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SMaRT lncRNA controls translation of a G-quadruplex containing mRNA antagonizing the DHX36 helicase

ABSTRACT: SMaRT lncRNA controls translation of a G-quadruplex containing mRNA antagonizing the DHX36 helicase

PROVIDER: PRJNA527830 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8745840_1.fastq.gz	Fastqsanger.gz
	SRR8745840_2.fastq.gz	Fastqsanger.gz
	SRR8745841_1.fastq.gz	Fastqsanger.gz
	SRR8745841_2.fastq.gz	Fastqsanger.gz
	SRR8745842_1.fastq.gz	Fastqsanger.gz

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SMaRT lncRNA controls translation of a G-quadruplex containing mRNA antagonizing the DHX36 helicase

Project description:Guanine-quadruplexes (G4) present in RNA and DNA exert a number of different functions in the nucleus and in the cytoplasm. However, the molecular mechanisms of G4-mediated regulation are still poorly understood. We describe a regulatory circuitry operating in the early phases of muscle differentiation in which a long non coding RNA (SMaRT) base pairs with a G4-containing mRNA (Mlx-g) and represses its translation in an antagonistic way with the RNA helicase DHX36. MLX-g is required to allow the nuclear translocation of the MLX-a and b dimerization partners and to control proper myogenesis. We show that by controlling MLX-g, lnc-SMaRT is able to regulate the overall quantity of nuclear MLX proteins and their transcriptional output. Therefore, the circuitry composed by lnc-SMaRT, Mlx-g and Dhx36 not only plays an important role in the control of myogenesis but unravels a molecular mechanism where G4 structures and G4 unwinding activities are controlled in vivo.

2020-03-18 | GSE128486 | GEO

DNA/RNA helicase DHX36 is required for late stages of spermatogenesis

Project description:Spermatogenesis is a highly complex developmental process that typically consists of mitosis, meiosis, and spermiogenesis. DNA/RNA helicase DHX36, a unique guanine-quadruplex (G4) resolvase, play crucial roles in a variety of biological processes. We previously showed that DHX36 is highly expressed in male germ cells with the highest level in zygotene spermatocytes. Here, we delete Dhx36 in advanced germ cells with Stra8-GFPCre, and found that a Dhx36 deficiency in the differentiated spermatogonia leads to meiotic defects and abnormal spermiogenesis. These defects in late stages of spermatogenesis arise from dysregulated transcription of G4-harboring genes, which are required for meiosis. Thus, this study reveals that Dhx36 play crucial roles in the late stages of spermatogenesis.

2022-11-24 | GSE218477 | GEO

DHX36 is the missing link to understand RNA G-quadruplex structures, mRNA stability, and translation [RNA-seq]

Project description:DHX36 is a ATP-dependent, 3´-5´ RNA helicase of the DEAH family. Previous publications reported this helicase to associate with AU-rich elements and to specifically unwind G-quadruplex structures. Here, we performed RNA-seq in triplicats of HEK293 wildtype cells and DHX36-KO-HEK293 cells to identify changes in RNA abundance upon presence or absence of this helicase. After sequencing and mapping to the human genome at nucleotide-resolution level we analysed the mRNA abundance of target mRNAs, identified in this study (see PAR-CLIP). Our analyses show that binding of DHX36 to 3´UTRS of target mRNAs significantly reduce their abundance.

2019-07-01 | GSE105173 | GEO

SMaRT lncRNA controls translation of a G-quadruplex-containing mRNA antagonizing the DHX36 helicase.

Project description:Guanine-quadruplexes (G4) included in RNA molecules exert several functions in controlling gene expression at post-transcriptional level; however, the molecular mechanisms of G4-mediated regulation are still poorly understood. Here, we describe a regulatory circuitry operating in the early phases of murine muscle differentiation in which a long non-coding RNA (SMaRT) base pairs with a G4-containing mRNA (Mlx-γ) and represses its translation by counteracting the activity of the DHX36 RNA helicase. The time-restricted, specific effect of lnc-SMaRT on the translation of Mlx-γ isoform modulates the general subcellular localization of total MLX proteins, impacting on their transcriptional output and promoting proper myogenesis and mature myotube formation. Therefore, the circuitry made of lnc-SMaRT, Mlx-γ, and DHX36 not only plays an important role in the control of myogenesis but also unravels a molecular mechanism where G4 structures and G4 unwinding activities are regulated in living cells.

