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rasiRNAs: a class of small regulatory RNAs

rasiRNAs: a class of small regulatory RNAs. Jasmine Lau 4 May 2009. The Family of small RNAs. Small noncoding regulatory RNAs. Shorter length 20-25 nucleotides. Longer length 24-27 nucleotides. piwi-interacting RNAs (piRNAs). small interfering RNAs (siRNAs). microRNAs (miRNAs).

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rasiRNAs: a class of small regulatory RNAs

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  1. rasiRNAs: a class of small regulatory RNAs Jasmine Lau 4 May 2009

  2. The Family of small RNAs Small noncoding regulatory RNAs Shorter length 20-25 nucleotides Longer length 24-27 nucleotides piwi-interacting RNAs (piRNAs) small interfering RNAs (siRNAs) microRNAs (miRNAs) 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

  3. First hints of rasiRNAs 2001 • Trypanosoma brucei • parasitic protist species • causes African trypanosomiasis (sleeping sickness) 2002 • Abundant 24-26 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 http://www.sanger.ac.uk/Projects/T_brucei/Tryp.cartoon.shtml

  4. First hints of rasiRNAs • Trypanosoma brucei • parasitic protist species • causes African trypanosomiasis (sleeping sickness) 2001 2002 • Abundant 24-26 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

  5. 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

  6. 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

  7. 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

  8. A A A A A U U U U U rasiRNA biogenesis AGO3 Adenine at nucleotide 10 Sense transcript: 3’ 5’ 10 complementary nucleotides Antisense transcript: 3’ 5’ Uridine at 5’ terminal end PIWI/ AUB Zucchini/ squash? 2’-O-Me AGO3 ? AGO3 3’ 5’ 5’ 3’ Pimet AGO3 5’ 3’ 3’ 5’ 5’ 3’ 5’ 3’ PIWI/ AUB 2’-O-Me Pimet 3’ 5’ 3’ 5’ ? PIWI/ AUB PIWI/ AUB Zucchini/ squash?

  9. 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

  10. 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

  11. How rasiRNAs work 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

  12. 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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