HOTAIR Forms an Intricate and Modular Secondary Structure

Somarowthu, Srinivas; Łęgiewicz, Michał; Chillón, Isabel; Marcia, Marco; Liu, Fei; Pyle, Anna Marie

doi:10.1016/j.molcel.2015.03.006

Cited by 291 publications

(347 citation statements)

References 38 publications

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“…1A; Porro et al 2014b). Validation of these interactions in vivo and in vitro (Porro et al 2014b) suggest that: (i) RNA binding to LSD1 is important at dysfunctional telomeres, and that (ii) TERRA may scaffold chromatin modifying enzyme complexes in a manner that is similar to other chromatin-associated lncRNAs such as HOTAIR and Xist (Tsai et al 2010;Engreitz et al 2014;Porro et al 2014b;Somarowthu et al 2015). Taken together, these data support a role for TERRA in recruiting proteins to modulate heterochromatin formation at chromosome ends.…”

Section: Introductionmentioning

confidence: 75%

G-quadruplex RNA binding and recognition by the lysine-specific histone demethylase-1 enzyme

Hirschi

Martin

Luka

et al. 2016

RNA

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Lysine-specific histone demethylase 1 (LSD1) is an essential epigenetic regulator in metazoans and requires the co-repressor element-1 silencing transcription factor (CoREST) to efficiently catalyze the removal of mono-and dimethyl functional groups from histone 3 at lysine positions 4 and 9 (H3K4/9). LSD1 interacts with over 60 regulatory proteins and also associates with lncRNAs (TERRA, HOTAIR), suggesting a regulatory role for RNA in LSD1 function. We report that a stacked, intramolecular G-quadruplex (GQ) forming TERRA RNA (GG[UUAGGG] 8 UUA) binds tightly to the functional LSD1-CoREST complex (K d ≈ 96 nM), in contrast to a single GQ RNA unit ([UUAGGG] 4 U), a GQ DNA ([TTAGGG] 4 T), or an unstructured single-stranded RNA. Stabilization of a parallel-stranded GQ RNA structure by monovalent potassium ions (K + ) is required for high affinity binding to the LSD1-CoREST complex. These data indicate that LSD1 can distinguish between RNA and DNA as well as structured versus unstructured nucleotide motifs. Further, cross-linking mass spectrometry identified the primary location of GQ RNA binding within the SWIRM/amine oxidase domain (AOD) of LSD1. An ssRNA binding region adjacent to this GQ binding site was also identified via X-ray crystallography. This RNA binding interface is consistent with kinetic assays, demonstrating that a GQ-forming RNA can serve as a noncompetitive inhibitor of LSD1-catalyzed demethylation. The identification of a GQ RNA binding site coupled with kinetic data suggests that structured RNAs can function as regulatory molecules in LSD1-mediated mechanisms.

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Section: Introductionmentioning

confidence: 75%

G-quadruplex RNA binding and recognition by the lysine-specific histone demethylase-1 enzyme

Hirschi

Martin

Luka

et al. 2016

RNA

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“…The 5 ′ domain of HOTAIR RNA (Rinn et al 2007), which was previously suggested to be responsible for the recruitment of PRC2 (Tsai et al 2010), has poor sequence conservation (Schorderet and Duboule 2011) but high structural conservation as inferred from covariation (Somarowthu et al 2015). The A-repeat in Xist and RepA RNA is evolutionary conserved (Nesterova et al 2001;Maenner et al 2010).…”

Section: Evolutionary Conservationmentioning

confidence: 99%

“…Protein recruitment by lncRNAs www.rnajournal.org 2015 in multiple studies (Davidovich et al 2013(Davidovich et al , 2014(Davidovich et al , 2015Wu et al 2013;Cifuentes-Rojas et al 2014;Somarowthu et al 2015) and will be valuable tools to rigorously test putative RNA-binding motifs for PRC2, if these are identified.…”

Section: Quantification Of Binding Specificitymentioning

confidence: 99%

“…A portion of this RNA, containing 89 nt, was later suggested to represent a highly structured minimal binding motif for PRC2 (Wu et al 2013). Yet, a large part of these 89 nt was later shown to form base pairs with nucleotides external to this region (Somarowthu et al 2015), therefore complicating their previous assignment as the minimal motif. PRC2 binds the entire 5 ′ domain of HOTAIR that is required for a stable fold and its partial 300-nt fragment with affinity differences of only twofold (Somarowthu et al 2015), as could be expected simply given their size difference (see above).…”

