Trans-acting siRNA

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Trans-acting siRNA (abbreviated "ta-siRNA" or "tasiRNA") are a class of small interfering RNA (siRNA) that repress gene expression through post-transcriptional gene silencing in land plants. [1] [2] [3] Precursor transcripts from TAS loci are polyadenylated and converted to double-stranded RNA, and are then processed into 21-nucleotide-long RNA duplexes with overhangs. [1] These segments are incorporated into an RNA-induced silencing complex (RISC) and direct the sequence-specific cleavage of target mRNA. Ta-siRNAs are classified as siRNA because they arise from double-stranded RNA (dsRNA). [4]

Contents

Discovery

ta-siRNA were originally detected in 2004 in the flowering plant Arabidopsis thaliana . [1] [2] Initial descriptions found involvement of the plant protein suppressor of gene silencing 3 (SGS3), and the enzyme RNA-dependant RNA polymerase 6 (RDR6).

Biogenesis

ta-siRNA Biogenesis in arabidopsis. Ta-siRNA Biogenesis in Arabidopsis.png
ta-siRNA Biogenesis in arabidopsis.

Ta-siRNAs are generated from non-coding transcripts through Argonaute-mediated miRNA-guided cleavage followed by conversion to double stranded RNA by RDR6. [5] The resulting dsRNA is further processed by dicer-like enzyme 4 (DCL4) to produce a phased array of 21-nt siRNAs from positions adjoining the miRNA cleavage site. [6]

There are four families of ta-siRNA-generating loci (TAS genes) in A. thaliana. TAS1, TAS2, and TAS4 families require one miRNA binding site for cleavage to occur while TAS3 requires two binding sites. [7] TAS gene family numbers do not generally indicate orthology, e.g. the moss TAS1 gene family does not share an ancestor gene with the Arabidopsis thalianaTAS1 gene family.

TAS1 and TAS2

TAS1/2 transcripts undergo an initial AGO1 mediated cleavage at the 5’ end that is guided by miR173. RDR6 then converts the transcript into a double strand RNA fragment which then gets processed by DCL4 to generate the 21-nt siRNA with 2 nucleotide 3’ overhangs that target complementary mRNAs in trans. [7]

TAS4

The initial steps for the TAS4 family of ta-siRNA is similar to that of TAS1 and TAS2. The TAS4 family of transcripts first undergo miR828 guided, AGO1 mediated cleavage, followed by dsRNA synthesis and processing by DCL4. [7]

TAS3

In contrast to the single mRNA binding family, TAS3 requires the guide mRNA miR390 bind the transcript at two sites. The transcript is then cleaved at the 3’ binding site only, by AGO7. As is the case for the TAS1, TAS2, and TAS3 families, RDR6 then synthesizes the dsRNA fragment which is further processed by DCL4. [7]

Mechanism

Endogenous ta-siRNAs act via hetero-silencing, which means that the genes they target for cleavage and repression do not have much resemblance to the genes from which the siRNAs derive. This differs from other endogenous siRNAs which are cis-acting and perform auto-silencing, repressing the expression of genes that are the same as or have a lot of resemblance to the genes from which they derive. It was previously thought that only miRNAs exhibited hetero-silencing. [1] Like other siRNAs, the ta-siRNAs are incorporated into RNA-induced silencing complexes (RISCs), where they guide the complex to cleave the target mRNAs in the middle of a single complementary site and repress translation. [1] [2] [8]

A member of the Argonaute protein family is a component of all RNA silencing effector complexes, including the RISCs that catalyze mRNA cleavage. [8] [9] Specifically in arabidopsis, it appears to be AGO7/ZIPPY that plays a role in the ta-siRNA pathway by acting during TAS3-derived ta-siRNA-mediated regulation. AGO7/ZIPPY does not play a role in the mechanisms for TAS1 or TAS2 ta-siRNA biogenesis. [9] ta-siRNAs can be loaded into AGO1 complexes to guide target mRNA cleavage. [10]

Presence in plants

In addition to being present in A. thaliana, [6] evidence of ta-siRNAs has also been found in the moss Physcomitrella patens , [5] maize, [11] Oryza sativa (rice), [12] and other plants. TAS3 trans-acting short-interfering RNA targeting auxin response factors ("tasiR-ARF") is an example of a ta-siRNA that has been shown to be present not only in arabidopsis, but in all of the previous examples. TasiR-ARF is responsible for regulating the signaling molecule auxin. It does this by targeting the mRNA that encodes several of the Auxin Response Factor (ARF) genes for degradation. [11]

Related Research Articles

microRNA Small non-coding ribonucleic acid molecule

MicroRNA (miRNA) are small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides. Found in plants, animals and some viruses, miRNAs are involved in RNA silencing and post-transcriptional regulation of gene expression. miRNAs base-pair to complementary sequences in mRNA molecules, then gene silence said mRNA molecules by one or more of the following processes:

  1. Cleavage of mRNA strand into two pieces,
  2. Destabilization of mRNA by shortening its poly(A) tail, or
  3. Translation of mRNA into proteins.
<span class="mw-page-title-main">Small interfering RNA</span> Biomolecule

Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA at first non-coding RNA molecules, typically 20-24 base pairs in length, similar to miRNA, and operating within the RNA interference (RNAi) pathway. It interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, preventing translation.

