Regulation of transcription by long noncoding RNAs

Abstract

Over the past decade there has been a greater understanding of genomic complexity in eukaryotes ushered in by the immense technological advances in high-throughput sequencing of DNA and its corresponding RNA transcripts. This has resulted in the realization that beyond protein-coding genes, there are a large number of transcripts that do not encode for proteins and, therefore, may perform their function through RNA sequences and/or through secondary and tertiary structural determinants. This review is focused on the latest findings on a class of noncoding RNAs that are relatively large (>200 nucleotides), display nuclear localization, and use different strategies to regulate transcription. These are exciting times for discovering the biological scope and the mechanism of action for these RNA molecules, which have roles in dosage compensation, imprinting, enhancer function, and transcriptional regulation, with a great impact on development and disease.

Keywords: RNA polymerase II; chromatin; chromatin-modifying complexes; enhancers; imprinting; transcriptional silencing.

Figure 1

Classes of lncRNAs (long noncoding RNAs). All known lncRNAs are divided into five classes, on the basis of their relationship with adjacent or overlapping genomic features. The initiation site for the noncoding transcript is shown in red, and the arrow indicates the direction of transcription. Less-common variants within the same class are indicated with dashed arrows. In the second column, existing names for the different classes are listed in gray within parentheses, and their corresponding names from our proposed new nomenclature are in black. Abbreviations: eRNAs, enhancer RNAs; gaRNAs, gene body–associated antisense RNAs; gsRNAs, gene body–associated sense RNAs; iRNAs, intervening long noncoding RNAs; lincRNAs, long intervening noncoding RNAs; NATs, natural antisense transcripts; ncRNAs-a, noncoding RNAs activating; pRNAs, promoter-associated RNAs; PROMPTs, promoter-associated pervasive transcripts; TSS, transcription start site; TTS, transcription termination site; uaRNAs, upstream antisense RNAs.

Figure 2

Mechanisms of ncRNA (noncoding RNA)-mediated regulation of PRC2. (a) The imprinted lncRNA (long noncoding RNA) Meg3 makes contact with EZH2 and JARID2 and stimulates their interaction on chromatin, facilitating PRC2 assembly, H3K27me3 deposition, and transcriptional repression of a subset of PRC2 targets in human and mouse stem cells (69). (b) The lncRNA HOTAIR has been reported to recruit PRC2 in trans to the HOXD locus in human fibroblasts (137). Later studies revealed that HOTAIR interacts directly with EZH2 and that phosphorylation of EZH2 at T345 stimulates ncRNA binding (70). (c) In embryonic stem cells, PRC2 is found at a majority of promoters, including those of active genes. However, interactions with nascent RNAs decrease the amount of deposited H3K27me3 either by inhibiting PRC2 function or by causing its release from chromatin (71). (d) SUZ12 was reported to interact with short ncRNAs originating from the region near the transcription start site (TSS) of Polycomb target genes, leading to PRC2 recruitment, H3K27me3 deposition, and silencing (72). SUZ12 also interacts with the lncRNA Braveheart (77). The center image is a schematic of the multiple mechanisms (a–d) by which ncRNAs have been shown to interact with PRC2.

Figure 3

Transcriptional activation by lncRNAs (long noncoding RNAs). (a) Several lncRNAs transcribed from a distal enhancer directly interact with subunits of Mediator and facilitate enhancer-promoter communication by promoting loop formation (86), which requires the function of cohesin (96). (b) In Schizosaccharomyces pombe, activation of fbp1 requires transcription of lncRNAs originating from an upstream transcription start site (TSS). This is followed by promoter remodeling via nucleosome depletion, which requires the transcribing polymerase (59). (c) Transcription of CEBPA in human cells is activated by an upstream sense lncRNA (ecCEBPA), which binds DNMT1 and sequesters it from chromatin, causing hypomethylation of the promoter. (d) Activation by an androgen receptor (AR) requires a complex cascade of post-translational modifications and lncRNA-protein interactions that culminates with the recruitment of PYGO2 via the lncRNA PCGEM1. In turn, PYGO2 stimulates transcription by strengthening enhancer-promoter looping (dashed arrows) (179).

Figure 4

Potential roles of lncRNAs (long noncoding RNAs) in nuclear organization. (a) In this speculative model, eRNAs (enhancer RNAs) mediate enhancer-promoter communication directly via base-pair interactions with uaRNAs (upstream antisense RNAs) and possibly facilitate chromatin looping. (b) The lncRNA Xist utilizes the three-dimensional organization of chromatin to spread its silencing activity over the whole X chromosome. Interactions with chromatin might be mediated via the matrix protein hnRNP U (41). At the target sites, Xist facilitates H3K27me3 deposition via PRC2 recruitment (187). (c) Roles of ncRNAs (noncoding RNAs) in CTCF function. (Left) Human CTCF binds RNA directly and RNA interactions mediate multimerization, which might guide chromatin looping and organization (141). (Middle) Human CTCF also binds RNA indirectly through its interactions with the RNA helicase DDX5, here bound to the lncRNA SRA (182). (Right) Drosophila CTCF and CP190 insulator proteins interact physically and genetically with AGO2, a small ncRNA-binding protein and key component of the RNAi machinery (92, 116).