Characterizing Transcriptomes from High-Throughput Sequencing Data

The DNA in our cells contains our genetic hereditary information, and is literally the blueprint of our body. The functional units of the genome are regions of continuous DNA sequence, and are called genes. According to the Central Dogma of Biology, the DNA sequence of the gene is transcribed into a messenger RNA (mRNA), which is in turn translated to proteins, which perform most tasks in the cell. All the cells in an organism share the same DNA, but there are dramatic morphological and functional differences between cells in various tissues and under different conditions. Many of these differences are mediated by regulation that determines which genes are “turned on”. Classically, regions in the DNA were considered as genes only if they encode proteins. Today, regions in the DNA that are transcribed to mRNA but do not encode proteins, and function at the RNA level are also considered genes, and are called non-coding RNAs. Antisense transcripts are a specific type of non-coding RNAs, that overlap a protein-coding gene on the opposite DNA strand. In this context, these are called the antisense and sense transcript, respectively. When the antisense gene is transcribed, it can down-regulate the expression of the sense gene. One of the first steps in understanding a newly sequenced organism is to annotate its genes, which will enable us to predict its repertoire of proteins. Ultimately we would like to annotate the genes, find their genomic position, and understand when, why and how they are turned on and off. The simplest task is to first identify their genomic position. In some simple eukaryote organisms (like the budding yeast), the genome is very dense with genes, and the vast majority of them are not spliced. In mammals, however, the genes comprise an extremely small part of the genomic sequence. For example, in humans only 2% of the genomic sequence is protein coding, making the task of finding the genes in the sea of the genomic sequence far from trivial. Thus, sequencing the genome is