fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins
Summary: Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) structure probing techniques characterize the secondary structure of RNA molecules, which influence their functions and interactions. A variation of SHAPE, footprinting SHAPE (fSHAPE), probes RNA in the presence and absenc...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2021-09-01
|
| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166721004688 |
| id |
doaj-9b2ac54000f94ebe9fde6319b126b28e |
|---|---|
| record_format |
Article |
| spelling |
doaj-9b2ac54000f94ebe9fde6319b126b28e2021-09-19T05:01:04ZengElsevierSTAR Protocols2666-16672021-09-0123100762fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteinsMeredith Corley0Ryan A. Flynn1Steven M. Blue2Brian A. Yee3Howard Y. Chang4Gene W. Yeo5Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Corresponding authorStem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USADepartment of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USADepartment of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USACenter for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USADepartment of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Corresponding authorSummary: Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) structure probing techniques characterize the secondary structure of RNA molecules, which influence their functions and interactions. A variation of SHAPE, footprinting SHAPE (fSHAPE), probes RNA in the presence and absence of protein to identify RNA bases that hydrogen-bond with protein. SHAPE or fSHAPE coupled with enhanced crosslinking and immunoprecipitation (SHAPE-eCLIP or fSHAPE-eCLIP) pulls down RNAs bound by any protein of interest and returns their structure or protein interaction information, respectively. Here, we describe detailed protocols for SHAPE-eCLIP and fSHAPE-eCLIP and an analysis protocol for fSHAPE.For complete details on the use and execution of these protocols, please refer to Corley et al. (2020).http://www.sciencedirect.com/science/article/pii/S2666166721004688GenomicsRNAseqMolecular BiologyAntibody |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Meredith Corley Ryan A. Flynn Steven M. Blue Brian A. Yee Howard Y. Chang Gene W. Yeo |
| spellingShingle |
Meredith Corley Ryan A. Flynn Steven M. Blue Brian A. Yee Howard Y. Chang Gene W. Yeo fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins STAR Protocols Genomics RNAseq Molecular Biology Antibody |
| author_facet |
Meredith Corley Ryan A. Flynn Steven M. Blue Brian A. Yee Howard Y. Chang Gene W. Yeo |
| author_sort |
Meredith Corley |
| title |
fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins |
| title_short |
fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins |
| title_full |
fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins |
| title_fullStr |
fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins |
| title_full_unstemmed |
fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins |
| title_sort |
fshape, fshape-eclip, and shape-eclip probe transcript regions that interact with specific proteins |
| publisher |
Elsevier |
| series |
STAR Protocols |
| issn |
2666-1667 |
| publishDate |
2021-09-01 |
| description |
Summary: Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) structure probing techniques characterize the secondary structure of RNA molecules, which influence their functions and interactions. A variation of SHAPE, footprinting SHAPE (fSHAPE), probes RNA in the presence and absence of protein to identify RNA bases that hydrogen-bond with protein. SHAPE or fSHAPE coupled with enhanced crosslinking and immunoprecipitation (SHAPE-eCLIP or fSHAPE-eCLIP) pulls down RNAs bound by any protein of interest and returns their structure or protein interaction information, respectively. Here, we describe detailed protocols for SHAPE-eCLIP and fSHAPE-eCLIP and an analysis protocol for fSHAPE.For complete details on the use and execution of these protocols, please refer to Corley et al. (2020). |
| topic |
Genomics RNAseq Molecular Biology Antibody |
| url |
http://www.sciencedirect.com/science/article/pii/S2666166721004688 |
| work_keys_str_mv |
AT meredithcorley fshapefshapeeclipandshapeeclipprobetranscriptregionsthatinteractwithspecificproteins AT ryanaflynn fshapefshapeeclipandshapeeclipprobetranscriptregionsthatinteractwithspecificproteins AT stevenmblue fshapefshapeeclipandshapeeclipprobetranscriptregionsthatinteractwithspecificproteins AT brianayee fshapefshapeeclipandshapeeclipprobetranscriptregionsthatinteractwithspecificproteins AT howardychang fshapefshapeeclipandshapeeclipprobetranscriptregionsthatinteractwithspecificproteins AT genewyeo fshapefshapeeclipandshapeeclipprobetranscriptregionsthatinteractwithspecificproteins |
| _version_ |
1717376145402363904 |