Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors

Przanowska, Roza; Weidmann, Chase A.; Saha, Shekhar; Cichewicz, Magdalena A.; Jensen, Kate; Przanowski, Piotr; Irving, Patrick S; Janes, Kevin A.; Guertin, Michael J.; Weeks, Kevin M.; Dutta, Anindya

doi:10.1016/j.celrep.2022.110361

Cited by 21 publications

(15 citation statements)

References 59 publications

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“…In addition, we conducted detailed analyses of human/mouse sequential homology of lnc-EST12 by analyzing GenBank databases for potential transcripts but could not identify a clear human sequential homolog for this lncRNA. Recently, a large number of studies on mouse lncRNAs have been reported and published [ 22 , 71 – 76 ], and no human/mouse homologies of these lncRNAs have been found in these studies [ 22 , 71 – 76 ]. For example, lncRNA MUNC regulates the transcription of different promyogenic factors in mice [ 71 ]; a novel mouse lncRNA Discn fine-tunes replication protein A (RPA) availability to promote genomic stability [ 72 ]; a mouse long noncoding RNA-lncFAO regulates inflammation resolution by mouse macrophages through fatty acid oxidation activation [ 73 ]; and a mouse macrophage-specific lncRNA-MAARS regulates apoptosis and atherosclerosis by tethering HuR in the nucleus [ 74 ].…”

Section: Discussionmentioning

confidence: 99%

“…Recently, a large number of studies on mouse lncRNAs have been reported and published [ 22 , 71 – 76 ], and no human/mouse homologies of these lncRNAs have been found in these studies [ 22 , 71 – 76 ]. For example, lncRNA MUNC regulates the transcription of different promyogenic factors in mice [ 71 ]; a novel mouse lncRNA Discn fine-tunes replication protein A (RPA) availability to promote genomic stability [ 72 ]; a mouse long noncoding RNA-lncFAO regulates inflammation resolution by mouse macrophages through fatty acid oxidation activation [ 73 ]; and a mouse macrophage-specific lncRNA-MAARS regulates apoptosis and atherosclerosis by tethering HuR in the nucleus [ 74 ]. LncRNAs exhibit low sequence conservation, and most mouse lncRNAs tend not to have sequences homologous to those in humans [ 77 – 81 ]; however, the mouse lncRNA research platform still provides a useful reference for research on human-related diseases [ 22 , 71 – 76 ].…”

Section: Discussionmentioning

confidence: 99%

“…For example, lncRNA MUNC regulates the transcription of different promyogenic factors in mice [ 71 ]; a novel mouse lncRNA Discn fine-tunes replication protein A (RPA) availability to promote genomic stability [ 72 ]; a mouse long noncoding RNA-lncFAO regulates inflammation resolution by mouse macrophages through fatty acid oxidation activation [ 73 ]; and a mouse macrophage-specific lncRNA-MAARS regulates apoptosis and atherosclerosis by tethering HuR in the nucleus [ 74 ]. LncRNAs exhibit low sequence conservation, and most mouse lncRNAs tend not to have sequences homologous to those in humans [ 77 – 81 ]; however, the mouse lncRNA research platform still provides a useful reference for research on human-related diseases [ 22 , 71 – 76 ]. Furthermore, although there have been reports about human lncRNAs with no homologous sequence to that of mouse lncRNAs, there remains a possibility for the existence of similar structures or functions between mouse and human lncRNAs [ 82 ].…”

Section: Discussionmentioning

confidence: 99%

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Lnc-EST12, which is negatively regulated by mycobacterial EST12, suppresses antimycobacterial innate immunity through its interaction with FUBP3

Yao

Xie

et al. 2022

Cell Mol Immunol

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Long noncoding RNAs (lncRNAs) have been implicated in the pathogenesis of intracellular pathogens. However, the role and mechanism of the important lncRNAs in Mycobacterium tuberculosis ( M.tb ) infection remain largely unexplored. Recently, we found that a secreted M.tb Rv1579c (an early secreted target with a molecular weight of 12 kDa, named EST12) protein activates NLRP3-gasdermin D (GSDMD)-mediated pyroptosis and plays a pivotal role in M.tb -induced immunity. In the present study, M.tb and the EST12 protein negatively regulated the expression of a key lncRNA (named lnc-EST12) in mouse macrophages by activating the JAK2-STAT5a signaling pathway. Lnc-EST12, with a size of 1583 bp, is mainly expressed in immune-related organs (liver, lung and spleen). Lnc-EST12 not only reduces the expression of the proinflammatory cytokines IL-1β, IL-6, and CCL5/8 but also suppresses the NLRP3 inflammasome and GSDMD pyroptosis-IL-1β immune pathway through its interaction with the transcription factor far upstream element-binding protein 3 (FUBP3). The KH3 and KH4 domains of FUBP3 are the critical sites for binding to lnc-EST12. Deficiency of mouse lnc-EST12 or FUBP3 in macrophages increased M.tb clearance and inflammation in mouse macrophages or mice. In conclusion, we report a new immunoregulatory mechanism in which mouse lnc-EST12 negatively regulates anti- M.tb innate immunity through FUBP3.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Lnc-EST12, which is negatively regulated by mycobacterial EST12, suppresses antimycobacterial innate immunity through its interaction with FUBP3

