Complexity of mammalian transcriptome analyzed by RNA deep sequencing

Genetic information in most living organisms on Earth is stored in the form of a chemical structure, known as deoxyribonucleic acid (DNA). Researchers discovered that pieces of long DNA molecules, called genes, are recognized by the nuclear multi-subunit complex of ribonucleic acid (RNA) polymerase, which then produces molecules of RNA, complementarily mirroring the original DNA. Some of these RNA molecules carry information that can be used to produce polypeptide chains with pre-defined amino acid sequences. These molecules have been named messenger RNAs (mRNAs). Others, such as ribosomal RNAs, transfer RNAs, and small nuclear RNAs, have been found to drive and regulate production of proteins. They are sometimes referred to as housekeeping or structural RNAs. However, sequences of mRNAs together with structural RNAs account for less than 10 % of animal and plant genomes. The rest of the genome was considered silent and non-functional, until on-going research revealed that about 80 % of DNA might be transcribed, producing numerous long noncoding RNA molecules with important functions. This chapter gives an overview of mammalian transcriptome research in recent decades. It discusses the main technology platforms, comparing their strong sides and disadvantages. Some of the most important findings are summarized, with an overview of the future prospectives in long noncoding RNA research. The chapter shows that the current understanding of what is a gene should be revised, in order to clearly define the complex relationship between product-coding regions, regulatory sequences, and the organism’s phenotype.