DMCA
The structure and repertoire of small interfering RNAs in Leishmania (Viannia) braziliensis reveal diversification in the trypanosomatid RNAi pathway
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Citations
1260 | Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25
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Citation Context ...siRNAs (see below) the two libraries gave essentially the same results (Fig. S1A), we will present the analysis of the second library because it had the highest number of reads (the sequence data from this study have been submitted to the NCBI Sequence Read Archive – SRA at http://www. ncbi.nlm.nih.gov/Traces/sra/sra.cgi – underAccession No. SRA059332). We obtained 27 868 280 RNA-Seq reads, which were pre-processed by clipping the 3′ adapter (5′- CTGTAGGCACCATCAAT-3′) and then aligned to the 35 L. braziliensis chromosomes of clone M2904 (MHOM/ BR/75 M2904) using the Bowtie Short Read Aligner (Langmead et al., 2009). Reads with more than two mismatches in the first 22 nucleotides were discarded and reads reporting multiple alignments were retained and aligned pseudorandomly (using Bowtie’s default options), resulting in 20 710 782 (74.3%) aligned reads. The reads not matching might arise from un-sequenced regions of the genome or from sequencing errors. The alignments were uploaded onto a customized local installation of the generic Genome Browser (Stein et al., 2002). To categorize siRNA-producing loci we manually inspected each chromosome for reads that aligned to annotated features as well as to regio... |
958 | Tandem Repeats Finder: a Program to Analyze DNA Sequences
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Citation Context ...d and aligned pseudorandomly (using Bowtie’s default options), resulting in 20 710 782 (74.3%) aligned reads. The reads not matching might arise from un-sequenced regions of the genome or from sequencing errors. The alignments were uploaded onto a customized local installation of the generic Genome Browser (Stein et al., 2002). To categorize siRNA-producing loci we manually inspected each chromosome for reads that aligned to annotated features as well as to regions without annotation. In addition, we surveyed short tandem repeats, which were catalogued using the program tandem repeats finder (Benson, 1999) and regions in-between CTUs. We also searched individual chromosomes for the presence of long inverted repeats (longer than 100 nt) using BLAST and the program inverted repeat finder (Warburton et al., 2004) and identified numerous regions ranging in size between 100 and 1800 nt. It is unknown whether or not hairpin RNA structures are generated from these inverted repeats. However, we did not find small RNA reads mapping to these regions of the genome suggesting that they do not form RNA hairpins recognized by the Lbr RNAi machinery. Our analysis identified four abundant categories of endogen... |
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The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
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Citation Context ...ication has occurred in the RNAi pathway during evolution of the trypanosomatid lineage. Introduction Gene silencing by small regulatory RNAs has been one of the major discoveries of the last two decades and has profoundly changed our view how gene expression is controlled in eukaryotes, shifting the emphasis from transcriptional and epigenetic regulation to post-transcriptional mechanisms. This field has been built on four fundamental discoveries. First, in the early 1990s genetic analysis in Caenorhabditis elegans brought to light two small noncoding RNAs, which regulate larval development (Lee et al., 1993; Wightman et al., 1993) and are the founders of the micro RNA (miRNA) family. Second, in 1998 Fire and Mello (Fire et al., 1998) made the seminal discovery that long double-stranded RNA (dsRNA) triggers degradation of homologous transcripts, a phenomenon dubbed RNA interference (RNAi). Third, Baulcombe and colleagues (Hamilton and Baulcombe, 1999) correlated posttranscriptional gene silencing (PTGS) in plants with the accumulation of a ~ 25 nt antisense RNA species, which they proposed ‘may represent the specificity determinant of PTGS’. Fourth, these small RNAs, which became known as small/s... |
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Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans
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Citation Context ...ed in the RNAi pathway during evolution of the trypanosomatid lineage. Introduction Gene silencing by small regulatory RNAs has been one of the major discoveries of the last two decades and has profoundly changed our view how gene expression is controlled in eukaryotes, shifting the emphasis from transcriptional and epigenetic regulation to post-transcriptional mechanisms. This field has been built on four fundamental discoveries. First, in the early 1990s genetic analysis in Caenorhabditis elegans brought to light two small noncoding RNAs, which regulate larval development (Lee et al., 1993; Wightman et al., 1993) and are the founders of the micro RNA (miRNA) family. Second, in 1998 Fire and Mello (Fire et al., 1998) made the seminal discovery that long double-stranded RNA (dsRNA) triggers degradation of homologous transcripts, a phenomenon dubbed RNA interference (RNAi). Third, Baulcombe and colleagues (Hamilton and Baulcombe, 1999) correlated posttranscriptional gene silencing (PTGS) in plants with the accumulation of a ~ 25 nt antisense RNA species, which they proposed ‘may represent the specificity determinant of PTGS’. Fourth, these small RNAs, which became known as small/short interfering RNAs (s... |
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Citation Context ...CAAT-3′) and then aligned to the 35 L. braziliensis chromosomes of clone M2904 (MHOM/ BR/75 M2904) using the Bowtie Short Read Aligner (Langmead et al., 2009). Reads with more than two mismatches in the first 22 nucleotides were discarded and reads reporting multiple alignments were retained and aligned pseudorandomly (using Bowtie’s default options), resulting in 20 710 782 (74.3%) aligned reads. The reads not matching might arise from un-sequenced regions of the genome or from sequencing errors. The alignments were uploaded onto a customized local installation of the generic Genome Browser (Stein et al., 2002). To categorize siRNA-producing loci we manually inspected each chromosome for reads that aligned to annotated features as well as to regions without annotation. In addition, we surveyed short tandem repeats, which were catalogued using the program tandem repeats finder (Benson, 1999) and regions in-between CTUs. We also searched individual chromosomes for the presence of long inverted repeats (longer than 100 nt) using BLAST and the program inverted repeat finder (Warburton et al., 2004) and identified numerous regions ranging in size between 100 and 1800 nt. It is unknown whether or not hair... |
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Biogenesis of small RNAs in animals.
