CLIP: a method for identifying protein-RNA interaction sites in living cells. Export

@article{citeulike:3732066, abstract = {Nucleic-acid binding proteins constitute nearly one-fourth of all functionally annotated human genes. Genome-wide analysis of protein-nucleic acid contacts has not yet been performed for most of these proteins, restricting attempts to establish a comprehensive understanding of protein function. UV cross-linking is a method typically used to determine the position of direct interactions between proteins and nucleic acids. We have developed the cross-linking and immunoprecipitation assay, which exploits the covalent protein-nucleic acid cross-linking to stringently purify a specific protein-RNA complex using immunoprecipitation followed by SDS-PAGE separation. In this way, the vast majority of non-specific contaminating RNA, which can bind to co-immunoprecipitated proteins or beads, can be removed. Here, we present an improved protocol that performs RNA linker ligation before the SDS-PAGE step, and describe its application to the specific purification and amplification of RNA ligands of Nova in neurons.}, author = {Ule, Jernej and Jensen, Kirk and Mele, Aldo and Darnell, Robert B.}, citeulike-article-id = {3732066}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ymeth.2005.07.018}, citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S1046202305001787}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16314267}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16314267}, doi = {10.1016/j.ymeth.2005.07.018}, issn = {1046-2023}, journal = {Methods (San Diego, Calif.)}, keywords = {biochemical, in\_vivo, method, rnp}, month = {December}, number = {4}, pages = {376--386}, posted-at = {2009-07-07 22:16:55}, priority = {2}, title = {CLIP: a method for identifying protein-RNA interaction sites in living cells.}, url = {http://dx.doi.org/10.1016/j.ymeth.2005.07.018}, volume = {37}, year = {2005} }

TY - JOUR ID - citeulike:3732066 L3 - citeulike-article-id:3732066 N2 - Nucleic-acid binding proteins constitute nearly one-fourth of all functionally annotated human genes. Genome-wide analysis of protein-nucleic acid contacts has not yet been performed for most of these proteins, restricting attempts to establish a comprehensive understanding of protein function. UV cross-linking is a method typically used to determine the position of direct interactions between proteins and nucleic acids. We have developed the cross-linking and immunoprecipitation assay, which exploits the covalent protein-nucleic acid cross-linking to stringently purify a specific protein-RNA complex using immunoprecipitation followed by SDS-PAGE separation. In this way, the vast majority of non-specific contaminating RNA, which can bind to co-immunoprecipitated proteins or beads, can be removed. Here, we present an improved protocol that performs RNA linker ligation before the SDS-PAGE step, and describe its application to the specific purification and amplification of RNA ligands of Nova in neurons. IS - 4 JF - Methods (San Diego, Calif.) SN - 1046-2023 EP - 386 TI - CLIP: a method for identifying protein-RNA interaction sites in living cells. VL - 37 SP - 376 KW - biochemical KW - in_vivo KW - method KW - rnp AU - Ule, Jernej AU - Jensen, Kirk AU - Mele, Aldo AU - Darnell, Robert PY - 2005/12// UR - http://dx.doi.org/10.1016/j.ymeth.2005.07.018 ER -