The Study Of Expression Pattern Of Mouse House-Keeping Gene On Isoforms Level Based On RNA-seq Data

Mus musculus is a commonly used model organism, also similar to human in physiology, so it is often used to study human diseases. The mouse genome was sequenced in 2002, and most of its genomic sequences are homologous with the human genome. It has an important role to annotate the human genome and improve the understanding of the functions of the human genes.House-keeping genes (HK genes) are genes required for maintaining basic vitality of cells and constantly expressed in different tissues, developmental or cell cycle. Study of HK genes will help understand the basic function of cells, as well as the minimum set of genes needed for life. Benefiting from the development of sequencing technology, the high-throughput and low-cost transcriptome sequencing enabled researchers to extract all mRNA from tissues to study gene functions and the content of interest and accelerated the speed of decoding the myth of the genome. By using RNA-seq data, identification of HK gene has become very efficient and accurate.In this study, RNA-seq data of 14 tissues of mouse from public databases was used and re-identified 8,648 HK genes and 1,828 of them have only one isoform. Filtering out unexpressed transcripts, a total of 4,208 HK genes which have a isoform played a major role in the gene expression were identified using our method, and we defined these transcripts as main isoforms. We carried out significance analysis of difference between main isoform and other isoforms and found they have significance difference. Correlation, cluster and content analysis showed the expression of main isoforms and their genes are highly correlated. As a result, the main isoform could represente their genes at expression level. Analyzing the structure of main isoforms, we found that the main isoforms were shorter and likely to have longer exons and shorter introns. The functions of main isoforms tend to enrich in fundamental pathways, such as oxidative phosphorylation and ubiquitination of protein, while others are significantly enriched in multiple signaling pathways.The study also identified specified expression of transcripts and found that these transcripts are mainly distributed in testicular cells, while there are still some exceptions, whose main isoforms are distinct in different tissues.