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Citation Context ...lton and Baulcombe, 1999) correlated posttranscriptional gene silencing (PTGS) in plants with the accumulation of a ~ 25 nt antisense RNA species, which they proposed ‘may represent the specificity determinant of PTGS’. Fourth, these small RNAs, which became known as small/short interfering RNAs (siRNAs), were shown to be the mediators of RNAi (Elbashir et al., 2001). After two decades of research it has become evident that small regulatory RNAs come in a variety of types, some of which are organism-specific, with the main known classes being siRNAs, miRNAs and Piwi-associated RNAs or piRNAs (Kim et al., 2009; Liu and Paroo, 2010) siRNAs are generated by cleavage of long dsRNA by Dicer, an RNase Accepted 29 November, 2012. *For correspondence. E-mail elisabetta.ullu@yale.edu; Tel. (+1) 203 785 3563; Fax (+1) 203 785 7329. Present addresses: †Department of Microbiology and Immunology, McGill University, Montreal, QC, H3A 2B4, Canada; ‡UCSFBerkeley Joint Graduate Group in Bioengineering 2. Gladstone Institute of Virology and Immunology; 1650 Owens St, San Francisco, CA 94158, USA. Molecular Microbiology (2013) 87(3), 580–593 doi:10.1111/mmi.12117 First published online 26 December 2012 © 2012 Blac... |
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Citation Context ...ease in a complex with a dsRNA-binding protein. The processing of miRNAs from their primary transcripts is more elaborate and in general requires the assistance of the microprocessor in the nucleus followed by export of precursors to the cytoplasm and cleavage by Dicer. However, in certain instances miRNA maturation can occur independently of Dicer (Cheloufi et al., 2010; Cifuentes et al., 2010; Yang et al., 2010). So far miRNAs have been shown to be derived from long, primary transcripts coding for multiple miRNAs, from introns or from other cellular RNAs, including the small nucleolar RNAs (Ender et al., 2008; Saraiya and Wang, 2008). Additionally, tRNAs have been implicated as sources of miRNAs (Cole et al., 2009; Lee et al., 2009; Haussecker et al., 2010). Invariably, small regulatory RNAs are found in a complex with a member of the Argonaute (AGO) protein family (Ender and Meister, 2010), which is characterized by conserved domains (MID, PAZ and Piwi). Certain AGO family members have been termed ‘slicers’ because they are endowed with an RNase H-like cleavage activity, which resides in the Piwi domain. siRNAs are associated with AGO slicers, are usually perfectly complementary to the target tra... |
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Double-stranded RNA induces mRNA degradation in Trypanosoma brucei
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Citation Context ...nt unclear. Furthermore, siRNAs derived from the pairing of gene and pseudogene transcripts have been implicated in regulating gene expression in certain organisms (Watanabe et al., 2008), including Trypanosoma brucei (Wen et al., 2011). Members of the order Kinetoplastida, which includes many human protozoan parasites, are considered early divergent eukaryotes and thus can inform us about ancient traits of the RNAi pathway. T. brucei, the causative agent of African sleeping sickness in humans and nagana in cattle, was the first member of this group where RNAi was experimentally demonstrated (Ngo et al., 1998). More recently, RNAi has been shown to be functional in Leishmania (Viannia) braziliensis and other members of the Viannia subgenus (Lye et al., 2010), the cause of cutaneous and mucocutaneous leishmaniasis in South America. Additionally, Crithidia fasciculata, a nonparasitic ‘outgroup’, is endowed with RNAi genes and generates siRNA-size molecules upon expression of a green fluorescent protein (GFP) hairpin (Lye et al., 2010). In T. brucei the RNAi pathway depends on five core components, which are also present in L. braziliensis (Lye et al., 2010; Barnes et al., 2012), namely a single Argon... |
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Citation Context ...n general requires the assistance of the microprocessor in the nucleus followed by export of precursors to the cytoplasm and cleavage by Dicer. However, in certain instances miRNA maturation can occur independently of Dicer (Cheloufi et al., 2010; Cifuentes et al., 2010; Yang et al., 2010). So far miRNAs have been shown to be derived from long, primary transcripts coding for multiple miRNAs, from introns or from other cellular RNAs, including the small nucleolar RNAs (Ender et al., 2008; Saraiya and Wang, 2008). Additionally, tRNAs have been implicated as sources of miRNAs (Cole et al., 2009; Lee et al., 2009; Haussecker et al., 2010). Invariably, small regulatory RNAs are found in a complex with a member of the Argonaute (AGO) protein family (Ender and Meister, 2010), which is characterized by conserved domains (MID, PAZ and Piwi). Certain AGO family members have been termed ‘slicers’ because they are endowed with an RNase H-like cleavage activity, which resides in the Piwi domain. siRNAs are associated with AGO slicers, are usually perfectly complementary to the target transcript and, upon binding of the ribonucleoprotein complex, target transcript cleavage ensues. In contrast, most miRNAs are o... |
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Citation Context ...r, 2010), which is characterized by conserved domains (MID, PAZ and Piwi). Certain AGO family members have been termed ‘slicers’ because they are endowed with an RNase H-like cleavage activity, which resides in the Piwi domain. siRNAs are associated with AGO slicers, are usually perfectly complementary to the target transcript and, upon binding of the ribonucleoprotein complex, target transcript cleavage ensues. In contrast, most miRNAs are only partially complementary to their targets and elicit downregulation of gene expression by accelerating transcript decay and/or inhibiting translation (Fabian et al., 2010; Guo et al., 2010; Bazzini et al., 2012; Djuranovic et al., 2012). The endogenous RNAi pathway triggered by long dsRNA is by and large a genome defence mechanism to control spreading of potentially dangerous parasitic nucleic acids, such as mobile elements, repeats and viruses (Huang et al., 2011). However, in the last few years deep sequencing of endogenous siRNAs has revealed further complexities of the siRNA repertoire with the identification of loci that upon transcription give rise to structured RNAs (long inverted repeats) or sense and antisense transcripts with the potential to form ds... |
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Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453:539–543
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Citation Context ...s deep sequencing of endogenous siRNAs has revealed further complexities of the siRNA repertoire with the identification of loci that upon transcription give rise to structured RNAs (long inverted repeats) or sense and antisense transcripts with the potential to form dsRNA, as it can occur at sites of convergent transcription. However, the functional significance of siRNAs from long hairpins and convergent transcription is at present unclear. Furthermore, siRNAs derived from the pairing of gene and pseudogene transcripts have been implicated in regulating gene expression in certain organisms (Watanabe et al., 2008), including Trypanosoma brucei (Wen et al., 2011). Members of the order Kinetoplastida, which includes many human protozoan parasites, are considered early divergent eukaryotes and thus can inform us about ancient traits of the RNAi pathway. T. brucei, the causative agent of African sleeping sickness in humans and nagana in cattle, was the first member of this group where RNAi was experimentally demonstrated (Ngo et al., 1998). More recently, RNAi has been shown to be functional in Leishmania (Viannia) braziliensis and other members of the Viannia subgenus (Lye et al., 2010), the cause of cuta... |
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A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity.
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Citation Context ...ogy and Immunology; 1650 Owens St, San Francisco, CA 94158, USA. Molecular Microbiology (2013) 87(3), 580–593 doi:10.1111/mmi.12117 First published online 26 December 2012 © 2012 Blackwell Publishing Ltd III-family endonuclease in a complex with a dsRNA-binding protein. The processing of miRNAs from their primary transcripts is more elaborate and in general requires the assistance of the microprocessor in the nucleus followed by export of precursors to the cytoplasm and cleavage by Dicer. However, in certain instances miRNA maturation can occur independently of Dicer (Cheloufi et al., 2010; Cifuentes et al., 2010; Yang et al., 2010). So far miRNAs have been shown to be derived from long, primary transcripts coding for multiple miRNAs, from introns or from other cellular RNAs, including the small nucleolar RNAs (Ender et al., 2008; Saraiya and Wang, 2008). Additionally, tRNAs have been implicated as sources of miRNAs (Cole et al., 2009; Lee et al., 2009; Haussecker et al., 2010). Invariably, small regulatory RNAs are found in a complex with a member of the Argonaute (AGO) protein family (Ender and Meister, 2010), which is characterized by conserved domains (MID, PAZ and Piwi). Certain AGO family member... |
53 |
Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes.
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Citation Context ...ncing errors. The alignments were uploaded onto a customized local installation of the generic Genome Browser (Stein et al., 2002). To categorize siRNA-producing loci we manually inspected each chromosome for reads that aligned to annotated features as well as to regions without annotation. In addition, we surveyed short tandem repeats, which were catalogued using the program tandem repeats finder (Benson, 1999) and regions in-between CTUs. We also searched individual chromosomes for the presence of long inverted repeats (longer than 100 nt) using BLAST and the program inverted repeat finder (Warburton et al., 2004) and identified numerous regions ranging in size between 100 and 1800 nt. It is unknown whether or not hairpin RNA structures are generated from these inverted repeats. However, we did not find small RNA reads mapping to these regions of the genome suggesting that they do not form RNA hairpins recognized by the Lbr RNAi machinery. Our analysis identified four abundant categories of endogenous siRNA-producing loci (Fig. 3A), which included SLACS, TATE, TAS-like repeats related to the previously identified TAS family (Fu and Barker, 1998; Fu et al., 1998), and the CIR74 family, a novel class of ... |
52 |
Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis.
