3D structure of DNA forms defined room for dissociated lncRNAs to activate gene expression

Berlin scientists propose novel mode of gene regulation through long non-coding RNAs

May 07, 2018
The DNA in our cells contains all genes as well as large regions that do not code for proteins, but, in many cases, have regulatory functions in the genome. Enhancers are a type of such regulatory regions, giving rise to so-called “long non-coding RNAs” (lncRNAs), which are known as crucial regulators of gene expression. Scientists from the Max Planck Institute for Molecular Genetics (MPIMG) in Berlin now have shown that a lncRNA called A-ROD is only functional the moment it is released from chromatin into the nucleoplasm. In the current issue of Nature Communications the researchers demonstrate that the regulatory interaction requires dissociation of A-ROD from chromatin, with target specificity ensured within the pre-established chromosomal proximity. This can heavily influence our understanding of dynamic regulation of gene expression in biological processes.

Mammalian genomes code not only for protein genes, but also for thousands of long non-coding RNAs (lncRNAs) that fulfill regulatory functions in development and disease. They are processed through the same molecular machinery as mRNAs, but to exert function, lncRNAs stay in the nucleus, where they can interact with proteins and direct their binding to DNA or enhance their enzymatic activity. They are often enriched in the nucleus and at chromatin, but whether their dissociation from chromatin is important for their role in transcription regulation is unclear.

Now, scientists from the research groups Long non-coding RNAs, headed by Ulf Ørom (now at Aarhus University, Denmark) and RNA Bioinformatics, headed by Annalisa Marsico, both from the Max Planck Institute for Molecular Genetics (MPIMG) in Berlin, analyzed a lncRNA called A-ROD (Activating Regulator Of DKK1 expression) that enhance expression of the DKK1 gene. They could show that A-ROD is only functional the moment it is released from chromatin into the nucleoplasm. Only then, it can bring transcription factors – proteins controlling the activity of genes – to specific sites of the DNA to enhance gene expression.

“Enhancers control the expression of genes over very long distances on the extended DNA thread”, explains Evgenia Ntini, first author of the study. “Interestingly, we found that lncRNAs transcribed from enhancers laying in a loop conformation with their target genes are less tethered to chromatin and are enriched in the soluble nucleoplasmic fraction of the cell. It seems that the release of the lncRNA from chromatin is important for their function.”

In its chromatin state, the linear DNA thread forms a three-dimensional structure with defined loops, which cause a close proximity of exactly defined DNA regions that are far away from each other on the linear thread. This is also the case for the A-ROD enhancer and its target gene. “Inside the loop, A-ROD can immediately interact with the DKK1 gene and regulatory RNA-binding proteins to activate gene expression”, Ntini says.

Based on their results, the scientists propose a novel mode of gene regulation mediated by lncRNAs. They suggest that the lncRNA will only mediate its effect after it has been fully transcribed and released from the site of transcription, with the A-ROD locus being in close proximity to DKK1. Thus, not the transcription of the lncRNA would be the critical step for gene activation, but rather its dissociation from chromatin where it becomes exposed to the nuclear environment and accessible to bind regulatory proteins.

The results are exciting both from an experimental and therapeutic point-of-view, as the strategies for targeting RNA expression in the cytoplasm, the nucleoplasm and at chromatin differ widely. The researchers believe that these differences can be exploited to optimize the approaches for targeting RNA-dependent processes in disease. A future scientific goal is to identify more of those enhancer-like non-coding RNAs to fully understand their potential and application in regulation of gene expression.

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