents the basics and most recent advancements in small RNA mediated plant genomics, metabolomics, proteomics and physiology. In addition, it emphasizes the various molecular mechanisms affected by small RNA and their applications in supporting plant growth and survival. Final sections cover the most recent advancements in small RNA mediated plant genomics, metabolomics, proteomics and physiology. Presents foundational information about small RNA biology and regulation in plants Includes small RNA pathway advances Describes the application and scope of small RNA technology for agricultural stability

Analysis of Small RNAs Associated with Plant Senescence

Analysis of Small RNAs Associated with Plant Senescence
A Book

by Amnon Lers

  • Publisher : Unknown Publisher
  • Release : 2013
  • Pages : 52
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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The Role of MicroRNAs in Plants

The Role of MicroRNAs in Plants
A Book

by Anthony A. Millar

  • Publisher : MDPI
  • Release : 2020-05-27
  • Pages : 174
  • ISBN : 3039287303
  • Language : En, Es, Fr & De
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Discovered in plants at the turn of the century, microRNAs (miRNAs) have been found to be fundamental to many aspects of plant biology. These small (20–24 nt) regulatory RNAs are derived via processing from longer imperfect double-stranded RNAs. They are then incorporated into silencing complexes, which they guide to (m)RNAs of high sequence complementarity, resulting in gene silencing outcomes, either via RNA degradation and/or translational inhibition. Some miRNAs are ancient, being present in all species of land plants and controlling fundamental processes such as phase change, organ polarity, flowering, and leaf and root development. However, there are many more miRNAs that are much less conserved and with less understood functions. This Special Issue contains seven research papers that span from understanding the function of a single miRNA family to examining how the miRNA profiles alter during abiotic stress or nutrient deficiency. The possibility of circular RNAs in plants acting as miRNA decoys to inhibit miRNA function is investigated, as was the hierarchical roles of miRNA biogenesis factors in the maintenance of phosphate homeostasis. Three reviews cover the potential of miRNAs for agronomic improvement of maize, the role of miRNA-triggered secondary small RNAs in plants, and the potential function of an ancient plant miRNA.

Identification of Small RNA Producing Genes in the Moss Physcomitrella Patens

Identification of Small RNA Producing Genes in the Moss Physcomitrella Patens
A Book

