COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

Hawkes, Emily; Hennelly, Scott P.; Novikova, Irina; Irwin, Judith A.; Dean, Caroline; Sanbonmatsu, Karissa Y.

doi:10.1016/j.celrep.2016.08.045

Cited by 133 publications

(134 citation statements)

References 47 publications

(68 reference statements)

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“…These results were reproducible across multiple RNAs and multiple target cell types. Importantly, recent work from numerous laboratories has used various SHAPE reagents in vitro, with results validated by a number of orthogonal techniques (Somarowthu et al 2015;Guo and Bartel 2016;Hawkes et al 2016;Pirakitikulr et al 2016). These published examples and our head-to-head comparison of SHAPE electrophiles provide clear and direct evidence that in vitro the reagents are largely equivalent.…”

Section: Resultsmentioning

confidence: 61%

Comparison of SHAPE reagents for mapping RNA structures inside living cells

Lee

Flynn

Kadina

et al. 2016

RNA

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Recent advances in SHAPE technology have converted the classic primer extension method to next-generation sequencing platforms, allowing transcriptome-level analysis of RNA secondary structure. In particular, icSHAPE and SHAPE-MaP, using NAI-N 3 and 1M7 reagents, respectively, are methods that claim to measure in vivo structure with high-throughput sequencing. However, these compounds have not been compared on an unbiased, raw-signal level. Here, we directly compare several in vivo SHAPE acylation reagents using the simple primer extension assay. We conclude that while multiple SHAPE technologies are effective at measuring purified RNAs in vitro, acylimidazole reagents NAI and NAI-N 3 give markedly greater signals with lower background than 1M7 for in vivo measurement of the RNA structurome.

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Section: Resultsmentioning

confidence: 61%

Comparison of SHAPE reagents for mapping RNA structures inside living cells

Lee

Flynn

Kadina

et al. 2016

RNA

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“…FLC reduction is associated with induction of long noncoding RNA (lncRNA) transcripts, both sense and antisense to FLC (Kim et al ., ). Antisense COOLAIR is a highly structured molecule (Hawkes et al ., ) that coats and downregulates the FLC locus upon cold exposure (Rosa et al ., ). Sense lncRNA COLDWRAP forms a repressive intragenic chromatin loop, whereas COLDAIR facilitates recruitment of Polycomb Repressive Complex 2 (PRC2) to FLC (Kim & Sung, ; Kim et al ., ).…”

Section: Convergence At Transcriptional Hubsmentioning

confidence: 99%

Light and temperature cues: multitasking receptors and transcriptional integrators

Casal

Qüesta

2017

New Phytologist

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Contents Summary1029I.Introduction1029II.Convergence at the receptor1030III.Convergence at transcriptional hubs1031IV.Convergence involving clock components1033V.Conclusions1033Acknowledgements1033References1033 Summary The combined information provided by light and temperature cues helps to optimise plant body architecture and physiology. Plants possess elaborate systems to sense and respond to these stimuli. Simultaneous perception of light and temperature by dual receptors such as phytochrome B and phototropin leads to immediate signalling convergence. Conversely, cue asynchronies initiate separate pathways and the information of the earliest cue is stored, awaiting the arrival of the later cue to control transcription. Storage mechanisms can involve changes in the activity of selected clock components or epigenetic modifications, depending on the time delay between cues (hours, days or several months). We propose a conceptual framework in which the mechanisms of integration relate to the timing of cue sensing.

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“…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]. By developing a picture of the partners that interact with lncRNAs, their mechanism of function can be inferred and further tested, through the removal or occlusion of the interacting domains, as revealed by the structure of the lncRNA.…”

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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COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

Cited by 133 publications

References 47 publications

Comparison of SHAPE reagents for mapping RNA structures inside living cells

Comparison of SHAPE reagents for mapping RNA structures inside living cells

Light and temperature cues: multitasking receptors and transcriptional integrators

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

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