Poster abstracts
Poster number 85 submitted by Yizhu Lin
Structural analyses of human and mouse NEAT1 lncRNAs suggest long-range RNA interactions contribute to paraspeckle architecture
Yizhu Lin (Carnegie Mellon Universty, Department of Biological Sciences), Gemma May (Carnegie Mellon Universty, Department of Biological Sciences), Joel McManus (Carnegie Mellon Universty, Department of Biological Sciences)
Abstract:
In the past decade, lncRNAs have been increasingly recognized as important regulators of gene expression. Because they don’t encode proteins, lncRNA structures and protein interactions are believed to be important for their functions. One relatively abundant lncRNA, NEAT1, functions in the formation of paraspeckles - nuclear bodies that have been implicated in multiple stress responses and diseases. NEAT1 has two isoforms produced by alternative 3’ end processing. The short isoform (NEAT1_v1) is 3.7 kb and contains a polyA tail, while the long isoform (NEAT1_v2) is 23 kb in length and has a 3’ end produced by RNase P cleavage. Though the NEAT1 primary sequence is not well conserved, the two isoforms and their function in paraspeckle formation were observed in both human and mouse cells. NEAT1 has a highly ordered spatial organization within the paraspeckle, in which NEAT1_v1 and both the 5’ and 3’ ends of NEAT1_v2 are localized to the periphery. The central sequences of NEAT1_v2 are found within the core 1 . The structural features that maintain this spatial organization remain unknown, however it was suggested that interactions among proteins bound to NEAT1 may help maintain paraspeckle structure 1 .
We combined experimental RNA secondary structure probing (Mod-seq 2 ) and computational structural analyses to investigate the structural features of NEAT1. The full length human and mouse NEAT1_v1 structures were probed using SHAPE and Mod-seq. By comparing the structures of human and mouse NEAT1, we identified conserved structural features. Our results indicate NEAT1_v1 is highly folded, and several regions have specific local secondary structural signatures conserved between human and mouse. Further computational analyses suggest that the 5’ end of NEAT1_v2 (or NEAT1_v1) and the 3’end of NEAT1_v2 form long-range base pairs with each other, which may contribute to the co-localization of NEAT1 5’ and 3’ ends. This interaction was verified in vitro using an RNA intermolecular gel-shift assay. Our results suggest that the secondary structure of NEAT1 and the long-range interactions among NEAT1 transcripts may have important architectural functions in paraspeckle formation.
References:
1. Souquere, S., Beauclair, G., Harper, F., Fox, A. & Pierron, G. Highly ordered spatial organization of the structural long noncoding NEAT1 RNAs within paraspeckle nuclear bodies. Mol Biol Cell 21, 4020–4027 (2010).
2. Talkish, J., May, G., Lin, Y., Woolford, J. L. & McManus, C. J. Mod-seq: high-throughput sequencing for chemical probing of RNA structure. RNA 20, 713–20 (2014).
Keywords: NEAT1, RNA structure, lncRNA