Long noncoding RNAs in innate lymphoid cell biology

项目总结:

Project Summary: Innate lymphoid cells (ILCs) are recently described groups of innate lymphocytes critical for defense against a variety of pathogens, and their dysfunction has been associated with multiple pathologies. Therefore, understanding how innate lymphoid cells are regulated in vivo is key to developing novel treatments for a variety of diseases. It has become clear recently that although the majority of the human genome does not encode for proteins, noncoding regions are transcribed nonetheless. Indeed, long intergenic noncoding RNA (lincRNA) transcripts have been shown to have key regulatory function in a variety of contexts, such as embryonic development. However, the roles of lincRNAs in the immune system in vivo are not well understood. Importantly, the loci encoding lincRNAs in mice and humans are often conserved. Furthermore, the expression of lincRNAs is often regulated in a cell type-specific manner, more so than protein coding genes. This implies both that lincRNAs play important roles in regulating specific cells in mice and humans, and that they may be useful targets in future therapeutics. Therefore, I hypothesize that cell type-specific lincRNA expression in ILCs is critical for their homeostasis. To this end, we found a specific lincRNA, Ak083360, that is expressed in group 1 ILCs, and in the absence of Ak083360 I have found that both the numbers and function of group 1 ILCs are significantly reduced in multiple tissues. Furthermore, I found that expression of the Id2 transcript is greatly reduced in Ak083360-/- NK cells. Thus, I hypothesize that Ak083360 is critical for the homeostasis of group 1 ILCs through regulation of group 1 ILC development, and that it does this through specific regulation of the Id2 gene. To test this hypothesis, I will determine both the developmental stages and biological process, such as cell proliferation or apoptosis, that are dysregulated in Ak083360-/- mice. I will also determine whether Ak083360 is required for group 1 ILC responses in inflammatory settings. Furthermore, I found that the expression of the Id2 gene is altered in Ak083360-deficient group 1 ILCs, and will determine whether dysregulation of Id2 expression is responsible for this phenotype. Finally, I predict that Ak083360 regulates chromatin accessibility at the Id2 locus. To test this, I will determine the state of chromatin accessibility in Ak083360-/- group 1 ILCs using ATAC-seq, and will combine this with RNA pulldown and Western blotting to determine if Ak083360 interacts with specific protein partners. Altogether, successful completion of the described experiments will further our understanding of both gene regulation by lincRNAs in general and specific factors regulating ILC populations.