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Citation Context ...e analysis was carried out on redundant reads. B. Analysis of the 3′ nucleotides of reads aligned to the genome with 0 mismatches. C. 3′ nucleotide prevalence of non-templated nucleotides expressed as percentage of total aligned reads. D. Percentage of reads with one or two non-templated 3′ nucleotides. 588 V. D. Atayde et al. © 2012 Blackwell Publishing Ltd, Molecular Microbiology, 87, 580–593 gene, which belongs to the family of HEN1 2′-Omethyltransferases, modifies the terminal ribose of siRNAs (H. Shi et al., unpubl. obs.). This modification was first discovered in Arabidopsis thaliana (Li et al., 2005), where both siRNAs and miRNAs are HEN1 substrates, and was later on described in a variety of non-coding RNAs, including the piRNAs (Kirino and Mourelatos, 2007; Saito et al., 2007), a class of small RNAs in Tetrahymena thermophila (Kurth and Mochizuki, 2009) and Drosophila siRNAs (Horwich et al., 2007; Pelisson et al., 2007). Additionally, Chlamydomonas reinhardtii small RNAs are modified at the 3′ end (Molnar et al., 2007). Consistent with the absence of a blocked siRNA 3′ terminus, the genome of L. braziliensis does not appear to code for a HEN1-like gene, as determined by using the BLAST ... |
47 |
A dicerindependent miRNA biogenesis pathway that requires Ago catalysis. Nature 465:584
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Citation Context ...tone Institute of Virology and Immunology; 1650 Owens St, San Francisco, CA 94158, USA. Molecular Microbiology (2013) 87(3), 580–593 doi:10.1111/mmi.12117 First published online 26 December 2012 © 2012 Blackwell Publishing Ltd III-family endonuclease in a complex with a dsRNA-binding protein. The processing of miRNAs from their primary transcripts is more elaborate and in general requires the assistance of the microprocessor in the nucleus followed by export of precursors to the cytoplasm and cleavage by Dicer. However, in certain instances miRNA maturation can occur independently of Dicer (Cheloufi et al., 2010; Cifuentes et al., 2010; Yang et al., 2010). So far miRNAs have been shown to be derived from long, primary transcripts coding for multiple miRNAs, from introns or from other cellular RNAs, including the small nucleolar RNAs (Ender et al., 2008; Saraiya and Wang, 2008). Additionally, tRNAs have been implicated as sources of miRNAs (Cole et al., 2009; Lee et al., 2009; Haussecker et al., 2010). Invariably, small regulatory RNAs are found in a complex with a member of the Argonaute (AGO) protein family (Ender and Meister, 2010), which is characterized by conserved domains (MID, PAZ and Piwi). C... |
41 |
Ribosome profiling shows that mir-430 reduces translation before causing mRNA decay in zebrafish.
- Bazzini, Lee, et al.
- 2012
(Show Context)
Citation Context ...served domains (MID, PAZ and Piwi). Certain AGO family members have been termed ‘slicers’ because they are endowed with an RNase H-like cleavage activity, which resides in the Piwi domain. siRNAs are associated with AGO slicers, are usually perfectly complementary to the target transcript and, upon binding of the ribonucleoprotein complex, target transcript cleavage ensues. In contrast, most miRNAs are only partially complementary to their targets and elicit downregulation of gene expression by accelerating transcript decay and/or inhibiting translation (Fabian et al., 2010; Guo et al., 2010; Bazzini et al., 2012; Djuranovic et al., 2012). The endogenous RNAi pathway triggered by long dsRNA is by and large a genome defence mechanism to control spreading of potentially dangerous parasitic nucleic acids, such as mobile elements, repeats and viruses (Huang et al., 2011). However, in the last few years deep sequencing of endogenous siRNAs has revealed further complexities of the siRNA repertoire with the identification of loci that upon transcription give rise to structured RNAs (long inverted repeats) or sense and antisense transcripts with the potential to form dsRNA, as it can occur at sites of converg... |
39 |
A common mechanism of stage-regulated gene expression in Leishmania mediated by a conserved 3′-untranslated region element.
- Boucher, Wu, et al.
- 2002
(Show Context)
Citation Context ...in L. braziliensis to decrease formation of sense and antisense transcripts from CTUs. In addition, we surveyed the reads for the presence of small RNAs derived from the SIDER family, which is found in T. brucei, T. cruzi and Leishmania ssp. (Bringaud et al., 2011). This family consists of short, truncated versions of ingi-related retroposons, has expanded in the genome of Divergent RNAi pathways in the trypanosomatid lineage 589 © 2012 Blackwell Publishing Ltd, Molecular Microbiology, 87, 580–593 Leishmania ssp., where it has acquired an independent function in regulation of gene expression (Boucher et al., 2002; McNicoll et al., 2005; Bringaud et al., 2007; Muller et al., 2010). L. braziliensis harbours about 2000 copies of SIDER (Smith et al., 2009), but we found no evidence of SIDER-derived reads, suggesting that these elements are not a significant source of dsRNA that is processed by the RNAi machinery. A standing question in the trypanosomatid RNAi pathway is whether miRNAs exist. As a first step towards answering this question we manually inspected each chromosome for reads that did not map to the major siRNA-producing loci and had a common 5′ end, the latter being a feature anticipated for mi... |
38 |
miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii
- r, Schwach, et al.
- 2007
(Show Context)
Citation Context ...e family of HEN1 2′-Omethyltransferases, modifies the terminal ribose of siRNAs (H. Shi et al., unpubl. obs.). This modification was first discovered in Arabidopsis thaliana (Li et al., 2005), where both siRNAs and miRNAs are HEN1 substrates, and was later on described in a variety of non-coding RNAs, including the piRNAs (Kirino and Mourelatos, 2007; Saito et al., 2007), a class of small RNAs in Tetrahymena thermophila (Kurth and Mochizuki, 2009) and Drosophila siRNAs (Horwich et al., 2007; Pelisson et al., 2007). Additionally, Chlamydomonas reinhardtii small RNAs are modified at the 3′ end (Molnar et al., 2007). Consistent with the absence of a blocked siRNA 3′ terminus, the genome of L. braziliensis does not appear to code for a HEN1-like gene, as determined by using the BLAST search algorithm at low stringency (Expected value = 10). Methylation of the terminal ribose is thought to protect the small RNA 3′ end from the attack by exonucleolytic and tailing activities (Cerutti and Ibrahim, 2010; Kim et al., 2010). For instance, in A. thaliana in the absence of HEN1 uridine residues are added to the 3′ end of mi- and siRNAs (Li et al., 2005), and recently it has been shown that the nucleotidyl transfe... |
30 |
Argonaute proteins at a glance.
