RNA immunoprecipitation chip: Difference between revisions
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'''RIP-chip (RNA immunoprecipitation chip)''' is a [[molecular biology]] technique which combines RNA [[immunoprecipitation]] with a [[DNA microarray|microarray]]. The purpose of this technique is to identify which [[RNA]] sequences interact with a particular [[RNA-binding protein|RNA binding protein]] of interest [[in vivo]]<ref>{{Citation|last=Gagliardi|first=Miriam|title=RIP: RNA Immunoprecipitation|date=2016|url=https://doi.org/10.1007/978-1-4939-6380-5_7|work=Polycomb Group Proteins: Methods and Protocols|pages=73–86|editor-last=Lanzuolo|editor-first=Chiara|series=Methods in Molecular Biology|place=New York, NY|publisher=Springer|language=en|doi=10.1007/978-1-4939-6380-5_7|isbn=978-1-4939-6380-5|access-date=2020-12-01|last2=Matarazzo|first2=Maria R.|editor2-last=Bodega|editor2-first=Beatrice}}</ref><ref>{{Cite journal|last=Townley-Tilson|first=W. H. Davin|last2=Pendergrass|first2=Sarah A.|last3=Marzluff|first3=William F.|last4=Whitfield|first4=Michael L.|date=2006-10-01|title=Genome-wide analysis of mRNAs bound to the histone stem–loop binding protein|url=http://rnajournal.cshlp.org/content/12/10/1853|journal=RNA|language=en|volume=12|issue=10|pages=1853–1867|doi=10.1261/rna.76006|issn=1355-8382|pmc=PMC1581977|pmid=16931877}}</ref><ref>{{Cite journal|last=Khalil|first=Ahmad M.|last2=Guttman|first2=Mitchell|last3=Huarte|first3=Maite|last4=Garber|first4=Manuel|last5=Raj|first5=Arjun|last6=Morales|first6=Dianali Rivea|last7=Thomas|first7=Kelly|last8=Presser|first8=Aviva|last9=Bernstein|first9=Bradley E.|last10=Oudenaarden|first10=Alexander van|last11=Regev|first11=Aviv|date=2009-07-14|title=Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression|url=https://www.pnas.org/content/106/28/11667|journal=Proceedings of the National Academy of Sciences|language=en|volume=106|issue=28|pages=11667–11672|doi=10.1073/pnas.0904715106|issn=0027-8424|pmc=PMC2704857|pmid=19571010}}</ref><ref name=":0">{{Cite journal|last=Hendrickson|first=David G.|last2=Hogan|first2=Daniel J.|last3=Herschlag|first3=Daniel|last4=Ferrell|first4=James E.|last5=Brown|first5=Patrick O.|date=2008-05-07|title=Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance|url=https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002126|journal=PLOS ONE|language=en|volume=3|issue=5|pages=e2126|doi=10.1371/journal.pone.0002126|issn=1932-6203|pmc=PMC2330160|pmid=18461144}}</ref>. It can also be used to determine relative levels of [[gene expression]], to identify subsets of RNAs which may be co-regulated, or to identify RNAs that may have related functions<ref name=":0" /><ref name=":1">{{Cite journal|last=Jayaseelan|first=Sabarinath|last2=Doyle|first2=Francis|last3=Tenenbaum|first3=Scott A.|date=2014-05-01|title=Profiling post-transcriptionally networked mRNA subsets using RIP-Chip and RIP-Seq|url=http://www.sciencedirect.com/science/article/pii/S1046202313004301|journal=Methods|series=Genomic approaches for studying transcriptional and post-transcriptional processes|language=en|volume=67|issue=1|pages=13–19|doi=10.1016/j.ymeth.2013.11.001|issn=1046-2023|pmc=PMC4004666|pmid=24257445}}</ref>. This technique provides insight into the post-transcriptional gene regulation which occurs between RNA and RNA binding proteins<ref name=":1" />. |
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'''RIP-chip (RNA immunoprecipitation chip)''' is a [[molecular biology]] technique which combines RNA [[immunoprecipitation]] with a [[DNA microarray|microarray]]. The purpose of this technique is to identify which [[RNA]] sequences interact with a particular [[RNA-binding protein|RNA binding protein]] of interest [[in vivo]]. It can also be used to determine relative levels of [[gene expression]], to identify subsets of RNAs which may be co-regulated, or to identify RNAs that may have related functions. This technique provides insight into the post-transcriptional gene regulation which occurs between RNA and RNA binding proteins. |
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== Development and Similar Techniques == |
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==RIP-Seq== |
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An alternative methodology (RIP-Seq) is to sequence the RNAs that were pulled down using [[high-throughput sequencing]] rather than analyze them with a microarray.{{cn|date=February 2018}} |
