Understanding Long Noncoding RNA and Chromatin Interactions: What We Know So Far

Abstract

With the evolution of technologies that deal with global detection of RNAs to probing of lncRNA-chromatin interactions and lncRNA-chromatin structure regulation, we have been updated with a comprehensive repertoire of chromatin interacting lncRNAs, their genome-wide chromatin binding regions and mode of action. Evidence from these new technologies emphasize that chromatin targeting of lncRNAs is a prominent mechanism and that these chromatin targeted lncRNAs exert their functionality by fine tuning chromatin architecture resulting in an altered transcriptional readout. Currently, there are no unifying principles that define chromatin association of lncRNAs, however, evidence from a few chromatin-associated lncRNAs show presence of a short common sequence for chromatin targeting. In this article, we review how technological advancements contributed in characterizing chromatin associated lncRNAs, and discuss the potential mechanisms by which chromatin associated lncRNAs execute their functions.

Keywords: RNA-chromatin interactions; chromatin; chromatin RNA; gene regulation; lncrna; long noncoding RNA.

Figure 1

Timeline of technological advances to study RNA-Protein and RNA-Chromatin interactions. Upper panel (light sea-green box) depicts in chronological order the prominent methods (in blue) to detect RNA interactions with chromatin. Examples of some of the functionally validated lncRNAs from each of these studies are shown (in black) below the corresponding method. Middle panel depicts the year in which these methodologies were published. Lower panel (light pink box) likewise shows in chronological order methods (in green) to identify RNA interactions with proteins.

Figure 2

Mechanisms of chromatin targeting of lncRNAs.Three broad mechanisms that explain both cis and trans acting lncRNAs targeting to the chromatin. (A–E) depicts possible mechanisms by which lncRNAs associate with chromatin through interacting with chromatin modifiers, chromatin readers and/or RNA binding proteins. LncRNAs that interact with proteins with dual RNA-DNA binding properties can bind to chromatin enriched with active (A) or inactive histone modifications (E), or interacts with RNA binding subunit of a heterocomplex chromatin modifiers (B), or lncRNAs can directly be targeted (triplex or R-loop) to chromatin as a complex with any RBP (C) or histone modification readers can recruit RBP bound lncRNAs that can subsequently interact with chromatin via histone modifications (D). Inactive chromatin associated lncRNAs (iCARs) can be recruited to chromatin by a single (E) or heterocomplex chromatin modifiers (not shown) with histone reading as well as modifying functions and such recruitments leads to spreading of inactive chromatin through repressive histone marks. (F–G) Triplex and R-loop forming lncRNAs can target chromatin in cis vs. trans (F–I). There might be a same (F) or different (G) group of protein complexes that might play a role in either stabilizing triplex formation by cis (F) or trans-acting (G) lncRNAs via binding to triplex forming oligos (TFOs). Similarly, R-loop formation might be coordinated by different protein complexes in cis (H) as compared to (if any) in-trans targeting (I).

Figure 3

Mechanism of in-cis chromatin targeting. Proposed model elucidating three different mechanisms of in-cis chromatin targeting of some of the well characterized lncRNAs. (A) Xist lncRNA upon transcription from the X-chromosome (red bar depicts the promoter) that is due to be inactivated, interacts with YY1 protein. YY1, being bifunctional RNA-DNA interacting protein, binds to YY1 binding sites (green bar) downstream of Xist promoter thereby retaining the newly transcribed Xist in cis. hnRNPU is another bifunctional protein, which can interact with both chromatin and RNA, binds at the 5′ end of Xist and targets it to chromatin. Nucleated Xist lncRNA then spreads along the entire X-chromosome using the three-dimensional folding of the chromatin with the aid of other transcriptional repressor complexes such as SHARP and PRC2. (B) Kcnq1ot1 lncRNA is exclusively transcribed (arrows depicting transcription) from an unmethylated paternal ICR (imprinted control region) (sky blue box), located within the intron 10 of its sense partner gene Kcnq1 gene. It functions in-cis to repress (blunted arrows represent transcriptional repression) lineage specific imprinted genes. Kcnq1ot1 (light green) interacts with and recruits G9a-PRC1-PRC2 complex to the promoters of placental linage genes (Blue boxes), while it additionally interacts with DNMT1 and targets G9a-PRC1-PRC2/DNMT1 complex to the promoters of genes that are silenced in all tissues in lineage independent fashion (Red boxes). The targeting and spreading to specific promoters across 1 mega-base region, unlike the whole X-chromosome spreading by Xist, is mediated by the three-dimensional folding of the chromatin. (C) Active XH lncCARs exemplify the case of in-cis targeting of lncRNAs to specific promoter regions of neighbouring protein coding genes to maintain their transcriptional activation. In the model, either the XH lncCARs first binds to WDR5-methyl transferase complex through the RNA binding pocket of WDR5 and then targeted (dashed black arrows) to chromatin at H3K4me2 (WDR5 reads H3K4me2), or they can directly bind H3K4me2 enriched chromatin (dashed red arrows) and act as a scaffold for the efficient docking of WDR5-methyl transferase complex which is necessary to maintain H3K4me2 levels and catalyse the conversion of H3K4me2 to H3K4me3. The maintenance of H3K4me2 marks is possibly mediated by a different WDR5- methyl transferase complex that is independent of the role of XH lncCARs.