Relevance Characteristics Analysis Of The Introns And Their Corresponding Mature MRNA In The Caenorhabditis Elegans

Introns are a kind of ncRNAs transcribed together with exons,and when pre-mRNAs form mature RNAs after transcriptional co-splicing,Intron are detached from the mRNAs.According to the understanding biological functions of the ncRNAs,post-spliced introns should have other biological functions.The latest studies show that post-spliced introns promote cell survival when nutrients are scarce,in addition to the functions that intron loss/gain can influence many stages of mRNA metabolism.Here,the protein coding genes of Caenorhabditis elegans genome are selected as our objects of study,interactive relationship between introns and their their corresponding mRNAs are analyzed systematically by the improved Smith-Waterman local alignment software?SW?,the binding free energy weighted local alignment algorithm?BEF?and the new symmetric relative entropy algorithm?NSRE?,sequence characteristics of interaction fragments and preference distribution of functional sites in the mRNA were studied.Similar analysis was carried out on the coding genes on in Drosophila melanogaster chromosome?.It is expected to reveal the interaction rules between introns and mRNA.The main contributions are summarized as follows:1.Base on the results of improved Smith-Waterman local alignment software?SW method?,the optimal matching segments between introns and their corresponding mature mRNAs were obtained,and then their relative matching frequency?RF?distribution were got.These results show that there are clear preferences in RF distribution;the match strengths are more significant in the UTRs than the ones in the CDS,especially in the 3?UTR.After classifying introns according to their length,it is found that short introns prefer to interact with the 5?UTR and long introns prefer to interact with the 3?UTR.The matched strengths are higher in the upstream region than in the downstream region from the exon-exon junction site,and the effect of short introns are more obvious.The matching rates of the optimal matching fragments are mainly in the range of 60-80%,and the length of the optmal matching fragments are mainly in the range of 20-30bp.This suggests that the interactions between introns and their corresponding mRNAs are a kind of weak RNA-RNA interactions.In addition,a very small number of the optmal matching fragments with 100%matching rates are found,but the length of these fragments are not more than 14bp.It shows that introns and mRNAs have intentionally avoided RNA interference mode in the process of co-evolution,and all adopt the regulation mode similar to that of miRNAs.From this point,we can confirm that the interactions between introns and mRNAs exist objectively.In addition,we also discussed the local alignments between intron sequences of other genes and the mRNA sequences.We find that there are still matching preferences in the 5'UTR and 3'UTR regions of the mRNAs,but the matching intensities are significantly lower than the matching intensities between introns and their corresponding mRNAs.These results indicate that there are also interactions between other introns and mRNAs.2.Base on the results of binding free energy weighted local alignment algorithm?BFE method?,the optimal matching segments between introns and their corresponding mature mRNAs were obtained,and then their relative matching frequency?RF?distribution were got.The results show that the distribution of relative matching frequencies on mRNAs obtained by BFE method is similar to that obtained by SW method,but the interaction intensity in 5'UTR and 3'UTR region is weaker than that in SW method.In the exon junction region,the relative matching frequency distribution is similar to that of SW method.The effects of long introns and short introns on mRNA and on the five functional sites are consistent with the results of SW method.The matching rate and length distribution shape of the optimal matching fragment are basically consistent with the results using SW method,but the difference is that the lengthes generally become longer.The most probable length using SW method is 23bp,but the most probable length using BFE method is 36bp.The distribution range of G+C content in the optimal matched fragment is still wide,but compared with SW method,the G+C content is generally higher.The most probable G+C content using SW method is 0.2,but the most probable G+C content using BFE method increases to 0.25.The base association of the optimal matched fragment is still strong,but slightly lower than the D₂ value using SW method.Again,it is shown that the optimal matching fragments are a special kind of sequence fragments with high structural organization or strong ordering structure.3.A new symmetric relative entropy local evolutionary relevance alignment algorithm?NSRE method?was used to obtain the optimal evolutionary relevance fragments between