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DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via m6A/YTHDF1

ABSTRACT: DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via m6A/YTHDF1

PROVIDER: PRJNA1103721 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28779964_1.fastq.gz	Fastqsanger.gz
	SRR28779964_2.fastq.gz	Fastqsanger.gz
	SRR28779965_1.fastq.gz	Fastqsanger.gz
	SRR28779965_2.fastq.gz	Fastqsanger.gz
	SRR28779966_1.fastq.gz	Fastqsanger.gz

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DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via m6A/YTHDF1

Project description:RNA structure constitutes a new layer of gene regulatory mechanisms. RNA binding proteins can modulate RNA secondary structures, thus participating in post-transcriptional regulation. The DEAH-box helicase 36 (DHX36) is known to bind and unwind RNA G-quadruplex (rG4) structure but the transcriptome-wide RNA structure remodeling induced by DHX36 binding and the impact on RNA fate remain poorly understood. Here, we investigate the RNA structurome alteration induced by DHX36 depletion. Our findings reveal that DHX36 binding induces structure remodeling not only at the localized binding sites but also on the entire mRNA transcript most pronounced in3’UTR regions. DHX36 binding increase structural accessibility at 3’UTRs which is correlated with decreased post-transcriptional mRNA abundance. Further analyses and experiments uncover that DHX36 binding sites are enriched for N6-methyladenosine (m6A) modification and YTHDF1 binding; and DHX36 induced structural change may facilitate YTHDF1 binding to m6A sites leading to RNA degradation. Altogether, our findings uncover the structural remodeling effect of DHX36 binding and its impact on RNA abundance through regulating m6A dependent YTHDF1 binding.

2024-10-03 | GSE264642 | GEO

YTHDF1 CLIP-seq in WT and DHX36-KO HEK293T cells

Project description:To identify the YTHDF1 binding changes upon DHX36 loss, we conducted and analyzed YTHDF1 CLIP-seq data in WT and DHX36-KO HEK293T cells.

2024-10-03 | GSE264498 | GEO

Transcriptomic RNA structure mapping unveils the structure dynamic induced by DHX36 binding (RBNS)

Project description:RNA binding proteins can modulate RNA secondary structures, thus participating in post-transcriptional regulation. The DEAH-box helicase 36 (DHX36) has a remarkable ability to bind and unwind RNA G-quadruplex (rG4) and duplex. However, the transcriptome-wide RNA structure dynamic induced by DHX36 and how structure change subsequently influences RNA fate remain poorly understood. Here, we first identify the endogenous binding sites and specificity of DHX36 based on binding profiles. Next, we capture in vivo RNA structuromes to investigate the structure change of DHX36-bound mRNAs following DHX36 knockout. DHX36 induces structure remodeling on not only the localized binding sites but also the other sites across the entire mRNA especially in 3’UTR. DHX36-induced more accessible structures of 3’UTR are revealed to correlate with post-transcriptional mRNA decrease. Furthermore, we demonstrate that DHX36 binding sites are enriched for N6-methyladenosine (m6A) modification and YTHDF1 binding. Finally, we experimentally validate that YTHDF1 binding is repelled to DHX36 loss-induced structure inaccessibility and YTHDF1 loss-induced mRNA stabilization could be a source of DHX36 loss-induced mRNA increase. Altogether, our findings uncover the effect of DHX36 binding on in vivo mRNA structure and propose a plausible mechanism of how RNA secondary structure change involves in post-transcriptional regulation through orchestrating YTHDF1 binding.

2024-10-03 | GSE237159 | GEO

Transcriptomic RNA structure mapping unveils the structure dynamic induced by DHX36 binding (Structure-seq)

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DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via m<sup>6</sup>A reader YTHDF1.

Project description:RNA structure constitutes a new layer of gene regulatory mechanisms. RNA binding proteins can modulate RNA secondary structures, thus participating in post-transcriptional regulation. The DEAH-box helicase 36 (DHX36) is known to bind and unwind RNA G-quadruplex (rG4) structure but the transcriptome-wide RNA structure remodeling induced by DHX36 binding and the impact on RNA fate remain poorly understood. Here, we investigate the RNA structurome alteration induced by DHX36 depletion. Our findings reveal that DHX36 binding induces structural remodeling not only at the localized binding sites but also on the entire mRNA transcript most pronounced in 3'UTR regions. DHX36 binding increases structural accessibility at 3'UTRs which is correlated with decreased post-transcriptional mRNA abundance. Further analyses and experiments uncover that DHX36 binding sites are enriched for N6-methyladenosine (m6A) modification and YTHDF1 binding; and DHX36 induced structural changes may facilitate YTHDF1 binding to m6A sites leading to RNA degradation. Altogether, our findings uncover the structural remodeling effect of DHX36 binding and its impact on RNA abundance through regulating m6A dependent YTHDF1 binding.

| S-EPMC11564809 | biostudies-literature

YTHDF1 CLIP-seq in WT and DHX36-KO HEK293T cells

Project description:YTHDF1 CLIP-seq in WT and DHX36-KO HEK293T cells

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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

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

2019-07-01 | GSE105170 | GEO

Tissue-specific structurome changes in the RNA structurome mediate salt salinity response in Arabidopsis

Project description:We employed Structure-seq2 method to probe RNA structure genome-wide in Arabidopsis shoot and root tissue separately and investigate the effect of salt stress on the RNA structurome in vivo.

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

2019-07-01 | GSE105169 | GEO