by Ceyda Coruh

  • Publisher : Unknown Publisher
  • Release : 2014
  • Pages : 129
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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In plants, a significant fraction of the genome is responsible for making regulatory small RNAs. These ubiquitous, endogenous small RNAs are currently categorized into two groups: microRNAs (miRNAs) and small interfering RNAs (siRNAs). They are produced by Dicer-Like (DCL) proteins and utilized by Argonaute (AGO) proteins to guide repressive regulation of target mRNAs and/or chromatin selected on the basis of small RNA-target complementarity at the transcriptional or post-transcriptional levels. 21 nt miRNAs and 24 nt heterochromatic siRNAs are the two major types of small RNAs found in angiosperms (flowering plants). The small RNA populations in angiosperms are dominated by 24 nt heterochromatic siRNAs which derive from intergenic, repetitive regions and mediate DNA methylation and repressive histone modifications to targeted loci in angiosperms. However, the existence and extent of heterochromatic siRNAs in other land plant lineages has been less clear. The failure to identify 24 nt heterochromatic siRNA accumulation by initial small RNA-seq attempts from several other species including gymnosperms (Dolgosheina et al. 2008), and the lycophyte Selaginella (Banks et al. 2011) has raised the question whether the heterochromatic siRNA pathway is angiosperm-specific. Previous work in Physcomitrella provides evidence that supports the hypothesis that the heterochromatic siRNA pathway is an ancestral trait that was present in the last common ancestor of bryophytes and all other subsequently diverged lineages of plants (Cho et al. 2008). However, comprehensive annotation of small RNA genes in the basal lineage Physcomitrella is still lacking and an investigation of small RNA populations in this model organism would shed more light on the evolution of regulatory small RNA pathways in land plants.With the advent of next-generation sequencing, small RNA-seq has become a good resource for producing enormous volumes of data on plant miRNA and siRNA expression. Therefore, we produced extensive small RNA-seq data (more than 108 mapped reads) to annotate small RNA genes in ten-day-old protonemata from wild-type Physcomitrella. ShortStack is a recently developed tool to analyze small RNA-seq data with respect to a reference genome and to provide a comprehensive annotation of de novo discovered small RNA genes. Utilizing ShortStack, we identified 16,024 distinct DCL-dependent small RNA producing loci and classified them into five different groupings based on the RNA secondary structure evaluation and the predominant small RNA size. These Physcomitrella small RNA producing loci is now available in our developing web server (plantsmallrnagenes.psu.edu).In order to investigate the features of heterochromatic siRNAs, we revisited the Physcomitrella genome to find functional orthologs of the heterochromatic siRNA genes. We identified candidate proteins that could potentially be involved in the accumulation of heterochromatic siRNAs and created mutants to perform genetic analysis. With the power of consistent biological replicates, differential expression analysis on small RNA-seq data revealed that the accumulation of siRNAs from 23-24 nt siRNA loci depends upon Physcomitrella homologs of DICER-LIKE 3 (DCL3), RNA-DEPENDENT RNA POLYMERASE 2 (RDR2), and the largest sub-unit of DNA-DEPENDENT RNA POLYMERASE IV (Pol IV), with the largest sub-unit of a Pol V homolog contributing to expression at a smaller subset of the loci. These data lead us to conclude that Physcomitrella utilizes a heterochromatic siRNA pathway fundamentally similar to that of flowering plants. In contrast to angiosperms, we identified a Physcomitrella-specific MINIMAL DICER-LIKE (mDCL) gene, which lacks the N-terminal helicase domain typical of DCL proteins, but contains the 'catalytic core' (the PAZ domain and the twin RNAseIII domains) of the DCL proteins. We showed that Physcomitrella heterochromatic siRNAs are not solely composed of 24 nt siRNAs as seen in angiosperms, but rather contain equal mixtures of 23 and 24 nt siRNAs. Interestingly, Physcomitrella-specific mDCL is found to be specifically required for 23 nt siRNA accumulation from these loci. Overall, our data lead us to conclude that heterochromatic siRNAs, and their biogenesis pathways, are largely but not completely identical between angiosperms and basal land plants, as represented by the bryophyte, Physcomitrella patens.Significant effort has been made in small RNA gene annotation, but this progress has been unevenly distributed, with MIRNA loci in particular receiving a disproportionate share of the attention. We believe that further efforts at comprehensive and consistent reference annotations of all types of small RNA producing genes, and improvements in the dissemination of such annotations, will greatly enhance the future of plant genomics. Our developing web server (plantsmallrnagenes.psu.edu), which currently hosts small RNA gene annotations of just two species, Amborella trichopoda and Physcomitrella patens, is intended to serve this purpose. In particular, we look forward to the day when researchers seeking to study small RNAs will be liberated from the need to "re-invent the wheel" by generating their own de novo annotations of small RNA-producing genes with each analysis.

Bioinformatics Tools to Classify and Characterize Plant Small RNAs

Bioinformatics Tools to Classify and Characterize Plant Small RNAs
A Book

by Reza Hammond

  • Publisher : Unknown Publisher
  • Release : 2019
  • Pages : 140
  • ISBN : 9781687974853
  • Language : En, Es, Fr & De
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Small RNAs (sRNAs) in plants are a highly abundant class of noncoding RNAs that regulate silencing processes, mostly on the basis of sequence complementarity. There are several classes of small RNA that differ in both their biogenesis and mode of silencing. With the advent of next generation sequencing technologies, sRNA presence can be quantified at a relatively low cost and in a short amount of time. Due to the large amount of data however, there are many challenges associated with the classification of individual sRNAs in these datasets. It is for this reason that I have developed several tools to assist in the classification of sRNAs. The first of these tools is miRador, a novel micro RNA (miRNA) prediction tool that I designed to predict miRNAs from a set of sRNA libraries. This tool utilizes a newly established set of criteria for annotating plant miRNAs which enable it to predict miRNAs with a high level of accuracy. sPARTA is a miRNA target prediction and validation tool which utilizes Parallel Analysis of RNA Ends (PARE) sequencing libraries to validate target cleavage facilitated by a miRNA. Utilizing sPARTA in conjunction with miRador allows for the prediction and validation of novel miRNAs for a variety of plant species. In this dissertation, I utilize this pipeline on maize sRNA data to predict four novel miRNAs. I also present a clustering script that makes use of the Meyers Lab database systems to quickly cluster a variety of sequencing data. Using this approach, I attempted to characterize 24-nt phasiRNA producing loci for two separate projects, presented as case studies. In the first case study, we identify that 24-nt phasiRNAs in maize may be required for robust fertility at higher growth temperatures. In the second case study, we identify that asparagus generates inverted repeat-derived phasiRNAs from mRNAs lacking a miR2275 target site. Taken together, these tools improve scientists ability to characterize various classes of small RNAs, and their effects on their encoding genomes.

RNA-Based Technologies for Functional Genomics in Plants

RNA-Based Technologies for Functional Genomics in Plants
A Book

by Guiliang Tang,Sachin Teotia,Xiaoqing Tang,Deepali Singh

  • Publisher : Springer
  • Release : 2021-05-13
  • Pages : 427
  • ISBN : 9783030649937
  • Language : En, Es, Fr & De
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This book offers a unique and comprehensive overview of key RNA-based technologies, as well as their development and applications for the functional genomics of plant coding and non-coding genes. It focuses on the latest as well as classical RNA-based techniques used for studies on small RNAs, long non-coding RNAs and protein-coding genes. These techniques chiefly focus on target mimics (TMs) and short tandem target mimics (STTMs) for small RNAs, and artificial microRNAs (amiRNAs), RNA interference (RNAi) and CRISPR/Cas for genes. Furthermore, the book discusses the latest trends in the field and various modifications of the above-mentioned approaches, and explores how these RNA-based technologies have been developed, applied and validated as essential technologies in plant functional genomics. RNA-based technologies, their mechanisms of action, their advantages and disadvantages, and insights into the further development and applications of these technologies in plants are discussed. These techniques will enable the users to functionally characterize genes and small RNAs through silencing, overexpression and editing. Gathering contributions by globally respected experts, the book will appeal to students, teachers and scientists in academia and industry who are interested in horticulture, genetics, pathology, entomology, physiology, molecular genetics and breeding, in vitro culture & genetic engineering, and functional genomics.

Origins and Evolution of Plant MicroRNA Genes

Origins and Evolution of Plant MicroRNA Genes
A Book

by Noah Fahlgren

  • Publisher : Unknown Publisher
  • Release : 2010
  • Pages : 122
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Eukaryotic small RNA (~20-30 nucleotides) are diverse regulatory molecules that repress gene expression at the transcriptional and post-transcriptional levels, defend hosts against invading viruses and defend genomes against selfish DNA elements. Small RNA populations are studied by high-throughput sequencing of the total small RNA fraction isolated from cells, however, the sequencing depth achieved by next-generation platforms makes genome mapping and analysis computationally intensive with standard methods. Here, methods to generate, parse, map, quantify, standardize and analyze large small RNA data sets are presented. This work demonstrates that small RNA profiling is quantitative and reproducible and that statistical methods can be adapted to facilitate objective comparisons between small RNA and small RNA populations. Plants RNA silencing systems, including microRNA (miRNA), are important components of complex regulatory networks. Several plant MIRNA gene families and their target gene families are ancient, but over two-thirds of Arabidopsis MIRNA families are species-specific or restricted to the Brassicaceae lineage. In this work, the repertoires of MIRNA in the closely related species A. thaliana, A. lyrata and Capsella rubella were studied. Despite the relatively recent speciation of A. thaliana and A. lyrata ~10 million years ago, at least 13% of the MIRNA from each is species-specific. Additionally, 24-46 Arabidopsis MIRNA families arose after the Arabidopsis-Capsella split ~20 million years ago, supporting a net birth-death rate of 1.2-2.3 MIRNA per million years. These data, and data from other species, suggest that MIRNA are born and lost frequently throughout the evolution of plants. Further, evidence for the recent origin of 32 MIRNA families by duplication events, mostly of protein-coding loci, was demonstrated, but only ~50% of these loci are predicted miRNA targets. Despite the link between MIRNA formation and potential target loci, only 25 young A. thaliana miRNA have verified targets. As a group, young miRNA tend to be expressed weakly, processed imprecisely and lack biologically relevant targets. Additionally, variation between young Arabidopsis miRNA was significantly higher than for ancient miRNA, suggesting that most of the young MIRNA are more likely evolving neutrally. Together, the data presented argue that most young MIRNA are evolutionarily transient.

Analysis of Arabidopsis Thaliana RNA Dependent RNA Polymerase Mutants Reveals Novel Small RNAs and Improves Existing Annotations

Analysis of Arabidopsis Thaliana RNA Dependent RNA Polymerase Mutants Reveals Novel Small RNAs and Improves Existing Annotations
A Book

by Seth Polydore

  • Publisher : Unknown Publisher
  • Release : 2019
  • Pages : 129
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Small RNAs are molecules that regulate key physiological functions in land plants through transcriptional and post-transcriptional silencing. Small RNAs can be divided into two major categories: microRNAs (miRNAs) which are precisely processed from single-stranded, stem-and-loop RNA precursors, and short interfering RNAs (siRNAs), which are derived from double-stranded RNA precursors. The processing of small RNA precursors is performed by RNASEIII-like endonucleases known as DICER-LIKE (DCL) proteins. DCLs hydrolyze small RNA precursors into 20-24 nt, double-stranded RNA molecules. One strand of these double-stranded RNA molecules is loaded into ARGONAUTE (AGO) proteins. AGO uses the loaded single-stranded RNA to target other RNA molecules for repression. Depending on the type of small RNA in question, a third type of protein family is necessary for small RNA biogenesis RNA DEPENDENT RNA POLYMERASE (RDR). RDRs convert single-stranded RNAs into double-stranded RNAs, which can be processed by DCL proteins. Small RNAs have been the subject of intense research since their discovery and much has been discovered about their modes of biogenesis and functions. However, some questions remain unanswered and some issues have arisen: Firstly, there are many multi-mapping reads, which comprise the majority of land plant small RNAs in a typical land plant small RNA transcriptome. Due to the difficulties in dealing with multi-mapped reads, in a typical small RNA study most small RNA data are ultimately ignored or incorrectly aligned. Secondly, many known types of small RNAs are incompletely or incorrectly annotated. Many MIRNA annotations in particular are known to be erroneous. In my research, I utilize mutants of the RDR genes known to be involved in small RNA biogenesis in order to re-examine known annotations of different types of small RNAs in Arabidopsis thaliana. I also utilize these mutants in order to determine if there are other, previously unknown types of small RNAs encoded in the A. thaliana genome. Ultimately, I found 58 erroneous MIRNA annotations and 38 small RNA loci that do not follow any known methods of small RNA biogenesis.siRNAs can be further subdivided into several different groups, including phased siRNAs (phasiRNAs) and heterochromatic siRNAs (hc-siRNAs). Predominantly 24 nt in length, hc-siRNAs are produced from the biochemical actions of DCL3, DNA DEPENDENT RNA POLYMERASE (Pol) IV, and RDR2. phasiRNAs are produced from the biochemical actions of Pol II, RDR6, and DCL4. In every land plant sequenced to date, 21-22 nt dominated phasiRNAs are well represented, but 24 nt-dominated phasiRNAs have only been identified in certain monocots thus far, especially Asparagus officinalis, Hemerocallis lilioasphodelus, Lilium maculatum, and the Poaceae family. I was interested in elucidating whether or not the A. thaliana genome encoded these 24 nt-dominated phasiRNAs. I therefore carefully examined A. thaliana 24 nt-dominated loci that consistently passed PHAS-locus detecting algorithms using multiple methods and found that they are likely just heterochromatic siRNAs (hc-siRNAs). Since 24 nt-dominated siRNA loci are very numerous in angiosperms, they serve as potential source of false-positives during searches for phasiRNA-generating loci. Overall, this analysis shows that using existing phasing score algorithms to detect novel PHAS loci can lead to false positives.

