The glucocorticoid receptor DNA-binding domain recognizes RNA hairpin structures with high affinity

Parsonnet, Nicholas Victor; Lammer, Nickolaus C.; Holmes, Zachariah E; Batey, Robert T.; Wuttke, Deborah S.

doi:10.1093/nar/gkz486

Cited by 30 publications

(79 citation statements)

References 96 publications

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“…hnRNPK participates in a broad range of biological processes, and this wide-spread participation is believed to be achieved through its direct interaction with a range of cellular RNAs that share the common characteristic of being cytosine rich ( 20 , 29 , 54 ). To determine if these interactions are indeed direct, as well as to characterize the range of affinities that define these interactions, we curated and created a set of hnRNPK-relevant RNAs as well as two unrelated control RNAs to test in vitro ( 43 , 55 ). These hnRNPK-relevant RNAs include elements from mouse Xist and other lncRNAs, several mRNAs ( 19 , 29 , 31 ), a nuclear enriched RNA motif ( 54 ), and two variations of a consensus motif generated in a yeast three-hybrid study that contain differential cytosine content ( 19 ) (Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

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hnRNPK recognition of the B motif of Xist and other biological RNAs

Nakamoto

Lammer

Batey

et al. 2020

Nucleic Acids Research

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Heterogeneous nuclear ribonuclear protein K (hnRNPK) is an abundant RNA-binding protein crucial for a wide variety of biological processes. While its binding preference for multi-cytosine-patch (C-patch) containing RNA is well documented, examination of binding to known cellular targets that contain C-patches reveals an unexpected breadth of binding affinities. Analysis of in-cell crosslinking data reinforces the notion that simple C-patch preference is not fully predictive of hnRNPK localization within transcripts. The individual RNA-binding domains of hnRNPK work together to interact with RNA tightly, with the KH3 domain being neither necessary nor sufficient for binding. Rather, the RG/RGG domain is implicated in providing essential contributions to RNA-binding, but not DNA-binding, affinity. hnRNPK is essential for X chromosome inactivation, where it interacts with Xist RNA specifically through the Xist B-repeat region. We use this interaction with an RNA motif derived from this B-repeat region to determine the RNA-structure dependence of C-patch recognition. While the location preferences of hnRNPK for C-patches are conformationally restricted within the hairpin, these structural constraints are relieved in the absence of RNA secondary structure. Together, these results illustrate how this multi-domain protein's ability to accommodate and yet discriminate between diverse cellular RNAs allows for its broad cellular functions.

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Section: Resultsmentioning

confidence: 99%

“…Purified RNA was 3′-end-labeled with fluorescein-5-thiosemicarbazide (FTSC) to perform fluorescence anisotropy binding assays using a previously published protocol ( 43 ). At typical labeling efficiencies we obtain good signal to noise for the use of RNA in binding assays at concentrations between 1 and 3 nM.…”

Section: Methodsmentioning

confidence: 99%

hnRNPK recognition of the B motif of Xist and other biological RNAs

Nakamoto

Lammer

Batey

et al. 2020

Nucleic Acids Research

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“…The GR recognizes and binds to the GRE in chromatin as a dimer [75]. As opposed to dimeric recognition of dsDNA, GR-DBD binds to RNA as a monomer and confers high affinity primarily through electrostatic contacts [76]. This contrast in how the GR recognizes dsDNA and the GAS5 stem (Figure 2) needs to be explored in more detail, including using an approach like SHAPE-MaP [77] to experimentally explore the two-dimensional folding of the GAS5 riborepressor, which currently is only backed by bioinformatics (i.e., folding algorithms, as in Figure 2).…”

Section: The Role Of Gas5 Lncrna As An Rna Mimic Of the Glucocortimentioning

confidence: 99%

The Growth-Arrest-Specific (GAS)-5 Long Non-Coding RNA: A Fascinating lncRNA Widely Expressed in Cancers

