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| Schematic of Xist interacting proteins. (A) Factors involved in the establishment of Xist silencing. These include Ncor/histone deacetylase-interacting proteins, and LBR, which tethers the inactive chromosome to the nuclear periphery allowing Xist to spread into active genes. (B) Factors involved in Xist-mediated maintenance of gene silencing. PRC1 (mediating H2A119ub) and PRC2 (mediating H3K27me3) complexes are recruited by Xist. (C) Proteins mediating Xist spreading: SAf-A, CIZ1 and YY1. (D) Proteins implicated in RNA methylation and early gene-silencing.
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Recent experimental evidence indicates that lncRNAs can act as regulatory molecules in the context of development and disease. Xist, the master regulator of X chromosome inactivation, is a classic example of how lncRNAs can exert multi-layered and fine-tuned regulatory functions, by acting as a molecular scaffold for recruitment of distinct protein...
Contexts in source publication
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... controversial is the interaction between certain subunits of the Polycomb2 (PRC2) complex (i.e., Ezh2 and Suz12) and Xist RNA ( Figure 3B). In fact, literature reports evidence arguing in favor ( Zhao et al., 2008;Kanhere et al., 2010) and against (Cerase et al., 2014;Almeida et al., 2017;Pintacuda et al., 2017) the idea that such interactions occur, or are critical, for PRC2 recruitment on the Xi. ...
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... consideration must be taken into account when critically assessing the lack of secondary structures reported through genome-sequencing based techniques. Nevertheless, the conservation of the B-repeats among mammals implies functionality, as recently confirmed in studies showing their role in binding to the nuclear matrix protein hnRNPK ( Chu et al., 2015;Cirillo et al., 2016), and in recruiting the Polycomb repressive complex 1 (PRC1) to Xist-bound chromatin (da Rocha et al., 2014;Almeida et al., 2017;Pintacuda et al., 2017) (Figure 3B). ...
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... et al. have highlighted the functional relevance of this repetitive region, using LNAs complementary to Xist C-repeat region, and showing a defect in localization of Xist, which was attributed to loss of binding of hnRNPU/Saf-A and YY1 (Sarma et al., 2010). Indeed, targeting the LNA-4978 to the Xist C-repeats is predicted to completely disrupt its structure and displace Xist from chromatin ( Figure 3C). ...
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... to the authors of the study, Xist localization and Xi positioning, result in the proper establishment of gene-silencing and its stabilization, respectively . However, it is likely that more factors, including SAF-A, are needed for Xist localization to the nuclear periphery or the nucleolus ( Figure 3A). ...
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... was one of the first characterized factors reported to accumulate on the Xi and directly interact with Xist RNA ( Helbig and Fackelmayer, 2003;Hasegawa et al., 2010). Under particular experimental conditions, SAF-A was shown to be both sufficient and necessary for Xist spreading over the Xi and, consequently, for Xist-mediated gene silencing ( Cerase et al., 2015;McHugh et al., 2015) ( Figure 3C). It is possible-however-that more factors are needed for Xist spreading along the Xi territory. ...
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... could mediate recruitment of YTHDC1, a known reader of methylated RNA, and consequent transcriptional silencing through a yet-undefined mechanism ( Figure 3D) (Patil et al., 2016). In the future, it will be crucial to clarify the contribution of m6A, as well as of other RNA modifications, to Xist structure(s). ...
Citations
... Other isoforms were specific to the primed or naive contexts and differed in their first and last exon. Importantly, all isoforms were produced from the same TSS and harbored all six repeat elements (A-F) important for XIST function and localization (Extended Data Fig. 3f) 31 . Altogether, these data reveal that XIST establishes distinct contacts on dampened and inactive X chromosomes, in line with the distinct activities of XIST in naive and primed pluripotent contexts. ...
XIST (X-inactive specific transcript) long noncoding RNA (lncRNA) is responsible for X chromosome inactivation (XCI) in placental mammals, yet it accumulates on both X chromosomes in human female preimplantation embryos without triggering X chromosome silencing. The XACT (X-active coating transcript) lncRNA coaccumulates with XIST on active X chromosomes and may antagonize XIST function. Here, we used human embryonic stem cells in a naive state of pluripotency to assess the function of XIST and XACT in shaping the X chromosome chromatin and transcriptional landscapes during preimplantation development. We show that XIST triggers the deposition of polycomb-mediated repressive histone modifications and dampens the transcription of most X-linked genes in a SPEN-dependent manner, while XACT deficiency does not significantly affect XIST activity or X-linked gene expression. Our study demonstrates that XIST is functional before XCI, confirms the existence of a transient process of X chromosome dosage compensation and reveals that XCI and dampening rely on the same set of factors.
