background: recently, the use of t7 rna polymerase instead of other viral and cellular promoters is increasing due to high efficacy of transcription in the cell cytoplasm by this polymerase. in order to translate the transcripts produced by t7 rna polymerase in mammalian cell lines, it is necessary to include internal ribosome entry site (ires) sequences. in addition, if sequence of poly a sign...

MicroRNAs (miRNAs) are short (~22 nucleotides), non-coding RNA molecules that post-transcriptionally regulate gene expression. As the miRNA field is still in its relative infancy, there is currently a lack of consensus regarding optimal methodologies for miRNA quantification, data analysis and data standardization. To investigate miRNA measurement we selected a panel of both synthetic miRNA spi...

RNA structural transitions are important in the function and regulation of RNAs. Here, we reveal a layer of transcriptome organization in the form of RNA folding energies. By probing yeast RNA structures at different temperatures, we obtained relative melting temperatures (Tm) for RNA structures in over 4000 transcripts. Specific signatures of RNA Tm demarcated the polarity of mRNA open reading...

The 2'-hydroxyl group in RNA plays an important structural role; it defines hydration in the minor groove, impacts thermodynamic stability of RNA, and often participates in RNA catalysis. To better study this important functional group in RNA, we describe a constant-time HMQC-IPAP-NOESY 3D NMR experiment. It simultaneously yields highly resolved 13C-separated NOEs from ribose protons to the 2'O...

the eukaryotic complexity involves the expression and regulation of genes via rna-dna, rna-rna, dna-protein and rna-protein interactions. recently, the role of rna molecules in the regulation of genes in higher organisms has become more evident, especially with the discovery that about 97% of the transcriptional output in higher organisms are represented as noncoding rnas: rrna, snornas, trna, ...

RNA sequencing (RNA-Seq) is a powerful method for discovering, annotating, and quantifying RNA transcripts that is currently revolutionizing the field of agrigenomics.1–9 RNA-Seq does not require speciesor transcript-specific probes, enabling precise quantification of both known and novel transcripts without prior knowledge. Beyond the measurement of gene expression changes, RNA-Seq can be used...