Characterization of a G-quadruplex structure at the 3' end of NEAT1_2 and its role in regulating its stability.

Abstract

Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease that causes deterioration of nerve cells, resulting in loss of muscle control and leads to paralysis. During the early stages of ALS, patients have an increased abundance of paraspeckles, membraneless organelles within nuclei that are comprised of RNA and proteins. The function of these subnuclear bodies is still largely unknown; however, they are created by a scaffold RNA, nuclear enriched abundant transcript 1 (NEAT1), a long noncoding RNA (lncRNA) that also has upregulated expression during ALS onset. Each paraspeckle may contain up to fifty NEAT1 RNAs. NEAT1 exists in two isoforms, NEAT1_1 of ∼3.7 kB and NEAT1_2 that is ∼22.7 kB, created by alternative 3’ splicing. Four G-rich regions common to both isoforms can fold into G-quadruplexes (GQ); however only NEAT1_2 contains a fifth GQ region near its 3’ end. At the 3’ terminus of NEAT1_2 there also exists a triple helix previously shown to affect its stability. Here we use different biophysical methods to analyze the role played by this fifth GQ upon the folding of the triple helix, and thus, the stability of NEAT1_2. Understanding the secondary structure of NEAT1 will help in expanding our breadth of knowledge surrounding neurodegenerative diseases like ALS by targeting the GQ and triple helix to disrupt their formation to alter its level of expression and its interaction with proteins necessary for paraspeckles.