High-throughput determination of RNA structures

Genome annotation by high-throughput 5' RNA end determination.

Complete gene identification and annotation, including alternative transcripts, remains a challenge in understanding genome organization. Such annotation can be achieved by a combination of computational analysis and experimental confirmation. Here, we describe a high-throughput technique, trans-spliced exon coupled RNA end determination (TEC-RED), that identifies 5' ends of expressed genes in ...

High-throughput characterization of protein–RNA interactions

RNA-binding proteins (RBPs) are important regulators of eukaryotic gene expression. Genomes typically encode dozens to hundreds of proteins containing RNA-binding domains, which collectively recognize diverse RNA sequences and structures. Recent advances in high-throughput methods for assaying the targets of RBPs in vitro and in vivo allow large-scale derivation of RNA-binding motifs as well as...

High-throughput isolation of Saccharomyces cerevisiae RNA.

The yeast Saccharomyces cerevisiae has long been an important model organism for biological investigation (1). More recently, high-throughput approaches using deletion libraries and fusion protein libraries have provided powerful techniques with which to study the entire yeast genome and proteome (2–6). However, the methods typically used for preparing high-quality RNA samples from yeast are im...

Fully asynchronous, robust, high-throughput arithmetic structures

PreRkTAG: Prediction of RNA Knotted Structures Using Tree Adjoining Grammars

Background: RNA molecules play many important regulatory, catalytic and structural <span style="font-variant: normal; font-style: norma...