Deciphering the role of nuclear organization in mRNA and lncRNA nuclear retention

点击翻译按钮获取中文摘要

The long-term objective of our research program is to develop and apply quantitative, single molecule and super-resolution microscopy RNA and protein imaging approaches, with the short-term objective to study the role of nuclear organization in modulating the selective nuclear retention of mRNAs and long-noncoding RNAs (lncRNAs). In eukaryotic cells, the site of genetic information storage is separated from the site of protein synthesis by packaging chromosomes in a separate cellular compartment, the nucleus. This separation required the co-evolution of a complex machinery that mediates the exchange of proteins and RNA between the two compartments. Within this regulatory framework, mRNA serves as a messenger molecule that, after synthesis in the nucleus, is transported to the cytoplasm for protein translation. In addition to mRNAs, eukaryotic genomes are transcribed into a vast variety of RNAs with little or no coding potential, the largest and possibly most diverse group of which is often summarized as lncRNAs. Most lncRNAs share many features with mRNAs, however, despite their similarities to mRNAs in terms of processing and composition, most lncRNAs are retained in the nucleus. Moreover, recent studies indicate that mRNAs can also be nuclear retained under certain conditions, suggesting that nuclear retention might be an important regulatory mechanism that modulates different aspects of gene expression; however, the mechanisms that modulate selective retention of lncRNAs and mRNAs are currently not understood. Sequestration within various nuclear compartments is thought to play a role in retention, yet, this process is not well studied and mechanistically ill defined. Our objective is therefore to develop and apply quantitative live-cell and single molecule microscopy approaches and assays that will allow us to study the mechanisms that mediate nuclear RNA retention and investigate the role of different nuclear compartments in this process. We hypothesize that different nuclear compartments modulate retention through different mechanisms. While retention in nuclear speckles (NP) may be a transient process that is mediated by frequent dynamic interactions of RNAs with NP components, allowing diffusion of molecules within and between NPs, retention in paraspeckles might be achieved by static retention facilitated by an RNA scaffold, enabling long term sequestration within a single paraspeckle. Completing this project will shed light onto the fundamental mechanisms of RNA retention and the role of different compartments in this process - a so far unappreciated and poorly studied aspect of gene regulation - leading to a better understanding of the underlying basic biology of gene expression. It will furthermore lead to the creation of quantitative tools to study RNA in cells that can be applied to investigate various aspects of RNA metabolism.