Computational Methods for Functional Analysis of Plant Small RNAs Using the RNA Degradome

Computational Methods for Functional Analysis of Plant Small RNAs Using the RNA Degradome
A Book

by Joshua Thody

  • Publisher : Unknown Publisher
  • Release : 2020
  • Pages : 129
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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RNA Interference

RNA Interference
Methods for Plants and Animals

by Dr. Tim Doran,Chris Helliwell

  • Publisher : CABI
  • Release : 2009
  • Pages : 257
  • ISBN : 1845934105
  • Language : En, Es, Fr & De
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This methods manual provides an introduction to RNA interference, the theory behind its many applications, and specific protocols for RNAi, in organisms from plants and C.elegans to Drosophila and mammals. There are also chapters covering small hairpin RNAs and viral-induced gene silencing.

Function and Maintenance of Trans-species Small RNAs in the Cuscuta Genus of Parasitic Plants

Function and Maintenance of Trans-species Small RNAs in the Cuscuta Genus of Parasitic Plants
A Book

by Nathan Johnson

  • Publisher : Unknown Publisher
  • Release : 2019
  • Pages : 129
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Regulatory small RNAs are important components involved in the regulation of many cellular processes in eukaryotes. Typically 20-24 nucleotides in length, small RNAs can repress gene expression through directed degradation of messenger RNA or through the recruitment/maintenance of repressive chromatin marks in the genome. In plants, large-scale annotations of small RNAs have languished despite the definition of several common classes (microRNAs, secondary siRNAs, heterochromatic siRNAs). ShortStack, a tool developed for the alignment and annotation of small RNAs from high-throughput sequencing reads has made large advancements in this process. The alignment step in small RNA analysis represents a particular challenge. In this step, reads are aligned to the genome based on sequence identity, however large proportions of small RNA sequencing reads (>50%) are known to map ambiguously to multiple places in the genome. This motivated the improvement of algorithms for the placement of these reads. Utilizing the density of unambiguously aligned reads in vicinity as a guiding principle, ShortStack chooses a place for ambiguously mapping reads in the genome. With both simulated and real datasets, this method greatly increases alignment precision for a modest reduction in sensitivity, compared to widely-used alternatives. It also improves the approximation of small RNA locus expression miRNAs. This tool was tested with small-RNA-sequencing libraries from three different plants, showing its superior performance with varied input. Through this improved algorithm, alignments and resulting annotations have minimized false positive rates, improving their quality and enhancing the results obtained from small-RNA-sequencing experiments. Species-species interactions are of a particular interest for small RNA research. Work on fungal and oomycete pathogens of plants show that small RNAs are able to regulate gene expression in trans-species manner. Recently, the parasitic plant genus Cuscuta has been a focus in this context, as it has been shown that bi-directional movement of biomolecules readily occurs in its interaction with hosts. Small-RNA-sequencing of Cuscuta campestris parasitizing the host Arabidopsis thaliana showed that numerous small RNAs are highly expressed in the host-parasite interface. Many of these were shown to be microRNAs and indeed target messenger RNAs originating from the host. These trans-species microRNAs were expressed similarly when parasitizing different hosts, but lack of expression on non-living hosts, hinting that a host-based trigger might be required. Secondary siRNAs resulting from targeting by these microRNAs are produced using protein machinery from the host, shown through their loss on mutant host plants. This implies processing takes place inside the host tissue. However, loss of secondary siRNAs did not measurably affect the growth of the parasite. Growing the parasite on hosts with loss of function mutations in targets of trans-species microRNAs showed enhanced growth for several targets, indicating their importance in host defense. These data broaden the picture of how small RNAs can be used in species interactions, making the case that this process may be used to enhance parasitic success. It is not clear how trans-species microRNAs from C. campestris are able to maintain targeting of host messenger RNAs in the light of adaptive pressures. To investigate this, small RNAs from host-parasite interactions in three more Cuscuta species were sequenced, including several different isolates within species. Many small RNAs were found to be highly expressed in the host-parasite interface. Targeting of host messenger RNAs was confirmed for several small RNAs in all species and isolates, indicating that the mechanism of trans-species small RNAs may be present throughout Cuscuta. Grouping distantly similar small RNAs based on sequence shows superfamilies that are retained between species groups. This analysis shows that several similar small RNAs are produced in a single species or isolate, accounting for variation in the target sites among possible hosts. This may also be used as a way to target numerous homologous messenger RNAs in a single host, regulating entire gene families. This provides a mechanism by which Cuscuta can ensure targeting despite any selection in the host to invalidate targeting. This discovery is a major expansion of the scope of trans-species small RNAs in plants and hints that this process may be widespread in nature.

