Showing papers on "MRNA modification published in 2007"

Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs.

Abstract: Small nucleolar RNAs (snoRNAs) and Cajal body-specific RNAs (scaRNAs) are named for their subcellular localization within nucleoli and Cajal bodies (conserved subnuclear organelles present in the nucleoplasm), respectively. They have been found to play important roles in rRNA, tRNA, snRNAs, and even mRNA modification and processing. All snoRNAs fall in two categories, box C/D snoRNAs and box H/ACA snoRNAs, according to their distinct sequence and secondary structure features. Box C/D snoRNAs and box H/ACA snoRNAs mainly function in guiding 2'-O-ribose methylation and pseudouridilation, respectively. ScaRNAs possess both box C/D snoRNA and box H/ACA snoRNA sequence motif features, but guide snRNA modifications that are transcribed by RNA polymerase II. Here we present a Web-based sno/scaRNA database, called sno/scaRNAbase, to facilitate the sno/scaRNA research in terms of providing a more comprehensive knowledge base. Covering 1979 records derived from 85 organisms for the first time, sno/scaRNAbase is not only dedicated to filling gaps between existing organism-specific sno/scaRNA databases that are focused on different sno/scaRNA aspects, but also provides sno/scaRNA scientists with an opportunity to adopt a unified nomenclature for sno/scaRNAs. Derived from a systematic literature curation and annotation effort, the sno/scaRNAbase provides an easy-to-use gateway to important sno/scaRNA features such as sequence motifs, possible functions, homologues, secondary structures, genomics organization, sno/scaRNA gene's chromosome location, and more. Approximate searches, in addition to accurate and straightforward searches, make the database search more flexible. A BLAST search engine is implemented to enable blast of query sequences against all sno/scaRNAbase sequences. Thus our sno/scaRNAbase serves as a more uniform and friendly platform for sno/scaRNA research. The database is free available at http://gene.fudan.sh.cn/snoRNAbase.nsf.

New mRNA modification

Abstract: Like the rough draft of a novel, a newly transcribed pre-mRNA molecule undergoes plenty of polishing before it's fit to be read. Custodio et al. now report evidence for a previously undiscovered editing step in the production of mRNA. Cells are fussy about mRNA. They detain a would-be strand in the nucleus until enzymes cleave the 3′ end, excise introns, stick a cap on the 5′ end, and affix a tail of multiple adenines. The carboxyl end of RNA polymerase II, the enzyme that transcribes RNA, orchestrates processing by latching onto editorial proteins. This end normally carries 52 copies of a 7-amino acid sequence. By deleting different combinations of these duplications, researchers previously determined that certain repeats attract proteins that perform specific mRNA alterations. Custodio et al. engineered mouse cells to make RNA polymerase molecules with untested combinations of deletions. The protein carrying five repeats was nonfunctional. But the one with 31 repeats could transcribe a human β-globin gene and complete the four processing steps. Nevertheless, the RNA strand remained stuck at the transcription site. Its retention suggests that the pre-mRNA must pass through an as-yet undefined editing round before the cell will release it into the cytoplasm. RNA polymerase presumably draws in proteins that perform this new alteration. The researchers hope to pin down these proteins by comparing the binding partners of RNA polymerases with truncated and full-length carboxyl ends. Once the team knows the proteins' identities, they can work out their functions. Reference: Custodio, N., et al. 2007. J. Cell Biol. 179:199–207. [PubMed]