MicroRNA-encoding long non-coding RNAs

• Published in: BMC genomics Vol. 9; no. 1; p. 236
• Main Authors: He, Shunmin, Su, Hua, Liu, Changning, Skogerbø, Geir, He, Housheng, He, Dandan, Zhu, Xiaopeng, Liu, Tao, Zhao, Yi, Chen, Runsheng
• Format: Journal Article
• Language: English
• Published: London BioMed Central 21.05.2008; BioMed Central Ltd; BMC
• Subjects: Animal Genetics and Genomics; Animals; Base Sequence; Biomedical and Life Sciences; Chromosome Mapping; Conserved Sequence; Databases, Nucleic Acid; DNA microarrays; Female; Genetic transcription; Health aspects; Life Sciences; Male; Mice; Mice, Inbred C57BL; Microarrays; Microbial Genetics and Genomics; MicroRNAs - chemistry; MicroRNAs - genetics; Molecular Sequence Data; Nucleic Acid Conformation; Oligonucleotide Array Sequence Analysis; Plant Genetics and Genomics; Pregnancy; Proteomics; Research Article; Reverse Transcriptase Polymerase Chain Reaction; RNA; RNA Splicing; RNA, Untranslated - chemistry; RNA, Untranslated - genetics; Software; China; Internal Motif; Position Weight Matrix; Xist Gene; Mature microRNA; Primary Transcript
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-9-236

Background Recent analysis of the mouse transcriptional data has revealed the existence of ~34,000 messenger-like non-coding RNAs (ml-ncRNAs). Whereas the functional properties of these ml-ncRNAs are beginning to be unravelled, no functional information is available for the large majority of these transcripts. Results A few ml-ncRNA have been shown to have genomic loci that overlap with microRNA loci, leading us to suspect that a fraction of ml-ncRNA may encode microRNAs. We therefore developed an algorithm (PriMir) for specifically detecting potential microRNA-encoding transcripts in the entire set of 34,030 mouse full-length ml-ncRNAs. In combination with mouse-rat sequence conservation, this algorithm detected 97 (80 of them were novel) strong miRNA-encoding candidates, and for 52 of these we obtained experimental evidence for the existence of their corresponding mature microRNA by microarray and stem-loop RT-PCR. Sequence analysis of the microRNA-encoding RNAs revealed an internal motif, whose presence correlates strongly ( R 2 = 0.9, P -value = 2.2 × 10 -16 ) with the occurrence of stem-loops with characteristics of known pre-miRNAs, indicating the presence of a larger number microRNA-encoding RNAs (from 300 up to 800) in the ml-ncRNAs population. Conclusion Our work highlights a unique group of ml-ncRNAs and offers clues to their functions.