... A small number of these lncRNAs that have been previously linked to particular biological pathways were also detected in the placenta, skin, colon, small intestine, and heart (Table 2). Secondary structures within these pathway-associated lncRNAs have previously been shown to coordinate lncRNA-protein interactions, highlighting their importance for function (Ghosh et al. 2022;Pintacuda et al. 2017;Simko et al. 2020;Uroda et al. 2019). Additionally, the formation of a DNA G4 in the H19 gene has been shown to regulate transcription of the H19 lncRNA with functional consequences (Fukuhara et al. 2017). ...
Secondary structure is a principal determinant of lncRNA function, predominantly regarding scaffold formation and interfaces with target molecules. Noncanonical secondary structures that form in nucleic acids have known roles in regulating gene expression and include G-quadruplexes (G4s), intercalated-motifs (iMs), and R-loops (RLs). In this paper, we utilized computational tools G4-iM Grinder and QmRLFS-finder to predict the formation of each of these structures throughout the lncRNA transcriptome in comparison to protein-coding transcripts. The importance of the predicted structures in lncRNA in biological contexts was assessed by combining our results with publicly available lncRNA tissue expression data followed by pathway analysis. The formation of predicted G4 (pG4) and iM (piM) structures in select lncRNA sequences was determined in vitro using biophysical experiments under near-physiological conditions. We found that the majority of the tested pG4s form highly stable G4 structures and identify many previously unreported G4s in biologically important lncRNAs. In contrast, none of the piM sequences were able to form iM structures, consistent with the idea that RNA is unable to form iMs. These C-rich sequences instead formed Z-RNA structures, which have not been previously observed in regions containing cytosine repeats and represent an interesting and under-explored target for protein-RNA interactions. Our results highlight the prevalence and potential structure-associated functions of noncanonical secondary structures in lncRNA and observe G4 and Z-RNA structure formation in many lncRNA sequences for the first time, furthering understanding of the structure-function relationship in lncRNAs.
... In addition, we identified upregulated common genes that may be involved in MLKL function in PD, such as Xist. The long non-coding RNA XIST (X-inactive specific transcripts) is derived from the XIST gene and is a key regulator of cell proliferation and differentiation [52]. A recent study demonstrated that lncRNA XIST sponges miR-199a-3P, thereby enhancing the expression of Sp1 and LRRK2, which accelerates PD progression [53]. ...
... In addition, we identified upregulated common genes that may be involved in MLKL function in PD, such as Xist. The long non-coding RNA XIST (X-inactive specific transcripts) is derived from the XIST gene and is a key regulator of cell proliferation and differentiation [52]. A recent study demonstrated that lncRNA XIST sponges miR-199a-3P, thereby enhancing the expression of Sp1 and LRRK2, which accelerates PD progression [53]. ...
Parkinson’s disease (PD), one of the most devastating neurodegenerative brain disorders, is characterized by the progressive loss of dopaminergic neurons in the substantia nigra (SN) and deposits of α-synuclein aggregates. Currently, pharmacological interventions for PD remain inadequate. The cell necroptosis executor protein
MLKL (Mixed-lineage kinase domain-like) is involved in various diseases, including inflammatory bowel disease
and neurodegenerative diseases; however, its precise role in PD remains unclear. Here, we investigated the neuroprotective role of MLKL inhibition or ablation against primary neuronal cells and human iPSC-derived midbrain organoids induced by toxic α-Synuclein preformed fibrils (PFFs). Using a mouse model (Tg-Mlkl−/−) generated by crossbreeding the SNCA A53T synuclein transgenic mice with MLKL knockout (KO)mice, we assessed the impact of MLKL deficiency on the progression of Parkinsonian traits. Our findings demonstrate that Tg-Mlkl−/− mice exhibited a significant improvement in motor symptoms and reduced phosphorylated α-synuclein expression compared to the classic A53T transgenic mice. Furthermore, MLKL deficiency alleviated tyrosine hydroxylase (TH)-positive neuron loss and attenuated neuroinflammation by inhibiting the activation of microglia and astrocytes. Single-cell RNA-seq (scRNA-seq) analysis of the SN of Tg-Mlkl−/− mice revealed a unique cell type-specific transcriptome profile, including downregulated prostaglandin D synthase (PTGDS) expression, indicating reduced microglial cells and dampened neuron death. Thus, MLKL represents a critical therapeutic target for reducing neuroinflammation and preventing motor deficits in PD.
