In a paper published online in advance in Nucleic Acids Research this week, investigators at Sloan-Kettering and Weill Cornell Medical College show that the activity of Nam8, a yeast U1 snRNP component that "collaborates with Mer1 to promote splicing of essential meiotic mRNAs," is weakened by "mutations in the putative RNA binding site of the RRM2 and RRM3 domains." More specifically, the team says SPO22 and PCH2 are targets of Nam8-dependent meiotic splicing; the researchers also show that while SPO22 splicing depends upon Mer1 recognition, "the Nam8-dependent PCH2 pre-mRNA ... lacks a Mer1 enhancer."
In an another advance online publication, researchers at the Academy of Sciences of the Czech Republic and their collaborators report their "homology search for bacterial non-coding RNAs using suboptimal RNA structures" among divergent species and their characterization of the structure of 6S RNA. The team shows that, in this non-coding RNA, "suboptimal structures are capable of capturing RNA homology even in divergent bacterial species." In addition, the team describes a computational method "for the identification of homologous ncRNAs using suboptimal structures."
The European Molecular Biology Laboratory's Peer Boork and his colleagues identify 11 conserved sequence motifs — which co-occur with one another and are over-represented near alternatively spliced exons — that they suggest could be involved in alternative splicing regulation. In the current issue of Nucleic Acids Research, Boork et al. describe this network of cis-element motifs, which they say is "likely to be the basis for context-dependent regulation." Using motif co-occurrence information, the EMBL-led team was able to predict alternatively skipped exons — it verified exon skipping in 29 cases of its 118 predictions, though it confirmed another 10 cases using RT-PCR and publicly available RNA-seq data.
In mapping "long-range associations between chromosomal regions," investigators at the Wistar Institute characterized the 3D structure of the fission yeast genome. Using this model, the team identified "new and important interactions" related to global genome organization and transcriptional regulation. In the current issue of Nucleic Acids Research, the authors say that their "study suggests the presence of a global genome organization in fission yeast that is functionally similar to the recently proposed mammalian transcription factory."