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HMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export II

ABSTRACT: To define the in vivo targets of the human nuclear exosome, we performed stranded RNA-seq using polyA RNAs isolated from nuclei of HeLa cells. To compare the RNA levels in each sample in an unbiased fashion, we added spike-in controls to equal amount of total nuclear RNAs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE77639 | GEO | 2017/12/06

SECONDARY ACCESSION(S): PRJNA311070

REPOSITORIES: GEO

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hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export I

Project description:To define the in vivo targets of the human nuclear exosome, we performed stranded RNA-seq using rRNA-depleted RNAs isolated from nuclei of HeLa cells. To compare the RNA levels in each sample in an unbiased fashion, we added spike-in controls to equal amount of total nuclear RNAs.

2017-12-06 | GSE77638 | GEO

hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export IV

Project description:To define the in vivo targets of the human nuclear exosome, we performed stranded RNA-seq using rRNA-depleted RNAs isolated from HeLa cells.

2018-07-09 | GSE89123 | GEO

hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export VI

Project description:To examine whether the competition between hMTR4 with ALYREF is important for the specific exosome recruitment, we performed stranded RNA-seq using rRNA-depleted nuclear RNAs isolated from ALYREF and control overexpression cells.

2017-12-06 | GSE100982 | GEO

hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export V

Project description:To examine whether the competition between hMTR4 with AlyREF is important for the specific exosome recruitment,we sequenced the RNAs associating with hMTR4 in control and AlyREF overexpression cells.

2017-12-06 | GSE100606 | GEO

hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export

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

2017-12-06 | GSE77641 | GEO

hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export III

Project description:To eliminate the possibility that for a particular gene the increased RNA level is an effect of enhanced transcription. We carried out ChIP-seq for RNAPII to compare transcription of mRNAs and lncRNAs in control, hRRP40 and hMTR4 knockdown cells. Among 15000 RNAPII binding peaks identified in these samples, only less than 50 peaks was significantly increased in hRRP40 or hMTR4 knockdown cells.

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hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export

Project description:hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export

| PRJNA311068 | ENA

Exosome cofactor hMTR4 competes with export adaptor ALYREF to ensure balanced nuclear RNA pools for degradation and export.

Project description:The exosome is a key RNA machine that functions in the degradation of unwanted RNAs. Here, we found that significant fractions of precursors and mature forms of mRNAs and long noncoding RNAs are degraded by the nuclear exosome in normal human cells. Exosome-mediated degradation of these RNAs requires its cofactor hMTR4. Significantly, hMTR4 plays a key role in specifically recruiting the exosome to its targets. Furthermore, we provide several lines of evidence indicating that hMTR4 executes this role by directly competing with the mRNA export adaptor ALYREF for associating with ARS2, a component of the cap-binding complex (CBC), and this competition is critical for determining whether an RNA is degraded or exported to the cytoplasm. Together, our results indicate that the competition between hMTR4 and ALYREF determines exosome recruitment and functions in creating balanced nuclear RNA pools for degradation and export.

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Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset

Project description:We present a new wholly defined Affymetrix spike-in dataset consisting of 18 microarrays. Over 5700 RNAs are spiked in at relative concentrations ranging from 1- to 4-fold, and the arrays from each condition are balanced with respect to both total RNA amount and degree of positive- versus negative-fold change. We use this new “Platinum Spike” dataset to evaluate microarray analysis routes and contrast the results to those achieved using our earlier Golden Spike dataset.

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Nuclear export of circular RNA

Project description:Circular RNAs (circRNAs), which can function as regulators of gene expression, are formed by back-splicing of precursor mRNAs in the nucleus. circRNAs are predominantly localized in the cytoplasm, indicating that they must be exported from the nucleus. Here, we uncover a pathway specific for nuclear export of circular RNA. This pathway requires Ran-GTP, Exportin-2 and IGF2BP1. Enhancing the nuclear Ran-GTP gradient by depletion or chemical inhibition of the major protein exporter, CRM1, selectively increases nuclear export of circRNAs, while reducing the nuclear Ran-GTP gradient selectively blocks circRNA export. Analysis of nuclear circRNA binding proteins reveals that interaction of IGF2BP1 with circRNA is enhanced by Ran-GTP, whereas its interaction with linear RNA is inhibited by Ran-GTP. Depletion or knockout of Exportin-2 specifically inhibits nuclear export of circRNA, while formation of an Exportin-2 circRNA export complex requires Ran-GTP and IGF2BP1. Our findings demonstrate that adaptors such as IGF2BP1 that bind directly to circular RNAs recruit Exportin-2 to export circRNAs in a mechanism analogous to protein export, rather than mRNA export.

2023-12-09 | GSE235899 | GEO

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