The Mechanism Of Interaction Between Mature MRNA And Its Intron Sequences

After the completion of model organism genome sequencing, nowadays we have got plenty of sequence information. Analyzing these sequences,we have found that coding sequences only take up a small part on the whole sequence, instead that most are non-coding sequences. However, it is less known what biological information and function these non-coding sequences contain. Studies show that these non-coding sequences can play a very important role in the vital life. So the biological sense has become a more and more hot subject. Introns as non-coding RNA transcribe together with mRNA. Results indicate that, there is interaction between introns and the corresponding mRNA, which is vital to gene expression. Based on this conclusion, we have applied this local matching method Smith-Waterman to acquire the optimal matching segments between introns and the corresponding mRNA, separately analyzed the characteristics of the F value distribution and the optimal matching segments on mRNA and introns and discussed the mechanism of interaction. Relative contents are as following.1. Spliced introns have a matching relationship with the corresponding mRNA and involve in gene epression and regulation. In order to reveal the sequence matching characteristics between the two referred, based on C. elegans genome-wide gene sequences and its ribonucleoprotein gene sequences we have applied this local matching method Smith-Waterman to acquire the optimal matching segments between exons and the corresponding introns and also done a research on the matching frequency distribution on exon-exon. We find that,1) the matching frequency distribution has a distinct difference on two sides of the joint, which gives exons’boundary. The average length and matching rate distribution of the optimal matching segments are similar to the binding characteristics between siRNA and miRNA.2) The first introns and long introns have a different bias of distribution on exon-exon from other introns.3) For the first introns and long introns, the optimal matching segments with high GC content, rich CG and high value of λCG display an obvious bias on exon-exon and there is a minimum of matching frequency on EJC binding region of upstream exons. Results show that, there are intercompetition and cooperation between EJC and introns when they bind with exons and introns and coding sequences are co-evolutionary to develop their own function.2. Local matching is made between mRNA and the corresponding introns of 27 species’Ribonucleoprotein genes to acquire the matching rate of each site on mRNA. Next length of mRNA is normalized to get the matching frequency distribution of the relative sites on mRNA along with its relative length. Then we have analyzed the regulation of the optimal matching region distribution on mRNA. We have found that there is a strong interaction between introns and UTR on mRNA. There are many optimal matching regions and low matching ones, so we have supposed that the low matching regions are binding regions of protein complexes. Near the functional sites on mRNA, such as translation initial and terminal sites, exon binding sites and EJC regions,the optimal matching frequency distributes differently from each other. Studies indicate that, gene expression and regulation depends on the network regulation among mRNA, introns and binding protein factors. The regulation by introns and binding protein can determinate the advanced structure of mRNA, help mRNA with nuclear export and regulate mRNA translation and so on. Conclusions have all proved that there is interaction between introns and mRNA.3. Similar to the method above-mentioned, choosing 27 Ribonucleoprotein species’Ribonucleoprotein genes as well, but we haven’t normalized introns uniformly. First, introns are grouped according to length. Then we make a local matching between introns and relative mRNA to get the matching strength distribution of the optimal matching segments at each site of introns. Result shows that, with intron length increasing, the distribution on introns gradually transfers from unimodal state to bimodal one even to multimodal state. The 5’region on introns, also called the first structure unit, is a mature sequence, while the 3’region is immature or evolving. The evolution of intron length is from 5’end to 3’end and the new units generate at 3’end one by one, which comes up with a probable mechanism of intron length evolution. Structure units on introns are 60bp long, but the binding sequence length between each two structure units is varied. Conclusion indicates that, introns with different length have a distinction in regulating mRNA structure. Introns contain plentiful functional units which have cooperative relationship of structure with sequences on mRNA, revealing evolution characteristics of intron structure and length.4. We have done a research on 13 whole-genomes and made a local matching based on the method of Smith-Waterman to obtain the optimal matching segments between mRNA and relative introns. We have analyzed the distribution regulation of the matching rate and the sequence characteristics of the optimal matching segments and learned about the universality of this interaction distribution. We have found that, the average length and matching rate distribution of the optimal matching segments are similar to the binding characteristics between siRNA and miRNA. On mRNA, UTR has a strong interaction with introns, low GC segments inclined to interact with 3’UTR and instead high GC segments inclined to interact with 5’UTR, moreover, translation initial and terminal sites can be recognized by their optimal matching rate distribution. As a result, the sequence characteristics of the optimal matching segments conform to the general regulation of RNA-RNA interaction and introns must be functional segments regulating gene expression. In the process of transportation and translation, the interaction between mRNA and introns has kept out binding proteins’ position. Introns and binding protein have competitive and cooperative mechanism in the process of interacting with mRNA. The interaction between introns and mature mRNA can regulate mRNA structure and guide mRNA nuclear-export.In a word, this thesis has mainly studied on the distribution regulation of the optimal matching rate and the sequence characteristics of the optimal matching segments of interaction between mRNA and relative introns, drawing some significant conclusions. Our research is of great biological significance to analyze intron function.