Supervised Machine Learning for Small RNA Informatics and Big Data Analytics in Plants

Supervised Machine Learning for Small RNA Informatics and Big Data Analytics in Plants
A Book

by Parth Patel

  • Publisher : Unknown Publisher
  • Release : 2019
  • Pages : 188
  • ISBN : 9781392010440
  • Language : En, Es, Fr & De
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My dissertation work focused on (1) the development of supervised machine learning approaches for plant small RNAs (i.e., microRNAs (miRNAs) and their secondary siRNA products, and heterochromatic siRNAs (hc-siRNAs)), and (2) the application of these data analytics tools to analyze next-generation sequencing (NGS) data of increasing size and complexity, bordering on 'big data'. Male germline associated 21- and 24-nt phased siRNAs (reproductive phasiRNAs) are highly enriched and numerous in the Poaceae (grasses) and crucial for reproductive tissue development and success. Little is known about the characteristics and functions of reproductive phasiRNAs in the grasses despite significant genomic resources, experimental data, and a growing set of computational tools. Given the important role grasses such as maize and rice play as a prime food-source in many countries and as influential factors in the global economy, a deeper understanding about their characteristics, possible targets and functions, and biogenesis is required. I present a new machine learning based approach for in-depth characterization of phasiRNAs, demonstrating highly informative sequence-based and positional features, strand specificity, and position-specific nucleotide biases potentially influencing AGO sorting. One major goal of my work was to utilize these tools as well as several other co-published tools to assess the landscape of sRNAs, including phasiRNAs and miRNAs (especially miR2118 and miR2275, triggers of reproductive phasiRNAs) in diverse 41 angiosperm species (38 monocot species, including families from the Acorales and Arecales to the Zingiberales) dating back to at least 200 million years ago. I demonstrate the origins and conservation of miR2118 and miR2275 across the monocot species and show that 21- and 24-PHAS loci (the sources of reproductive phasiRNAs) are particularly numerous and abundant in the inflorescence tissues of the grasses. I show that in silico trigger identification indicates diverse mechanisms for the production of 21- and 24-nt phasiRNAs. I conclude that the prevalence of reproductive phasiRNAs in the flowering plants beyond the grasses shows their broad roles and importance in plant reproductive tissue development.

Gating of Small RNA Mobility in Plant Stem Cell Niches

Gating of Small RNA Mobility in Plant Stem Cell Niches
A Book

by Simon Klesen

  • Publisher : Unknown Publisher
  • Release : 2020
  • Pages : 129
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Testing the Complementarity Requirements of Plant MicroRNA-target Interactions

Testing the Complementarity Requirements of Plant MicroRNA-target Interactions
A Book

