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rasiRNAs: a class of small regulatory RNAs
Jasmine Lau 4 May 2009
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The Family of small RNAs
Small noncoding regulatory RNAs Shorter length 20-25 nucleotides Longer length 24-27 nucleotides small interfering RNAs (siRNAs) microRNAs (miRNAs) piwi-interacting RNAs (piRNAs) rasiRNAs – repeat-associated siRNA Other piRNAs rasiRNAs rasiRNAs = Repeat-associated small interfering RNAs sequence-specific gene silencing (RNAi mechanism) forms RNA-protein complexes with Piwi subfamily proteins sequences correspond to genomic repeats and transposons
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First hints of rasiRNAs
2001 Trypanosoma brucei parasitic protist species causes African trypanosomiasis (sleeping sickness) 2002 Abundant nucleotide long siRNA-like RNAs Represented 2 retrotransposons in the genome Both sense and antisense polarity 2003 2004 Regulatory mechanism to silence retrotransposon transcription and mobilization? 2005 2006 2007 2008 Present
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First hints of rasiRNAs
2001 Trypanosoma brucei parasitic protist species causes African trypanosomiasis (sleeping sickness) 2002 Abundant nucleotide long siRNA-like RNAs Represented 2 retrotransposons in the genome Both sense and antisense polarity 2003 2004 Regulatory mechanism to silence retrotransposon transcription and mobilization? 2005 Nicotiana and Arabidopsis thaliana plants 2006 24-26 nucleotide long endogenous siRNA species Represented 2 retrotransposons in Nicotiana genome, 1 retrotransposon in Arabidopsis genome Both sense and antisense polarity 2007 2008 Linked to DNA methylation and systemic silencing Mechanism to keep retrotransposon silent? Present
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rasiRNAs: new class of RNAs
2001 Drosophila melanogaster small RNA profiling 2 distinct classes of small RNAs: 21-23 nt RNAs 24-26 nt RNAs 2002 2003 Sequences correspond to genomic repeats or transposons 2004 Sequences correspond to genomic repeats/transposons Class of RNAs called repeat-associated siRNAs (rasiRNAs) 2005 Also described in zebrafish, fission yeast 2006 Sense & antisense orientation of repetitive sequence elements: Long Terminal Repeat (LTR) and non-LTR retrotransposons DNA transposons Satellite and microsatellite sequences Complex repeats 2007 2008 Present
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rasiRNAs: subclass of piRNAs
2001 Longer length 24-27 nucleotides 2002 2003 piwi-interacting RNAs (piRNAs) 2004 24-26 nucleotide long RNAs BUT lack transposon or repetitive seqeuences 2005 Other piRNAs rasiRNAs 2006 2007 2008 Present
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rasiRNA biogenesis Argonaute protein family Ago subfamily Piwi subfamily Ago1 Ago2 Ago3 Aubergine (Aub) Piwi Associate with miRNAs Associate with siRNAs Associate with rasiRNAs, present in germline cells and early embryos Dicer-dependent production to produce double-stranded precursor Dicer-independent production
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rasiRNA biogenesis ? ? AGO3 Adenine at nucleotide 10 Sense transcript:
5’ 3’ A 10 complementary nucleotides Antisense transcript: U 3’ 5’ Uridine at 5’ terminal end PIWI/ AUB Zucchini/ squash? 2’-O-Me AGO3 ? AGO3 5’ 5’ 3’ A 3’ Pimet A AGO3 To add in? It also remains unclear how the ping-pong biogenesis mechanism is initiated. In the fly, aub and possibly piwi are accumulated at the posterior pole in the oocytes and remains in the polar granules in the early embryos. It is then deposited in the pole cells which are the progenitor germ cells. Hence, this suggests that rasiRNAs which are associated with Piwi proteins can be transmitted via the germline for the next generation, acting as ‘primary seeds’ to launch the rasiRNA biogenesis cycle in the embryos. 5’ 3’ 5’ 3’ A A 3’ U 5’ U 3’ 5’ PIWI/ AUB 2’-O-Me Pimet U 3’ 5’ 3’ U 5’ ? PIWI/ AUB PIWI/ AUB Zucchini/ squash?
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What do rasiRNAs do? Present in fission yeast, plants, fly, zebrafish
Functions mainly in the germline and early embryo development in fly and zebrafish, found at very low levels in the adult fly. Maintaining genomic stability Silencing and suppressing mobilization of retrotransposons and other selfish genetic transposable elements Guide transcriptional and post-transcriptional gene silencing of repetitive sequence elements Guide chromatin silencing to establish and maintain heterochromatin Also in particular for flies: Maintaining germ cell self-renewal Establishing axis polarity of the early embryo Regulating pole cell formation and oocyte maturation Maintaining telomeres
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How rasiRNAs work Fission yeast :
Gene silencing and establishing heterochromatin Transcriptional silencing complex in nucleus Ago1, Chp1 and Tas3 Binds DNA/ chromatin, induce DNA and histone methylation Dicer cleaves long dsRNA Plants : Similar mechanism to yeast (above), also repress repetitive transposable elements Induce systemic gene silencing, Histone H3 lysine-9 methylation, DNA methylation Direct chromatin modifications Ago4-dependent mechanisms
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How rasiRNAs work Downstream effector mechanisms and pathways
Drosophila melanogaster: Induce histone H3 Lysine 9 methylation and association of HP1 chromatin binding protein with heterochromatin rasiRNAs associate with piwi Argonaute proteins, and RNA helicases (Spindle-E and Armitage) Downstream effector mechanisms and pathways are not yet known Literature between piRNAs and rasiRNAs are merging
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piwi-interacting RNAs (piRNAs)
Summary: rasiRNAs rasiRNAs = Repeat-associated small interfering RNAs Longer length 24-27 nucleotides sequence-specific gene silencing (RNAi mechanism) piwi-interacting RNAs (piRNAs) forms RNA-protein complexes with Piwi subfamily proteins Other piRNAs rasiRNAs sequences correspond to genomic repeats and transposons
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