Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures
AUTOR(ES)
Kitagawa, Junji
FONTE
Oxford University Press
RESUMO
It is an outstanding problem to clarify how the RNA sequence is related to its structure and biological functions. We developed a simplified definition of a metric for tree representation of RNA secondary structures and analyzed the conformational energy landscapes of human spliceosomal snRNAs. We discuss the structural properties of the biological sequence by calculating the conformational energy landscapes based on the structural distance between each of the pairs in the set of suboptimal structures. The new index value is introduced for estimating the shapes of distribution patterns in conformational energy landscapes. We apply our method to the five human snRNAs and show that U1 snRNA has a multi-valley profile of the landscape, whereas the landscapes of the other four snRNAs have one steep valley. This result reflects different biological functions of these snRNAs in the pre-mRNA splicing process. The results of analyzing tRNAs and rRNAs show that the conformational energy landscapes of these sequences have multi-valley profiles.
ACESSO AO ARTIGO
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=152804Documentos Relacionados
- Elements required for transcription initiation of the human U2 snRNA gene coincide with elements required for snRNA 3' end formation.
- Increasing the distance between the snRNA promoter and the 3' box decreases the efficiency of snRNA 3'-end formation.
- NMR structure of the 3′ stem–loop from human U4 snRNA
- Sequence-specific interaction of U1 snRNA with the SMN complex
- Orientation-dependent transcriptional activator upstream of a human U2 snRNA gene.