| S-EPMC7271651 | biostudies-literature

SMaRT lncRNA controls translation of a G-quadruplex containing mRNA antagonizing the DHX36 helicase

Project description:Guanine-quadruplexes (G4) included in RNA molecules exert several functions in controlling gene expression at post-transcriptional level; however, the molecular mechanisms of G4-mediated regulation are still poorly understood. Here we describe a regulatory circuitry operating in the early phases of murine muscle differentiation in which a long non coding RNA (SMaRT) base pairs with a G4-containing mRNA (Mlx-gamma) and represses its translation by counteracting the activity of the DHX36 RNA helicase. The time-restricted, specific effect of lnc-SMaRT on the translation of Mlx-gamma isoform modulates the general subcellular localization of total MLX proteins, impacting on their transcriptional output and promoting proper myogenesis and mature myotube formation. Therefore, the circuitry made of lnc-SMaRT, Mlx-gamma and DHX36 not only plays an important role in the control of myogenesis but also unravels a molecular mechanism where G4 structures and G4 unwinding activities are regulated in living cells.

| S-SCDT-EMBOR-2019-49942V1 | biostudies-other

Rapid degradation of DHX36 revealing its transcriptional role by interacting with G-quadruplex

Project description:More evident supports G-quadruplex are involved in transcription. Recent research revealed that DHX36 preferentially resolves G-quadruplex (G4) structure over the canonical G4, raising the possibility that DHX36 could bind and resolve G4 structures to regulate gene transcription. However, the hypothesis has yet been validated systematically in vivo.In this study, we investigated the role of DHX36 interacting with G4s in transcription. Firstly, we performed CUT&TAG to map the binding sites in chromatin of MCF7. Next, we utilized nascent RNA-seq and AID protein degradation system to identify the direct gene targets by transcriptional regulation of DHX36 and found these sites are enriched with G4 structure. We picked three G4 sequences in oncogene from these sites and found DHX36 binds and resolves these G4 structures in vitro, suggesting DHX36 may be recruited to these promoter G4 sites and regulate gene transcription by resolving G4 structure.

2024-08-13 | GSE228815 | GEO

lncSMaRT translational regulation of Spire1, a new player in muscle differentiation

Project description:Total RNA of DHX36 RIP experiment in Human differentiating myoblasts at DM1 was extracted and subjected to unstranded paired end library prep and sequencing. DHX36 is an ATP-dependent helicase of the DEAH family that is known to be involved in unwinding of G-Quadruplex structures, regulating mRNA metabolism and translation. We demonstrated that mouse DHX36 and the lncRNA lnc-SMaRT are involved in muscle differentiation by translationally regulating G-Quadruplex containing mRNAs (Mlx and Spire1). Here, we characterize the human DHX36 interactome in differentiating myoblasts in order to find out a lnc-SMaRT analogous gene.

2022-04-14 | GSE181308 | GEO

DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation [PAR-CLIP-seq]

Project description:DHX36 is a ATP-dependent, 3´-5´ RNA helicase of the DEAH family. Previous publications reported this helicase to associate with AU-rich elements and to specifically unwind G-quadruplex structures. Here, we performed PAR-CLIP in duplicates to specifically crosslink DHX36 and helicase-dead DHX36 E335A to its RNA binding targets in HEK293 cells. After sequencing and mapping to the human genome at nucleotide-resolution level we combined sequencing reads to a total of over 60000 binding clusters on more than 9000 transcripts. Distribution analyses revealed that DHX36 binds mainly to CDSs and 3´UTRS of mRNAs. Also, a G-rich binding motif for DHX36 was identified.

2019-07-01 | GSE105171 | GEO

DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation [Ribo-Seq]

Project description:DHX36 is a ATP-dependent, 3´-5´ RNA helicase of the DEAH family. Previous publications reported this helicase to associate with AU-rich elements and to specifically unwind G-quadruplex structures. Here, we performed Ribosome footprintin in triplicats of HEK293 wildtype cells and DHX36-KO-HEK293 cells to identify changes in ribosome occupancy on mRNAs upon presence or absence of this helicase. After sequencing and mapping to the human genome at nucleotide-resolution level we analysed the coverage of ribosomes on target mRNAs, identified in this study (see PAR-CLIP). Our analyses show that only minor changes upon DHX36 knockout can be observed.

2019-07-01 | GSE105172 | GEO

DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation [ChrRNA-seq]

2019-07-01 | GSE105169 | GEO