Interaction Between Exon-exon Sequences And Intron Sequences

As a kind of non-coding RNA, introns are transcribed together with mRNA. Many indirect evidences suggest that there is a kind of interaction between mRNA sequences and the corresponding introns after splicing. We think that this kind of interaction is showed by the matching segments between them, which plays a significant role in gene expression regulation process and undertakes important biological functions. Based on this idea, Smith-Waterman local alignment methods were used to obtain the optimal matching segments between exon-exon sequences and their corresponding intron. sequences. Their distributions on exon-exon sequences and the characteristics of optimal matching segments were analyzed, and the mechanisms of the interactions were discussed. The main contributions are summarized as follows:1. The ribosomal protein genes of27genomes were analyzed. The conclusions as follows:1) The bonding information of EJC are shown on the distributions of matching frequency in exon-exon sequences in some lower eukaryotes. Some higher eukaryotes do not show this kind of character. Sequence analysis point out that the sequence composition of EJC bonding region for all of the genomes has lower composed order or the sequences constitution are more random compared with the other part of an exon. Results indicate that EJC and introns as two kind of regulating elements exists competitive and cooperative relations in the process of bonding on exons.2) The average length of the optimal matching segments is about20bp and their matching rates are mainly distributed between65%and80%, but a few of the elements have perfect matching. These matching characters are the same as the two non-coding genes siRNA and miRNA.2. On the Genome-wide level, the distributions of optimal matched frequencies on the exon-exon sequences of Caenorhabditis elegans, Arabidopsis thaliana and Drosophila melanogaster are analyzed. Results show that:1) obvious changes occur on the exon junction regions; The distributions of optimal matching frequencies for first introns are different with the other introns on the exon-exon sequences. The bonding strength of long and short introns on the corresponding exon-exon sequence also has differences. These indicate that the first introns and the long introns have special biological functions, and reveals that there are interactions between introns and the coding sequences.2) The most probable length of the optimal matching length distribution is all about20bp, and the matching rate of the optimal matching segments are identical to the analysis of the ribosomal genes. Optimal matching segments between introns and coding sequences are RNA-RNA interactions, and their characters are the same as miRNA and siRNA, which indicate that this kind of interactions is of great significance. We think that these optimal matching regions may play very important roles in gene regulation and gene expression. As a kind sequence set of RNA-RNA interaction, introns should be the third kind of non-coding functional segments.3. The GC content of the optimum matching segments in all exon-exon sequences of the Caenorhabditis elegans, Arabidopsis thaliana and Drosophila melanogaster are analyzed. Results indicate that1) the distributions of the matching frequencies of exon-exon sequences with all optimum matching segments are almost the same as those with their GC content among0.3-0.5. When the GC content among0.0-0.3, the distributions of matching frequencies in upstream region of exon-exon sequences are obviously higher than its downstream region, when the GC content among0.5-1.0, the distribution characters are opposite.2) All of the optimal matching segments of exon-exon sequences are divided into three groups according to their GC content and the sequences features analyzed. The segments of GC content among0.0-0.3have the highest D2. The segments of GC content among0.5-1.0have the lowest D2compared with the all optimal matching segments. The segments of GC content among0.3-0.5have the D2values between the former two. This sequence character is similar in the3genomes. Results show that the optimal matching segments with low GC content have stronger structure orders, but the optimal matching segments with high GC content have lowest structure orders or the sequence randomness is stronger. This result shows that the exon-exon sequences have the distinct internal structures.In a word, this paper mainly studies the interactions between exon-exon sequences and intron sequences in the junctions and the interactions are characterized by the optimal matching regions on the two kinds of sequences. The distributions of optimal matching frequencies on exon-exon sequences and the characters of optimal matching segments were analyzed. Some of significant results were obtained. All of the results support the idea that the interactions do exist on the introns and exon-exon sequences. Our analysis has important meanings to understand intron functions.