- Ender, Meister
- 2010
(Show Context)
Citation Context ...n certain instances miRNA maturation can occur independently of Dicer (Cheloufi et al., 2010; Cifuentes et al., 2010; Yang et al., 2010). So far miRNAs have been shown to be derived from long, primary transcripts coding for multiple miRNAs, from introns or from other cellular RNAs, including the small nucleolar RNAs (Ender et al., 2008; Saraiya and Wang, 2008). Additionally, tRNAs have been implicated as sources of miRNAs (Cole et al., 2009; Lee et al., 2009; Haussecker et al., 2010). Invariably, small regulatory RNAs are found in a complex with a member of the Argonaute (AGO) protein family (Ender and Meister, 2010), which is characterized by conserved domains (MID, PAZ and Piwi). Certain AGO family members have been termed ‘slicers’ because they are endowed with an RNase H-like cleavage activity, which resides in the Piwi domain. siRNAs are associated with AGO slicers, are usually perfectly complementary to the target transcript and, upon binding of the ribonucleoprotein complex, target transcript cleavage ensues. In contrast, most miRNAs are only partially complementary to their targets and elicit downregulation of gene expression by accelerating transcript decay and/or inhibiting translation (Fabian e... |
30 |
Evolution of nuclear ribosomal RNAs in kinetoplastid protozoa: perspectives on the age and origins of parasitism. Proc Natl Acad Sci U
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- 1993
(Show Context)
Citation Context ...2009). Past (Djikeng et al., 2001) and recent (Tschudi et al., 2012) siRNA profiling in T. brucei procyclic forms indicates that the endogenous siRNA-producing loci have been conserved from trypanosomes to animals and include retroposons, satellite-like repeats, long inverted repeats, sites of convergent transcription and two pseudogenes. Although T. brucei and L. braziliensis belong to the same family and have conserved mechanisms of gene expression, including polycistronic transcription of long gene arrays and trans-splicing of pre-mRNA, these organisms are evolutionarily distantly related (Fernandes et al., 1993), raising the question whether the structure of siRNAs and the scope of the RNAi pathway have been conserved through the evolution of the trypanosomatid lineage. Here, we have undertaken an in-depth analysis of siRNAs in L. braziliensis promastigotes. Structurally, Leishmania siRNAs are slightly shorter than those in T. brucei and, importantly, are not modified at the 3′ end. As in T. brucei (Djikeng et al., 2001; Tschudi et al., 2012) the major classes of Leishmania siRNAs are derived from putative mobile elements and repeats, namely the SLACS retroposon [Spliced Leader Associated Conserved S... |
30 |
The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC.
- Horwich, Matranga, et al.
- 2007
(Show Context)
Citation Context ...des. 588 V. D. Atayde et al. © 2012 Blackwell Publishing Ltd, Molecular Microbiology, 87, 580–593 gene, which belongs to the family of HEN1 2′-Omethyltransferases, modifies the terminal ribose of siRNAs (H. Shi et al., unpubl. obs.). This modification was first discovered in Arabidopsis thaliana (Li et al., 2005), where both siRNAs and miRNAs are HEN1 substrates, and was later on described in a variety of non-coding RNAs, including the piRNAs (Kirino and Mourelatos, 2007; Saito et al., 2007), a class of small RNAs in Tetrahymena thermophila (Kurth and Mochizuki, 2009) and Drosophila siRNAs (Horwich et al., 2007; Pelisson et al., 2007). Additionally, Chlamydomonas reinhardtii small RNAs are modified at the 3′ end (Molnar et al., 2007). Consistent with the absence of a blocked siRNA 3′ terminus, the genome of L. braziliensis does not appear to code for a HEN1-like gene, as determined by using the BLAST search algorithm at low stringency (Expected value = 10). Methylation of the terminal ribose is thought to protect the small RNA 3′ end from the attack by exonucleolytic and tailing activities (Cerutti and Ibrahim, 2010; Kim et al., 2010). For instance, in A. thaliana in the absence of HEN1 uridine resi... |
27 |
Pimet, the Drosophila homolog of HEN1, mediates 2'-O-methylation of Piwi- interacting RNAs at their 3' ends
- Saito, Sakaguchi, et al.
- 2007
(Show Context)
Citation Context ...leotides expressed as percentage of total aligned reads. D. Percentage of reads with one or two non-templated 3′ nucleotides. 588 V. D. Atayde et al. © 2012 Blackwell Publishing Ltd, Molecular Microbiology, 87, 580–593 gene, which belongs to the family of HEN1 2′-Omethyltransferases, modifies the terminal ribose of siRNAs (H. Shi et al., unpubl. obs.). This modification was first discovered in Arabidopsis thaliana (Li et al., 2005), where both siRNAs and miRNAs are HEN1 substrates, and was later on described in a variety of non-coding RNAs, including the piRNAs (Kirino and Mourelatos, 2007; Saito et al., 2007), a class of small RNAs in Tetrahymena thermophila (Kurth and Mochizuki, 2009) and Drosophila siRNAs (Horwich et al., 2007; Pelisson et al., 2007). Additionally, Chlamydomonas reinhardtii small RNAs are modified at the 3′ end (Molnar et al., 2007). Consistent with the absence of a blocked siRNA 3′ terminus, the genome of L. braziliensis does not appear to code for a HEN1-like gene, as determined by using the BLAST search algorithm at low stringency (Expected value = 10). Methylation of the terminal ribose is thought to protect the small RNA 3′ end from the attack by exonucleolytic and tailing ... |
24 |
Biochemical principles of small RNA pathways.
- Liu, Paroo
- 2010
(Show Context)
Citation Context ..., 1999) correlated posttranscriptional gene silencing (PTGS) in plants with the accumulation of a ~ 25 nt antisense RNA species, which they proposed ‘may represent the specificity determinant of PTGS’. Fourth, these small RNAs, which became known as small/short interfering RNAs (siRNAs), were shown to be the mediators of RNAi (Elbashir et al., 2001). After two decades of research it has become evident that small regulatory RNAs come in a variety of types, some of which are organism-specific, with the main known classes being siRNAs, miRNAs and Piwi-associated RNAs or piRNAs (Kim et al., 2009; Liu and Paroo, 2010) siRNAs are generated by cleavage of long dsRNA by Dicer, an RNase Accepted 29 November, 2012. *For correspondence. E-mail elisabetta.ullu@yale.edu; Tel. (+1) 203 785 3563; Fax (+1) 203 785 7329. Present addresses: †Department of Microbiology and Immunology, McGill University, Montreal, QC, H3A 2B4, Canada; ‡UCSFBerkeley Joint Graduate Group in Bioengineering 2. Gladstone Institute of Virology and Immunology; 1650 Owens St, San Francisco, CA 94158, USA. Molecular Microbiology (2013) 87(3), 580–593 doi:10.1111/mmi.12117 First published online 26 December 2012 © 2012 Blackwell Publishing Ltd I... |
24 |
Conserved vertebrate mir-451 provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis.
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- 2010
(Show Context)
Citation Context ... Owens St, San Francisco, CA 94158, USA. Molecular Microbiology (2013) 87(3), 580–593 doi:10.1111/mmi.12117 First published online 26 December 2012 © 2012 Blackwell Publishing Ltd III-family endonuclease in a complex with a dsRNA-binding protein. The processing of miRNAs from their primary transcripts is more elaborate and in general requires the assistance of the microprocessor in the nucleus followed by export of precursors to the cytoplasm and cleavage by Dicer. However, in certain instances miRNA maturation can occur independently of Dicer (Cheloufi et al., 2010; Cifuentes et al., 2010; Yang et al., 2010). So far miRNAs have been shown to be derived from long, primary transcripts coding for multiple miRNAs, from introns or from other cellular RNAs, including the small nucleolar RNAs (Ender et al., 2008; Saraiya and Wang, 2008). Additionally, tRNAs have been implicated as sources of miRNAs (Cole et al., 2009; Lee et al., 2009; Haussecker et al., 2010). Invariably, small regulatory RNAs are found in a complex with a member of the Argonaute (AGO) protein family (Ender and Meister, 2010), which is characterized by conserved domains (MID, PAZ and Piwi). Certain AGO family members have been termed ‘... |
19 | snoRNA, a novel precursor of microRNA in Giardia lamblia.
