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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE105173 | GEO | 2019/07/01

REPOSITORIES: GEO

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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.

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

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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 [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 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.

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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.

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

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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

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Project description:In this study, we deciphered the functions of Dhx36 and related molecular mechanisms in muscle stem cells and muscle regeneration. We found Dhx36 was highly induced in activated muscle stem cells during regeneration induced by injury. Conditional inactivation of Dhx36 in mouse muscle stem cells caused significant impaired regeneration, which was due to the dramatically decreased cell proliferation. Dhx36 was a well-known RNA helicase for binding/unbinding DNA/RNA G-quadruplexes and it was dominantly expressed in cytoplasm of proliferating myoblast. Therefore CLIP-seq was conducted to identify the mRNAs interacting with Dhx36 in myoblast cells.

2021-04-27 | GSE151122 | GEO

System-wide analysis of Dhx36 function in skeletal muscle satellite cells reveals its binding with 5’UTR G4 structure to promote Gnai2 RNA translation

Project description:In this study, we deciphered the functions of Dhx36 and related molecular mechanisms in muscle stem cells and muscle regeneration. We found Dhx36 was highly induced in activated muscle stem cells during regeneration induced by injury. Conditional inactivation of Dhx36 in mouse muscle stem cells caused significant impaired regeneration, which was due to the dramatically decreased cell proliferation. Dhx36 was a well-known RNA helicase for binding/unwinding DNA/RNA G-quadruplexes and it was dominantly expressed in cytoplasm of proliferating myoblast. CLIP-seq was conducted to identify the mRNAs interacting with Dhx36 in myoblast cells. To examine whether Dhx36 regulates translation process, we also conducted polysome profiling followed by RNA-seq in WT and Dhx36 KO myoblast cells. This SuperSeries is composed of the SubSeries listed below.

2021-04-27 | GSE151124 | GEO

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