Yao

Xie

et al. 2022

Cell Mol Immunol

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“…In this regard, the primary sequence of lncRNAs is only poorly informative of the function of a given lncRNA, and curiously also less conserved than higher-order structures (Johnsson et al, 2014). It is however conceivable that, just alike proteins, lncRNAs may act through discrete, modular functional elements (Przanowska et al, 2022). Recognition of such structural motifs is together the main obstacle and the key to define the exact mechanism of action of lncRNAs.…”

Section: Discussionmentioning

confidence: 99%

MIR205HG/LEADR Long Noncoding RNA Binds to Primed Proximal Regulatory Regions in Prostate Basal Cells Through a Triplex- and Alu-Mediated Mechanism

Bezzecchi¹,

Pagani²,

Forte³

et al. 2022

Front. Cell Dev. Biol.

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Aside serving as host gene for miR-205, MIR205HG transcribes for a chromatin-associated long noncoding RNA (lncRNA) able to restrain the differentiation of prostate basal cells, thus being reannotated as LEADR (Long Epithelial Alu-interacting Differentiation-related RNA). We previously showed the presence of Alu sequences in the promoters of genes modulated upon MIR205HG/LEADR manipulation. Notably, an Alu element also spans the first and second exons of MIR205HG/LEADR, suggesting its possible involvement in target selection/binding. Here, we performed ChIRP-seq to map MIR205HG/LEADR chromatin occupancy at genome-wide level in prostate basal cells. Our results confirmed preferential binding to regions proximal to gene transcription start site (TSS). Moreover, enrichment of triplex-forming sequences was found upstream of MIR205HG/LEADR-bound genes, peaking at −1,500/−500 bp from TSS. Triplexes formed with one or two putative DNA binding sites within MIR205HG/LEADR sequence, located just upstream of the Alu element. Notably, triplex-forming regions of bound genes were themselves enriched in Alu elements. These data suggest, from one side, that triplex formation may be the prevalent mechanism by which MIR205HG/LEADR selects and physically interacts with target DNA, from the other that direct or protein-mediated Alu (RNA)/Alu (DNA) interaction may represent a further functional requirement. We also found that triplex-forming regions were enriched in specific histone modifications, including H3K4me1 in the absence of H3K27ac, H3K4me3 and H3K27me3, indicating that in prostate basal cells MIR205HG/LEADR may preferentially bind to primed proximal regulatory elements. This may underscore the need for basal cells to keep MIR205HG/LEADR target genes repressed but, at the same time, responsive to differentiation cues.

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“…LncRNAs can have a variety of regulatory mechanisms depending on its localization in the cell. In the nucleus, lncRNAs can act molecular scaffolds or decoys so as to bind regulatory elements or they can recruit transcription factors to mediate gene transcription ( 37 – 40 ). In the cytoplasm, lncRNAs can act as ceRNAs to competitively bind to miRNAs, thereby reducing their inhibitory effects on target gene ( 41 – 45 ).…”

Section: Discussionmentioning

confidence: 99%

Buffalo long non-coding RNA gene11007 promotes myoblasts proliferation

Zhang

Xu²,

Sun³

et al. 2022

Front. Vet. Sci.

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Buffalo meat is of good quality because it is lean and tender, and could bring significant cardiovascular benefits. The underlying difference in muscle development and meat quality is a complex and precisely orchestrated process which has been demonstrated to be regulated by long non-coding RNAs (lncRNAs). However, the regulatory role of lncRNAs in the growth and development of buffalo skeletal muscle is still unclear. In this study, the Ribo-Zero RNA-Seq method was used to explore the lncRNA expression profiles of buffalo myoblasts during the proliferation and differentiation phases. A specific set of 9,978 lncRNAs was found. By comparing the expression profiles of lncRNAs, it was found that there were 1,576 differentially expressed lncRNAs (DELs) during buffalo myoblast differentiation. Twelve DELs were chosen and subsequently verified in eight different buffalo tissues during fetal and adult stages by using qPCR. Gene11007 was found to be one of the most down-regulated lncRNAs during buffalo myoblasts differentiation and it was subsequently characterized. EdU, CCK-8, qPCR and western blotting assays showed that gene11007 promoted the proliferation of buffalo myoblasts but it had no effect on cell differentiation. Our research may enrich the genome annotations of buffalo and provide a new molecular target for the in-depth understanding of the regulation of lncRNAs in skeletal muscle.

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Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors

Cited by 21 publications

References 59 publications

Lnc-EST12, which is negatively regulated by mycobacterial EST12, suppresses antimycobacterial innate immunity through its interaction with FUBP3

Lnc-EST12, which is negatively regulated by mycobacterial EST12, suppresses antimycobacterial innate immunity through its interaction with FUBP3

MIR205HG/LEADR Long Noncoding RNA Binds to Primed Proximal Regulatory Regions in Prostate Basal Cells Through a Triplex- and Alu-Mediated Mechanism

Buffalo long non-coding RNA gene11007 promotes myoblasts proliferation

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