Novel cell type-specific epigenetic role of nuclear lncRNAs in 3D heterochromatization and transcriptional repatterning in the MDD brain

Converging evidence suggests that major depressive disorder (MDD) involves maladaptive processes impairing the ability of individuals to appropriately interface with the environment leading to compromised structural and synaptic plasticity in the cortico-limbic brain areas. So far, no coherent hypothesis fully explains this phenomenon. Fine-tuning of transcriptional regulation by gene x environment interaction is central to MDD etiology. In this regard, long-non-coding RNAs (lncRNAs), a class of regulatory RNAs, are gaining traction for their role in key brain functions and behavior, including MDD. How lncRNAs participate in MDD pathogenesis is not clearly understood; however, their potential engagement in epigenomic reprogramming and subsequent fine- tuning of the transcriptome at the genome-wide level is being considered a paradigm shift in understanding the refinement of cellular processes. Remarkably, a majority of lncRNAs are selectively expressed in the brain in a cell and tissue-specific manner. More importantly, lncRNAs have access to chromatin due to their permanent presence in the nucleus, where they can participate in the programmed arrangement of linear chromatin structure to conformational compactness, a process pivotal to epigenetic reprogramming. Specifically, nuclear lncRNAs may cause a facultative progression of a heterochromatin state following a higher-order chromatin structure formation in 3-dimensional (3D) space, which can initiate genome-wide silencing of transcriptional activity. This can possibly be achieved through nuclear lncRNA-mediated recruitment of chromatin modifier PRC2 in conjunction with methyltransferases EZH2 and SUZ12, thereby facilitating the placement of H3K27me3 repressive histone marks on chromatin. Interestingly, both lncRNAs and chromatin conformational changes are highly sensitive to environmental cues. Using a multitude of innovative approaches, the proposed study seeks to mechanistically examine nuclear lncRNA regulation of 3D chromatin organization and its functional significance in MDD. We propose an overarching hypothesis that a dynamic shift in the expression of a unique pool of nuclear lncRNAs, their interactions with specific RNA binding chromatin modifiers, and consequent repatterning of global gene expression via a facultative progression of 3D heterochromatin state in a cell type- specific manner will be central to MDD pathogenesis. To test this, in the prefrontal cortex and hippocampus from MDD and well-matched controls, we propose to examine: 1) global shift in nuclear lncRNA transcriptome and its correlatedness within an expression framework in a cell type-specific manner; 2) cell type-specific 3D chromatin conformation changes mediated via a specific repertoire of nuclear lncRNAs following genome-wide analysis of higher-order chromatin organization; 3) role of chromatin modifier PRC2 complex and its interaction with nuclear lncRNAs in reshaping 3D heterochromatin organization; and 4) impact of nuclear lncRNA-mediated 3D heterochromatinization on global gene expression and consequent functional responses in a cell type-specific manner. If proven, the study will provide novel avenues to develop lncRNA-based therapeutic interventions.