Urb-RIP - An Adaptable and Efficient Approach for Immunoprecipitation of RNAs and Associated RNAs/Proteins.
Post-transcriptional regulation of gene expression is an important process that is mediated by interactions between mRNAs and RNA binding proteins (RBP), non-coding RNAs (ncRNA) or ribonucleoproteins (RNP). Key to the study of post-transcriptional regulation of mRNAs and the function of ncRNAs such...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2016-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5145212?pdf=render |
| _version_ | 1818290378507288576 |
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| author | Kyle A Cottrell Sergej Djuranovic |
| author_facet | Kyle A Cottrell Sergej Djuranovic |
| author_sort | Kyle A Cottrell |
| collection | DOAJ |
| description | Post-transcriptional regulation of gene expression is an important process that is mediated by interactions between mRNAs and RNA binding proteins (RBP), non-coding RNAs (ncRNA) or ribonucleoproteins (RNP). Key to the study of post-transcriptional regulation of mRNAs and the function of ncRNAs such as long non-coding RNAs (lncRNAs) is an understanding of what factors are interacting with these transcripts. While several techniques exist for the enrichment of a transcript whether it is an mRNA or an ncRNA, many of these techniques are cumbersome or limited in their application. Here we present a novel method for the immunoprecipitation of mRNAs and ncRNAs, Urb-RNA immunoprecipitation (Urb-RIP). This method employs the RRM1 domain of the "resurrected" snRNA-binding protein Urb to enrich messages containing a stem-loop tag. Unlike techniques which employ the MS2 protein, which require large repeats of the MS2 binding element, Urb-RIP requires only one stem-loop. This method routinely provides over ~100-fold enrichment of tagged messages. Using this technique we have shown enrichment of tagged mRNAs and lncRNAs as well as miRNAs and RNA-binding proteins bound to those messages. We have confirmed, using Urb-RIP, interaction between RNA PolIII transcribed lncRNA BC200 and polyA binding protein. |
| first_indexed | 2024-12-13T02:27:13Z |
| format | Article |
| id | doaj.art-9eb8e58bf31c4a13b0ff624df94d4611 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-13T02:27:13Z |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-9eb8e58bf31c4a13b0ff624df94d46112022-12-22T00:02:36ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-011112e016787710.1371/journal.pone.0167877Urb-RIP - An Adaptable and Efficient Approach for Immunoprecipitation of RNAs and Associated RNAs/Proteins.Kyle A CottrellSergej DjuranovicPost-transcriptional regulation of gene expression is an important process that is mediated by interactions between mRNAs and RNA binding proteins (RBP), non-coding RNAs (ncRNA) or ribonucleoproteins (RNP). Key to the study of post-transcriptional regulation of mRNAs and the function of ncRNAs such as long non-coding RNAs (lncRNAs) is an understanding of what factors are interacting with these transcripts. While several techniques exist for the enrichment of a transcript whether it is an mRNA or an ncRNA, many of these techniques are cumbersome or limited in their application. Here we present a novel method for the immunoprecipitation of mRNAs and ncRNAs, Urb-RNA immunoprecipitation (Urb-RIP). This method employs the RRM1 domain of the "resurrected" snRNA-binding protein Urb to enrich messages containing a stem-loop tag. Unlike techniques which employ the MS2 protein, which require large repeats of the MS2 binding element, Urb-RIP requires only one stem-loop. This method routinely provides over ~100-fold enrichment of tagged messages. Using this technique we have shown enrichment of tagged mRNAs and lncRNAs as well as miRNAs and RNA-binding proteins bound to those messages. We have confirmed, using Urb-RIP, interaction between RNA PolIII transcribed lncRNA BC200 and polyA binding protein.http://europepmc.org/articles/PMC5145212?pdf=render |
| spellingShingle | Kyle A Cottrell Sergej Djuranovic Urb-RIP - An Adaptable and Efficient Approach for Immunoprecipitation of RNAs and Associated RNAs/Proteins. PLoS ONE |
| title | Urb-RIP - An Adaptable and Efficient Approach for Immunoprecipitation of RNAs and Associated RNAs/Proteins. |
| title_full | Urb-RIP - An Adaptable and Efficient Approach for Immunoprecipitation of RNAs and Associated RNAs/Proteins. |
| title_fullStr | Urb-RIP - An Adaptable and Efficient Approach for Immunoprecipitation of RNAs and Associated RNAs/Proteins. |
| title_full_unstemmed | Urb-RIP - An Adaptable and Efficient Approach for Immunoprecipitation of RNAs and Associated RNAs/Proteins. |
| title_short | Urb-RIP - An Adaptable and Efficient Approach for Immunoprecipitation of RNAs and Associated RNAs/Proteins. |
| title_sort | urb rip an adaptable and efficient approach for immunoprecipitation of rnas and associated rnas proteins |
| url | http://europepmc.org/articles/PMC5145212?pdf=render |
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