Biotech Articles
Publish Your Research Online
Get Recognition - International Audience

Request for an Author Account   |   Login   |   Submit Article
 
 
HOME FAQ TOP AUTHORS FORUMS PUBLISH ARTICLE
 
 

Biogenesis of siRNA: Exogenous or Endogenous?

BY: Dr. Kishor Uttamrao Tribhuvan | Category: Biotech-Research | Submitted: 2017-03-21 11:32:14
       No Photo
Article Summary: "siRNA generated in plants and animals not only exogenously originated in response to infection of viruses, bacteria or other parasitic organism but also it originated from genes located in pericentromeric, transposable element and repetitive region of the host genome. RNA polymerase IV and RNA polymerase V is responsible for bi.."


Share with Facebook Share with Linkedin Share with Twitter Share with Pinterest Email this article
     


Biogenesis of siRNA: Exogenous or Endogenous?
Authors: Kishor U Tribhuvan1, Deepak V Pawar1, Anshul Watts1, Archana Watts2, Ravi Prakash Saini1
1ICAR-National Research Centre on Plant Biotechnology, New Delhi110012
2 ICAR-Division of Plant Physiology, Indian Agriculture Research Institute, New Delhi 110012


In the last decade utilization double stranded small RNA was started for silencing of desired genes through the phenomenon of RNA interference (RNAi). There are many types of small RNAs that have been discovered [microRNA (miRNA), Piwi-interacting RNA (piRNA), small interfering RNA (siRNA), small nucleolar RNA (snoRNAs), tRNA-derived small RNA (tsRNA), small rDNA-derived RNA (srRNA), small nuclear RNA/ U-RNA], among these miRNAs and siRNAs are rigorously utilized in RNAi gene silencing experiment. The miRNAs originate from endogenously microRNA (MIR) gene families, whereas siRNA originate exogenously in the host organism from genome of infected viruses, bacteria or other parasitic organism. With the advancement of sequencing technologies high throughput sequencing is presently being applied for sequencing of small RNA libraries and it became evident that miRNA represent only a tiny fraction of the total complement of small RNA present in the plant genome. For example in A. thaliana only ~1200 to 1300 MIR genes are present whereas more than ten thousands of small RNAs are found in inflorescence tissue. This variation between miRNA genes and number of small RNA present in the cell enforce to think about biogenesis of small RNA source.

Recent studies carried out in flies and mammals using high throughput sequencing show that endogenous biogenesis of small RNAs can take place from genes other than MIR gene family, called endogenous siRNA (endo-siRNA). These studies have also helped to understand that miRNAs are endogenously originated from MIR genes and siRNAs can be originated from pericentromeric region, transposable element and repetitive region of the genome. Transcription of MIR genes is carried out by RNA polymerase II (RNA Pol II) to produce precursor miRNA in plant and animal. In yeast (Schizosaccharomyces pombe) RNA Pol II is also carries out synthesis of siRNAs from pericentromeric repeat region and these processed siRNAs direct pericentromeric heterochromatin formation by recruiting histone methyltransferases to modify the chromatin. In case of plants, RNA polymerase IV (RNA Pol IV) and RNA polymerase V (RNA Pol V) is responsible for biosynthesis of siRNAs from pericentromeric, transposable element and other repeat regions of the genome. The subunit composition of these two polymerases indicate that these polymerases are evolved from RNA polymerase II because they share a number of subunits with RNA polymerase II. Around 90% of all endogenous siRNA are produced from RNA polymerase IV. It is thought that RNA pol IV transcribes heterochromatic DNA to produce siRNA precursor, although presence DNA dependent RNA polymerase activity is not detected so far and requires a putative chromatin remolding protein CLASSY1 for siRNA biogenesis. It is also found that majority of endogenous siRNAs is disappear in RNA pol IV mutant, the small quantity of siRNAs that exists in these mutants may be produced from other polymerase such as RNA Pol I, II and III. It is also well known that RNA Pol V is essential for siRNA mediated DNA methylation and also promotes siRNA accumulation at some loci. The main function of RNA Pol V is to methylate DNA or histone at the siRNA generating loci, promoting siRNAs biogenesis in indirect way, because DNA and histone methylation may in turn mark these regions for siRNA production in a feed forward loop. With the help of DRD1 (a chromatin remolding protein) and DMS3 (structural maintenance of chromosome hinge domain protein) RNA Pol V generates noncoding transcript which is further used for siRNA mediated heterochromatin formation. RNA Pol V is also required for siRNA mediated DNA methylation and histone H3 lysine 9 (H3K9) methylation at heterochromatic loci hence it is thought that these transcripts recruit siRNAs to the genomic loci for chromatin modification. In addition to these, RNA Pol V can also physically interact with AGO4 through its GW-WG motifs, hence RNA pol V may serve the dual function of generating transcript targeted by AGO4 bound siRNA and recruiting AGO4 and associated siRNA through physical interaction.

