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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE105175 | 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.

2019-07-01 | GSE105169 | 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 [cPDS-RNA-seq]

2019-07-01 | GSE105170 | 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

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 [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 [Ribo-Seq]

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

| PRJNA415033 | 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

A U-rich element in the 5' untranslated region is necessary for the translation of p27 mRNA.

Project description:Increased translation of p27 mRNA correlates with withdrawal of cells from the cell cycle. This raised the possibility that antimitogenic signals might mediate their effects on p27 expression by altering complexes that formed on p27 mRNA, regulating its translation. In this report, we identify a U-rich sequence in the 5' untranslated region (5'UTR) of p27 mRNA that is necessary for efficient translation in proliferating and nonproliferating cells. We show that a number of factors bind to the 5'UTR in vitro in a manner dependent on the U-rich element, and their availability in the cytosol is controlled in a growth- and cell cycle-dependent fashion. One of these factors is HuR, a protein previously implicated in mRNA stability, transport, and translation. Another is hnRNP C1 and C2, proteins implicated in mRNA processing and the translation of a specific subset of mRNAs expressed in differentiated cells. In lovastatin-treated MDA468 cells, the mobility of the associated hnRNP C1 and C2 proteins changed, and this correlated with increased p27 expression. Together, these data suggest that the U-rich dependent RNP complex on the 5'UTR may regulate the translation of p27 mRNA and may be a target of antimitogenic signals.

| S-EPMC86072 | biostudies-literature

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