It is thought that virtually all protein-coding genes in the human genome have already been discovered, yet a significant fraction of genetic variants associated with human disease map to the intergenic space. Furthermore, genome-wide studies of transcription have found that these intergenic regions are pervasively transcribed into different classes of RNA molecules. These include long intervening noncoding RNAs (lincRNAs), which contain at least 200 bases, and similarly to mRNAs, begin with a 5' cap and end with a poly(A) tail. Thousands of lincRNA genes were recently reported in human and mouse and several lines of evidence suggest that many of them are functionally important. For example, lincRNA expression varies across tissues and is commonly dysregulated in human disease, including cancer. Furthermore, the sequences of lincRNA exons were significantly conserved during vertebrate evolution. Accumulating evidence shows that lincRNAs play pivotal regulatory roles in diverse biological processes, such as dosage compensation, transcriptional regulation, DNA damage response and establishment of cell identity. Some of these lincRNAs were shown to recruit protein complexes to chromatin, or to act as scaffolds or decoys, but the mode of action currently remains unknown for the vast majority of lincRNAs. Our goal is to understand the functionality of lincRNAs and the ways it manifests itself in their sequences.