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

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

PROVIDER: PRJNA603461 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10973988.fastq.gz	Fastqsanger.gz
	SRR10973989.fastq.gz	Fastqsanger.gz
	SRR10973990.fastq.gz	Fastqsanger.gz
	SRR10973991.fastq.gz	Fastqsanger.gz
	SRR10973992.fastq.gz	Fastqsanger.gz

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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

Altered expression of genes in lncRNA-LBCS, hnRNPK and PTBP1 knockdown

Project description:We identify a lncRNA which low expresses and regulates self-renewal of bladder cancer stem cell. So we named it lncRNA-LBCS (low expresses in bladder cancer stem cell). Further study finds that lncRNA-LBCS bind to hnRNPK and PTBP1. To investigate the genes regulated by these, we knockdown lncRNA-LBCS, hnRNPK and PTBP1 by siRNA, respectively, and perform high-throughput sequence. So we identify a series of genes regulated by lncRNA-LBCS, hnRNPK and PTBP1, respectively.

2017-08-13 | GSE79832 | GEO

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 assemblies.

Project description:SINEUPs are long non-coding RNAs (lncRNAs) that contain a SINE element, and which up-regulate the translation of target mRNA. They have been studied in a wide range of applications, as both biological and therapeutic tools, although the underpinning molecular mechanism is unclear. Here, we focused on the sub-cellular distribution of target mRNAs and SINEUP RNAs, performing co-transfection of expression vectors for these transcripts into human embryonic kidney cells (HEK293T/17), to investigate the network of translational regulation. The results showed that co-localization of target mRNAs and SINEUP RNAs in the cytoplasm was a key phenomenon. We identified PTBP1 and HNRNPK as essential RNA binding proteins. These proteins contributed to SINEUP RNA sub-cellular distribution and to assembly of translational initiation complexes, leading to enhanced target mRNA translation. These findings will promote a better understanding of the mechanisms employed by regulatory RNAs implicated in efficient protein translation.

| S-EPMC7672464 | biostudies-literature

iiCLIP protocol benchmarking with PTBP1

Project description:We describe an improved individual nucleotide resolution CLIP protocol (iiCLIP), which can be completed within 4 days from UV crosslinking to libraries for sequencing. For benchmarking, we directly compared PTBP1 iiCLIP libraries with the iCLIP2 protocol produced under standardised conditions with 1 million HEK293 cells, and with public eCLIP and iCLIP PTBP1 data. There are 3 PTBP1 iiCLIP libraries, 1 input iiCLIP library and 1 PTBP1 iCLIP2 library produced in this study.

2022-08-01 | E-MTAB-10881 | biostudies-arrayexpress

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

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

| PRJNA944232 | ENA

Enhanced CLIP-seq analysis of PTBP1 and IGF2BP2 binding targets

Project description:To investigate the binding targets of PTBP1 (PTB) and IGF2BP2 (IMP2) in glioma cells, we carried out an unbiased analysis of transcripts bound by PTBP1 and IGF2BP2 using enhanced crosslinking immunoprecipitation followed by high-throughput sequencing (eCLIP) in A172 glioma cells. We repeated the eCLIP method twice in each experiment, and found that the ratio of PTBP1 and IGF2BP2 binding mRNAs overlap was very high.

2022-01-02 | GSE192792 | 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

eCLIP from K562 (ENCSR268ETU)

Project description:eCLIP experiment on K562 against HNRNPK For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2017-01-04 | GSE91621 | GEO

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