Fu Liang Xie

Publications (2)5.88 Total impact

• Article: Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags.

  Cheng Xiang Qiu, Fu Liang Xie, Yi Yong Zhu, Kai Guo, Si Qi Huang, Li Nie, Zhi Min Yang
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  ABSTRACT: MicroRNAs (miRNAs) are a class of non-coding RNAs that regulate gene post-transcriptional expression in animals and plants. Comparatively genomic computational methods have been developed to predict new miRNAs in worms, humans, and Arabidopsis. Here we present an EST (Expressed Sequence Tags)--and GSS (Genomic Survey Sequences)-based combined approach for the detection of novel miRNAs in Gossypium hirsutum. This was initiated by using previously known miRNA sequences from Arabidopsis, rice and other plant species and an algorithm called miRNAassist to blast the databases of G. hirsutum EST and GSS. A total of 37 potential miRNAs were detected following a range of filtering criteria. Using these potential miRNAs sequences, we further blasted the publicly available mRNA database and detected 96 potential targets in G. hirsutum. According to the mRNA information provided by the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/), most of the miRNA targeted genes were predicted to encode transcription factors that regulate cell growth and development, signaling, and metabolism. So far, little is known about experimental or computational identification of miRNA in G. hirsutum species. These new miRNAs and their targets in G. hirsutum have been run through miRNAassist to yield data that may help us better understanding of the possible role of miRNAs in regulating the growth and development of G. hirsutum.
  Gene 07/2007; 395(1-2):49-61. · 2.34 Impact Factor
• Article: Computational identification of novel microRNAs and targets in Brassica napus.

  Fu Liang Xie, Si Qi Huang, Kai Guo, An Ling Xiang, Yi Yong Zhu, Li Nie, Zhi Min Yang
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  ABSTRACT: MicroRNAs (miRNAs) are a newly discovered class of non-protein-coding small RNAs with roughly 22 nucleotide-long. Increasing evidence has shown that miRNAs play multiple roles in biological processes, including development, cell proliferation and apoptosis and stress responses. In this research, several approaches were combined to make computational prediction of potential miRNAs and their targets in Brassica napus. We used previously known miRNAs from Arabidopsis, rice and other plant species against both expressed sequence tags (EST) and genomic survey sequence (GSS) databases to search for potential miRNAs in B. napus. A total of 21 potential miRNAs were detected following a range of strict filtering criteria. Using these potential miRNA sequences, we could further blast the mRNA database and found 67 potential targets in this species. According to the mRNA target information provided by NCBI (http://www.ncbi.nlm.nih.gov/), most of the target mRNAs appeared to be involved in plant growth, development and stress responses. To validate the prediction of miRNAs in B. napus, we performed a RT-PCR based assay of mature miRNA expression. Five miRNAs were identified in response to auxin, cadmium stress and phosphate starvation. So far, little is known about experimental or computational identification of miRNA in B. napus species. To improve efficiency for blast search, we developed an implementation (miRNAassist) that can identify homologs of miRNAs and their targets, with high sensitivity and specificity. The program is allowed to be run on Windows Operation System platform. miRNAassist is freely available if required.
  FEBS Letters 05/2007; 581(7):1464-74. · 3.54 Impact Factor