Section: Considering Rna Motifs For Prc2 Bindingmentioning

confidence: 99%

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The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2

Davidovich

Cech

2015

RNA

261

224

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Polycomb repressive complex-2 (PRC2) is a histone methyltransferase required for epigenetic silencing during development and cancer. Among chromatin modifying factors shown to be recruited and regulated by long noncoding RNAs (lncRNAs), PRC2 is one of the most studied. Mammalian PRC2 binds thousands of RNAs in vivo, and it is becoming a model system for the recruitment of chromatin modifying factors by RNA. Yet, well-defined PRC2-binding motifs within target RNAs have been elusive. From the protein side, PRC2 RNA-binding subunits contain no known RNA-binding domains, complicating functional studies. Here we provide a critical review of existing models for the recruitment of PRC2 to chromatin by RNAs. This discussion may also serve researchers who are studying the recruitment of other chromatin modifiers by lncRNAs.

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“…By resolving this, a deeper insight into the molecular properties that are required for the lncRNA to mediate these interactions and its functions, is revealed. For example, by combining the structures of SHAPE [66], DMS [67] and terbium structure probing [68], it has been shown that Hotair forms intricate structural modules that are essential in binding to PRC2 to carry out its function [69]. Coolair is another lncRNA with a complex structure that includes multi-helix junctions and two right-hand turn motifs, which appear to impact its function [70].…”

Section: Determining the Mechanism Of Lncrna Functionmentioning

confidence: 99%

The emerging molecular biology toolbox for the study of long noncoding RNA biology

et al. 2017

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Long noncoding RNAs (lncRNAs) have been implicated in many biological processes. However, due to the unique nature of lncRNAs and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lncRNAs are being discovered and the assignment of biological function to these transcripts. Here we present a molecular biology toolbox equipped to help dissect aspects of lncRNA biology and reveal functionality. We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lncRNA candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely. This involves the use of imaging-based strategies to validate these candidates and observe the behaviors of these transcripts at single molecule resolution in individual cells. We also describe the use of gene editing tools and interactome capture techniques to interrogate functionality and infer mechanism, respectively. With the emergence of lncRNAs as important molecules in healthy and diseased cellular function, it remains crucial to deepen our understanding of their biology. One of the greatest challenges in modern day genomics is ascribing function to genes and genetic elements. It has become apparent that most of the human genome is pervasively transcribed, but less than 2% of these outputs are putatively functional RNAs that encode for proteins [1][2][3][4]. The functions of the remaining proportion of the transcriptome and the genomic regions from which they arise, mostly remain uncharacterized and make up the 'dark matter' of the genome. With the advent and development of RNA deep sequencing technologies, long noncoding RNAs (lncRNAs) have been revealed to emanate from these dark regions of the genome [5]. For a long time, the biological utility of these transcripts remained unknown and highly controversial, with many believing that they were functionless due to their lack of any protein-coding potential. In short, they were thought to simply be the result of transcriptional noise. This skepticism was further compounded by evidence pointing to the poor specificity of RNA PolII binding and transcription initiation, their low abundance and poor conservation [6][7][8]. However, over the last decade, several examples of well-studied lncRNAs have been identified that show they are indeed functional molecules and play important roles in many biological processes [5].LncRNAs are generally products of RNA PolII activity and are arbitrarily defined as being greater than 200 nucleotides in length [9]. These transcripts can arise from genomic regions that intervene (lincRNAs) or are within protein-coding genes (i.e., introns, overlapping exons, antisense transcripts) as well as enhancer regions and promoter regions [5]. Nascent lncRNA transcripts undergo post-transcriptional modifications resulting in products that are capped at the 5 -end and often spliced and polyadenylated [9]. Furthermore, cert...

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HOTAIR Forms an Intricate and Modular Secondary Structure

Cited by 291 publications

References 38 publications

G-quadruplex RNA binding and recognition by the lysine-specific histone demethylase-1 enzyme

G-quadruplex RNA binding and recognition by the lysine-specific histone demethylase-1 enzyme

The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2

The emerging molecular biology toolbox for the study of long noncoding RNA biology

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