Each method has unique strengths and limitations, which makes it important to select optimal approaches for the biological question being addressed. Here we review methods for the study of RNA–protein interact
研究人员可通过RNA-蛋白质交联鉴定体内两者的相互作用,原理是在变性情况下,排除非共价结合的相互作用,纯化RNA,接着只提取发生交联的蛋白以用于鉴定。 甲醛是一种小的双功能交联剂,可以很容易地渗透细胞并交联2Å距离内的大分子,包括蛋白质—蛋白质,蛋白质—DNA和蛋白质—RNA复合物,形成可逆的共价连接,导致很难区分...
Correspondence to Paul A. Khavari. Rights and permissions Reprints and permissions About this article Cite this article Ramanathan, M., Porter, D.F. & Khavari, P.A. Author Correction: Methods to study RNA–protein interactions. Nat Methods 16, 351 (2019). https://doi.org/10.1038/s41592-01...
protein–RNA interactions, both the RNA and protein(s) must be correctly folded to allow proper binding. RNA is very susceptible to degradation, so special care must be taken not to introduce RNases into the reaction. ...
This is mainly due to technical difficulties in their identification and in differentiating between interactors of circRNAs and their linear counterparts. Here we review the currently used methodology to systematically study circRNA-protein complexes (circRNPs), focusing either on a specific RNA or ...
in vivoprofiling of protein-RNA interactions is subject to the transcript abundances in the experimental cell type. Thus, researchers must instead rely on computational methods to impute missing binding sites on non-expressed transcripts or to characterize RBP binding sites in settings where no ...
As long-read sequencing technologies continue to advance, the possibility of obtaining maps of DNA and RNA modifications at single-molecule resolution has become a reality. Here we highlight the opportunities and challenges posed by the use of long-read sequencing technologies to study epigenetic and...
Protein-RNA interactions select article Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions Review articleAbstract only Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein...
Protein–protein interactions (PPIs) drive cellular processes and responses to environmental cues, reflecting the cellular state. Here we develop Tapioca, an ensemble machine learning framework for studying global PPIs in dynamic contexts. Tapioca predicts de novo interactions by integrating mass spectrometr...
To apply PCR to the study of RNA, the RNA sample must first be converted to cDNA to provide the necessary DNA template for the thermostable polymerase (Figure 1). This process is called reverse transcription (RT), hence the name RT-PCR. Reverse transcriptases (RTs) are RNA-directed DNA ...