- Saraiya, Wang
- 2008
(Show Context)
Citation Context ...th a dsRNA-binding protein. The processing of miRNAs from their primary transcripts is more elaborate and in general requires the assistance of the microprocessor in the nucleus followed by export of precursors to the cytoplasm and cleavage by Dicer. However, in certain instances miRNA maturation can occur independently of Dicer (Cheloufi et al., 2010; Cifuentes et al., 2010; Yang et al., 2010). So far miRNAs have been shown to be derived from long, primary transcripts coding for multiple miRNAs, from introns or from other cellular RNAs, including the small nucleolar RNAs (Ender et al., 2008; Saraiya and Wang, 2008). Additionally, tRNAs have been implicated as sources of miRNAs (Cole et al., 2009; Lee et al., 2009; Haussecker et al., 2010). Invariably, small regulatory RNAs are found in a complex with a member of the Argonaute (AGO) protein family (Ender and Meister, 2010), which is characterized by conserved domains (MID, PAZ and Piwi). Certain AGO family members have been termed ‘slicers’ because they are endowed with an RNase H-like cleavage activity, which resides in the Piwi domain. siRNAs are associated with AGO slicers, are usually perfectly complementary to the target transcript and, upon binding... |
18 |
Target RNAdirected trimming and tailing of small silencing RNAs.
- Ameres, Horwich, et al.
- 2010
(Show Context)
Citation Context ...minal ribose is thought to protect the small RNA 3′ end from the attack by exonucleolytic and tailing activities (Cerutti and Ibrahim, 2010; Kim et al., 2010). For instance, in A. thaliana in the absence of HEN1 uridine residues are added to the 3′ end of mi- and siRNAs (Li et al., 2005), and recently it has been shown that the nucleotidyl transferase AtHESO1 uridylates unmethylated small RNAs to trigger their degradation (Zhao et al., 2012). Similarly, in HEN1-deficient Drosophila AGO2-associated siRNAs, which normally carry a 2′-O-methyl group on the terminal ribose, are tailed and trimmed (Ameres et al., 2010). The important role that 3′ end remodelling by nucleotydyl transferases play in small RNA metabolism is also underscored by the findings that in C. elegans the absence of the nucleotidyl transferase CDE-1, which uridylates siRNAs bound to a specific AGO protein, results in increased levels of such siRNAs and in defects in chromosome segregation, and in C. reinhardtii the MUT68 nucleotidyl transferase, which adds uridines to a small proportion of unmodified and shorter than average small RNAs, has been shown to cooperate with the exosome subunit RRP6 to eliminate these RNAs (Ibrahim et al., 20... |
18 |
Modifications of small RNAs and their associated proteins.
- Kim, Heo, et al.
- 2010
(Show Context)
Citation Context ...thermophila (Kurth and Mochizuki, 2009) and Drosophila siRNAs (Horwich et al., 2007; Pelisson et al., 2007). Additionally, Chlamydomonas reinhardtii small RNAs are modified at the 3′ end (Molnar et al., 2007). Consistent with the absence of a blocked siRNA 3′ terminus, the genome of L. braziliensis does not appear to code for a HEN1-like gene, as determined by using the BLAST search algorithm at low stringency (Expected value = 10). Methylation of the terminal ribose is thought to protect the small RNA 3′ end from the attack by exonucleolytic and tailing activities (Cerutti and Ibrahim, 2010; Kim et al., 2010). For instance, in A. thaliana in the absence of HEN1 uridine residues are added to the 3′ end of mi- and siRNAs (Li et al., 2005), and recently it has been shown that the nucleotidyl transferase AtHESO1 uridylates unmethylated small RNAs to trigger their degradation (Zhao et al., 2012). Similarly, in HEN1-deficient Drosophila AGO2-associated siRNAs, which normally carry a 2′-O-methyl group on the terminal ribose, are tailed and trimmed (Ameres et al., 2010). The important role that 3′ end remodelling by nucleotydyl transferases play in small RNA metabolism is also underscored by the findings ... |
16 |
Regulation of small RNA stability: methylation and beyond.
- Ji, Chen
- 2012
(Show Context)
Citation Context ... two major classes of known L. braziliensis putative transposable elements. After CIP treatment (Fig. 1A), SLACS- and TATE-derived small RNAs showed a slightly diminished electrophoretic mobility as compared with the untreated sample, consistent with the presence of a phosphate group at the 5′ end. Cleavage of dsRNA by Dicer produces a 3′ OH, but in a number of organisms, including T. brucei (Patrick et al., 2009), the 2′-O position of the ribose of certain siRNAs and miRNAs is modified by the addition of a methyl group, a reaction carried out by a member of the HEN1 methyltransferase family (Ji and Chen, 2012). As a result, these small RNAs become resistant to periodate oxidation and b-elimination. Figure 1B shows that this chemical treatment resulted in an increased mobility of SLACS and TATE small RNAs, which is expected if the siRNAs are unmodified. Thus, on the basis of the above observations and the association of small RNAs with LbrAGO1 (see below), we concluded that these small RNAs represent authentic siRNAs, and, in contrast to T. brucei (Patrick et al., 2009), they are not modified at the 3′ end. Lastly, by Northern blot analysis we compared the size distribution of SLACS siRNAs in T. bru... |
16 |
The mouse homolog of HEN1 is a potential methylase for Piwi-interacting RNAs.
- Kirino, Mourelatos
- 2007
(Show Context)
Citation Context ...evalence of non-templated nucleotides expressed as percentage of total aligned reads. D. Percentage of reads with one or two non-templated 3′ nucleotides. 588 V. D. Atayde et al. © 2012 Blackwell Publishing Ltd, Molecular Microbiology, 87, 580–593 gene, which belongs to the family of HEN1 2′-Omethyltransferases, modifies the terminal ribose of siRNAs (H. Shi et al., unpubl. obs.). This modification was first discovered in Arabidopsis thaliana (Li et al., 2005), where both siRNAs and miRNAs are HEN1 substrates, and was later on described in a variety of non-coding RNAs, including the piRNAs (Kirino and Mourelatos, 2007; Saito et al., 2007), a class of small RNAs in Tetrahymena thermophila (Kurth and Mochizuki, 2009) and Drosophila siRNAs (Horwich et al., 2007; Pelisson et al., 2007). Additionally, Chlamydomonas reinhardtii small RNAs are modified at the 3′ end (Molnar et al., 2007). Consistent with the absence of a blocked siRNA 3′ terminus, the genome of L. braziliensis does not appear to code for a HEN1-like gene, as determined by using the BLAST search algorithm at low stringency (Expected value = 10). Methylation of the terminal ribose is thought to protect the small RNA 3′ end from the attack by exonuc... |
14 | Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania.
- Bringaud, Muller, et al.
- 2007
(Show Context)
Citation Context ...ense and antisense transcripts from CTUs. In addition, we surveyed the reads for the presence of small RNAs derived from the SIDER family, which is found in T. brucei, T. cruzi and Leishmania ssp. (Bringaud et al., 2011). This family consists of short, truncated versions of ingi-related retroposons, has expanded in the genome of Divergent RNAi pathways in the trypanosomatid lineage 589 © 2012 Blackwell Publishing Ltd, Molecular Microbiology, 87, 580–593 Leishmania ssp., where it has acquired an independent function in regulation of gene expression (Boucher et al., 2002; McNicoll et al., 2005; Bringaud et al., 2007; Muller et al., 2010). L. braziliensis harbours about 2000 copies of SIDER (Smith et al., 2009), but we found no evidence of SIDER-derived reads, suggesting that these elements are not a significant source of dsRNA that is processed by the RNAi machinery. A standing question in the trypanosomatid RNAi pathway is whether miRNAs exist. As a first step towards answering this question we manually inspected each chromosome for reads that did not map to the major siRNA-producing loci and had a common 5′ end, the latter being a feature anticipated for miRNA-derived reads. Unfortunately, we did not f... |
14 | An unusual Dicerlike1 protein fuels the RNA interference pathway in Trypanosoma brucei.
- Shi, Tschudi, et al.