Goustin

Thepsuwan

Kosir

et al. 2019

ncRNA

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Long non-coding RNA (lncRNA) genes encode non-messenger RNAs that lack open reading frames (ORFs) longer than 300 nucleotides, lack evolutionary conservation in their shorter ORFs, and do not belong to any classical non-coding RNA category. LncRNA genes equal, or exceed in number, protein-coding genes in mammalian genomes. Most mammalian genomes harbor ~20,000 protein-coding genes that give rise to conventional messenger RNA (mRNA) transcripts. These coding genes exhibit sweeping evolutionary conservation in their ORFs. LncRNAs function via different mechanisms, including but not limited to: (1) serving as “enhancer” RNAs regulating nearby coding genes in cis; (2) functioning as scaffolds to create ribonucleoprotein (RNP) complexes; (3) serving as sponges for microRNAs; (4) acting as ribo-mimics of consensus transcription factor binding sites in genomic DNA; (5) hybridizing to other nucleic acids (mRNAs and genomic DNA); and, rarely, (6) as templates encoding small open reading frames (smORFs) that may encode short proteins. Any given lncRNA may have more than one of these functions. This review focuses on one fascinating case—the growth-arrest-specific (GAS)-5 gene, encoding a complicated repertoire of alternatively-spliced lncRNA isoforms. GAS5 is also a host gene of numerous small nucleolar (sno) RNAs, which are processed from its introns. Publications about this lncRNA date back over three decades, covering its role in cell proliferation, cell differentiation, and cancer. The GAS5 story has drawn in contributions from prominent molecular geneticists who attempted to define its tumor suppressor function in mechanistic terms. The evidence suggests that rodent Gas5 and human GAS5 functions may be different, despite the conserved multi-exonic architecture featuring intronic snoRNAs, and positional conservation on syntenic chromosomal regions indicating that the rodent Gas5 gene is the true ortholog of the GAS5 gene in man and other apes. There is no single answer to the molecular mechanism of GAS5 action. Our goal here is to summarize competing, not mutually exclusive, mechanistic explanations of GAS5 function that have compelling experimental support.

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“…In a recent study, Parsonnete et al [184] describes the physical association of both GRwt and GRdim protein with non-coding RNA hairpin structures via the DBD of the receptor. Additionally, Parsonnete et al [184] illustrates that the GRwt binds to the RNA as a monomer and that the Gas5 hairpin RNA, an RNA repressor of the GR [185,186], competes for GRwt binding, with dsDNA containing a consensus GRE with a binding affinity that is in the same range.…”

Section: Grα Downregulation and Receptor Conformationmentioning

confidence: 99%

Acquired Glucocorticoid Resistance Due to Homologous Glucocorticoid Receptor Downregulation: A Modern Look at an Age-Old Problem

Spies

Verhoog

Louw

2021

Cells

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For over 70 years, the unique anti-inflammatory properties of glucocorticoids (GCs), which mediate their effects via the ligand-activated transcription factor, the glucocorticoid receptor alpha (GRα), have allowed for the use of these steroid hormones in the treatment of various autoimmune and inflammatory-linked diseases. However, aside from the onset of severe side-effects, chronic GC therapy often leads to the ligand-mediated downregulation of the GRα which, in turn, leads to a decrease in GC sensitivity, and effectively, the development of acquired GC resistance. Although the ligand-mediated downregulation of GRα is well documented, the precise factors which influence this process are not well understood and, thus, the development of an acquired GC resistance presents an ever-increasing challenge to the pharmaceutical industry. Recently, however, studies have correlated the dimerization status of the GRα with its ligand-mediated downregulation. Therefore, the current review will be discussing the major role-players in the homologous downregulation of the GRα pool, with a specific focus on previously reported GC-mediated reductions in GRα mRNA and protein levels, the molecular mechanisms through which the GRα functional pool is maintained and the possible impact of receptor conformation on GC-mediated GRα downregulation.

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The glucocorticoid receptor DNA-binding domain recognizes RNA hairpin structures with high affinity

Cited by 30 publications

References 96 publications

hnRNPK recognition of the B motif of Xist and other biological RNAs

hnRNPK recognition of the B motif of Xist and other biological RNAs

The Growth-Arrest-Specific (GAS)-5 Long Non-Coding RNA: A Fascinating lncRNA Widely Expressed in Cancers

Acquired Glucocorticoid Resistance Due to Homologous Glucocorticoid Receptor Downregulation: A Modern Look at an Age-Old Problem

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