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

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

PROVIDER: PRJNA415033 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6191040.fastq.gz	Fastqsanger.gz
	SRR6191041.fastq.gz	Fastqsanger.gz
	SRR6191042.fastq.gz	Fastqsanger.gz
	SRR6191037.fastq.gz	Fastqsanger.gz
	SRR6191038.fastq.gz	Fastqsanger.gz

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DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation

Project description:DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation

| PRJNA415014 | ENA

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]

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

| PRJNA415030 | ENA

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

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

| PRJNA415031 | ENA

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

Project description:DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation [cPDS-RNA-seq]

| PRJNA415032 | ENA

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 [ChrRNA-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 | GSE105169 | GEO

DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation [cPDS-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 | GSE105170 | GEO

DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-07-01 | GSE105175 | GEO

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

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