MicroRNAs (miRNAs) are a class of non-coding RNA that post-transcriptionally regulates the expression of target genes by binding to mRNAs. As one form of alternative splicing, intron retention has influence upon mRNA modification and protein encoding. The effect of miRNA on mRNA containing retained intron within 30 UTR, however, has not been systematically elucidated. Here, we examined a total of 2864 human genes which contain at least one retained intron from the MAASE and ASD databases and found 387 genes having contained retained introns within 30 UTR. The effect of retained introns upon miRNA targets was explored with three web-based programs for miRNA prediction including miRanda, TargetScanS and PicTar. The results showed that retained introns can increase putative miRNA targets in human mRNA. Retained introns have higher chances than other regions of 30 UTR in involving the site of miRNAs targets of most genes which contain putative miRNA targets within it. Furthermore, some transcripts contain miRNA targets solely because of the retained introns in 30 UTR. In addition, we examined those ‘Ignored’ retained introns by miRanda software and the results indicated that miRNAs may contain many more putative targets.

Kininogens, the precursors of bradykinins, vary extremely in both structure and function among different taxa of animals, in particular between mammals and amphibians. This includes even the most conserved bradykinin domain in terms of biosynthesis mode and structure. To elucidate the evolutionary dynamics of kininogen genes, we have identified 19 novel amino acid sequences from EST and genomic databases (for mammals, birds, and fishes) and explored their phylogenetic relationships using combined amino acid sequence and gene structure as markers. Our results show that there were initially two paralogous kininogen genes in vertebrates. During their evolution, the original gene was saved with frequent multiplication in amphibians, but lost in fishes, birds, and mammals, while the novel gene was saved with multiple functions in fishes, birds, and mammals, but became a pseudogene in amphibians. We also propose that the defense mechanism against specific predators in amphibian skin secretions has been bradykinin receptor dependent. Our findings may provide a foundation for identification and structural, functional, and evolutionary analyses of more kininogen genes and other gene families.

To further elucidate the characteristics and potential functions of non-coding region of certain genes, we here systematically examined alternative promoter regions and repeated elements in non-coding regulatory regions of human tissue-specific genes. The results demonstrated that the different types of tissue-specific gene show distinct characteristics, such as the type of alternative promoters, CpG islands, initiating intervallic dinucleotides, and repeat elements. Surprisingly, 74.8% of selected genes contain more than one putative alternative promoter (PAP), and about 92.11% of signal receptors (membrane-bound) possess PAPs. Moreover, a specific PAP type (GC-GC type: both the downstream (?300) and the upstream (-700) regions of transcription start sites are GC-rich) is dominant in human tissue-specific genes and the tissue-specific transcription factors have significantly higher proportion of GC-GC type PAPs. Notably, our data indicated that more than 80% of PAPs are CpG-poor in the considered genes. Furthermore, our findings revealed an inverse tendency between transposable elements and other repeated elements in the 50 flanking regions. These results seem to imply that the distinct alternative promoters and repeated elements may contribute to the regulation and divergence of human tissue-specific genes.

Chitinases (E.3.2.1.14) are ubiquitous hydrolases capable of cleaving the b-1,4-glycosidic bonds in chitin polymers. The physiological significance of these enzymes in the development and immunity of various animals has recently been reported [Badariotti F, Thuau R, Lelong C, Dubos MP, Favrel P. Characterization of an atypical family 18 chitinase from the oyster Crassostrea gigas: evidence for a role in early development and immunity. Dev Comp Immunol 2007;31(6):559–70]. Lampreys are regarded as the most phylogenetically primitive species that may have an adaptive immune system. However, no chitinase gene has yet been identified in lamprey. We report here the identification and characterization of a chitinase-coding gene from the lamprey Lampetra japonica. The predicted amino acid sequence of the chitinase gene consisted of a typical catalytic domain and a peritrophin-A type chitin-binding domain. Real time RT-PCR analysis showed that the chitinase gene was expressed in various tissues of adult L. japonica, particularly in the liver, where a significant difference between male and female was observed during the pre-spawning period. A significant increase in expression was also observed in vivo following stimulation by bacteria or fungi. These findings seemed to suggest that in L. japonica, chitinase probably plays an important role in gonadal development as well as in innate immunity in response to invasion by microorganisms.