- 2006
(Show Context)
Citation Context ...of the Viannia subgenus (Lye et al., 2010), the cause of cutaneous and mucocutaneous leishmaniasis in South America. Additionally, Crithidia fasciculata, a nonparasitic ‘outgroup’, is endowed with RNAi genes and generates siRNA-size molecules upon expression of a green fluorescent protein (GFP) hairpin (Lye et al., 2010). In T. brucei the RNAi pathway depends on five core components, which are also present in L. braziliensis (Lye et al., 2010; Barnes et al., 2012), namely a single Argonaute, AGO1 (Durand-Dubief and Bastin, 2003; Shi et al., 2004), two Dicer-like enzymes, the cytoplasmic DCL1 (Shi et al., 2006) and the nuclear DCL2 (Patrick et al., 2009), and two novel factors termed RIF4, an exonuclease that together with AGO1 is required for the maturation of siRNAs from duplex to single-stranded form, and RIF5, a DCL1 cofactor (Barnes et al., 2012). Trypanosome siRNAs are produced by both Dicers and are characterized by a 5′ phosphate and a blocked 3′ end (Patrick et al., 2009). Past (Djikeng et al., 2001) and recent (Tschudi et al., 2012) siRNA profiling in T. brucei procyclic forms indicates that the endogenous siRNA-producing loci have been conserved from trypanosomes to animals and include re... |
14 | CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs. - Wolfswinkel, Claycomb, et al. - 2009 |
14 |
The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation.
- Zhao, Yu, et al.
- 2012
(Show Context)
Citation Context ... braziliensis does not appear to code for a HEN1-like gene, as determined by using the BLAST search algorithm at low stringency (Expected value = 10). Methylation of the terminal ribose is thought to protect the small RNA 3′ end from the attack by exonucleolytic and tailing activities (Cerutti and Ibrahim, 2010; Kim et al., 2010). For instance, in A. thaliana in the absence of HEN1 uridine residues are added to the 3′ end of mi- and siRNAs (Li et al., 2005), and recently it has been shown that the nucleotidyl transferase AtHESO1 uridylates unmethylated small RNAs to trigger their degradation (Zhao et al., 2012). Similarly, in HEN1-deficient Drosophila AGO2-associated siRNAs, which normally carry a 2′-O-methyl group on the terminal ribose, are tailed and trimmed (Ameres et al., 2010). The important role that 3′ end remodelling by nucleotydyl transferases play in small RNA metabolism is also underscored by the findings that in C. elegans the absence of the nucleotidyl transferase CDE-1, which uridylates siRNAs bound to a specific AGO protein, results in increased levels of such siRNAs and in defects in chromosome segregation, and in C. reinhardtii the MUT68 nucleotidyl transferase, which adds uridines... |
12 |
Uridylation of miRNAs by hen1 suppressor1 in Arabidopsis.
- Ren, Chen, et al.
- 2012
(Show Context)
Citation Context ... untemplated nucleotides on all size classes of siRNAs and the significant fraction of tailed molecules (~ 20%) suggest that tailing of Lbr siRNAs does not preferentially target shorter molecules and is a rather frequent occurrence. This phenomenon clearly indicates that the 3′ end of certain siRNAs is exposed to the action of nucleotydyl transferases. Establishing whether tailing occurs before or after the loading of siRNAs into LbrAGO1 and whether tailed siRNAs are eliminated will require further investigation. By analogy to other systems (van Wolfswinkel et al., 2009; Ibrahim et al., 2010; Ren et al., 2012; Zhao et al., 2012) tailing of Lbr siRNAs is most likely carried out by one or more nucleotidyl transferases. The Leishmania homologues of T. brucei cytosolic terminal uridilyl transferase (TUTase) 3 (LbrM19.1680) and TUTase 4 [LbrM32.2690 (Aphasizhev et al., 2004; Stagno et al., 2007)], are good candidates for adding uridine to siRNAs and we are currently exploring this possibility. In L. braziliensis we found four major classes of siRNAproducing loci (Table 1), all derived from either putative mobile elements or repeats, mirroring in this respect the siRNA repertoire in T. brucei (Djikeng e... |
11 |
Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in Chlamydomonas.
- Ibrahim, Rymarquis, et al.
- 2010
(Show Context)
Citation Context ...eres et al., 2010). The important role that 3′ end remodelling by nucleotydyl transferases play in small RNA metabolism is also underscored by the findings that in C. elegans the absence of the nucleotidyl transferase CDE-1, which uridylates siRNAs bound to a specific AGO protein, results in increased levels of such siRNAs and in defects in chromosome segregation, and in C. reinhardtii the MUT68 nucleotidyl transferase, which adds uridines to a small proportion of unmodified and shorter than average small RNAs, has been shown to cooperate with the exosome subunit RRP6 to eliminate these RNAs (Ibrahim et al., 2010). It has been proposed that MUT68/RRP6 is part of a quality control that eliminates damaged or ‘dysfunctional’ small RNAs, although what constitutes a ‘dysfunctional’ small RNA is not yet understood (Ibrahim et al., 2010). Thus, it was unsurprising to find that in L. braziliensis a proportion of siRNAs carried untemplated nucleotides at the 3′ end, with uridine being the most frequent addition. We estimated that about 20% of endogenous siRNAs are tailed, but this is probably an underestimate, considering that a single nucleotide addition may frequently match the genomic sequence. In contrast, ... |
11 | Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania. - HG, Farris, et al. - 2012 |
11 |
A novel repeat-associated small interfering RNAmediated silencing pathway downregulates complementary sense gypsy transcripts in somatic cells of the Drosophila ovary.
- Pelisson, Sarot, et al.
- 2007
(Show Context)
Citation Context ...et al. © 2012 Blackwell Publishing Ltd, Molecular Microbiology, 87, 580–593 gene, which belongs to the family of HEN1 2′-Omethyltransferases, modifies the terminal ribose of siRNAs (H. Shi et al., unpubl. obs.). This modification was first discovered in Arabidopsis thaliana (Li et al., 2005), where both siRNAs and miRNAs are HEN1 substrates, and was later on described in a variety of non-coding RNAs, including the piRNAs (Kirino and Mourelatos, 2007; Saito et al., 2007), a class of small RNAs in Tetrahymena thermophila (Kurth and Mochizuki, 2009) and Drosophila siRNAs (Horwich et al., 2007; Pelisson et al., 2007). Additionally, Chlamydomonas reinhardtii small RNAs are modified at the 3′ end (Molnar et al., 2007). Consistent with the absence of a blocked siRNA 3′ terminus, the genome of L. braziliensis does not appear to code for a HEN1-like gene, as determined by using the BLAST search algorithm at low stringency (Expected value = 10). Methylation of the terminal ribose is thought to protect the small RNA 3′ end from the attack by exonucleolytic and tailing activities (Cerutti and Ibrahim, 2010; Kim et al., 2010). For instance, in A. thaliana in the absence of HEN1 uridine residues are added to the 3′... |
10 |
2'-O-methylation stabilizes Piwi-associated small RNAs and ensures DNA elimination in Tetrahymena. RNA
- Kurth, Mochizuki
- 2009
(Show Context)
Citation Context ...of reads with one or two non-templated 3′ nucleotides. 588 V. D. Atayde et al. © 2012 Blackwell Publishing Ltd, Molecular Microbiology, 87, 580–593 gene, which belongs to the family of HEN1 2′-Omethyltransferases, modifies the terminal ribose of siRNAs (H. Shi et al., unpubl. obs.). This modification was first discovered in Arabidopsis thaliana (Li et al., 2005), where both siRNAs and miRNAs are HEN1 substrates, and was later on described in a variety of non-coding RNAs, including the piRNAs (Kirino and Mourelatos, 2007; Saito et al., 2007), a class of small RNAs in Tetrahymena thermophila (Kurth and Mochizuki, 2009) and Drosophila siRNAs (Horwich et al., 2007; Pelisson et al., 2007). Additionally, Chlamydomonas reinhardtii small RNAs are modified at the 3′ end (Molnar et al., 2007). Consistent with the absence of a blocked siRNA 3′ terminus, the genome of L. braziliensis does not appear to code for a HEN1-like gene, as determined by using the BLAST search algorithm at low stringency (Expected value = 10). Methylation of the terminal ribose is thought to protect the small RNA 3′ end from the attack by exonucleolytic and tailing activities (Cerutti and Ibrahim, 2010; Kim et al., 2010). For instance, in A. ... |
10 |
Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome.
