a unique rna structure formed by a long-distance ... singh.pdf · natalia singh and ravindra singh...
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Natalia Singh and Ravindra Singh Department of Biomedical Sciences
Iowa State University, USA [email protected]
A unique RNA structure formed by a long-distance interaction uncovers the therapeutic potential of a deep
intronic sequence
July 5, 2014, Salzburg, Austria
Organization of SMN protein
Howell et al., Future Med Chemistry, 6 (9), 1081-1099, 2014
Two SMN Genes as inverted repeats on 5q11-q13!
NAIP SMN2
AG-1 C212 NAIP SMN1
AG-1 C212
1 2a 2b 3 4 5 6 7 8
G C C
A A
1 2a 2b 3 4 5 6 7 8
A T T
C C
500 Kb 500 Kb
282 aa! 294 aa!
Spinal Muscular Atrophy (SMA)!!SMN1
!"#$%
!"#&%
'()*%+%,%*-.)%/%01233*4%
5% /% 6%5% 6%
$% &%5% 67%
Regulatory elements of SMN pre-mRNA
Master checkpoint
Howell et al., Future Med Chemistry, 6 (9), 1081-1099, 2014
8!!9#$%
:-5% :-/% :-6%8);<.)%/%
GUAAGUCUGCCAGCAUUAUGAAAGUGAAUCUUACUUUUGUAAAACUUUAUGGUUUGUGG!#$!$=9$>%?@()*%>A%#$!$B9$C%?@()*%BA%
#$!$=9$C%?@()*%CA%
#$!&=9&>%?@()*%5A%
#$!$B9&>%?@()*%$=A%
#$!&B9&C%?@()*%/A%#$!7=97>%?@()*%6A%
#$!&=9&C%?@()*%$$%#$!&B97>%?@()*%$&A%
#$!$B9&C%?@()*%$>A%#$!&=97>%?@()*%$BA%#$!&B97C%?@()*%$5A%
#$!$=97>%?@()*%$6A%#$!$=9&C%?@()*%$/A%
!"#&%?@()*%7A%
ISS-N1 is a strong intronic splicing silencer
$% &% 7% /%5%B%>%
5% /% 6%5% 6%
'()*%+%,%*-.)%/%01233*4%
$$% $&% $7%6% C% $=% $>% $B%#D% >% 6$% />%$C%6C%>$% /% 7% 6&%6C% B>% &C% B% B%
!"#$%
!"#&%
#$!
$=9$>%
#$!
$B9$C%
#$!
$=9$C%
#$!
&=9&>%
#$!
$B9&>%
#$!
&B9&C%
#$!
7=97>%
#$!
&=9&C%
#$!
&B97>%
#$!
$=9&>%
#$!
$B9&C%
#$!
&=97>%
#$!
&B97C%
#$!
$=9&C%
#$!
$=97>%
E*F;.<%
$5% $/% $6%&/%7C%6$%
#$!$=9&>%?@()*%$7A%
5´SS !
Singh et al. Mol. Cell. Biol. 26, 1333-1346, 2006!
ISS-N1 is a target for an antisense oligonucleotide (ASO)-mediated correction of SMN2 exon 7 splicing
#.)
*%
".F1%
D)G9#$%
D)G9#$H$=%
D)G9#$H&=%
D)G9#$H7=%
5% /% 6%5% 6%
'()*%+%
,%*-.)%/%01233*4%$% &% 7% 5%B%>%/% 6$% 66%5/%/$%>%
GUAAGUCUGCCAGCAUUAUGAAAGUGAAUCUUACUUUUGUAAAACUUUAUGGUUUGUGG!
D)G9#$% D)G9#$H$=% D)G9#$H&=% D)G9#$H7=%
8!!9#$%
:-5% :-/% :-6%8);<.)%/%
:-B% :->% :-7% :-&I% :-&(% :-$%
!"D%J(G*);%K2I<.I@(0;% H%9% H% H% H% H%#.<L(@%K2I<.I@(0;% 9%H% 9% 9% 9% 9%
5´SS !
Singh et al. Mol. Cell. Biol. 26, 1333-1346, 2006!US Patent # US 2007/0292408 !
Mutation!
3´SS !
Studies with ISS-N1-targeting ASOs
Sivanesan et al., Transl. Neurosci., 4, 1-7, 2013!
Relative efficacy of drug candidates in !7SMA mice!
Seo et al., Biochim. Biophys Acta, 1126, 271-83 2013!
ISS-N1 targeting ASO
ISS-N1 targeting ASO
Gene Therapy
days
Singh et al., RNA 16, 1167-1181, 2010
Antagonistic response of two ASOs that bind to targets differing in a single nucleotide
RNA 16, 1167-1181, 2010
ASO-based approach reveals a long-distance interaction (LDI)
Primary site of LDI
Nucleic Acids Research 41, 8144-8165, 2013!
Smallest motif for LDI
Nucleic Acids Research 41, 8144-8165, 2013!
Effect of point mutations within the smallest motif for LDI
Nucleic Acids Research 41, 8144-8165, 2013!
Effect of structure-associated mutations on LDI
Nucleic Acids Research 41, 8144-8165, 2013!
Effect of compensatory mutations on LDI
Nucleic Acids Research 41, 8144-8165, 2013!
Effect of negative regulators on LDI
Nucleic Acids Research 41, 8144-8165, 2013!
Structure of SMN2 intron 7 (Probed by SHAPE)
ISS-N2!
Nucleic Acids Research 41, 8144-8165, 2013!
Validation of the 5" strand of ISTL1
NAR 41, 8144-8165, 2013
Validation of the 3" strand of ISTL1 formation
Nucleic Acids Research 41, 8144-8165, 2013!
Effect of L14 and F14 on RNA secondary structure of SMN2 intron 7
Nucleic Acids Research 41, 8144-8165, 2013!
Structural basis of the effect of ASOs F14 pathway ! Exon 7 inclusion
L14 pathway ! Exon 7 exclusion
Nucleic Acids Research 41, 8144-8165, 2013!
Is ISS-N2 a new antisense target ?
ISS-N2
Nucleic Acids Research 41, 8144-8165, 2013!
Effect of ISS-N2-targeting ASOs on SMN2 exon 7 splicing
:-5% :-/% :-6%8);<.)%/%
:-B% :->% :-7% :-&I% :-&(% :-$%5´SS !
Mutation!
Nucleic Acids Research 41, 8144-8165, 2013!
Mechanism of splicing correction by a deep intronic target
Nucleic Acids Research 41, 8144-8165, 2013!