Optimal antisense target reducing INS intron 1 retention is adjacent to a parallel G quadruplex. Kralovicova, J., Lages, A., Patel, A., Dhir, A., Buratti, E., Searle, M., & Vorechovsky, I. Nucleic acids research, 42(12):8161–8173, June, 2014. ![Optimal antisense target reducing INS intron 1 retention is adjacent to a parallel G quadruplex. [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Splice-switching oligonucleotides (SSOs) have been widely used to inhibit exon usage but antisense strategies that promote removal of entire introns to increase splicing-mediated gene expression have not been developed. Here we show reduction of INS intron 1 retention by SSOs that bind transcripts derived from a human haplotype expressing low levels of proinsulin. This haplotype is tagged by a polypyrimidine tract variant rs689 that decreases the efficiency of intron 1 splicing and increases the relative abundance of mRNAs with extended 5' untranslated region (5' UTR), which curtails translation. Co-expression of haplotype-specific reporter constructs with SSOs bound to splicing regulatory motifs and decoy splice sites in primary transcripts revealed a motif that significantly reduced intron 1-containing mRNAs. Using an antisense microwalk at a single nucleotide resolution, the optimal target was mapped to a splicing silencer containing two pseudoacceptor sites sandwiched between predicted RNA guanine (G) quadruplex structures. Circular dichroism spectroscopy and nuclear magnetic resonance of synthetic G-rich oligoribonucleotide tracts derived from this region showed formation of a stable parallel 2-quartet G-quadruplex on the 3' side of the antisense retention target and an equilibrium between quadruplexes and stable hairpin-loop structures bound by optimal SSOs. This region interacts with heterogeneous nuclear ribonucleoproteins F and H that may interfere with conformational transitions involving the antisense target. The SSO-assisted promotion of weak intron removal from the 5' UTR through competing noncanonical and canonical RNA structures may facilitate development of novel strategies to enhance gene expression.
@article{Kralovicova2014,
title = {Optimal antisense target reducing {INS} intron 1 retention is adjacent to a parallel {G} quadruplex.},
volume = {42},
issn = {1362-4962},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24944197},
doi = {10.1093/nar/gku507},
abstract = {Splice-switching oligonucleotides (SSOs) have been widely used to inhibit exon usage but antisense strategies that promote removal of entire introns to increase splicing-mediated gene expression have not been developed. Here we show reduction of INS intron 1 retention by SSOs that bind transcripts derived from a human haplotype expressing low levels of proinsulin. This haplotype is tagged by a polypyrimidine tract variant rs689 that decreases the efficiency of intron 1 splicing and increases the relative abundance of mRNAs with extended 5' untranslated region (5' UTR), which curtails translation. Co-expression of haplotype-specific reporter constructs with SSOs bound to splicing regulatory motifs and decoy splice sites in primary transcripts revealed a motif that significantly reduced intron 1-containing mRNAs. Using an antisense microwalk at a single nucleotide resolution, the optimal target was mapped to a splicing silencer containing two pseudoacceptor sites sandwiched between predicted RNA guanine (G) quadruplex structures. Circular dichroism spectroscopy and nuclear magnetic resonance of synthetic G-rich oligoribonucleotide tracts derived from this region showed formation of a stable parallel 2-quartet G-quadruplex on the 3' side of the antisense retention target and an equilibrium between quadruplexes and stable hairpin-loop structures bound by optimal SSOs. This region interacts with heterogeneous nuclear ribonucleoproteins F and H that may interfere with conformational transitions involving the antisense target. The SSO-assisted promotion of weak intron removal from the 5' UTR through competing noncanonical and canonical RNA structures may facilitate development of novel strategies to enhance gene expression.},
number = {12},
journal = {Nucleic acids research},
author = {Kralovicova, Jana and Lages, Ana and Patel, Alpa and Dhir, Ashish and Buratti, Emanuele and Searle, Mark and Vorechovsky, Igor},
month = jun,
year = {2014},
pmid = {24944197},
keywords = {\#nosource},
pages = {8161--8173},
}
Downloads: 0
{"_id":"qabR24eM9W2wEE2wX","bibbaseid":"kralovicova-lages-patel-dhir-buratti-searle-vorechovsky-optimalantisensetargetreducinginsintron1retentionisadjacenttoaparallelgquadruplex-2014","author_short":["Kralovicova, J.","Lages, A.","Patel, A.","Dhir, A.","Buratti, E.","Searle, M.","Vorechovsky, I."],"bibdata":{"bibtype":"article","type":"article","title":"Optimal antisense target reducing INS intron 1 retention is adjacent to a parallel G quadruplex.","volume":"42","issn":"1362-4962","url":"http://www.ncbi.nlm.nih.gov/pubmed/24944197","doi":"10.1093/nar/gku507","abstract":"Splice-switching oligonucleotides (SSOs) have been widely used to inhibit exon usage but antisense strategies that promote removal of entire introns to increase splicing-mediated gene expression have not been developed. Here we show reduction of INS intron 1 retention by SSOs that bind transcripts derived from a human haplotype expressing low levels