... Nanobodies have potential to interrupt lncRNA-RNA binding protein (RBP) interaction [122]. Nanobodies can be designed to specifically target structured RNA molecules [123], and since many lncRNAs such as MALAT1 [124], NEAT1 [125], XIST [126], or HOTAIR [127] are well-identified, this approach has a potential to use in GI cancers which those lncRNAs are dysregulated. Inhibition of the target/downstream proteins by functional lncRNA-RBP complexes constructed by RNA decoys or imitators of lncRNAs may also be used for anticancer strategies [128]. ...
Long non-coding RNAs (lncRNAs) play a significant biological role in the regulation of various cellular processes such as cell proliferation, differentiation, apoptosis and migration. In various malignancies, lncRNAs interplay with some main cancer-associated signaling pathways, including the Hippo signaling pathway to regulate the various cellular processes. It has been revealed that the cross-talking between lncRNAs and Hippo signaling pathway involves in gastrointestinal (GI) cancers development and progression. Considering the clinical significance of these lncRNAs, they have also been introduced as potential biomarkers in diagnostic, prognostic and therapeutic strategies in GI cancers. Herein, we review the mechanisms of lncRNA-mediated regulation of Hippo signaling pathway and focus on the corresponding molecular mechanisms and clinical significance of these non-coding RNAs in GI cancers.
... Other isoforms are specific to the primed or naïve contexts and differ in their first and last exon. Importantly, all the isoforms are produced from the same TSS and harbor all 6 repeat elements (A-F) that are important for XIST function and localization (Supplementary Figure 2F) (Pintacuda et al., 2017b). Altogether, these data reveal that XIST establishes distinct contacts on dampened and inactive X chromosomes, in line with distinct activities of XIST in naïve and primed pluripotent contexts. ...
XIST long non-coding RNA is responsible for X chromosome inactivation (XCI) in placental mammals, yet it accumulates on both X chromosomes in human female pre-implantation embryos without triggering X chromosome silencing. The long non-coding RNA XACT co-accumulates with XIST on active Xs and may antagonize XIST function. Here we used human ES cells in a naive state of pluripotency to assess the function of XIST and XACT in shaping the X chromosome chromatin and transcriptional landscapes during pre-implantation development. We show that XIST triggers the deposition of polycomb-mediated repressive histone modifications and attenuates transcription of most X-linked genes in a SPEN-dependent manner, while XACT deficiency does not significantly affect XIST activity or X-linked gene expression. Our study demonstrates that XIST is functional prior to XCI, confirms the existence of a transient process of X chromosome dosage compensation, and reveals that X chromosome inactivation and dampening rely on the same set of factors.
... The formation of RNA secondary structures has been shown to drive the scaffolding activities of lncRNAs [18,96]. In fact, the spatial arrangement achieved through dynamic base-pairing interactions can facilitate interactions of lncRNAs with distinct molecules, thus forming proper ribonucleoprotein hubs for the downstream modulation of gene expression. ...
In recent years, research on long non-coding RNAs (lncRNAs) has gained considerable attention due to the increasing number of newly identified transcripts. Several characteristics make their functional evaluation challenging, which called for the urgent need to combine molecular biology with other disciplines, including bioinformatics. Indeed, the recent development of computational pipelines and resources has greatly facilitated both the discovery and the mechanisms of action of lncRNAs. In this review, we present a curated collection of the most recent computational resources, which have been categorized into distinct groups: databases and annotation, identification and classification, interaction prediction, and structure prediction. As the repertoire of lncRNAs and their analysis tools continues to expand over the years, standardizing the computational pipelines and improving the existing annotation of lncRNAs will be crucial to facilitate functional genomics studies.
... A total of 300 upregulated DEGs and 481 downregulated DEG found in HPV-positive HNSCC samples compared to HPV-negative HNSCC sam Among these DEGs, X Inactive Specific Transcript (XIST) was the most significant regulated. XIST is involved in cell differentiation, cell proliferation, and genome m nance in human cells [33]. Abnormal XIST expression plays a vital role in the occu and development of many cancers [34]. ...
... Among these DEGs, X Inactive Specific Transcript (XIST) was the most significantly upregulated. XIST is involved in cell differentiation, cell proliferation, and genome maintenance in human cells [33]. Abnormal XIST expression plays a vital role in the occurrence and development of many cancers [34]. ...