by Qikun Liu

  • Publisher : Unknown Publisher
  • Release : 2014
  • Pages : 129
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Small RNAs are a group of regulatory RNAs of 20-30 nucleotides (nt) that are involved in diverse cellular processes across multiple eukaryotic kingdoms, including animals, plants and fungi. In complex with Argonaute (AGO) effector proteins, they recognize target RNA transcripts (coding and non-coding) based on sequence complementarity, and function as negative regulators at both transcriptional and post-transcriptional levels.It is widely accepted that plant microRNA-target interactions usually require a high degree of complementarity to trigger target cleavage. However, the sequence requirements for target repression at protein level through slicing independent mechanisms have never been systematically studied.Utilzing a self-designed dual-luciferase reporter system, I systematically examined the complementarity requirements for microRNA function through Nicotiana benhtamiana transient assay. I found that changes of the mRNA accumulation accounts for almost all observed regulatory effects. Comparison among those naturally occurring targets indicated that mismatches located near the miRNA 5'ends were more disruptive to miRNA function than those occurred near miRNA 3'ends. Actually, certain naturally occurring targets with unpaired bases only present at the miRNA 3'ends can even carry stronger regulatory efficiency than perfectly paired sites when position in 3'-untranslated region (UTR), but not open reading frame (ORF). I found that this was largely due to different behavior of perfectly paired sites, when placed in different contexts (ORF vs. 3'-UTR). While up to 3 mismatches could be tolerated at the 3'end without affecting the target efficacy, base pairing patterns that are typical of the known configuration of animal microRNA-target duplex did not trigger any detectable level of target down-regulation.Through collaboration we identified a non-canonical plant miRNA-target pairing pattern, where a 6-nt bulge on the target in between nucleotide 6 and 7 relative to the miRNA was tolerated. I demonstrated that this is very unique in terms of both the miRNA involved and the position of the bulge.De novo annotation and quantification of small RNA producing loci were also carried out in N. benthamiana. A total of 43652 small RNA producing loci, including 177 MIRNA, 4573 hairpin_RNA (hpRNA), and 38902 siRNA loci were identified. 95 MIRNA loci belonging to 37 plant known microRNA families were found. Comparing to the novel MIRNAs, these known MIRNA genes are processed with higher accuracy, and expressed more abundantly. Although small RNA clusters mainly producing 23 to 24 nt siRNA dominated hpRNA and siRNA loci, and 24-nt small RNAs are the most abundant small RNA species, 20 to 21 nt siRNAs are more robustly generated from certain highly active loci. Loci that give rise to longer small RNAs (23-24 nts) are generally less repetitive than those producing short small RNAs (20-22 nts). This is true for all types of annotated loci (MIRNA, hpRNA, and siRNA). MIRNA loci are enriched in genic regions and depleted in repeat regions, whereas siRNA loci, especially 23-24 nt groups, tend to occupy regions enriched for repetitive elements.

Regulation of Gene Expression by Small RNAs

Regulation of Gene Expression by Small RNAs
A Book

by Rajesh K. Gaur,John J. Rossi

  • Publisher : CRC Press
  • Release : 2009-04-27
  • Pages : 440
  • ISBN : 1420008706
  • Language : En, Es, Fr & De
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New Findings Revolutionize Concepts of Gene FunctionEndogenous small RNAs have been found in various organisms, including humans, mice, flies, worms, fungi, and bacteria. Furthermore, it's been shown that microRNAs acting as cellular rheostats have the ability to modulate gene expression. In higher eukaryotes, microRNAs may regulate as much as 50 p

Plant Genomes

Plant Genomes
A Book

by Jean-Nicolas Volff

  • Publisher : Karger Medical and Scientific Publishers
  • Release : 2008-01-01
  • Pages : 145
  • ISBN : 3805584911
  • Language : En, Es, Fr & De
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Recent major advances in the field of comparative genomics and cytogenomics of plants, particularly associated with the completion of ambitious genome projects, have uncovered astonishing facets of the architecture and evolutionary history of plant genomes. The aim of this book was to review these recent developments as well as their implications in our understanding of the mechanisms which drive plant diversity. New insights into the evolution of gene functions, gene families and genome size are presented, with particular emphasis on the evolutionary impact of polyploidization and transposable elements. Knowledge on the structure and evolution of plant sex chromosomes, centromeres and microRNAs is reviewed and updated. Taken together, the contributions by internationally recognized experts present a panoramic overview of the structural features and evolutionary dynamics of plant genomes.This volume of Genome Dynamics will provide researchers, teachers and students in the fields of biology and agronomy with a valuable source of current knowledge on plant genomes.