Sequence And Structure Analysis Of LincRNA Binded To MiRNA Competing With Target MRNA

Large intergenic non-coding RNAs(linc RNAs) refer to intergenic non-coding RNAs whose lengths are more than 200 nt. Initially linc RNA was considered to be “noise” in the genomic transcription. However, since the development of second-generation sequencing technology and a large amount of data generated by sequencing technology, the growing number of linc RNAs are identified, causing people's attention. There are more than 12,000 linc RNAs included in the human genome. Linc RNAs involve in transcriptional control and epigenetic regulation, and play a role in many diseases. In addition, linc RNA can bind to mi RNA just as m RNA, and then regulate m RNA expression indirectly. Based on the function of linc RNA that combine with mi RNA, we analyzed the sequence and structure of linc RNA and compared with m RNA's.First, gene expression profiles of ovarian serous adenocarcinoma were downloaded from TCGA and converted into the form of linc RNA, m RNA and mi RNA expression data matrix. MINDy algorithm was used to identify linc RNAs which influence m RNA and mi RNA expression relationship. Linc RNA, mi RNA and m RNA can form a triplet. According linc RNA expression value, samples were divided into two subsets, and ?I represents the mutual information difference between the two subsets of m RNA and mi RNA. The greater the absolute value of ?I, the greater the influence of linc RNA on the relationship between mi RNA and m RNA expression. As a result, there are millions of triplets whose ?I is not equal to zero. The result showed that linc RNA can regulate m RNA and mi RNA expression relationship to some extent.Second, we analyzed the relationship between sequence and structure of linc RNA and the regulation of m RNA and mi RNA expression relation. The result showed that features of linc RNA such as sequence length and secondary structure can impact this regulation. Moreover, this regulation is determined by characteristics of target sites and linc RNA-mi RNA combination including AU content, binding site and the minimum free energy hybridization of linc RNA and mi RNA. Furthermore, some special SNPs would break linc RNA local and even whole structure, and then influence linc RNA's ability to bind to mi RNA.Last, we selected triplets which with ?I is greater than 0.2 and compared the binding features of linc RNA and m RNA from these triplets. The results showed that the length of m RNA 3' UTR is longer than linc RNA and m RNA's AU content is more than linc RNA's. Thses characters indicated that m RNA is more easily to combine with mi RNA than linc RNA. Moreover, m RNA-mi RNA double strands structures are more stable than linc RNA-mi RNA, and binding sites distribute on both end of m RNA 3'UTR while binding sites evenly distribute in linc RNA. As a whole, m RNA sequence and structure features have more advantages than linc RNA for binding to mi RNA.