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

Written By Saima Shahid
Discovery of Endogenous Plant Small RNAs and Their Role in Trans species Gene Regulation
  • Publsiher : Unknown
  • Release : 20 June 2021
  • ISBN : 0987654321
  • Pages : 212 pages
  • Rating : 4/5 from 21 reviews
GET THIS BOOKDiscovery of Endogenous Plant Small RNAs and Their Role in Trans species Gene Regulation


Read or download book entitled Discovery of Endogenous Plant Small RNAs and Their Role in Trans species Gene Regulation written by Saima Shahid which was release on 20 June 2021, this book published by Unknown. Available in PDF, EPUB and Kindle Format. Book excerpt: 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.

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
  • Author : Saima Shahid
  • Publisher : Unknown
  • Release Date : 2017
  • Total pages : 212
  • ISBN : 0987654321
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Summary : 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 ...

Non Coding RNAs in Plants

Non Coding RNAs in Plants
  • Author : Volker A. Erdmann,Jan Barciszewski
  • Publisher : Springer Science & Business Media
  • Release Date : 2011-07-20
  • Total pages : 510
  • ISBN : 0987654321
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Summary : 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 ...

Plant Small RNA

Plant Small RNA
  • Author : Praveen Guleria,Vineet Kumar
  • Publisher : Academic Press
  • Release Date : 2020-02-19
  • Total pages : 635
  • ISBN : 0987654321
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Summary : 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 Small RNA

Plant Small RNA
  • Author : Praveen Guleria,Vineet Kumar
  • Publisher : Academic Press
  • Release Date : 2020-02
  • Total pages : 660
  • ISBN : 0987654321
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Summary : 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 ...

Identification of Small RNA Producing Genes in the Moss Physcomitrella Patens

Identification of Small RNA Producing Genes in the Moss Physcomitrella Patens
  • Author : Ceyda Coruh
  • Publisher : Unknown
  • Release Date : 2014
  • Total pages : 212
  • ISBN : 0987654321
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Summary : 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 ...

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
  • Author : Nathan Johnson
  • Publisher : Unknown
  • Release Date : 2019
  • Total pages : 212
  • ISBN : 0987654321
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Summary : 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 ...

The Role of MicroRNAs in Plants

The Role of MicroRNAs in Plants
  • Author : Anthony A. Millar
  • Publisher : MDPI
  • Release Date : 2020-05-27
  • Total pages : 174
  • ISBN : 0987654321
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Summary : 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 ...

RNA Based Technologies for Functional Genomics in Plants

RNA Based Technologies for Functional Genomics in Plants
  • Author : Guiliang Tang,Sachin Teotia,Xiaoqing Tang,Deepali Singh
  • Publisher : Springer
  • Release Date : 2021-05-13
  • Total pages : 427
  • ISBN : 0987654321
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Summary : 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 ...

Bioinformatics Tools to Classify and Characterize Plant Small RNAs

Bioinformatics Tools to Classify and Characterize Plant Small RNAs
  • Author : Reza Hammond
  • Publisher : Unknown
  • Release Date : 2019
  • Total pages : 140
  • ISBN : 0987654321
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Summary : 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 ...

Analysis of Small RNAs Associated with Plant Senescence

Analysis of Small RNAs Associated with Plant Senescence
  • Author : Amnon Lers
  • Publisher : Unknown
  • Release Date : 2013
  • Total pages : 52
  • ISBN : 0987654321
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Summary : Download or read online Analysis of Small RNAs Associated with Plant Senescence written by Amnon Lers, published by which was released on 2013. Get Analysis of Small RNAs Associated with Plant Senescence Books now! Available in PDF, ePub and Kindle....

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
  • Author : Seth Polydore
  • Publisher : Unknown
  • Release Date : 2019
  • Total pages : 212
  • ISBN : 0987654321
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Summary : 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 ...

Testing the Complementarity Requirements of Plant MicroRNA target Interactions

Testing the Complementarity Requirements of Plant MicroRNA target Interactions
  • Author : Qikun Liu
  • Publisher : Unknown
  • Release Date : 2014
  • Total pages : 212
  • ISBN : 0987654321
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Summary : 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 ...

Genome wide Analysis of Plant Heterochromatic Short interfering RNAs

Genome wide Analysis of Plant Heterochromatic Short interfering RNAs
  • Author : Feng Wang
  • Publisher : Unknown
  • Release Date : 2016
  • Total pages : 212
  • ISBN : 0987654321
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Summary : 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 (...

Gating of Small RNA Mobility in Plant Stem Cell Niches

Gating of Small RNA Mobility in Plant Stem Cell Niches
  • Author : Simon Klesen
  • Publisher : Unknown
  • Release Date : 2020
  • Total pages : 212
  • ISBN : 0987654321
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Summary : Download or read online Gating of Small RNA Mobility in Plant Stem Cell Niches written by Simon Klesen, published by which was released on 2020. Get Gating of Small RNA Mobility in Plant Stem Cell Niches Books now! Available in PDF, ePub and Kindle....

Origins and Evolution of Plant MicroRNA Genes

Origins and Evolution of Plant MicroRNA Genes
  • Author : Noah Fahlgren
  • Publisher : Unknown
  • Release Date : 2010
  • Total pages : 122
  • ISBN : 0987654321
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Summary : 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 ...