<span class="mw-page-title-main">Dicer</span> Enzyme that cleaves double-stranded RNA (dsRNA) into short dsRNA fragments

Dicer, also known as endoribonuclease Dicer or helicase with RNase motif, is an enzyme that in humans is encoded by the DICER1 gene. Being part of the RNase III family, Dicer cleaves double-stranded RNA (dsRNA) and pre-microRNA (pre-miRNA) into short double-stranded RNA fragments called small interfering RNA and microRNA, respectively. These fragments are approximately 20–25 base pairs long with a two-base overhang on the 3′-end. Dicer facilitates the activation of the RNA-induced silencing complex (RISC), which is essential for RNA interference. RISC has a catalytic component Argonaute, which is an endonuclease capable of degrading messenger RNA (mRNA).

The RNA-induced silencing complex, or RISC, is a multiprotein complex, specifically a ribonucleoprotein, which functions in gene silencing via a variety of pathways at the transcriptional and translational levels. Using single-stranded RNA (ssRNA) fragments, such as microRNA (miRNA), or double-stranded small interfering RNA (siRNA), the complex functions as a key tool in gene regulation. The single strand of RNA acts as a template for RISC to recognize complementary messenger RNA (mRNA) transcript. Once found, one of the proteins in RISC, Argonaute, activates and cleaves the mRNA. This process is called RNA interference (RNAi) and it is found in many eukaryotes; it is a key process in defense against viral infections, as it is triggered by the presence of double-stranded RNA (dsRNA).

<span class="mw-page-title-main">Argonaute</span> Protein that plays a role in RNA silencing process

The Argonaute protein family, first discovered for its evolutionarily conserved stem cell function, plays a central role in RNA silencing processes as essential components of the RNA-induced silencing complex (RISC). RISC is responsible for the gene silencing phenomenon known as RNA interference (RNAi). Argonaute proteins bind different classes of small non-coding RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). Small RNAs guide Argonaute proteins to their specific targets through sequence complementarity, which then leads to mRNA cleavage, translation inhibition, and/or the initiation of mRNA decay.

Piwi-interacting RNA (piRNA) is the largest class of small non-coding RNA molecules expressed in animal cells. piRNAs form RNA-protein complexes through interactions with piwi-subfamily Argonaute proteins. These piRNA complexes are mostly involved in the epigenetic and post-transcriptional silencing of transposable elements and other spurious or repeat-derived transcripts, but can also be involved in the regulation of other genetic elements in germ line cells.

<span class="mw-page-title-main">Piwi</span>

Piwi genes were identified as regulatory proteins responsible for stem cell and germ cell differentiation. Piwi is an abbreviation of P-elementInduced WImpy testis in Drosophila. Piwi proteins are highly conserved RNA-binding proteins and are present in both plants and animals. Piwi proteins belong to the Argonaute/Piwi family and have been classified as nuclear proteins. Studies on Drosophila have also indicated that Piwi proteins have no slicer activity conferred by the presence of the Piwi domain. In addition, Piwi associates with heterochromatin protein 1, an epigenetic modifier, and piRNA-complementary sequences. These are indications of the role Piwi plays in epigenetic regulation. Piwi proteins are also thought to control the biogenesis of piRNA as many Piwi-like proteins contain slicer activity which would allow Piwi proteins to process precursor piRNA into mature piRNA.

RNA silencing or RNA interference refers to a family of gene silencing effects by which gene expression is negatively regulated by non-coding RNAs such as microRNAs. RNA silencing may also be defined as sequence-specific regulation of gene expression triggered by double-stranded RNA (dsRNA). RNA silencing mechanisms are conserved among most eukaryotes. The most common and well-studied example is RNA interference (RNAi), in which endogenously expressed microRNA (miRNA) or exogenously derived small interfering RNA (siRNA) induces the degradation of complementary messenger RNA. Other classes of small RNA have been identified, including piwi-interacting RNA (piRNA) and its subspecies repeat associated small interfering RNA (rasiRNA).

