Transcriptome Profiling

Transcriptional regulation plays a critical role in determining cellular identity and function. We are interested in characterizing gene expression of tissue specific genes during normal development and also under pathological conditions. Microarray is the classical method which has long been used for transcriptome profiling but it is limited to known genome sequences and has low sensitivity.  A recently developed highly quantitative method called RNA-Sequencing or RNA-Seq, provides base pair resolution with absolute number of reads and has the ability to detect novel exons, transcripts and transcript isoforms.  Compiling and comparing RNA-Seq data for macrophages and thymocytes will provide transcriptome insights of tissue specific gene expression. Initial analysis of the data showed that most tissue restricted genes have very high expression in their respective tissue types.  In addition, genome tracks from previous studies were uploaded to assess for common patterns of chromatin signatures based on known histone modifications: H3K4me1 marks enhancers; H3K9me1 and H3K9acetyl are active chromatin marks while H3K27me3 and H3K9me3 are repressive marks. Characterization of genome-wide gene expression from cells of distinct tissue types will refine the definition for classifying genes required for tissue specificity and provide information about how tissue specific gene expression programs are implemented.