of proinsulin. This haplotype is tagged by a polypyrimidine tract variant rs689 that decreases the efficiency of intron 1 splicing and increases the relative abundance of mRNAs with extended 5' untranslated region (5' UTR), which curtails translation. Co-expression of haplotype-specific reporter constructs with SSOs bound to splicing regulatory motifs and decoy splice sites in primary transcripts revealed a motif that significantly reduced intron 1-containing mRNAs. Using an antisense microwalk at a single nucleotide resolution, the optimal target was mapped to a splicing silencer containing two pseudoacceptor sites sandwiched between predicted RNA guanine (G) quadruplex structures. Circular dichroism spectroscopy and nuclear magnetic resonance of synthetic G-rich oligoribonucleotide tracts derived from this region showed formation of a stable parallel 2-quartet G-quadruplex on the 3' side of the antisense retention target and an equilibrium between quadruplexes and stable hairpin-loop structures bound by optimal SSOs. This region interacts with heterogeneous nuclear ribonucleoproteins F and H that may interfere with conformational transitions involving the antisense target. The SSO-assisted promotion of weak intron removal from the 5' UTR through competing noncanonical and canonical RNA structures may facilitate development of novel strategies to enhance gene expression.","number":"12","journal":"Nucleic acids research","author":[{"propositions":[],"lastnames":["Kralovicova"],"firstnames":["Jana"],"suffixes":[]},{"propositions":[],"lastnames":["Lages"],"firstnames":["Ana"],"suffixes":[]},{"propositions":[],"lastnames":["Patel"],"firstnames":["Alpa"],"suffixes":[]},{"propositions":[],"lastnames":["Dhir"],"firstnames":["Ashish"],"suffixes":[]},{"propositions":[],"lastnames":["Buratti"],"firstnames":["Emanuele"],"suffixes":[]},{"propositions":[],"lastnames":["Searle"],"firstnames":["Mark"],"suffixes":[]},{"propositions":[],"lastnames":["Vorechovsky"],"firstnames":["Igor"],"suffixes":[]}],"month":"June","year":"2014","pmid":"24944197","keywords":"#nosource","pages":"8161–8173","bibtex":"@article{Kralovicova2014,\n\ttitle = {Optimal antisense target reducing {INS} intron 1 retention is adjacent to a parallel {G} quadruplex.},\n\tvolume = {42},\n\tissn = {1362-4962},\n\turl = {http://www.ncbi.nlm.nih.gov/pubmed/24944197},\n\tdoi = {10.1093/nar/gku507},\n\tabstract = {Splice-switching oligonucleotides (SSOs) have been widely used to inhibit exon usage but antisense strategies that promote removal of entire introns to increase splicing-mediated gene expression have not been developed. Here we show reduction of INS intron 1 retention by SSOs that bind transcripts derived from a human haplotype expressing low levels of proinsulin. This haplotype is tagged by a polypyrimidine tract variant rs689 that decreases the efficiency of intron 1 splicing and increases the relative abundance of mRNAs with extended 5' untranslated region (5' UTR), which curtails translation. Co-expression of haplotype-specific reporter constructs with SSOs bound to splicing regulatory motifs and decoy splice sites in primary transcripts revealed a motif that significantly reduced intron 1-containing mRNAs. Using an antisense microwalk at a single nucleotide resolution, the optimal target was mapped to a splicing silencer containing two pseudoacceptor sites sandwiched between predicted RNA guanine (G) quadruplex structures. Circular dichroism spectroscopy and nuclear magnetic resonance of synthetic G-rich oligoribonucleotide tracts derived from this region showed formation of a stable parallel 2-quartet G-quadruplex on the 3' side of the antisense retention target and an equilibrium between quadruplexes and stable hairpin-loop structures bound by optimal SSOs. This region interacts with heterogeneous nuclear ribonucleoproteins F and H that may interfere with conformational transitions involving the antisense target. The SSO-assisted promotion of weak intron removal from the 5' UTR through competing noncanonical and canonical RNA structures may facilitate development of novel strategies to enhance gene expression.},\n\tnumber = {12},\n\tjournal = {Nucleic acids research},\n\tauthor = {Kralovicova, Jana and Lages, Ana and Patel, Alpa and Dhir, Ashish and Buratti, Emanuele and Searle, Mark and Vorechovsky, Igor},\n\tmonth = jun,\n\tyear = {2014},\n\tpmid = {24944197},\n\tkeywords = {\\#nosource},\n\tpages = {8161--8173},\n}\n\n","author_short":["Kralovicova, J.","Lages, A.","Patel, A.","Dhir, A.","Buratti, E.","Searle, M.","Vorechovsky, I."],"key":"Kralovicova2014","id":"Kralovicova2014","bibbaseid":"kralovicova-lages-patel-dhir-buratti-searle-vorechovsky-optimalantisensetargetreducinginsintron1retentionisadjacenttoaparallelgquadruplex-2014","role":"author","urls":{"Paper":"http://www.ncbi.nlm.nih.gov/pubmed/24944197"},"keyword":["#nosource"],"metadata":{"authorlinks":{}},"html":""},"bibtype":"article","biburl":"https://bibbase.org/zotero/eric.larG4","dataSources":["4i5C7S78DvJNsaHyg","5L2zM5wNE5CBYNuea"],"keywords":["#nosource"],"search_terms":["optimal","antisense","target","reducing","ins","intron","retention","adjacent","parallel","quadruplex","kralovicova","lages","patel","dhir","buratti","searle","vorechovsky"],"title":"Optimal antisense target reducing INS intron 1 retention is adjacent to a parallel G quadruplex.","year":2014}