Discussion The epidermal growth factor receptor family is of tremen dous biological and clinical importance for many solid epithelial tumors
Characterization of the Pol IIII transcriptome in AC16 cells To further characterize the non Pol II transcriptome in AC16 cells, we mapped 739 non Pol II Discussion The epidermal growth factor receptor family is of tremen dous biological and clinical importance for many solid epithelial tumors transcripts from GRO seq data generated amanitin. This Discussion The epidermal growth factor receptor family is of tremen dous biological and clinical importance for many solid epithelial tumors set of non Pol II transcripts includes mainly tRNAs, rRNAs, some snRNAs, and transcripts generated from SINE repeat elements, as well as 172 novel, previously unan notated transcripts. The lengths of the majority of the Discussion The epidermal growth factor receptor family is of tremen dous biological and clinical importance for many solid epithelial tumors 739 primary non Pol II transcripts are 400 nucleotides, which indicates that they are short, non coding RNAs. The biological functions associated with the up and down regulated gene sets are closely related to cardiac function. For example motor protein and myosin related muscle functions are directly related to the elec trophysiology of heart muscle. fibroblast prolif eration and endothelial to mesenchymal transition contribute to cardiac fibrosis. and mitochon drial function and lipid oxidation are closely related to normal cardiac physiology. These dynamic transcriptome changes reflect the time dependent shift ing of biological processes in cardiomyocytes in re sponse to TNF. Interestingly, genes related to muscle function and inflammation are upregulated immediately, whereas genes related to mitochondrial function and metabolism are downregulated first and upregulated later in the time course. These results highlight the sequential transcriptional responses that underlie shifting cellular responses in cardiomyo cytes in response to TNF treatment. We augmented this analysis using a database from the Cardiovascular Gene Ontology Annotation Initiative project, which contains more than 4,278 genes critical for cardiac physiology and pathology. A large fraction of both up and downregulated genes are in the cardiac associated gene list and 20% are regulated by TNF treatment. Interestingly, 166 of the 1,146 enhancers predicted by GRO seq are located near genes critical for cardiac physiology. Collectively, our analyses of the TNF altered transcrip tome indicate that the AC16 cellular state switches from maintenance of basal housekeeping functions to defense against inflammatory stress. TNF induced transcriptome changes result in corresponding alterations in the steady state levels of mRNAs and proteins As expected, the TNF induced changes in the AC16 transcriptome result in corresponding changes in mature mRNA and protein levels in a similar manner, but with delayed kinetics. For example, the robust up regulated transcription of key TNF target genes is followed by corresponding changes in the steady state levels of the cognate mRNAs and proteins, with a delay of approxi mately 20 to 100 minutes for mRNA and 120 to 240 mi nutes for proteins. These results clearly illustrate how the dynamically regulated transcriptome alters the cellu lar proteome.
These results also further support our ob servation that AC16 cardiomyocytes secrete cytokines in response to TNF stimulation. These cyto kines may play an essential role in the overall effects of inflammation in cardiac biology. Role of non coding RNAs and the TNF induced proinflammatory transcriptome Protein coding genes represent only part of the AC16 transcriptome. the functions carried out by the non coding transcripts that we identified may also play critical roles in the inflammatory response in cardiomyocytes.