introns and their corresponding mRNAs,and the relative evolutionary relevance frequency distribution near functional sites.The results show that the relative evolutionary relevance frequency distribution still showed a preferential distribution at both ends of the mRNA,but the interaction intensity at the 5'end is significantly higher than that using SW and BFE methods,and the interaction intensity at the 3'end is lower than that of the other two methods.In addition,the regions with strong preference distribution are different from those obtained by other two methods.In the AUG region,significant strong interaction distributions occur upstream of the relative matching frequency preference regions using SW and BFE methods.In the UAA region,the significant strong interaction distribution is closer to the UAA site,and also at the front end of the relative matching frequency preference distribution.The results show that base match is a form of interaction between introns and mRNAs,and the evolutionary relevance of fragments should be another association mode.The distributions of relative evolutionary relevance frequency distribution in three types of exon junction regions are similar to that using SW and BFE methods.However,downstream of the junction point,the minimal distribution appeared in the junction regions of the three exons.In SW method and BFE method,there is no obvious minimum distribution in downstream of the junction point of the middle exon junction region.The length distribution of the optimal evolutionary relevance fragments has obvious characteristics and is more conservative.Most of the optimal evolutionary relevance fragments are about 16bp in length,which is different from the length distribution using SW method and BFE method.The distribution of G+C content in the optimal evolutionary relevance fragments is more similar to that using the BFE method,and the G+C content is significantly higher than that using the SW method.However,the base relevance?D₂ value?of the optimal evolutionary relevance fragments is similar to other types of sequences,and does not show strong correlation characteristics.These results suggest that these interaction patterns?evolutionary associations?are dominated by short fragments with no specific sequence structure.4.The protein coding gene of Drosophila melanogaster chromosome I were selected as the analysis sample,the interaction between introns and their corresponding mRNA were characterized by local base matching,and all the optimal matching fragments and the relative matching frequency distribution of the mRNA sequence were obtained.The results show that the distribution of relative matching frequencies on the mRNA is similar to that in the Caenorhabditis elegans gene.However,in the 5'UTR region,the relative matching frequency distribution preference is significantly higher than that of Caenorhabditis elegans.In the 3'UTR region,the preferences are almost the same,but the peak distribution of the Drosophila melanogaster is farther from UAA site.The matching rate and length distribution of the optimal matching fragments are basically the same as that of the Caenorhabditis elegans.The distribution of G+C content in the optimal matching fragments of introns is similar to that of the Caenorhabditis elegans,but the G+C content of the optimal matching fragment of the Drosophila melanogaster is generally higher than that of the Caenorhabditis elegans,and the most probable G+C content of the Drosophila melanogaster is higher than that of Caenorhabditis elegans,and the difference value is about 0.1.The G+C content distributions of 5'UTR and CDS for the Caenorhabditis elegans gene are almost the same,while the distribution of G+C content of 5'UTR for the Drosophila melanogaster gene is significantly lower than that of CDS.We believe that this difference contributes to the fact that Drosophila melanogaster has a higher preference for relative matching frequencies than that of Caenorhabditis elegans at the 5'end of the RNA sequence.In short,there are interactions between mature mRNAs and introns in the protein coding genes of Caenorhabditis elegans and Drosophila melanogaster,and the interaction distribution on the mRNA shows a basically consistent internal regularity.Sequence characteristics of the optimal matched fragments show that they,similar to miRNAs,are a class of unique functional fragments.The interaction patterns based on SW and BFE methods are different from those based on NSRE methods.It shows that there are at least two interaction patterns between introns and mRNAs,which should play corresponding biological functions simultaneously.We believe that the interaction between introns and mRNAs is the result of the cooperative evolution of different types of sequences in the process of life evolution.It is a positive adaptive strategy to exert the cooperative function and reflects the evolutionary mechanism of organisms under functional constraints.