- Smith, Bringaud, et al.
- 2009
(Show Context)
Citation Context ...mall RNAs derived from the SIDER family, which is found in T. brucei, T. cruzi and Leishmania ssp. (Bringaud et al., 2011). This family consists of short, truncated versions of ingi-related retroposons, has expanded in the genome of Divergent RNAi pathways in the trypanosomatid lineage 589 © 2012 Blackwell Publishing Ltd, Molecular Microbiology, 87, 580–593 Leishmania ssp., where it has acquired an independent function in regulation of gene expression (Boucher et al., 2002; McNicoll et al., 2005; Bringaud et al., 2007; Muller et al., 2010). L. braziliensis harbours about 2000 copies of SIDER (Smith et al., 2009), but we found no evidence of SIDER-derived reads, suggesting that these elements are not a significant source of dsRNA that is processed by the RNAi machinery. A standing question in the trypanosomatid RNAi pathway is whether miRNAs exist. As a first step towards answering this question we manually inspected each chromosome for reads that did not map to the major siRNA-producing loci and had a common 5′ end, the latter being a feature anticipated for miRNA-derived reads. Unfortunately, we did not find evidence of such reads. Since our analysis was carried out on small RNAs associated with AGO... |
9 |
Dual role of the RNA substrate in selectivity and catalysis by terminal uridylyl transferases.
- Stagno, Aphasizheva, et al.
- 2007
(Show Context)
Citation Context ...of certain siRNAs is exposed to the action of nucleotydyl transferases. Establishing whether tailing occurs before or after the loading of siRNAs into LbrAGO1 and whether tailed siRNAs are eliminated will require further investigation. By analogy to other systems (van Wolfswinkel et al., 2009; Ibrahim et al., 2010; Ren et al., 2012; Zhao et al., 2012) tailing of Lbr siRNAs is most likely carried out by one or more nucleotidyl transferases. The Leishmania homologues of T. brucei cytosolic terminal uridilyl transferase (TUTase) 3 (LbrM19.1680) and TUTase 4 [LbrM32.2690 (Aphasizhev et al., 2004; Stagno et al., 2007)], are good candidates for adding uridine to siRNAs and we are currently exploring this possibility. In L. braziliensis we found four major classes of siRNAproducing loci (Table 1), all derived from either putative mobile elements or repeats, mirroring in this respect the siRNA repertoire in T. brucei (Djikeng et al., 2001; Tschudi et al., 2012). Thus, similarly to trypanosomes and many other organisms one of the functions of the RNAi pathway in Leishmania is to downregulate expression of putative mobile elements that may affect genome integrity. Indeed, genetic ablation of LbrAGO1 leads to th... |
8 | Multiple copies of a retroposon interrupt spliced leader RNA genes in the African trypanosome, Trypanosoma gambiense. - Aksoy, Lalor, et al. - 1987 |
8 |
Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei.
- Patrick, Shi, et al.
- 2009
(Show Context)
Citation Context ...0), the cause of cutaneous and mucocutaneous leishmaniasis in South America. Additionally, Crithidia fasciculata, a nonparasitic ‘outgroup’, is endowed with RNAi genes and generates siRNA-size molecules upon expression of a green fluorescent protein (GFP) hairpin (Lye et al., 2010). In T. brucei the RNAi pathway depends on five core components, which are also present in L. braziliensis (Lye et al., 2010; Barnes et al., 2012), namely a single Argonaute, AGO1 (Durand-Dubief and Bastin, 2003; Shi et al., 2004), two Dicer-like enzymes, the cytoplasmic DCL1 (Shi et al., 2006) and the nuclear DCL2 (Patrick et al., 2009), and two novel factors termed RIF4, an exonuclease that together with AGO1 is required for the maturation of siRNAs from duplex to single-stranded form, and RIF5, a DCL1 cofactor (Barnes et al., 2012). Trypanosome siRNAs are produced by both Dicers and are characterized by a 5′ phosphate and a blocked 3′ end (Patrick et al., 2009). Past (Djikeng et al., 2001) and recent (Tschudi et al., 2012) siRNA profiling in T. brucei procyclic forms indicates that the endogenous siRNA-producing loci have been conserved from trypanosomes to animals and include retroposons, satellite-like repeats, long inve... |
7 | Comparative genomics reveals two novel RNAi factors in Trypanosoma brucei and provides insight into the core machinery.
- Barnes, Shi, et al.
- 2012
(Show Context)
Citation Context ...erimentally demonstrated (Ngo et al., 1998). More recently, RNAi has been shown to be functional in Leishmania (Viannia) braziliensis and other members of the Viannia subgenus (Lye et al., 2010), the cause of cutaneous and mucocutaneous leishmaniasis in South America. Additionally, Crithidia fasciculata, a nonparasitic ‘outgroup’, is endowed with RNAi genes and generates siRNA-size molecules upon expression of a green fluorescent protein (GFP) hairpin (Lye et al., 2010). In T. brucei the RNAi pathway depends on five core components, which are also present in L. braziliensis (Lye et al., 2010; Barnes et al., 2012), namely a single Argonaute, AGO1 (Durand-Dubief and Bastin, 2003; Shi et al., 2004), two Dicer-like enzymes, the cytoplasmic DCL1 (Shi et al., 2006) and the nuclear DCL2 (Patrick et al., 2009), and two novel factors termed RIF4, an exonuclease that together with AGO1 is required for the maturation of siRNAs from duplex to single-stranded form, and RIF5, a DCL1 cofactor (Barnes et al., 2012). Trypanosome siRNAs are produced by both Dicers and are characterized by a 5′ phosphate and a blocked 3′ end (Patrick et al., 2009). Past (Djikeng et al., 2001) and recent (Tschudi et al., 2012) siRNA prof... |
6 |
Rapid decay of unstable Leishmania mRNAs bearing a conserved retroposon signature 3′-UTR motif is initiated by a site-specific endonucleolytic cleavage without prior deadenylation.
- Muller, Padmanabhan, et al.
- 2010
(Show Context)
Citation Context ...scripts from CTUs. In addition, we surveyed the reads for the presence of small RNAs derived from the SIDER family, which is found in T. brucei, T. cruzi and Leishmania ssp. (Bringaud et al., 2011). This family consists of short, truncated versions of ingi-related retroposons, has expanded in the genome of Divergent RNAi pathways in the trypanosomatid lineage 589 © 2012 Blackwell Publishing Ltd, Molecular Microbiology, 87, 580–593 Leishmania ssp., where it has acquired an independent function in regulation of gene expression (Boucher et al., 2002; McNicoll et al., 2005; Bringaud et al., 2007; Muller et al., 2010). L. braziliensis harbours about 2000 copies of SIDER (Smith et al., 2009), but we found no evidence of SIDER-derived reads, suggesting that these elements are not a significant source of dsRNA that is processed by the RNAi machinery. A standing question in the trypanosomatid RNAi pathway is whether miRNAs exist. As a first step towards answering this question we manually inspected each chromosome for reads that did not map to the major siRNA-producing loci and had a common 5′ end, the latter being a feature anticipated for miRNA-derived reads. Unfortunately, we did not find evidence of such r... |
4 |
Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.
- Huang, Houwing, et al.
