Long Noncoding RNAs with Enhancer-like Function in Human Cells

Long Noncoding RNAs (lncRNA) constitute a large portion of the mammalian transcriptome even though their biological functions remained unclear. In 2009 we participated in a study that analyzed a set of 3,019 lncRNAs that did not overlap protein-coding loci (equivalent to lincRNAs) from GENCODE.  In the course of this project we found that these lncRNAs also display evolutionary sequence conservation and a specific pattern of splicing distinct from that of protein-coding transcripts. A number of these RNAs cluster in well-defined gene families, and within some of these we have found a large number of compensating mutations, suggesting the presence of a common structural fold. Using RNAseq we have shown that lncRNAs display differential tissue expression, which is closely correlated with the presence of active or repressive chromatin signatures.  Importantly, we found increased expression of a number of lncRNAs following differentiation of adult human stem cells. Functional analysis of these lncRNAs in multiple cell lines revealed their positive regulation of neighboring protein-coding transcripts. This work was published in the journal Cell in 2010 (Orom et al.,2010).

Furthermore, during 2011 we have developed a new custom microarray platform to measure lncRNA expression. We are using these arrays with various collaborators to study lncRNA involvement in (1) haematopoeitic cell differentiation (with Thomas Graf of the CRG), (2) cardiac progenitor cell differentiation (with Thierry Pedrazzinni). In parallel, we are developing tools to study candidate lncRNAs in loss-of-function assays. We have adapted retroviral delivery systems and short hairpin technology to target lncRNAs in a high-throughput manner, and are currently testing this as a method for functional lncRNA discovery.  In addition, we have submitted a manuscrit to be submitted to the journal genome research, within the ENCODE project consortium, describing the gene structure and expression of the largest collection of human lncRNAs to date: “The GENCODE v7 catalogue of human long non-coding RNAs: Analysis of their gene structure, evolution and expression” (Derrien et al. Including the group members R. Guigo, A. Tanzer, S. Djebali, H.Tilgner, D. Martin,  D. Gonzalez, J. Lagarde, R. Johnson and A. Merkel).  We have also been investigating into the function of lncRNAs by statistical analysis of high-throughput RNA-seq data, particularly focusing on the possible association between lncRNA expression and splicing. Complementary to this, we have been analyzing lncRNA patterns in RIP-SEQ experiments involving HuR and Pabpc1 proteins (with Scott Tenenbaum) within the ENCODE project.