Long noncoding RNAs: an emerging link between gene regulation and nuclear organization

Abstract

Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs) that play important roles in diverse biological processes. As a class, lncRNAs are generally enriched in the nucleus and, specifically, within the chromatin-associated fraction. Consistent with their localization, many lncRNAs have been implicated in the regulation of gene expression and in shaping 3D nuclear organization. In this review, we discuss the evidence that many nuclear-retained lncRNAs can interact with various chromatin regulatory proteins and recruit them to specific sites on DNA to regulate gene expression. Furthermore, we discuss the role of specific lncRNAs in shaping nuclear organization and their emerging mechanisms. Based on these examples, we propose a model that explains how lncRNAs may shape aspects of nuclear organization to regulate gene expression.

Keywords: chromatin regulation; genome organization; long noncoding RNA (lncRNA); nuclear domains.

Figure 1. lncRNA-mediated regulation of gene expression through the recruitment of chromatin regulatory proteins

(a) Different cell types express distinct lncRNAs that can differentially recruit these same chromatin regulatory proteins, including the repressive PRC2 complex and the activating WDR5 chromatin modifying protein, to specific genes. Inset: lncRNAs can recruit these complexes by binding to target sites through three mechanisms: tethering to its nascent transcription locus (top panel), directly hybridizing to genomic targets (middle panel), or interacting with a DNA-binding protein (bottom panel). (b) Different lncRNAs can scaffold unique assemblies of chromatin regulatory complexes. lncRNAs are generally expressed at lower levels relative their associated chromatin proteins (background). (c) lncRNAs may act to coordinate the regulation of gene expression at specific target locations. In this illustration, a lncRNA that can scaffold PRC2, Jarid1C, and ESET may act to remove H3K4me3 and place H3K27me3 and H3K9me2, thereby coordinating the repression of transcription.

Figure 2. lncRNAs can utilize a proximity-guided search to localize to target genes

(a) lncRNAs can regulate genes (green box) on its own chromosome (left panel). In the nucleus, this regulation can occur if the lncRNA locus is in close physical proximity to its target sites (middle panel). For instance, Xist localizes to genes across the X-chromosome (right panel). (b) lncRNAs can also regulate expression of genes on different chromosomes (blue box, left panel). In the nucleus, this can also occur when the lncRNA locus and its targets are in close proximity (middle panel). An example is Firre, which localizes to targets that are present across several chromosomes (right panel). (c) The concentration of a lncRNA will be highest (dark red – inner circle) near its site of transcription and will decrease (light red – outer circles) the further the distance is from its site of transcription, creating a concentration gradient of lncRNA abundance (red cloud, intensity indicates average lncRNA concentration). This spatial gradient establishes a nuclear domain with a high lncRNA concentration, where they can interact with site-specific targets (dark blue arrows). Conversely, lncRNAs outside of the nuclear domain will have a lower probability of interacting with site-specific targets (light blue arrows) due to decreased lncRNA concentration.

Figure 3. lncRNAs can shape three-dimensional nuclear architecture across various levels of organization

(a) Actively transcribed Neat1 (red line) is required to establish the formation of the paraspeckle nuclear body (red cloud), which is an RNA-protein (gray) nuclear domain that is the site of nuclear retention of RNAs such as the CTN RNA (black). (b) Xist (red line) establishes an intrachromosomal nuclear domain (red cloud) by nucleating near its transcription site (white box) and spreading to DNA sites in spatial proximity to its locus. (c) Firre establishes an interchromosomal nuclear domain and brings together targets on chromosomes 2, 15, and 17 into close physical proximity to its transcriptional locus on the X-chromosome. (d) Enhancer RNAs (eRNAs) maintain the interaction between enhancer and promoter regions and may do this by interacting with proteins that can modify chromatin.

Figure 4. A model for how lncRNAs can dynamically shape nuclear organization

The proposed steps involved in lncRNA mediated assembly of nuclear organization roughly based on the proposed models for the Neat1 and Xist lncRNAs. (i) Transcription of a lncRNA can seed the formation of a lncRNA nuclear domain. (ii) lncRNAs can bind to proteins in the nucleus (gray circles) to scaffold protein complexes. Formation of these complexes will nucleate the formation of a spatial compartment (red cloud, dashed lines) near the transcriptional locus of the lncRNA. (iii) lncRNAs can bind to specific DNA sites (white squares) to recruit lncRNA-protein complexes to target sites. (iv) By recruiting these complexes to DNA, lncRNAs can guide chromatin modifications (blue histones), such as repressive histone modification (red marks). (v) Modified chromatin may be compressed and repositioned into a new nuclear region. (vi) As the lncRNA continues to be transcribed from its transcriptional locus, it may iteratively bind to DNA sites (green regions), modify target sites, and reposition DNA into the lncRNA nuclear domain. This continuous process may act to maintain the nuclear domain established by a lncRNA.

Figure 5. A hypothesis for how lncRNAs may act to assemble dynamic and specific nuclear domains

(a) Nuclear domains that share the same proteins can interact in different regions of the nucleus. Zoom-in panels: We hypothesize that different lncRNAs may act to distinguish between these domains by scaffolding and assembling distinct domains. (b) Through linear co-regulation, operons can simultaneously regulate sets of genes (A, B, C and D, E, F) with shared regulatory functions. Activators (pink triangles) and repressor (green boxes) control operon expression under a particular cell state. We hypothesize that through spatial co-regulation, lncRNAs may nucleate the formation of nuclear domains to co-localize target genes upon induction of lncRNA expression. For instance, upon induction of lncRNA1, genes A, B, and C are co-regulated in a nuclear domain (red cloud, dashed lines). Under a different cell state, lncRNA1 expression is repressed, leading to the breakdown of the lncRNA1 nuclear domain and expression of lncRNA2 leads to formation of another nuclear domain (blue cloud, dashed lines) containing genes D, E, and F.