Interactions between various events are essential for complex and delicate transcriptional regulation. To delineate the features and potential roles of alternative promoters (APs) correlated with alternative splicing (AS), we have systematically analyzed 9908 putative alternative promoters (PAPs) from 3797 human genes. Our results showed that ~65% of AS events are associated with PAPs. Intriguingly, PAPs per human AS gene only averaged 2.6 for our dataset, which was significantly lower than previously reported. This seems to imply that the human genome contains a small pool of appropriable PAPs for AS genes. Exploration of the characteristics of PAPs such as CpG islands, TATA boxes, GC-content, transcription factor binding sites (TFBSs) and repetitive elements suggested that, respectively, 87% and 90% of PAPs of human AS genes are CpG- and TATA box-poor. The GC-content is significantly higher in the downstream of transcription start sites (TSSs) than upstream (58% vs. 53%), and there is a strong negative correlation between the GC-content and the number of PAPs. These suggested that GC-content around the TSSs plays an important role in the regulation of AS. Moreover, different APs contain distinct densities of repetitive elements and TFBSs, indicating that such sequences have an intrinsic role in the divergent regulation of PAPs and AS. Substantial difference was also found between human AS genes in terms of PAP numbers. A close connection between PAPs and AS may play a critical role in the choice of APs and regulation of AS genes. Furthermore, the distribution of AS genes on different human chromosomes also influences the numbers of PAPs and isoforms of AS genes. Our results may provide important clues for further studies on regulatory network of transcription-related events.

Transcriptional isoforms are not just random combinations of exons. What has caused exons to be differentially spliced and whether exons with different splicing frequencies are subjected to divergent regulation by potential elements or splicing signals? Beyond the conventional classification for alternatively spliced exons (ASEs) and constitutively spliced exons (CSEs), we have classified exons from alternatively spliced human genes and their mouse orthologs (12,314 and 5,464, respectively) into four types based on their splicing frequencies. Analysis has indicated that different groups of exons presented divergent compositional and regulatory properties. Interestingly, with the decrease of splicing frequency, exons tend to have greater lengths, higher GC content, and contain more splicing elements and repetitive elements, which seem to imply that the splicing frequency is influenced by such factors. Comparison of non-alternatively spliced (NAS) mouse genes with alternatively spliced human orthologs also suggested that exons with lower splicing frequencies may be newly evolved ones which gained functions with splicing frequencies altered through the evolution. Our findings have revealed for the first time that certain factors may have critical influence on the splicing frequency, suggesting that exons with lower splicing frequencies may originate from old repetitive sequences, with splicing sites altered by mutation, gaining novel functions and become more frequently spliced.

Alternative splicing has been discovered in nearly all metazoan organisms as a mechanism to increase the diversity of gene products. However, the origin and evolution of alternatively spliced genes are still poorly understood. To understand the mechanisms for the evolution of alternatively spliced genes, it may be important to study the differences between alternatively and non-alternatively spliced genes. The aim of this research was to compare amino acid usage and protein length distribution between alternatively and non-alternatively spliced genes across six nearly complete eukaryotic genomes, including those of human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), fruit fly (Drosophila melanogaster), Caenorhabditis elegans, and bovine (Bos taurus). Our results have suggested the following: (1) across the six species, alternatively and non-alternatively spliced genes have very similar tendency for amino acids usage for not only the overall scale but also those highly expressed genes, with all of the highly expressed genes having preferred amino acids including A, E, G, K, L, P, S, V, R, T, and D. (2) For not only the overall genes but also those highly expressed ones, the average length of the protein products of alternatively spliced genes is significantly greater than that of non-alternatively spliced ones. In contrast, distributions of protein lengths for the two groups of genes are very similar among all six species. Based on these results, we propose that alternatively spliced genes may have originated from non-alternatively spliced ones through events such as DNA mutations or gene fusion.