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DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation [ChrRNA-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: GSE105169 | GEO | 2019/07/01

REPOSITORIES: GEO

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

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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

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.

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

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

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

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

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. To examine whether Dhx36 regulates translation process, we conducted polysome profiling followed by RNA-seq in WT and Dhx36 KO myoblast cells.

2021-04-27 | GSE151123 | GEO

piR-36249 and DHX36 together inhibit testicular cancer cell progression by upregulating OAS2

Project description:PIWI-interacting RNAs (piRNAs) have been identified in mammalian germline initially and later also found to be aberrantly expressed in various cancers. However, their functions in cancer is not very clear. Here, we studied the role of piR-36249, a member of the piRNA family, in testicular cancer. We show that piR-36249 is significantly downregulated in testicular cancer tissues comparing to tumor-adjacent tissues. Functional studies demonstrate that piR-36249 inhibits testicular cancer cell proliferation, migration and invasion. Mass Spectrometry (MS) analysis of piR-36249 pull-downed proteins reveals that piR-36249 interacts with ATP-dependent DNA/RNA helicase (DHX36). Dual-luciferase assays shows that piR-36249 binds to the 3'UTR of 2'-5'-oligoadenylate synthetase 2 (OAS2) mRNA. OAS2 has been shown in literature as a tumor suppressor modulating the occurrence and development of some tumors, such as colorectal cancer and breast cancer. In this study, OAS2 knockdown also promotes testicular cancer cell proliferation and migration. Furthermore, RNA immunoprecipitation assay reveals that DHX36 can also bind to OAS2 mRNA, and knockdown of DHX36 increases OAS2 mRNA yet downregulates its protein, indicating the enhancing OAS2 protein expression level effect of DHX36. All these data suggest that piR-36249, together with DHX36, functions in inhibiting testicular cancer cells proliferation, migration and invasion by upregulating OAS2 protein, and piR-36249 may serve as a potential predictor for the prognosis of testicular cancer.

2023-01-25 | GSE213411 | GEO

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