RasiRNAs: a class of small regulatory RNAs Jasmine Lau 4 May 2009.
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Transcript of RasiRNAs: a class of small regulatory RNAs Jasmine Lau 4 May 2009.
Small noncoding regulatory RNAs
Longer length 24-27 nucleotides
small interfering RNAs
(siRNAs)
microRNAs (miRNAs)
Shorter length 20-25 nucleotides
piwi-interacting RNAs (piRNAs)
Other piRNAs
rasiRNAs
The Family of small RNAs
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
First hints of rasiRNAsTrypanosoma brucei • parasitic protist species• causes African trypanosomiasis (sleeping sickness)
2001
2002
2003
2004
2005
2006
2007
2008
Present
Abundant 24-26 nucleotide long siRNA-like RNAs Represented 2 retrotransposons in the genome Both sense and antisense polarity
Regulatory mechanism to silence retrotransposon transcription and mobilization?
http://www.sanger.ac.uk/Projects/T_brucei/Tryp.cartoon.shtml
First hints of rasiRNAsTrypanosoma brucei • parasitic protist species• causes African trypanosomiasis (sleeping sickness) 2002
2001
2003
2004
2005
2006
2007
2008
Present
Abundant 24-26 nucleotide long siRNA-like RNAs Represented 2 retrotransposons in the genome Both sense and antisense polarity
Regulatory mechanism to silence retrotransposon transcription and mobilization?
Nicotiana and Arabidopsis thaliana plants
24-26 nucleotide long endogenous siRNA species Represented 2 retrotransposons in Nicotiana genome, 1 retrotransposon in Arabidopsis genome Both sense and antisense polarity
Linked to DNA methylation and systemic silencing Mechanism to keep retrotransposon silent?
rasiRNAs: new class of RNAs
2003
2001
2002
2004
2005
2006
2007
2008
Present
Drosophila melanogaster small RNA profiling
2 distinct classes of small RNAs:(i) 21-23 nt RNAs(ii) 24-26 nt RNAs
Sequences correspond to genomic repeats/transposons Class of RNAs called repeat-associated siRNAs (rasiRNAs)
Sequences correspond to genomic repeats or transposons
Also described in zebrafish, fission yeast
Sense & antisense orientation of repetitive sequence elements:• Long Terminal Repeat (LTR) and non-LTR retrotransposons• DNA transposons• Satellite and microsatellite sequences• Complex repeats
rasiRNAs: subclass of piRNAs
2006
2001
2002
2004
2005
2003
2007
2008
Present
Longer length 24-27 nucleotides
piwi-interacting RNAs (piRNAs)
Other piRNAs
rasiRNAs
24-26 nucleotide long RNAsBUT lack transposon or repetitive seqeuences
rasiRNA biogenesisArgonaute
protein family
Piwi subfamily
Ago1
Ago subfamily
Ago2 Ago3Aubergine
(Aub)Piwi
Associate with rasiRNAs, present in germline cells and early embryos
Associate with miRNAs
Associate with siRNAs
Dicer-dependent production to produce
double-stranded precursor
Dicer-independent production
rasiRNA biogenesisSense transcript:
Antisense transcript:
5’3’
AGO3
5’ 3’A
PIWI/ AUB
3’ 5’U
Adenine at nucleotide 10
Uridine at 5’ terminal end
UA
PIWI/ AUB
5’3’ U
5’ 3’
PIWI/ AUB
5’3’ U
10 complementary nucleotides
5’ 3’A
AGO3
5’ 3’A
AGO3
5’3’ U
? PIWI/ AUB
A5’ 3’
?AGO3
Zucchini/ squash?
Zucchini/ squash?
2’-O-Me
Pimet
Pimet
2’-O-Me
What do rasiRNAs do?
• 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
Maintaining genomic stability
Present in fission yeast, plants, fly, zebrafishFunctions mainly in the germline and early embryo development in fly and zebrafish, found at very low levels in the adult fly.
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
How rasiRNAs work
Fission yeast : Gene silencing and establishing heterochromatin
Dicer cleaves long dsRNA
Transcriptional silencing complex in nucleus Ago1, Chp1 and Tas3
Binds DNA/ chromatin, induce DNA and histone methylation
Plants : Similar mechanism to yeast (above), also repress repetitive transposable elements
Ago4-dependent mechanisms
Induce systemic gene silencing, Histone H3 lysine-9 methylation, DNA methylation Direct chromatin modifications
How rasiRNAs work
Drosophila melanogaster:
rasiRNAs associate with piwi Argonaute proteins, and RNA helicases (Spindle-E and Armitage)
Induce histone H3 Lysine 9 methylation and association of HP1 chromatin binding protein with heterochromatin
Downstream effector mechanisms and pathways are not yet known Literature between piRNAs and rasiRNAs are merging
Longer length 24-27 nucleotides
piwi-interacting RNAs (piRNAs)
Other piRNAs
rasiRNAs
Summary: 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