Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq.
Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq.
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DOI：
10.1016/j.xpro.2022.101823
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发表时间：
2022-12-16
期刊：
影响因子：
--
通讯作者：
Tebaldi, Toma
中科院分区：
文献类型：
--
作者：
Biancon, Giulia;Busarello, Emma;Joshi, Poorval;Lesch, Bluma J.;Halene, Stephanie;Tebaldi, Toma
成千上万的RNA结合蛋白协调RNA加工，改变蛋白质-RNA相互作用经常导致疾病。在这里，我们提出了分级eCLIP-seq（freCLIP-seq）的实验和计算分析管道，这是一种增强UV交联和RNA免疫沉淀的修饰，然后进行测序。FreCLIP-seq允许在单核苷酸水平上对蛋白质-RNA相互作用进行全转录组分析，并通过分离多组分复合物中单个RNA结合蛋白的结合信号提供额外的分辨率。结合占有率可以从读段计数和交联事件推断。有关本方案使用和执行的完整详细信息，请参阅。交联细胞沉淀和免疫沉淀的产生通过膜大小分级分离复合物内不同的RBP-RNA接触通过转录组范围或区域特异性方法识别结合峰结合占位符的注释和差异分析出版商注：进行任何实验方案都需要遵守当地机构的实验室安全和伦理指南。成千上万的RNA结合蛋白协调RNA加工，改变蛋白质-RNA相互作用经常导致疾病。在这里，我们提出了分级eCLIP-seq（freCLIP-seq）的实验和计算分析管道，这是一种增强UV交联和RNA免疫沉淀的修饰，然后进行测序。FreCLIP-seq允许在单核苷酸水平上对蛋白质-RNA相互作用进行全转录组分析，并通过分离多组分复合物中单个RNA结合蛋白的结合信号提供额外的分辨率。结合占有率可以从读段计数和交联事件推断。
Thousands of RNA-binding proteins orchestrate RNA processing and altered protein-RNA interactions frequently lead to disease. Here, we present experimental and computational analysis pipelines of fractionated eCLIP-seq (freCLIP-seq), a modification of enhanced UV-crosslinking and RNA immunoprecipitation followed by sequencing. FreCLIP-seq allows transcriptome-wide analysis of protein-RNA interactions at single-nucleotide level and provides an additional level of resolution by isolating binding signals of individual RNA-binding proteins within a multicomponent complex. Binding occupancy can be inferred from read counts and crosslinking events. For complete details on the use and execution of this protocol, please refer to. Generation of crosslinked cell pellets and immunoprecipitation Isolation of distinct RBP-RNA contacts within a complex by membrane size fractionation Identification of binding peaks by a transcriptome-wide or region-specific approach Annotation and differential analysis of binding occupancies Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Thousands of RNA-binding proteins orchestrate RNA processing and altered protein-RNA interactions frequently lead to disease. Here, we present experimental and computational analysis pipelines of fractionated eCLIP-seq (freCLIP-seq), a modification of enhanced UV-crosslinking and RNA immunoprecipitation followed by sequencing. FreCLIP-seq allows transcriptome-wide analysis of protein-RNA interactions at single-nucleotide level and provides an additional level of resolution by isolating binding signals of individual RNA-binding proteins within a multicomponent complex. Binding occupancy can be inferred from read counts and crosslinking events.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
48
作者：
Van Nostrand EL;Pratt GA;Shishkin AA;Gelboin-Burkhart C;Fang MY;Sundararaman B;Blue SM;Nguyen TB;Surka C;Elkins K;Stanton R;Rigo F;Guttman M;Yeo GW
通讯作者：
Yeo GW
影响因子：
16
作者：
Biancon G;Joshi P;Zimmer JT;Hunck T;Gao Y;Lessard MD;Courchaine E;Barentine AES;Machyna M;Botti V;Qin A;Gbyli R;Patel A;Song Y;Kiefer L;Viero G;Neuenkirchen N;Lin H;Bewersdorf J;Simon MD;Neugebauer KM;Tebaldi T;Halene S
通讯作者：
Halene S
影响因子：
7
作者：
Griffin, Kimberly N.;Walters, Benjamin William;Li, Haixin;Wang, Huafeng;Biancon, Giulia;Tebaldi, Toma;Kaya, Carolyn B.;Kanyo, Jean;Lam, TuKiet T.;Cox, Andy L.;Halene, Stephanie;Chung, Jean-Ju;Lesch, Bluma J.
通讯作者：
Lesch, Bluma J.
影响因子：
4.8
作者：
Huppertz, Ina;Attig, Jan;D'Ambrogio, Andrea;Easton, Laura E.;Sibley, Christopher R.;Sugimoto, Yoichiro;Tajnik, Mojca;Koenig, Julian;Ule, Jernej
通讯作者：
Ule, Jernej