RNA molecules interact by forming inter-molecular base pairs that compete with the intramolecular base pairs of their secondary structures. Here we investigate the patterns of neutral mutations in RNAs whose function is the interaction with other RNAs, i.e., of co-folding RNAs. We find that (1) the degree of neutrality is much smaller in interacting RNAs compared to RNAs that just have to cofor...

Noncoding RNAs have been implicated in the regulation of expression of numerous genes; however, the mechanism is not fully understood. We identified bidirectional, long noncoding RNAs upstream of the TNF gene using five different methods. They arose in a region where the repressors LRRFIP1, EZH2, and SUZ12 were demonstrated to bind, suggesting a role in repression. The noncoding RNAs were polya...

Ribonuclease P (RNase P) is the ribonucleoprotein endonuclease that processes the 5' ends of precursor tRNAs. Bacterial and eukaryal RNase P RNAs had the same primordial ancestor; however, they were molded differently by evolution. RNase P RNAs of eukaryotes, in contrast to bacterial RNAs, are not catalytically active in vitro without proteins. By comparing the bacterial and eukaryal RNAs, we c...

The Ro 60 kDa autoantigen is a major target of the immune response in patients with systemic lupus erythematosus. In vertebrate cells, Ro binds misfolded small RNAs and likely functions in RNA quality control. In eukaryotes and bacteria, Ro also associates with small RNAs called Y RNAs. We present structures of unliganded Ro and Ro complexed with two RNAs at 1.95 and 2.2 A resolution, respectiv...

Adenosine to inosine (A-to-I) editing consists of an RNA modification where single adenosines along the sequence are converted into inosines. Such a biochemical transformation is catalyzed by enzymes belonging family adenosine deaminases acting on (ADARs) and occurs either co- or post-transcriptionally. The employment powerful, high-throughput detection methods has recently revealed that A-to-I...

Tiny non-coding RNAs called microRNAs (miRNAs) are crucial for cell survival and differentiation. Numerous cancer varieties, including acute myeloid leukemia, have been linked to abnormal miRNA expression (AML). Objective: