The Application Of An Integrated Differential Transcriptome Bioinformatics System In Mouse And Human Transcriptomic Studies

Defining the precise map of the transcriptome, which is all the transcripts encoded in the genome, is critical for understanding the initiation and progression of disease and the identification of putative diagnostic and prognostic biomarkers for the disease. Bioinformatics is necessary for interpreting the biological features from the massive transcriptomic data derived from RNA-seq or DNA microarray.Here, we first established the bioinformatics analysis system for differential transcriptome. We then performed RNA-seq of mouse testis exposed to cadmium. By analyzing the raw data using the bioinformatics analysis system, we investigated the molecular mechanism of cadmium caused male reproductive toxicity and identified several putative biomarkers successfully. We then used this bioinformatics system in studying the dynamic transcriptomic changes during heart development from our human cardiac RNA-seq data and other public data.Part ?:Integrated Differential Transcriptome Analysis SystemUnderstanding the transcriptome is essential for interpreting the functional elements of the genome and revealing the molecular constituents of cells and tissues, and also for understanding development and disease. Moreover, transcriptome studies can facilitate the identification of diagnostic and prognostic biomarkers for disease. At present, RNA-seq has been the most popular method in transcriptome studies. Bininformatics community has developed many RNA-seq analysis tools based on various algorithms and statistical models in order to address the computational analysis issues, including reads mapping, transcriptome reconstruction, transcriptome quantification, differential analysis and downstream functional or regulatory analysis. The most important thing is to select a set of suitable software to build the transcriptome analysis pipeline for better understanding development and disease. In this study, we established an integrated analysis system of differential transcriptome used for each process of computational transcriptomic studies. Part ?:Differential Analysis of Mouse Testicular Transcriptome Exposed to CadmiumCadmium is a common toxicant that is detrimental to many tissues. Although a number of transcriptional signatures have been revealed in different tissues after cadmium treatment, the genes involved in the cadmium caused male reproductive toxicity, and the underlying molecular mechanism remains unclear. Here we observed that the mice treated with different amount of cadmium in their rodent chow for six months exhibited reduced serum testosterone. We then performed RNA-seq to comprehensively investigate the mice testicular transcriptome to further elucidate the mechanism by using our established bioinformatics analysis system. Our bioinformatics analysis results showed that hundreds of genes expression altered significantly in response to cadmium treatment. In particular, we found several transcriptional signatures closely related to the biological processes of regulation of hormone, gamete generation, and sexual reproduction, respectively. The expression of several testosterone synthetic key enzyme genes, such as Star, Cypllal, and Cyp17a1, were inhibited by the cadmium exposure. For better understanding of the cadmium-mediated transcriptional regulatory mechanism of the genes, we computationally analyzed the transcription factors binding sites and the mircoRNAs targets of the differentially expressed genes. Our findings suggest that the reproductive toxicity by cadmium exposure is implicated in multiple layers of deregulation of several biological processes and transcriptional regulation in mice. Part ?:Differential Transcriptomic Analysis of Human Heart DevelopmentHeart is the first functional organ during embryogenesis. Normal heart development and function is essential for embryonic or postnatal life, and defects in heart formation cause congenital heart disease. Even in adulthood, heart disease may occur in response to stimulations. Thus, the study of the regulatory transcriptional programs of heart development is particularly important for understanding the molecular mechanisms of congenital heart disease and for developing strategies for cardiac regeneration. Although studies have been focused on the transcriptional signatures for the differentiation course from mouse and human embryonic stem cell to cardiomyocytes in vitro, and mouse model has been used to study the transcriptome between embryonic and adult heart, the direct evidence of human embryonic and adult heart transcriptomic landscape is limited.Here, we obtained the transcriptome of human embryonic and adult heart tissue based on RNA-seq and compared the transcriptional patterns. By using our bioinformatics analysis system, we found6,104cardiac expressed lncRNAs with RPKM>0and1,581cardiac actively expressed lncRNAs with RPKM>1in at least one sample. Differentially expressed analysis showed that2,692mRNA and306 lncRNA were significantly differentially expressed between fetal and adult heart, and these transcripts exhibited dynamic patterns during heart development. Functional annotation of the differentially expressed mRNAs and lncRNAs suggested that they were highly associated with cardiac functions. The chromatin marks and DNA methylation states also showed dynamic changes during heart development and coordinated regulate gene transcription. Furthermore, we discovered genome-wide putative distal enhancers by mapping histone marks. De novo motif analysis of these putative distal enhancers revealed the existence of several cardiac transcriptional factors motifs. Finally, we identified both active and poised enhancers in human heart. Functional annotations of these different classes of enhances revealed their distinct roles in cardiac development and diseases. Collectively, our integrative study have shed light on the understanding of heart development, diseases and regeneration.