Because the chemical and biological properties of many RNAs are determined by their conformations, an RNA equivalent exists to the protein folding problem. The RNA folding problem has both a practical side and an academic side. If the practical problem were solved, it would be possible to predict the conformations of RNAs of known sequence. The academic problem has to do with determining what h...

The role of small RNAs as critical components of global regulatory networks has been highlighted by several recent studies. An important class of such small RNAs is represented by CsrB and CsrC of Escherichia coli, which control the activity of the global regulator CsrA. Given the critical role played by CsrA in several bacterial species, an important problem is the identification of CsrA-regul...

Small non-coding RNAs, including microRNAs (miRNAs), endogenous small interfering RNAs (endo-siRNAs) and Piwiinteracting RNAs (piRNAs), play essential roles in mammalian development. The function and timing of expression of these three classes of small RNAs differ greatly. piRNAs are expressed and play a crucial role during male gametogenesis, whereas endo-siRNAs are essential for oocyte meiosi...

Non-coding small RNAs (19-24 nucleotide long) have recently been recognized as the important regulator of gene expression in both plants and animals. Several classes of endogenous short RNAs have partial or near perfect complementarity to mRNAs and a protein complex is guided by short RNAs to target mRNAs. The targeted mRNA is either cleaved or its translation is suppressed. Initially, short RN...

Recent analyses based on high-throughput transcriptome data have revealed that the fraction of the genome that is transcribed largely exceeds the fraction encoding protein. Transcription of unconventional genes into noncoding RNAs is widespread and, in mammals, these RNAs comprise at least half the total number of RNAs transcribed by RNA polymerase II. Although the function of the majority of n...

Small noncoding RNAs (ncRNAs) are a novel class of gene regulators that modulate gene expression at transcriptional, post-transcriptional, and epigenetic levels, and they play crucial roles in almost all cellular processes in eukaryotes. Recent studies have indicated that several types of small noncoding RNAs, including microRNAs (miRNAs), endo-small interference RNAs (endo-siRNAs), and Piwi-in...