For several decades, only a limited number of noncoding RNAs, such as ribosomal and transfer RNA, have been studied in any depth. In recent years, additional species of noncoding RNAs have increasingly been discovered. Of these, small RNA species attract particular interest because of their essential roles in processes such as RNA silencing and modifications. Detailed analyses revealed several ...

A range of noncoding RNAs are transcribed by pol III. A lot of them such as tRNA, 7SL RNA, 7SK RNA, 5S RNA, MRP RNA, Y RNAs, H1 RNA, and vault RNAs are considered as "house keeping" RNAs essential for eukaryotic cells. In recent years, researchers started to recognize the existence of unconventional functions of many pol III transcripts other than classical "house keeping" roles. Therefore, the...

Posttranscriptional chemical modification of RNA bases is a widespread and physiologically relevant regulator of RNA maturation, stability, and function. While modifications are best characterized in short, noncoding RNAs such as tRNAs, growing evidence indicates that mRNAs and long noncoding RNAs (lncRNAs) are likewise modified. Here, we apply our high-throughput annotation of modified ribonuc...

More than 98% of the mammalian genome is noncoding, and interspersed transposable elements account for ∼50% of noncoding space. Here, we demonstrate that a specific interaction between the polycomb protein EZH2 and RNA made from B2 SINE retrotransposons controls stress-responsive genes in mouse cells. In the heat-shock model, B2 RNA binds stress genes and suppresses their transcription. Upon st...

DNA methylation is a mechanism of epigenetic gene regulation and genome defense conserved in many eukaryotic organisms. In Arabidopsis, the DNA methyltransferase domains rearranged methylase 2 (DRM2) controls RNA-directed DNA methylation in a pathway that also involves the plant-specific RNA Polymerase V (Pol V). Additionally, the Arabidopsis genome encodes an evolutionarily conserved but catal...

Termination of RNA polymerase II (RNAPII) transcription is associated with RNA 3' end formation. For coding genes, termination is initiated by the cleavage/polyadenylation machinery. In contrast, a majority of noncoding transcription events in Saccharomyces cerevisiae does not rely on RNA cleavage for termination but instead terminates via a pathway that requires the Nrd1-Nab3-Sen1 (NNS) comple...