Biomedical subjects

Xiaowo Wang

Publications and source records attributed to Xiaowo Wang.

2 recordsLinked to original sources

PubMed2006

Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking sequences.

MicroRNAs (miRNAs) are a class of approximately 22-nt small RNAs that regulate posttranscriptional gene expression. Thousands of expressed sequence tags (ESTs) have been identified by using upstream 2500-nt and downstream 4000-nt flanking sequences to BLAST in the dbEST database. The cotranscription of the miRNAs and their flanking sequences covered by the matched ESTs is verified by RT-PCR. It directly reveals that a large portion of mammalian intergenic miRNAs are first transcribed as long primary transcripts (pri-miRNAs). Also, the transcripts' ranges of tens of pri-miRNAs are predicted by the EST-extension method. We then extracted the tissue-specific expression information from the annotations of the matched ESTs and established the expression profile of the studied miRNAs for tens of tissues. This provided a new way to establish the expression profiles of miRNAs. Results show that the human brain, lung, liver, and eye and the mouse brain, eye, and mammary gland are tissues in which enriched numbers of miRNAs are expressed.

3' Flanking Region↗

PubMed2005

MicroRNA identification based on sequence and structure alignment.

MOTIVATION: MicroRNAs (miRNA) are approximately 22 nt long non-coding RNAs that are derived from larger hairpin RNA precursors and play important regulatory roles in both animals and plants. The short length of the miRNA sequences and relatively low conservation of pre-miRNA sequences restrict the conventional sequence-alignment-based methods to finding only relatively close homologs. On the other hand, it has been reported that miRNA genes are more conserved in the secondary structure rather than in primary sequences. Therefore, secondary structural features should be more fully exploited in the homologue search for new miRNA genes. RESULTS: In this paper, we present a novel genome-wide computational approach to detect miRNAs in animals based on both sequence and structure alignment. Experiments show this approach has higher sensitivity and comparable specificity than other reported homologue searching methods. We applied this method on Anopheles gambiae and detected 59 new miRNA genes. AVAILABILITY: This program is available at http://bioinfo.au.tsinghua.edu.cn/miralign. SUPPLEMENTARY INFORMATION: Supplementary information is available at http://bioinfo.au.tsinghua.edu.cn/miralign/supplementary.htm.

Algorithms↗