All RNA molecules are subject to post-transcriptional gene regulation, including mechanisms such as splicing, cleavage and polyadenylation, editing, transport, stability, and translation. These mechanisms rely on the specific recognition of functional RNA elements by RNA-binding proteins (RBPs) and a range ...
Read More »RNA-Seq and quantitative modeling unravel the contributions of regulated transcription and mRNA decay to the dynamics of gene expression
Organisms have acquired sophisticated regulatory networks that control gene expression in response to cellular perturbations. Understanding of the mechanisms underlying the coordinated changes in gene expression in response to external and internal stimuli is a fundamental issue in biology. Recent ...
Read More »Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites
Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. Tsinghua University researchers apply a soft-clustering method, RBPgroup, to various CLIP-seq datasets to group together RBPs that specifically bind the ...
Read More »PAR-CLIP and Streamlined Small RNA cDNA Library Preparation Protocol for the Identification of RNA Binding Protein Target Sites
The study of protein-RNA interactions is critical for our understanding of cellular processes and regulatory circuits controlled by RNA binding proteins (RBPs). Recent next generation sequencing-based approaches significantly promoted our understanding of RNA biology and its importance for cell function. ...
Read More »Identifying RBP Targets with RIP-seq
One of the challenges to assess the impact of RBPs on posttranscriptional gene regulation is identifying and quantifying the RNA and protein components of ribonucleoprotein complexes (RNPs) in a cellular context. The human genome is estimated to contain 1542 RBPs. ...
Read More »Integrating Large-Scale RNA-Seq and CLIP-Seq Datasets Enables Study of lncRNA
Long non-coding RNAs (lncRNAs) are emerging as important regulatory molecules in developmental, physiological, and pathological processes. However, the precise mechanism and functions of most of lncRNAs remain largely unknown. Recent advances in high-throughput sequencing of immunoprecipitated RNAs after cross-linking (CLIP-Seq) ...
Read More »