mir-156 microRNA precursor

MicroRNA (miRNA) precursor miR156 is a family of plant non-coding RNA. This microRNA has now been predicted or experimentally confirmed in a range of plant species. Animal miRNAs are transcribed as ~70 nucleotide precursors and subsequently processed by the Dicer enzyme to give a ~22 nucleotide product. miR156 functions in the induction of flowering by suppressing the transcripts of SQUAMOSA-PROMOTER BINDING LIKE (SPL) transcription factors gene family. It was suggested that the loading into ARGONAUTE1 and ARGONAUTE5 is required for miR156 functionality in Arabidopsis thaliana. In plants the precursor sequences may be longer, and the carpel factory (caf) enzyme appears to be involved in processing. In this case the mature sequence comes from the 5' arm of the precursor, and both Arabidopsis thaliana and rice genomes contain a number of related miRNA precursors which give rise to almost identical mature sequences. The extents of the hairpin precursors are not generally known and are estimated based on hairpin prediction. The products are thought to have regulatory roles through complementarity to mRNA.

mir-160 microRNA precursor family

In molecular biology, mir-160 is a microRNA that has been predicted or experimentally confirmed in a range of plant species including Arabidopsis thaliana and Oryza sativa (rice). miR-160 is predicted to bind complementary sites in the untranslated regions of auxin response factor genes to regulate their expression. The hairpin precursors are predicted based on base pairing and cross-species conservation; their extents are not known. In this case, the mature sequence is excised from the 5' arm of the hairpin.

RNA polymerase IV is an enzyme that synthesizes small interfering RNA (siRNA) in plants, which silence gene expression. RNAP IV belongs to a family of enzymes that catalyze the process of transcription known as RNA Polymerases, which synthesize RNA from DNA templates. Discovered via phylogenetic studies of land plants, genes of RNAP IV are thought to have resulted from multistep evolution processes that occurred in RNA Polymerase II phylogenies. Such an evolutionary pathway is supported by the fact that RNAP IV is composed of 12 protein subunits that are either similar or identical to RNA polymerase II, and is specific to plant genomes. Via its synthesis of siRNA, RNAP IV is involved in regulation of heterochromatin formation in a process known as RNA directed DNA Methylation (RdDM).

<span class="mw-page-title-main">RNA interference</span> Biological process of gene regulation

RNA interference (RNAi) is a biological process in which RNA molecules are involved in sequence-specific suppression of gene expression by double-stranded RNA, through translational or transcriptional repression. Historically, RNAi was known by other names, including co-suppression, post-transcriptional gene silencing (PTGS), and quelling. The detailed study of each of these seemingly different processes elucidated that the identity of these phenomena were all actually RNAi. Andrew Fire and Craig C. Mello shared the 2006 Nobel Prize in Physiology or Medicine for their work on RNAi in the nematode worm Caenorhabditis elegans, which they published in 1998. Since the discovery of RNAi and its regulatory potentials, it has become evident that RNAi has immense potential in suppression of desired genes. RNAi is now known as precise, efficient, stable and better than antisense therapy for gene suppression. Antisense RNA produced intracellularly by an expression vector may be developed and find utility as novel therapeutic agents.

In molecular biology mir-390 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms.

In molecular biology mir-828 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms.

Transposon silencing is a form of transcriptional gene silencing targeting transposons. Transcriptional gene silencing is a product of histone modifications that prevent the transcription of a particular area of DNA. Transcriptional silencing of transposons is crucial to the maintenance of a genome. The “jumping” of transposons generates genomic instability and can cause extremely deleterious mutations. Transposable element insertions have been linked to many diseases including hemophilia, severe combined immunodeficiency, and predisposition to cancer. The silencing of transposons is therefore extremely critical in the germline in order to stop transposon mutations from developing and being passed on to the next generation. Additionally, these epigenetic defenses against transposons can be heritable. Studies in Drosophila, Arabidopsis thaliana, and mice all indicate that small interfering RNAs are responsible for transposon silencing. In animals, these siRNAS and piRNAs are most active in the gonads.

RDE-1 (RNAi-DEfective 1) is a primary Argonaute protein required for RNA-mediated interference (RNAi) in Caenorhabditis elegans. The rde-1 gene locus was first characterized in C. elegans mutants resistant to RNAi, and is a member of a highly conserved Piwi gene family that includes plant, Drosophila, and vertebrate homologs.

RNA polymerase V, previously known as RNA polymerase IVb, is a multisubunit plant specific RNA polymerase. It is required for normal function and biogenesis of small interfering RNA (siRNA). Together with RNA polymerase IV, Pol V is involved in an siRNA-dependent epigenetic pathway known as RNA-directed DNA methylation (RdDM), which establishes and maintains heterochromatic silencing in plants.

<span class="mw-page-title-main">DCL1</span> Protein coding gene in plants

DCL1 is a gene in plants that codes for the DCL1 protein, a ribonuclease III enzyme involved in processing double-stranded RNA (dsRNA) and microRNA (miRNA). Although DCL1, also called Endoribonuclease Dicer homolog 1, is named for its homology with the metazoan protein Dicer, its role in miRNA biogenesis is somewhat different, due to substantial differences in miRNA maturation processes between plants and animals, as well due to additional downstream plant-specific pathways, where DCL1 paralogs like DCL4 participate, such Trans-acting siRNA biogenesis.