BA_3829

Fig. 1: Biogenesis of heterochromatic siRNAs. 1) heterochromatic loci are transcribed by RNAPol IV into ssRNA transcript, 2) ssRNA are copied into dsRNA by RDR2, 3) 24 nucleotide siRNA are processed from the dsRNA by DCL3 and methylated by HEN1, 4) Loaded in to AGO4 containing RISCs, 5) The siRNA recruited to the source loci by transcript generated by RNA Pol V

In animal system Dicer is one of the important enzyme that cleaves double stranded RNA (dsRNAs) and pre-micro RNAs into 20–25 bp dsRNA fragments and miRNAs, respectively. In plants, homolog of dicer is Dicer like (DCL) protein involved in similar kind of function. Majority of miRNAs are processed by DCL1 but in some cases it is replaced by DCL4. Whereas, DCL3 involved in processing of heterochromatic loci and produces 24 nt long siRNAs. In plant every DCL have specificity for its substrate and other DCL access the substrate in the absence of primary DCL such as production of transgene, viral and endogenous siRNA.

Argonaute (AGO) family proteins play an important role in RNAi as they are components of the RNA-induced silencing complex (RISC). These proteins bind to different classes of small non-coding RNAs, miRNAs, siRNAs and piRNAs. Small RNAs guide AGO proteins to their specific targets through sequence complementarity, which then leads to either cleavage of the mRNAs or translation inhibition. AGO proteins contain four characteristic domains: N- terminal, PAZ, Mid and a C-terminal PIWI domain. The PAZ domain is an RNA binding domain which recognizes the 3' end of both siRNA and miRNA, in a sequence independent manner and also targets the mRNA for cleavage or translation inhibition. PAZ domain bind to 2-nucleotide single stranded overhang in small RNA duplex and play a role in loading of duplex on to the protein, then the dsRNA unwound such that only one strand retained in the RISC. The PIWI domain possess RNase activity essential for small RNA guided cleavage of target mRNA. There are ten AGO protein found in A. thaliana among these AGO1 bind most of miRNAs, trans acting siRNA (ta-siRNA) and transgene siRNA and possesses slicing activity and mediate the function these small RNA in vivo. AGO1 and AGO10 are most related to each other and both are involved in miRNA mediated translational repression of target mRNA. Whereas AGO4 and AGO6 are involved for processing of endogenous siRNA to silence transposons and repeat sequences.

RNA dependent RNA polymerase (RDR) is required for amplification siRNA or miRNA, it uses ssRNAs as templates and generate ds RNA. In case of A. thaliana among the six RDR genes, RDR1, RDR2 and RDR6 have been involved in amplification of siRNA generated from plant viruses. RDR2 also a crucial player for amplification of siRNA synthesized from heterochromatic region.

References:

  1. Xuemei Chen (2009) Small RNAs and their roles in plant development. Annu. Rev. Cell Dev. Biol.35:21- 44
  2. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ (2005) Elucidation of the small RNA component of the transcriptome. Science 309: 1567-69


About Author / Additional Info:


Search this site & forums
Share this article with friends:



Share with Facebook Share with Linkedin Share with Twitter Share with Pinterest Email this article

More Social Bookmarks (Digg etc..)


Comments on this article: (0 comments so far)

Comment By Comment

Leave a Comment   |   Article Views: 199



Additional Articles:

•   Autoradiography - Types of Radiations Used and Measuring Autoradiography

•   Garlic : The Bulb of Wonder

•   Comparative Advantages of Genic-SSRs Over Genomic SSRs for Crop Improvement

•   Growing of Bougainvillea in Farm Houses




Latest Articles in "Biotech-Research" category:
•   Human Longevity: A Revolution in Biotechnology and Nanotechnology.

•   Nanoparticles as Delivery Device For Gene Therapy

•   Biotechnology as a Tool in Medicine: Focus on Artemisinin

•   Tissue Cells and Skin Cells Reprogrammed Into Embryonic Stem Cells:-

•   Polymerase Chain Reaction (or PCR) - Technique For Amplifying DNA

•   Treatment of Heart Disease With Stem Cells

•   Biological Activities and Bioassays

•   DNA Sequencing: Maxam Gilbert Method

•   PCR Aspects and its Future | PCR versus Cloning

•   Plasmid as Vectors For Plant Transformation

•   Gene Isolation and Characterisation

•   Apoptosis and Cancer: A Review

•   Extraction of Nucleic Acids (DNA and RNA) From Plant Tissues

•   Stem Cells From Bone Marrow and Vein Leftovers Can Heal Damaged Hearts

•   Gene Transfer Techniques: Biolistics, Bacterial and Viral Transformation

•   Breast Cancer: Cactus For Womens Life

•   Mtt Assay: Assess The Viability Of Cell In Culture

•   Medicinal Plants: Source Of Medicine

•   Biotechnology Impact on Alzheimer's Disease



Important Disclaimer: All articles on this website are for general information only and is not a professional or experts advice. We do not own any responsibility for correctness or authenticity of the information presented in this article, or any loss or injury resulting from it. We do not endorse these articles, we are neither affiliated with the authors of these articles nor responsible for their content. Please see our disclaimer section for complete terms.
Page copy protected against web site content infringement by Copyscape
Copyright © 2010 biotecharticles.com - Do not copy articles from this website.

ARTICLE CATEGORIES :
Agriculture Bioinformatics Applications Biotech Products Biotech Research
Biology Careers College/Edu DNA Environmental Biotech
Genetics Healthcare Industry News Issues Nanotechnology
Others Stem Cells Press Release Toxicology  


  |   Disclaimer/Privacy/TOS   |   Submission Guidelines   |   Contact Us