![]() ![]() Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Causes and effects of N-terminal codon bias in bacterial genes. Advances in RNA structure analysis by chemical probing. Illuminating the silence: understanding the structure and function of small RNAs. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. ![]() icSHAPE reactivities can additionally be used to constrain and improve RNA secondary structure prediction models.Ĭooper, T.A., Wan, L. Comparing in vivo and in vitro icSHAPE measurements can reveal in vivo RNA-binding protein imprints or facilitate the dissection of RNA post-transcriptional modifications. The entire experimental procedure can be completed in ∼5 d, and the sequencing and bioinformatics data analysis take an additional 4–5 d with no extensive computational skills required. After deep sequencing of cDNA, computational analysis yields flexibility scores for every base across the starting RNA population. Purified RNA is then reverse-transcribed to produce cDNA, with SHAPE-modified bases leading to truncated cDNA. Living cells are treated with the icSHAPE chemical NAI-N 3 followed by selective chemical enrichment of NAI-N 3–modified RNA, which provides an improved signal-to-noise ratio compared with similar methods leveraging deep sequencing. IcSHAPE ( in vivo click selective 2-hydroxyl acylation and profiling experiment) captures RNA secondary structure at a transcriptome-wide level by measuring nucleotide flexibility at base resolution. ![]()
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