irCLIP platform for efficient characterization of protein-RNA interactions

被引：0
|
作者：
Zarnegar, Brian J. [1 ]
Flynn, Ryan A. [1 ,2 ]
Shen, Ying [1 ]
Do, Brian T. [1 ,2 ]
Chang, Howard Y. [1 ,2 ]
Khavari, Paul A. [1 ,3 ]
机构：
[1] Stanford Univ, Sch Med, Program Epithelial Biol, Stanford, CA 94305 USA
[2] Stanford Univ, Sch Med, Ctr Personal Dynam Regulomes, Stanford, CA 94305 USA
[3] Palo Alto Healthcare Syst, Vet Affairs, Palo Alto, CA 94304 USA
来源：
NATURE METHODS | 2016年 / 13卷 / 06期
关键词：
BINDING PROTEIN; HITS-CLIP; NUCLEOTIDE RESOLUTION; WIDE ANALYSIS; TRANSCRIPTOME; SITES; CELLS; ARGONAUTE; INSIGHTS;
D O I：
10.1038/NMETH.3840
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
The complexity of transcriptome-wide protein-RNA interaction networks is incompletely understood. While emerging studies are greatly expanding the known universe of RNA-binding proteins, methods for the discovery and characterization of protein-RNA interactions remain resource intensive and technically challenging. Here we introduce a UV-C crosslinking and immunoprecipitation platform, irCLIP, which provides an ultraefficient, fast, and nonisotopic method for the detection of protein-RNA interactions using far less material than standard protocols.
引用
收藏
页码：489 / +
页数：7
相关论文
共 50 条
  • [1] High-throughput characterization of protein-RNA interactions
    Cook, Kate B.
    Hughes, Timothy R.
    Morris, Quaid D.
    BRIEFINGS IN FUNCTIONAL GENOMICS, 2015, 14 (01) : 74 - 89
  • [2] CLIPdb: a CLIP-seq database for protein-RNA interactions
    Yang, Yu-Cheng T.
    Di, Chao
    Hu, Boqin
    Zhou, Meifeng
    Liu, Yifang
    Song, Nanxi
    Li, Yang
    Umetsu, Jumpei
    Lu, Zhi John
    BMC GENOMICS, 2015, 16
  • [3] Advances and challenges in the detection of transcriptome-wide protein-RNA interactions
    Wheeler, Emily C.
    Van Nostrand, Eric L.
    Yeo, Gene W.
    WILEY INTERDISCIPLINARY REVIEWS-RNA, 2018, 9 (01)
  • [4] iCLIP: Protein-RNA interactions at nucleotide resolution
    Huppertz, Ina
    Attig, Jan
    D'Ambrogio, Andrea
    Easton, Laura E.
    Sibley, Christopher R.
    Sugimoto, Yoichiro
    Tajnik, Mojca
    Koenig, Julian
    Ule, Jernej
    METHODS, 2014, 65 (03) : 274 - 287
  • [5] Clip for studying protein-RNA interactions that regulate virus replication
    Mugisha, Christian Shema
    Tenneti, Kasyap
    Kutluay, Sebla B.
    METHODS, 2020, 183 : 84 - 92
  • [6] SpyCLIP: an easy-to-use and high-throughput compatible CLIP platform for the characterization of protein-RNA interactions with high accuracy
    Zhao, Ya
    Zhang, Yao
    Teng, Yilan
    Liu, Kai
    Liu, Yanqing
    Li, Weihua
    Wu, Ligang
    NUCLEIC ACIDS RESEARCH, 2019, 47 (06)
  • [7] Protein-RNA interactions: new genomic technologies and perspectives
    Koenig, Julian
    Zarnack, Kathi
    Luscombe, Nicholas M.
    Ule, Jernej
    NATURE REVIEWS GENETICS, 2012, 13 (02) : 77 - 83
  • [8] Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions
    Van Nostrand, Eric L.
    Huelga, Stephanie C.
    Yeo, Gene W.
    RNA PROCESSING: DISEASE AND GENOME-WIDE PROBING, 2016, 907 : 1 - 28
  • [9] omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data
    Drewe-Boss, Philipp
    Wessels, Hans-Hermann
    Ohler, Uwe
    GENOME BIOLOGY, 2018, 19
  • [10] Quantifying sequence and structural features of protein-RNA interactions
    Li, Songling
    Yamashita, Kazuo
    Amada, Karlou Mar
    Standley, Daron M.
    NUCLEIC ACIDS RESEARCH, 2014, 42 (15) : 10086 - 10098
12345