Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity
The control and function of RNA are governed by the specificity of RNA binding proteins. Here, we describe a method for global unbiased analysis of RNA-protein interactions that uses in vitro selection, high-throughput sequencing, and sequence-specificity landscapes. The method yields affinities for...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2012-05-01
|
| Series: | Cell Reports |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124712001167 |
| _version_ | 1818037640853716992 |
|---|---|
| author | Zachary T. Campbell Devesh Bhimsaria Cary T. Valley Jose A. Rodriguez-Martinez Elena Menichelli James R. Williamson Aseem Z. Ansari Marvin Wickens |
| author_facet | Zachary T. Campbell Devesh Bhimsaria Cary T. Valley Jose A. Rodriguez-Martinez Elena Menichelli James R. Williamson Aseem Z. Ansari Marvin Wickens |
| author_sort | Zachary T. Campbell |
| collection | DOAJ |
| description | The control and function of RNA are governed by the specificity of RNA binding proteins. Here, we describe a method for global unbiased analysis of RNA-protein interactions that uses in vitro selection, high-throughput sequencing, and sequence-specificity landscapes. The method yields affinities for a vast array of RNAs in a single experiment, including both low- and high-affinity sites. It is reproducible and accurate. Using this approach, we analyzed members of the PUF (Pumilio and FBF) family of eukaryotic mRNA regulators. Our data identify effects of a specific protein partner on PUF-RNA interactions, reveal subsets of target sites not previously detected, and demonstrate that designer PUF proteins can precisely alter specificity. The approach described here is, in principle, broadly applicable for analysis of any molecule that binds RNA, including proteins, nucleic acids, and small molecules. |
| first_indexed | 2024-12-10T07:30:04Z |
| format | Article |
| id | doaj.art-c925452b081e4831ab860a8043418d2e |
| institution | Directory Open Access Journal |
| issn | 2211-1247 |
| language | English |
| last_indexed | 2024-12-10T07:30:04Z |
| publishDate | 2012-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj.art-c925452b081e4831ab860a8043418d2e2022-12-22T01:57:36ZengElsevierCell Reports2211-12472012-05-011557058110.1016/j.celrep.2012.04.003Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding SpecificityZachary T. Campbell0Devesh Bhimsaria1Cary T. Valley2Jose A. Rodriguez-Martinez3Elena Menichelli4James R. Williamson5Aseem Z. Ansari6Marvin Wickens7Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1554, USADepartment of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1554, USAGraduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1554, USADepartment of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1554, USADepartment of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USADepartment of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USADepartment of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1554, USADepartment of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1554, USAThe control and function of RNA are governed by the specificity of RNA binding proteins. Here, we describe a method for global unbiased analysis of RNA-protein interactions that uses in vitro selection, high-throughput sequencing, and sequence-specificity landscapes. The method yields affinities for a vast array of RNAs in a single experiment, including both low- and high-affinity sites. It is reproducible and accurate. Using this approach, we analyzed members of the PUF (Pumilio and FBF) family of eukaryotic mRNA regulators. Our data identify effects of a specific protein partner on PUF-RNA interactions, reveal subsets of target sites not previously detected, and demonstrate that designer PUF proteins can precisely alter specificity. The approach described here is, in principle, broadly applicable for analysis of any molecule that binds RNA, including proteins, nucleic acids, and small molecules.http://www.sciencedirect.com/science/article/pii/S2211124712001167 |
| spellingShingle | Zachary T. Campbell Devesh Bhimsaria Cary T. Valley Jose A. Rodriguez-Martinez Elena Menichelli James R. Williamson Aseem Z. Ansari Marvin Wickens Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity Cell Reports |
| title | Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity |
| title_full | Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity |
| title_fullStr | Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity |
| title_full_unstemmed | Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity |
| title_short | Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity |
| title_sort | cooperativity in rna protein interactions global analysis of rna binding specificity |
| url | http://www.sciencedirect.com/science/article/pii/S2211124712001167 |
| work_keys_str_mv | AT zacharytcampbell cooperativityinrnaproteininteractionsglobalanalysisofrnabindingspecificity AT deveshbhimsaria cooperativityinrnaproteininteractionsglobalanalysisofrnabindingspecificity AT carytvalley cooperativityinrnaproteininteractionsglobalanalysisofrnabindingspecificity AT josearodriguezmartinez cooperativityinrnaproteininteractionsglobalanalysisofrnabindingspecificity AT elenamenichelli cooperativityinrnaproteininteractionsglobalanalysisofrnabindingspecificity AT jamesrwilliamson cooperativityinrnaproteininteractionsglobalanalysisofrnabindingspecificity AT aseemzansari cooperativityinrnaproteininteractionsglobalanalysisofrnabindingspecificity AT marvinwickens cooperativityinrnaproteininteractionsglobalanalysisofrnabindingspecificity |