Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of nucleus and cytoplasm-specific HNRNPK binding on SINEUP RNA by seCLIP

ABSTRACT: Analysis of nucleus and cytoplasm-specific HNRNPK binding on SINEUP RNA by seCLIP

PROVIDER: PRJNA944232 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23851747.fastq.gz	Fastqsanger.gz
	SRR23851748.fastq.gz	Fastqsanger.gz
	SRR23851749.fastq.gz	Fastqsanger.gz
	SRR23851750.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Analysis of nucleus and cytoplasm-specific HNRNPK binding on SINEUP RNA by seCLIP

Project description:To check the subcellular location-specific HNRNPK binding sites on mouse SINEB2 repeat element, we prepared seCLIP (single-end enhanced crosslinking and immunoprecipitation assay) libraries from SINEUP-GFP transfected nuclear and cytoplasmic fractions from HEK293T/17 cells.

2023-03-16 | GSE227250 | GEO

SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assembly [eCLIP-seq]

Project description:We found novel functional long non-coding RNAs (lncRNAs) that contain a SINE element, and which up-regulate the translation of target mRNA, named SINEUPs. To investigate the network of translational regulation, we focused on the sub-cellular distribution of target mRNAs and SINEUP RNAs and SINEUP RNA binding proteins (RBPs). We identified PTBP1 and HNRNPK as essential RBPs. These proteins contributed to SINEUP RNA sub-cellular distribution and to assembly of translational initiation complexes, leading to enhancement of the target mRNA translation. To prove the SINEUP RBPs binding regions on SINEUP-GFP transcripts, we performed seCLIP; single-end enhanced crosslinking and immunoprecipitation assay to determine the specific binding sites of PTBP1 and HNRNPK on SINEUP-GFP RNA. These findings will promote a better understanding of the mechanisms on the fate of regulatory RNAs implicated in efficient protein translation.

2020-02-09 | GSE144345 | GEO

Detection of SINEUP RNA modification by Oxford Nanopore direct-RNA sequencing

Project description:To detect the modifed bases in SINEUP RNA, we compared chemically modified in vitro transcribed (IVT) SINEUP-GFP RNA and in-cell transcribed (ICT) SINEUP RNA from SINEUP-GFP and sense EGFP co-transfected HEK293T/17 cells. Comparative study of Nanopore direct RNA sequencing data from non-modified and modified IVT samples against the data from ICT SINEUP RNA sample revealed modified k-mers positions in SINEUP RNA in the cell.

2023-02-04 | GSE224018 | GEO

In vivo structure analysis of SINEUP RNA

Project description:To analyze SINEUP RNA secondary structure in living cells, multiple SINEUP RNA and target EGFP mRNA plasmids were transfected in HEK293T/17 cells and icSHAPE libraries were prepared.

2020-03-06 | GSE146407 | GEO

Reversible internalization of cytoplasm into the nucleus in senescent cells

Project description:Reversible internalization of cytoplasm into the nucleus in senescent cells

| PRJNA1014412 | ENA

SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assembly [eCLIP-seq]

Project description:SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assembly [eCLIP-seq]

| PRJNA603461 | ENA

hnRNPK knock down in Ewing cell line

Project description:Ewing sarcoma is a highly aggressive tumor characterized by a translocation between members of the FET family of RNA binding proteins and one of several ETS transcription factors, with the most common translocation being EWS-FLI1. EWS-FLI1 leads to changes in gene expression through mechanisms that are not completely understood. We performed RNA sequencing analysis on primary pediatric human mesenchymal progenitor cells (pMPCs) expressing EWS-FLI1 in order to identify novel target genes. This analysis identified lnc277 as a previously uncharacterized long non-coding RNA upregulated by EWS-FLI1 in pMPCs. Inhibiting the expression of lnc277 diminished the ability of Ewing sarcoma cell lines to proliferate and form colonies in soft agar whereas inhibiting lnc277 had no effect on other cell types tested. By analyzing gene expression after shRNA knockdown, we found that both EWS-FLI1 and lnc277 repressed many more genes that they induced and that a significant fraction of EWS-FLI1 repressed targets were also repressed by lnc277. Analysis of primary human Ewing sarcoma RNA sequencing data further supports a role for lnc277 in mediating gene repression. We identified hnRNPK as an RNA binding protein that interacts directly with lnc277. We found a significant overlap in the genes repressed by hnRNPK and those repressed by both EWS-FLI1 and lnc277, suggesting that hnRNPK participates in lnc277 mediated gene repression. Thus, lnc277 is a previously uncharacterized long non-coding RNA downstream of EWS-FLI1 that facilitates the development of Ewing sarcoma via the repression of target genes. Our studies identify a novel mechanism of oncogenesis downstream of a chromosomal translocation and underscore the importance of lncRNA-mediated gene repression as a mechanism of EWS-FLI1 transcriptional regulation. A673 Ewing cells expressing an shRNA targeting hnRNPK or control were subjected to paired end RNA sequencing and compared to shGFP control.

2014-11-01 | E-GEOD-60890 | biostudies-arrayexpress

Functional Antagonism Between CELF and Mbnl Proteins in Cytoplasm and Nucleus

Project description:Functional Antagonism Between CELF and Mbnl Proteins in Cytoplasm and Nucleus

| PRJNA262626 | ENA

Effect of overexpressing HNRNPK in glioblastoma stem cell

Project description:The mechanisms underlys GBM cellular transitions remain unclear.In our study, we overexpressed HNRNPK in three different types of GSCs. HNRNPK (WT) leads to high expression of core markers in GSCs, and its characteristics are similar to those of the MES subtype, exhibiting stronger invasive abilities and tumorigenic potential. We mutated 422 site from lysine(K) to argnine(R) to study the function of SUMOylation in HNRNPK. Sequencing of GSCs with overexpression of HNRNPK (K422R) mutation confirmed the upregulation of infiltrating markers within the GSCs. The changes in GSC subtypes driven by overexpression of HNRNPK (WT or K422R) were not restricted by GSC mutation features.

2024-12-13 | GSE262681 | GEO

N6-methyladenosine profiling on SINEUP non-coding RNA by Nanopore Sequencing

Project description:SINEUP Nanopore m6A

| PRJEB55645 | ENA