I learned this amazing fact from a talk I went to last week: currently, somewhere between 70% and 90% of DNA is estimated to be transcribed into RNA but not translated into proteins. So, the question is: if it's not making proteins, what's all this non-coding RNA doing?
In mammalians in particular, more than a thousand large (over 5 kb) intergenic noncoding RNAs (lincRNA) have been identified  and, by looking at expression patterns, researchers were able to see that they are involved in many different biological processes. They are evolutionary conserved across species, indicating that they are indeed functional, yet very little is known of their function. Two 2009 papers [1,2] investigated whether lincRNA are involved in the establishment of chromatin states by creating "genome-wide chromatin-state maps."
We need a refresher here. I discussed chromatin (the package of DNA and proteins inside the nucleus) in this post. The structure and topology of the chromatin changes from cell line to cell line and also during a cell's life, allowing for different genes to be activated or deactivated as needed (for example during cell differentiation). These modifications in the way the DNA is packaged are called chromatin states and are key to understand how and which genes are expressed inside the cell. In particular, there exists a whole family of proteins, called chromatin-modifying complexes, that modify the structure of chromatin to promote or inhibit access genes.
in , Guttman et al. looked at a particular genome domain called K4-K36 in genome-wide chromatin-state maps in 4 mouse cell lines. This chromatin signature marks actively transcribed genes, hence, they were able to find lincRNAs "by identifying K4-K36 structures that reside outside protein-coding gene loci."
"These lincRNAs show similar expression levels as protein-coding genes, but lack any protein-coding capacity. Importantly, lincRNAs show significant evolutionary conservation relative to neutral sequences, providing strong evidence that they have been functional in the mammalian lineage ."In , Khalil et al. extended the results found in  by mapping the K4-K36 domain to 6 human cell types. They found 1,703 new human lincRNA genes and estimated the total number of human lincRNAs to be roughly 4,500. Of all newly discovered lincRNAs, a substantial fraction was found to be associated with PCR2, one of the chromatin-modifying complexes I mentioned above.
"Collectively, these results suggest that many lincRNAs collaborate with chromatin-modifying proteins to repress gene expression at specific loci. [...] Our results suggest an intriguing hypothesis that lincRNAs bind to chromatin-modifying complexes to guide them to specific locations in the genome. [...] Under our model, differentially expressed lincRNAs could bind to these complexes and help establish cell type specific epigenetic states."The specific experiments conducted by Khalil et al. identified associations with chromatin-modifying complexes that have a repressive role, but the researchers suggest that, with different experiments, one could find additional lincRNA that instead are associated with activating chromatin-modifying complexes.
 Guttman, M., Amit, I., Garber, M., French, C., Lin, M., Feldser, D., Huarte, M., Zuk, O., Carey, B., Cassady, J., Cabili, M., Jaenisch, R., Mikkelsen, T., Jacks, T., Hacohen, N., Bernstein, B., Kellis, M., Regev, A., Rinn, J., & Lander, E. (2009). Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals Nature, 458 (7235), 223-227 DOI: 10.1038/nature07672
 Khalil, A., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B., van Oudenaarden, A., Regev, A., Lander, E., & Rinn, J. (2009). Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression Proceedings of the National Academy of Sciences, 106 (28), 11667-11672 DOI: 10.1073/pnas.0904715106