Gene processing control loops suggested by sequencing, splicing, and RNA folding

BMC Bioinformatics

Research Article

Xiaojun Guan¹  Diana O Perkins²  Clark D Jeffries³ 

[1] Center for Bioinformatics, University of North Carolina at Chapel Hill, NC, USA;Department of Psychiatry, University of North Carolina at Chapel Hill, NC, USA;Eshelman School of Pharmacy and Renaissance Computing Institute, University of North Carolina at Chapel Hill, NC, USA;Renaissance Computing Institute, University of North Carolina at Chapel Hill, NC, USA;

关键词: Small RNAs;    Neural Stem Cell;    Spliceosome Assembly;    Minimal Folding Free Energy Index;    Spliceosome Protein;   

DOI  :  10.1186/1471-2105-11-602

 received in 2010-09-09, accepted in 2010-12-20,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundSmall RNAs are known to regulate diverse gene expression processes including translation, transcription, and splicing. Among small RNAs, the microRNAs (miRNAs) of 17 to 27 nucleotides (nts) undergo biogeneses including primary transcription, RNA excision and folding, nuclear export, cytoplasmic processing, and then bioactivity as regulatory agents. We propose that analogous hairpins from RNA molecules that function as part of the spliceosome might also be the source of small, regulatory RNAs (somewhat smaller than miRNAs).ResultsDeep sequencing technology has enabled discovery of a novel 16-nt RNA sequence in total RNA from human brain that we propose is derived from RNU1, an RNA component of spliceosome assembly. Bioinformatic alignments compel inquiring whether the novel 16-nt sequence or its precursor have a regulatory function as well as determining aspects of how processing intersects with the miRNA biogenesis pathway. Specifically, our preliminary in silico investigations reveal the sequence could regulate splicing factor Arg/Ser rich 1 (SFRS1), a gene coding an essential protein component of the spliceosome. All 16-base source sequences in the UCSC Human Genome Browser are within the 14 instances of RNU1 genes listed in wgEncodeGencodeAutoV3. Furthermore, 10 of the 14 instances of the sequence are also within a common 28-nt hairpin-forming subsequence of RNU1.ConclusionsAn abundant 16-nt RNA sequence is sourced from a spliceosomal RNA, lies in a stem of a predicted RNA hairpin, and includes reverse complements of subsequences of the 3'UTR of a gene coding for a spliceosome protein. Thus RNU1 could function both as a component of spliceosome assembly and as inhibitor of production of the essential, spliceosome protein coded by SFRS1. Beyond this example, a general procedure is needed for systematic discovery of multiple alignments of sequencing, splicing, and RNA folding data.

【 授权许可】

CC BY   
© Jeffries et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.