The pathogenesis of head and neck squamous cell carcinoma (HNSCC) is associated with human papillomavirus (HPV) infection. However, the molecular mechanisms underlying the interactions between HNSCC and HPV remain unclear. Bioinformatics was used to analyze the gene expression dataset of HPV-associated HNSCC based on the Cancer Genome Atlas (TCGA) database. Differentially expressed genes (DEGs) in HPV-positive and HPV-negative HNSCC were screened. Gene function enrichment, protein–protein interactions (PPI), survival analysis, and immune cell infiltration of DEGs were performed. Furthermore, the clinical data of HNSCC tissue samples were analyzed using immunohistochemistry. In total, 194 DEGs were identified. A PPI network was constructed and 10 hub genes (EREG, PLCG1, ERBB4, HBEGF, ZFP42, CBX6, NFKBIA, SOCS1, ATP2B2, and CEND1) were identified. Survival analysis indicated that low expression of SOCS1 was associated with worse overall survival. Immunohistochemistry demonstrated that SOCS1 expression was higher in HPV-negative HNSCC than in HPV-positive HNSCC, and there was a positive correlation between SOCS1 expression and patient survival. This study provides new information on biological targets that may be relevant to the molecular mechanisms underpinning the occurrence and development of HNSCC. SOCS1 may play an important role in the interaction between HPV and HNSCC and serve as a potential biomarker for future therapeutic targets.
... Second, also lncRNA Xist interacts extensively with proteins, although most interactions sites are not yet defined [24,109]. Some Xist motifs that are heavily involved in protein interactions are the so-called A-and E-repeats, regions for which several structural models have been proposed [24,110]. According to the full-length Xist structure described by Smola and colleagues, the structural domains that contain the A and E repeats are dynamic and flexible, but their minimal free energy structure presents a G$U content of 15% and 19% respectively, both higher than the overall content of the entire Xist (12% G$U content) [24] (Table S1, Figs. ...
Long non-coding RNAs (lncRNAs) are recently-discovered transcripts involved in gene expression regulation and associated with diseases. Despite the unprecedented molecular complexity of these transcripts, recent studies of the secondary and tertiary structure of lncRNAs are starting to reveal the principles of lncRNA structural organization, with important functional implications. It therefore starts to be possible to analyze lncRNA structures systematically. Here, using a set of prototypical and medically-relevant lncRNAs of known secondary structure, we specifically catalogue the distribution and structural environment of one of the first-identified and most frequently occurring non-canonical Watson-Crick interactions, the G·U base pair. We compare the properties of G·U base pairs in our set of lncRNAs to those of the G·U base pairs in other well-characterized transcripts, like rRNAs, tRNAs, ribozymes, and riboswitches. Furthermore, we discuss how G·U base pairs in these targets participate in establishing interactions with proteins or miRNAs, and how they enable lncRNA tertiary folding by forming intramolecular or metal-ion interactions. Finally, by identifying highly-G·U-enriched regions of yet unknown function in our target lncRNAs, we provide a new rationale for future experimental investigation of these motifs, which will help obtain a more comprehensive understanding of lncRNA functions and molecular mechanisms in the future.
... In addition, we identi ed upregulated common genes that may be involved in MLKL function in PD, such as Xist. The long noncoding RNA XIST (X-inactive speci c transcripts) is derived from the XIST gene and is a key regulator of cell proliferation and differentiation 52 . A recent study demonstrated that lncRNA XIST sponges miR-199a-3P, thereby enhancing the expression of Sp1 and LRRK2, which accelerates PD progression 53 . ...
Parkinson’s disease (PD), one of the most devastating neurodegenerative brain disorders, is characterized by the progressive loss of dopaminergic neurons in the substantia nigra (SN) and deposits of α-synuclein aggregates. Currently, pharmacological interventions for PD remain inadequate. The cell necroptosis executor protein MLKL (Mixed-lineage kinase domain-like) is involved in various diseases, including inflammatory bowel disease and neurodegenerative diseases; however, its precise role in PD remains unclear. Here, we investigated the neuroprotective role of MLKL inhibition or ablation against neuronal cell death induced by 6-OHDA and TNF-α. Using a mouse model (Tg- Mlkl −/− ) generated by crossbreeding the SNCA A53T synuclein transgenic mice with MLKL knockout (KO)mice, we assessed the impact of MLKL deficiency on the progression of Parkinsonian traits. Our findings demonstrate that Tg- Mlkl −/− mice exhibited a significant improvement in motor symptoms and reduced phosphorylated α-synuclein expression compared to that in the classic A53T transgenic mice. Furthermore, MLKL deficiency alleviated tyrosine hydroxylase (TH)-positive neuron loss and attenuated neuroinflammation by inhibiting the activation of microglia and astrocytes. Single-cell RNA-seq (scRNA-seq) analysis of the SN of Tg- Mlkl −/ − mice revealed a unique cell type-specific transcriptome profile, including downregulated prostaglandin D synthase (PTGDS) expression, indicating reduced microglial cells and dampened neuron death. Thus, MLKL represents a critical therapeutic target for reducing neuroinflammation and preventing motor deficits in PD.