An alternative methodology (RIP-Seq) is to sequence the RNAs that were pulled down using [[high-throughput sequencing]] rather than analyze them with a microarray.{{cn|date=February 2018}} |
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==ChIP-on-chip== |
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A similar technique is [[ChIP-on-chip]], which detects the binding of proteins to genomic DNA rather than RNA.{{cn|date=February 2018}} |
A similar technique is [[ChIP-on-chip]], which detects the binding of proteins to genomic DNA rather than RNA.{{cn|date=February 2018}} |
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==CLIP-Seq== |
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A competing technique is [[CLIP-Seq]], where the RNA binding protein is cross-linked to the RNA via the use of UV light, followed by nuclease digestion and analyzed with high-throughput sequencing.{{cn|date=February 2018}} |
A competing technique is [[CLIP-Seq]], where the RNA binding protein is cross-linked to the RNA via the use of UV light, followed by nuclease digestion and analyzed with high-throughput sequencing.{{cn|date=February 2018}} |
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Revision as of 05:13, 1 December 2020
RIP-chip (RNA immunoprecipitation chip) is a molecular biology technique which combines RNA immunoprecipitation with a microarray. The purpose of this technique is to identify which RNA sequences interact with a particular RNA binding protein of interest in vivo[1][2][3][4]. It can also be used to determine relative levels of gene expression, to identify subsets of RNAs which may be co-regulated, or to identify RNAs that may have related functions[4][5]. This technique provides insight into the post-transcriptional gene regulation which occurs between RNA and RNA binding proteins[5].
Development and Similar Techniques
An alternative methodology (RIP-Seq) is to sequence the RNAs that were pulled down using high-throughput sequencing rather than analyze them with a microarray.[citation needed]
A similar technique is ChIP-on-chip, which detects the binding of proteins to genomic DNA rather than RNA.[citation needed]
A competing technique is CLIP-Seq, where the RNA binding protein is cross-linked to the RNA via the use of UV light, followed by nuclease digestion and analyzed with high-throughput sequencing.[citation needed]
References
- ^ Gagliardi, Miriam; Matarazzo, Maria R. (2016), Lanzuolo, Chiara; Bodega, Beatrice (eds.), "RIP: RNA Immunoprecipitation", Polycomb Group Proteins: Methods and Protocols, Methods in Molecular Biology, New York, NY: Springer, pp. 73–86, doi:10.1007/978-1-4939-6380-5_7, ISBN 978-1-4939-6380-5, retrieved 2020-12-01
- ^ Townley-Tilson, W. H. Davin; Pendergrass, Sarah A.; Marzluff, William F.; Whitfield, Michael L. (2006-10-01). "Genome-wide analysis of mRNAs bound to the histone stem–loop binding protein". RNA. 12 (10): 1853–1867. doi:10.1261/rna.76006. ISSN 1355-8382. PMC 1581977. PMID 16931877.
{{cite journal}}: CS1 maint: PMC format (link) - ^ Khalil, Ahmad M.; Guttman, Mitchell; Huarte, Maite; Garber, Manuel; Raj, Arjun; Morales, Dianali Rivea; Thomas, Kelly; Presser, Aviva; Bernstein, Bradley E.; Oudenaarden, Alexander van; Regev, Aviv (2009-07-14). "Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression". Proceedings of the National Academy of Sciences. 106 (28): 11667–11672. doi:10.1073/pnas.0904715106. ISSN 0027-8424. PMC 2704857. PMID 19571010.
{{cite journal}}: CS1 maint: PMC format (link) - ^ a b Hendrickson, David G.; Hogan, Daniel J.; Herschlag, Daniel; Ferrell, James E.; Brown, Patrick O. (2008-05-07). "Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance". PLOS ONE. 3 (5): e2126. doi:10.1371/journal.pone.0002126. ISSN 1932-6203. PMC 2330160. PMID 18461144.
{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link) - ^ a b Jayaseelan, Sabarinath; Doyle, Francis; Tenenbaum, Scott A. (2014-05-01). "Profiling post-transcriptionally networked mRNA subsets using RIP-Chip and RIP-Seq". Methods. Genomic approaches for studying transcriptional and post-transcriptional processes. 67 (1): 13–19. doi:10.1016/j.ymeth.2013.11.001. ISSN 1046-2023. PMC 4004666. PMID 24257445.
{{cite journal}}: CS1 maint: PMC format (link)
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