<span class="mw-page-title-main">RNA-directed DNA methylation</span> RNA-based gene silencing process

RNA-directed DNA methylation (RdDM) is a biological process in which non-coding RNA molecules direct the addition of DNA methylation to specific DNA sequences. The RdDM pathway is unique to plants, although other mechanisms of RNA-directed chromatin modification have also been described in fungi and animals. To date, the RdDM pathway is best characterized within angiosperms, and particularly within the model plant Arabidopsis thaliana. However, conserved RdDM pathway components and associated small RNAs (sRNAs) have also been found in other groups of plants, such as gymnosperms and ferns. The RdDM pathway closely resembles other sRNA pathways, particularly the highly conserved RNAi pathway found in fungi, plants, and animals. Both the RdDM and RNAi pathways produce sRNAs and involve conserved Argonaute, Dicer and RNA-dependent RNA polymerase proteins.

<span class="mw-page-title-main">DCL2</span> Dicer-like gene in plants

DCL2 is a gene in plants that codes for the DCL2 protein, a ribonuclease III enzyme involved in processing exogenous double-stranded RNA (dsRNA) into 22 nucleotide small interference RNAs (siRNAs).

References

  1. 1 2 3 4 5 Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert JL, Bartel DP, Crété P (October 2004). "Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs". Mol. Cell. 16 (1): 69–79. doi: 10.1016/j.molcel.2004.09.028 . PMID   15469823.
  2. 1 2 3 Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS (October 2004). "SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis". Genes Dev. 18 (19): 2368–79. doi:10.1101/gad.1231804. PMC   522987 . PMID   15466488.
  3. ↑ Axtell MJ, Jan C, Rajagopalan R, Bartel DP (November 2006). "A two-hit trigger for siRNA biogenesis in plants". Cell. 127 (3): 565–77. doi: 10.1016/j.cell.2006.09.032 . PMID   17081978.
  4. ↑ Axtell, Michael J. (29 April 2013). "Classification and Comparison of Small RNAs from Plants". Annual Review of Plant Biology. 64 (1): 137–159. doi:10.1146/annurev-arplant-050312-120043. PMID   23330790.
  5. 1 2 Talmor-Neiman M, Stav R, Klipcan L, Buxdorf K, Baulcombe DC, Arazi T (November 2006). "Identification of trans-acting siRNAs in moss and an RNA-dependent RNA polymerase required for their biogenesis". Plant J. 48 (4): 511–21. doi: 10.1111/j.1365-313X.2006.02895.x . PMID   17076803.
  6. 1 2 Allen E, Xie Z, Gustafson AM, Carrington JC (April 2005). "microRNA-directed phasing during trans-acting siRNA biogenesis in plants". Cell. 121 (2): 207–21. doi: 10.1016/j.cell.2005.04.004 . PMID   15851028.
  7. 1 2 3 4 Allen E, Howell MD (October 2010). "miRNAs in the biogenesis of trans-acting siRNAs in higher plants". Semin. Cell Dev. Biol. 21 (8): 798–804. doi:10.1016/j.semcdb.2010.03.008. PMID   20359543.
  8. 1 2 Tomari Y, Zamore PD (March 2005). "Perspective: machines for RNAi". Genes Dev. 19 (5): 517–29. doi: 10.1101/gad.1284105 . PMID   15741316.
  9. 1 2 Adenot X, Elmayan T, Lauressergues D, Boutet S, Bouché N, Gasciolli V, Vaucheret H (May 2006). "DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7". Curr. Biol. 16 (9): 927–32. doi: 10.1016/j.cub.2006.03.035 . PMID   16682354.
  10. ↑ Wu L, Mao L, Qi Y (October 2012). "Roles of dicer-like and argonaute proteins in TAS-derived small interfering RNA-triggered DNA methylation". Plant Physiol. 160 (2): 990–9. doi:10.1104/pp.112.200279. PMC   3461571 . PMID   22846193.
  11. 1 2 Williams L, Carles CC, Osmont KS, Fletcher JC (July 2005). "A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the arabidopsis ARF2, ARF3, and ARF4 genes". Proc. Natl. Acad. Sci. U.S.A. 102 (27): 9703–8. doi: 10.1073/pnas.0504029102 . PMC   1172271 . PMID   15980147.
  12. ↑ Heisel SE, Zhang Y, Allen E, Guo L, Reynolds TL, Yang X, Kovalic D, Roberts JK (2008). "Characterization of unique small RNA populations from rice grain". PLOS ONE. 3 (8): e2871. doi: 10.1371/journal.pone.0002871 . PMC   2518513 . PMID   18716673.
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