- 2011
(Show Context)
Citation Context ...tary to the target transcript and, upon binding of the ribonucleoprotein complex, target transcript cleavage ensues. In contrast, most miRNAs are only partially complementary to their targets and elicit downregulation of gene expression by accelerating transcript decay and/or inhibiting translation (Fabian et al., 2010; Guo et al., 2010; Bazzini et al., 2012; Djuranovic et al., 2012). The endogenous RNAi pathway triggered by long dsRNA is by and large a genome defence mechanism to control spreading of potentially dangerous parasitic nucleic acids, such as mobile elements, repeats and viruses (Huang et al., 2011). However, in the last few years deep sequencing of endogenous siRNAs has revealed further complexities of the siRNA repertoire with the identification of loci that upon transcription give rise to structured RNAs (long inverted repeats) or sense and antisense transcripts with the potential to form dsRNA, as it can occur at sites of convergent transcription. However, the functional significance of siRNAs from long hairpins and convergent transcription is at present unclear. Furthermore, siRNAs derived from the pairing of gene and pseudogene transcripts have been implicated in regulating gene ex... |
4 |
Small interfering RNA-producing loci in the ancient parasitic eukaryote Trypanosoma brucei.
- Tschudi, Shi, et al.
- 2012
(Show Context)
Citation Context ... al., 2010; Barnes et al., 2012), namely a single Argonaute, AGO1 (Durand-Dubief and Bastin, 2003; Shi et al., 2004), two Dicer-like enzymes, the cytoplasmic DCL1 (Shi et al., 2006) and the nuclear DCL2 (Patrick et al., 2009), and two novel factors termed RIF4, an exonuclease that together with AGO1 is required for the maturation of siRNAs from duplex to single-stranded form, and RIF5, a DCL1 cofactor (Barnes et al., 2012). Trypanosome siRNAs are produced by both Dicers and are characterized by a 5′ phosphate and a blocked 3′ end (Patrick et al., 2009). Past (Djikeng et al., 2001) and recent (Tschudi et al., 2012) siRNA profiling in T. brucei procyclic forms indicates that the endogenous siRNA-producing loci have been conserved from trypanosomes to animals and include retroposons, satellite-like repeats, long inverted repeats, sites of convergent transcription and two pseudogenes. Although T. brucei and L. braziliensis belong to the same family and have conserved mechanisms of gene expression, including polycistronic transcription of long gene arrays and trans-splicing of pre-mRNA, these organisms are evolutionarily distantly related (Fernandes et al., 1993), raising the question whether the structure ... |
3 |
Multiple terminal uridylyltransferases of trypanosomes.
- Aphasizhev, Aphasizheva, et al.
- 2004
(Show Context)
Citation Context ...ndicates that the 3′ end of certain siRNAs is exposed to the action of nucleotydyl transferases. Establishing whether tailing occurs before or after the loading of siRNAs into LbrAGO1 and whether tailed siRNAs are eliminated will require further investigation. By analogy to other systems (van Wolfswinkel et al., 2009; Ibrahim et al., 2010; Ren et al., 2012; Zhao et al., 2012) tailing of Lbr siRNAs is most likely carried out by one or more nucleotidyl transferases. The Leishmania homologues of T. brucei cytosolic terminal uridilyl transferase (TUTase) 3 (LbrM19.1680) and TUTase 4 [LbrM32.2690 (Aphasizhev et al., 2004; Stagno et al., 2007)], are good candidates for adding uridine to siRNAs and we are currently exploring this possibility. In L. braziliensis we found four major classes of siRNAproducing loci (Table 1), all derived from either putative mobile elements or repeats, mirroring in this respect the siRNA repertoire in T. brucei (Djikeng et al., 2001; Tschudi et al., 2012). Thus, similarly to trypanosomes and many other organisms one of the functions of the RNAi pathway in Leishmania is to downregulate expression of putative mobile elements that may affect genome integrity. Indeed, genetic ablation ... |
3 |
Turnover of mature miRNAs and siRNAs in plants and algae.
- Cerutti, Ibrahim
- 2010
(Show Context)
Citation Context ... small RNAs in Tetrahymena thermophila (Kurth and Mochizuki, 2009) and Drosophila siRNAs (Horwich et al., 2007; Pelisson et al., 2007). Additionally, Chlamydomonas reinhardtii small RNAs are modified at the 3′ end (Molnar et al., 2007). Consistent with the absence of a blocked siRNA 3′ terminus, the genome of L. braziliensis does not appear to code for a HEN1-like gene, as determined by using the BLAST search algorithm at low stringency (Expected value = 10). Methylation of the terminal ribose is thought to protect the small RNA 3′ end from the attack by exonucleolytic and tailing activities (Cerutti and Ibrahim, 2010; Kim et al., 2010). For instance, in A. thaliana in the absence of HEN1 uridine residues are added to the 3′ end of mi- and siRNAs (Li et al., 2005), and recently it has been shown that the nucleotidyl transferase AtHESO1 uridylates unmethylated small RNAs to trigger their degradation (Zhao et al., 2012). Similarly, in HEN1-deficient Drosophila AGO2-associated siRNAs, which normally carry a 2′-O-methyl group on the terminal ribose, are tailed and trimmed (Ameres et al., 2010). The important role that 3′ end remodelling by nucleotydyl transferases play in small RNA metabolism is also underscor... |
2 |
TSIDER1, a short and non-autonomous Salivarian trypanosome-specific retroposon related to the ingi6 subclade.
- Bringaud, Berriman, et al.
- 2011
(Show Context)
Citation Context ... in much lower amounts than in T. brucei or are not processed by the Dicer enzymes. Importantly, it has been recently shown that in Leishmania major and L. tarentolae modified thymine residues, termed base J, are present at the ends of CTUs and appear to prevent readthrough transcription (van Luenen et al., 2012). A similar mechanism is likely to operate in L. braziliensis to decrease formation of sense and antisense transcripts from CTUs. In addition, we surveyed the reads for the presence of small RNAs derived from the SIDER family, which is found in T. brucei, T. cruzi and Leishmania ssp. (Bringaud et al., 2011). This family consists of short, truncated versions of ingi-related retroposons, has expanded in the genome of Divergent RNAi pathways in the trypanosomatid lineage 589 © 2012 Blackwell Publishing Ltd, Molecular Microbiology, 87, 580–593 Leishmania ssp., where it has acquired an independent function in regulation of gene expression (Boucher et al., 2002; McNicoll et al., 2005; Bringaud et al., 2007; Muller et al., 2010). L. braziliensis harbours about 2000 copies of SIDER (Smith et al., 2009), but we found no evidence of SIDER-derived reads, suggesting that these elements are not a significant... |
2 |
Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei.
- Wen, Zheng, et al.
- 2011
(Show Context)
Citation Context ...rther complexities of the siRNA repertoire with the identification of loci that upon transcription give rise to structured RNAs (long inverted repeats) or sense and antisense transcripts with the potential to form dsRNA, as it can occur at sites of convergent transcription. However, the functional significance of siRNAs from long hairpins and convergent transcription is at present unclear. Furthermore, siRNAs derived from the pairing of gene and pseudogene transcripts have been implicated in regulating gene expression in certain organisms (Watanabe et al., 2008), including Trypanosoma brucei (Wen et al., 2011). Members of the order Kinetoplastida, which includes many human protozoan parasites, are considered early divergent eukaryotes and thus can inform us about ancient traits of the RNAi pathway. T. brucei, the causative agent of African sleeping sickness in humans and nagana in cattle, was the first member of this group where RNAi was experimentally demonstrated (Ngo et al., 1998). More recently, RNAi has been shown to be functional in Leishmania (Viannia) braziliensis and other members of the Viannia subgenus (Lye et al., 2010), the cause of cutaneous and mucocutaneous leishmaniasis in South Am... |
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