Function by Structure: Spotlights on Xist Long Non-coding RNA

Pintacuda, Greta; Young, Alexander N.; Cerase, Andrea

doi:10.3389/fmolb.2017.00090

Cited by 88 publications

(84 citation statements)

References 77 publications

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“…In the last few years, a number of Xist partners have been identified, and their specific interaction with one of the repeat modules in Xist has been characterized 6 . This has led to the establishment of a preliminary but highly interesting repeat-to-function correlation through which Xist is beginning to be better understood 15 . Here, we review the latest advances in understanding mouse Xist, highlighting important insights and raising questions that remain unanswered.…”

Section: Introductionmentioning

confidence: 99%

The B-side of Xist

Monfort

Wutz

2020

F1000Res

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Female mammals express the long noncoding X inactivation-specific transcript (Xist) RNA to initiate X chromosome inactivation (XCI) that eventually results in the formation of the Barr body. Xist encompasses half a dozen repeated sequence stretches containing motifs for RNA-binding proteins that recruit effector complexes with functions for silencing genes and establishing a repressive chromatin configuration. Functional characterization of these effector proteins unveils the cooperation of a number of pathways to repress genes on the inactive X chromosome. Mechanistic insights can be extended to other noncoding RNAs with similar structure and open avenues for the design of new therapies to switch off gene expression. Here we review recent advances in the understanding of Xist and on this basis try to synthesize a model for the initiation of XCI.

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Section: Introductionmentioning

confidence: 99%

The B-side of Xist

Monfort

Wutz

2020

F1000Res

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“…These approaches have been especially important for understanding noncoding RNAs such as ribosomal RNAs (Lempereur et al 1985;Moazed et al 1986), spliceosomes (Black and Pinto 1989;Murphy and Cech 1993), and 7SK (Wassarman and Steitz 1991). The development of more sensitive and scalable approaches to RNA probing have made these experiments particularly useful for larger RNAs such as the long noncoding RNA (lncRNA) Xist (Maenner et al 2010;Fang et al 2015;Smola et al 2016;Liu et al 2017;Pintacuda et al 2017), which are not readily amenable to structure determination by other means.…”

Section: Introductionmentioning

confidence: 99%

Carbodiimide reagents for the chemical probing of RNA structure in cells

Wang

Sexton

Culligan

et al. 2018

RNA

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Deciphering the conformations of RNAs in their cellular environment allows identification of RNA elements with potentially functional roles within biological contexts. Insight into the conformation of RNA in cells has been achieved using chemical probes that were developed to react specifically with flexible RNA nucleotides, or the Watson-Crick face of singlestranded nucleotides. The most widely used probes are either selective SHAPE (2 ′ ′ ′ ′ ′ -hydroxyl acylation and primer extension) reagents that probe nucleotide flexibility, or dimethyl sulfate (DMS), which probes the base-pairing at adenine and cytosine but is unable to interrogate guanine or uracil. The constitutively charged carbodiimide N-cyclohexyl-N ′ ′ ′ ′ ′ -(2morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMC) is widely used for probing G and U nucleotides, but has not been established for probing RNA in cells. Here, we report the use of a smaller and conditionally charged reagent, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), as a chemical probe of RNA conformation, and the first reagent validated for structure probing of unpaired G and U nucleotides in intact cells. We showed that EDC demonstrates similar reactivity to CMC when probing transcripts in vitro. We found that EDC specifically reacted with accessible nucleotides in the 7SK noncoding RNA in intact cells. We probed structured regions within the Xist lncRNA with EDC and integrated these data with DMS probing data. Together, EDC and DMS allowed us to refine predicted structure models for the 3 ′ ′ ′ ′ ′ extension of repeat C within Xist. These results highlight how complementing DMS probing experiments with EDC allows the analysis of Watson-Crick base-pairing at all four nucleotides of RNAs in their cellular context.

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“…X‐inactive specific transcript (Xist) is one of the first discovered and most well characterized lncRNAs (Pintacuda, Young, & Cerase, ; Simon et al, ). Xist functions as the major effector of the X chromosome inactivation (XCI) process in mammals and has been implicated in oncogenic processes (Fang, Sun, & Gong, ; Lee & Bartolomei, ; Plath, Mlynarczyk‐Evans, Nusinow, & Panning, ).…”

Section: Underexplored Mammalian Rna Targets For Small Molecule Intermentioning

confidence: 99%

“…Importantly, mutational studies revealed that specific structural domains, namely six tandem hairpin repeats (A–F) are crucial for its function in XCI (Wutz, Rasmussen, & Jaenisch, ). The mechanisms through which individual structural domains and protein interactions mediate the functions of Xist are currently under investigation (Pintacuda et al, ). Structural insights into the A‐ and F‐repeat region (RepA) of Xist by Pyle and co‐workers revealed an intricate tertiary architecture within specific functional modules (Liu et al, ).…”

Section: Underexplored Mammalian Rna Targets For Small Molecule Intermentioning

confidence: 99%

Targeting RNA in mammalian systems with small molecules

2018

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The recognition of RNA functions beyond canonical protein synthesis has challenged the central dogma of molecular biology. Indeed, RNA is now known to directly regulate many important cellular processes, including transcription, splicing, translation, and epigenetic modifications. The misregulation of these processes in disease has led to an appreciation of RNA as a therapeutic target. This potential was first recognized in bacteria and viruses, but discoveries of new RNA classes following the sequencing of the human genome have invigorated exploration of its disease-related functions in mammals. As stable structure formation is evolving as a hallmark of mammalian RNAs, the prospect of utilizing small molecules to specifically probe the function of RNA structural domains and their interactions is gaining increased recognition. To date, researchers have discovered bioactive small molecules that modulate phenotypes by binding to expanded repeats, microRNAs, G-quadruplex structures, and RNA splice sites in neurological disorders, cancers, and other diseases. The lessons learned from achieving these successes both call for additional studies and encourage exploration of the plethora of mammalian RNAs whose precise mechanisms of action remain to be elucidated. Efforts toward understanding fundamental principles of small molecule-RNA recognition combined with advances in methodology development should pave the way toward targeting emerging RNA classes such as long noncoding RNAs. Together, these endeavors can unlock the full potential of small molecule-based probing of RNA-regulated processes and enable us to discover new biology and underexplored avenues for therapeutic intervention in human disease. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA in Disease and Development > RNA in Disease.

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Function by Structure: Spotlights on Xist Long Non-coding RNA

Cited by 88 publications

References 77 publications

The B-side of Xist

The B-side of Xist

Carbodiimide reagents for the chemical probing of RNA structure in cells

Targeting RNA in mammalian systems with small molecules

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