FUS-dependent loading of SUV39H1 to OCT4 pseudogene-lncRNA programs a silencing complex with OCT4 promoter specificity

Scarola, Michele; Comisso, Elisa; Rosso, Massimo; Sal, Giannino Del; Schneider, Claudio; Schoeftner, Stefan; Benetti, Roberta

doi:10.1038/s42003-020-01355-9

Cited by 4 publications

(3 citation statements)

References 46 publications

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“…The pioneer transcription factor CBP also binds RNAs, including those transcribed from enhancers, to stimulate histone acetylation and consequently transcription 276 . Some transcription factors (OCT4, NANOG, SOX2 and SOX9) are also regulated by lncRNAs, including pseudogene-derived lncRNAs [277][278][279][280][281] , and reciprocally regulate the expression of lncRNAs 282 . Enhancer-derived lncRNAs also regulate the expression of the nuclear hormone receptor ESR1 (ref.…”

Section: Control Of Chromatin Architecturementioning

confidence: 99%

Long non-coding RNAs: definitions, functions, challenges and recommendations

Mattick

Amaral

Carninci

et al. 2023

Nat Rev Mol Cell Biol

857

384

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Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease. Sections Consensus statement Purpose of this Consensus StatementIn this Consensus Statement we present a current and coherent picture of the roles of lncRNAs in cell and developmental biology, identify the key issues in understanding their functions and chart the path forward. We address lncRNA definition, nomenclature, conservation, expression, phenotypic visibility, functional assays and molecular mechanisms encompassing lncRNA connections to chromatin architecture, epigenetic processes, enhancer function and biomolecular condensates, as well as the roles of lncRNAs outside the nucleus. We argue that loci expressing lncRNAs should be recognized as bona fide genes and discuss lncRNA structure-function relationships as the means to parse mechanisms and pathways. Finally, we identify the current challenges and offer recommendations for understanding the relationship of lncRNAs to genome architecture, gene regulation and cellular organization.The authors of this Consensus Statement were suggested by recommendations of colleagues. Consensus was reached by group e-mail and discussion. Definition and nomenclature of lncRNAslncRNAs have been arbitrarily defined as non-coding transcripts of more than 200 nucleotides (200 nt), which is a convenient size cutoff in biochemical and biophysical RNA purification protocols that deplete most infrastructural RNAs, such as 5S rRNAs, tRNAs, snRNAs and snoRNAs, as well as miRNAs, siRNAs and piRNAs 23 . This definition also excludes some other well-known short RNAs such as the primatespecific snaRs (~80-120 nt), which associate with nuclear factor 90 (ref. 24); Y ...

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Section: Control Of Chromatin Architecturementioning

confidence: 99%

Long non-coding RNAs: definitions, functions, challenges and recommendations

Mattick

Amaral

Carninci

et al. 2023

Nat Rev Mol Cell Biol

857

384

View full text Add to dashboard Cite

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“…A study has shown that circFndc3b interacted with RNA-binding protein FUS in sarcomas to decrease FUS level, thereby upregulating vascular endothelial growth factor (VEGFA) expression and activating VEGFA signaling [ 29 ]. FUS could interact with downstream mRNA to silence its expression [ 30 ]. In the present study, lncRNA HOTAIR bound to FUS and negatively regulated its expression.…”

Section: Discussionmentioning

confidence: 99%

HOTAIR regulates SIRT3-mediated cardiomyocyte survival after myocardial ischemia/reperfusion by interacting with FUS

Liu

Sun

Wang

et al. 2023

BMC Cardiovasc Disord

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Background Myocardial ischemia/reperfusion (I/R) contributes to serious myocardial injury and even death. Therefore, prevention and mitigation of myocardial I/R is particularly important. LncRNA HOTAIR has been reported to be implicated in myocardial I/R progression. However, the detailed molecular mechanism of HOTAIR in cardiomyocyte was explored in myocardial I/R. Methods Firstly, cell model of myocardial I/R was established through hypoxia/reoxygenation (H/R). Apoptosis and cell cycle were evaluated utilizing flow cytometry. The corresponding test kits were conducted to monitor the levels of LDH, Caspase3 and Caspase9. The gene expression and protein levels were detected by qPCR and western blot, respectively. RNA pull-down and RIP were performed to verify the interaction between FUS and lncRNA HOTAIR. Results In AC16 cardiomyocytes treated with H/R, lncRNA HOTAIR and SIRT3 expression were obviously decreased. Overexpression of HOTAIR or SIRT3 could ameliorate H/R-induced cardiomyocyte injury by promoting cell viability, lowering LDH levels, and suppressing cell apoptosis. Further, lncRNA HOTAIR upregulated the expression of SIRT3 via interacting with FUS, thereby promoting the survival of H/R-injured cardiomyocytes. Conclusion LncRNA HOTAIR can improve myocardial I/R by affecting cardiomyocyte survival through regulation of SIRT3 by binding to the RNA binding protein FUS.

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“…The OCT4-encoding gene POU5F1 has 8 pseudogenes ( hPOU5F1P1-8 ) in Homo sapiens and 5 pseudogenes ( mPOU5F1P1-5 ) in Mus musculus [ 16 ]. Scarola et al [ 16 , 17 ] reported that OCT4-pg4 (transcript of mPou5F1P4 ) can change its spatial conformation by recruiting the RNA-binding protein FUS, exposing specific functional domains and binding to histone methyltransferase SUV39H1 to form the mOCT4P4-FUS-SUV39H1 complex, which then targeted the OCT4 promoter region, promoted H3K9me3 and inhibited OCT4 expression. Parental OCT4 does not have the ability to bind FUS and SUV39H1 to further regulate its transcription.…”

Section: Lncrnas Regulate Oct4 Expression At the Transcriptional Levelmentioning

confidence: 99%

The roles of long noncoding RNAs in the regulation of OCT4 expression

Zhou

Zeng

2022

Stem Cell Res Ther

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OCT4 is a major transcription factor that maintains the pluripotency of stem cells, including embryonic stem cells, induced pluripotent stem cells and cancer stem cells. An increasing number of long noncoding RNAs have been reported to participate in the regulation of OCT4 expression through various mechanisms, including binding with the OCT4 gene promoter to regulate local methylation; promoting chromosomal spatial folding to form an inner ring, thereby aggregating OCT4 cis-acting elements scattered in discontinuous sites of the chromosome; competitively binding microRNAs with OCT4 to upregulate OCT4 expression at the posttranscriptional level; and sharing a promoter with OCT4. Moreover, the transcription of some long noncoding RNAs is regulated by OCT4, and certain long noncoding RNAs form feedback regulatory loops with OCT4. In this review, we summarized the research progress of the long noncoding RNAs involved in the regulation of OCT4 expression.

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FUS-dependent loading of SUV39H1 to OCT4 pseudogene-lncRNA programs a silencing complex with OCT4 promoter specificity

Cited by 4 publications

References 46 publications

Long non-coding RNAs: definitions, functions, challenges and recommendations

Long non-coding RNAs: definitions, functions, challenges and recommendations

HOTAIR regulates SIRT3-mediated cardiomyocyte survival after myocardial ischemia/reperfusion by interacting with FUS

The roles of long noncoding RNAs in the regulation of OCT4 expression

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