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High-throughput sequencing of pluripotent cells

ABSTRACT: We report HERV-K rec iCLIP-seq binding data, ribosome profiling data, and RNA-seq from ELF1 naïve hESC and RNA-seq from NCCIT cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE63570 | GEO | 2015/04/21

SECONDARY ACCESSION(S): PRJNA268222

REPOSITORIES: GEO

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High-throughput sequencing of pluripotent cells

Project description:We report HERV-K rec iCLIP-seq binding data, ribosome profiling data, and RNA-seq from ELF1 naïve hESC and RNA-seq from NCCIT cells. HERV-K Rec iCLIP-seq: 2 replicates in NCCIT. Ribosome profiling: 4 replicates each of Rec-overexpressing NCCIT vs. control NCCIT; RNAseq: 3 replicates each of HERV-K Rec siRNA vs. control siRNA in NCCIT; RNA-seq: 3 replicates each of ELF1 naïve hESC vs. primed hESC.

2015-04-21 | E-GEOD-63570 | biostudies-arrayexpress

Expression data from human embryonic kidney 293 (HEK-293) cells transiently transfected with Human endogenous retrovirus (HERV) (K-HML2) Rec protein compared to empty expression vector control

Project description:HERV-K protein Rec functions as RNA transport protein shuttling unspliced viral genomic RNA from the nucleus to the cytoplasm. Rec was found to be expressed in several tumors and transformed cell lines and contributes to cell transformation by inhibiting the transcription factor Promyelocytic Leukemia Zinc Finger Protein

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Regulation of Endogenous Retroviruses and Cellular Genes by HIV-1 Rev [cytoplasmic RNA]

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rec and np9 in normal human tissues

Project description:HERV-K(HML-2) rec and np9 transcripts in normal human tissues

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Project description:TDP-43 iCLIP in mESC and hESC

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Project description:To investigate the role and mechanism of miR-125b on NCCIT cells without bias, we analyzed differentially expression RNA profile among miR-125b antagomir-, miR-125b agomir-, and negative control-transfected NCCIT tumor cells by RNA-seq.

2018-11-30 | GSE123113 | GEO

microRNA-seq reveals microRNAs under the regulation of miR-125b in NCCIT tumor cells

Project description:To investigate the role and mechanism of miR-125b on NCCIT cells without bias, we analyzed differentially expression microRNA profile among miR-125b antagomir-, miR-125b agomir-, and negative control-transfected NCCIT tumor cells by microRNA-seq.

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The RNA m6A reader YTHDC2 recruits TET1 to demethylate transposable elements DNA and prevent neural fate of human pluripotent stem cells [ChIP-seq_2]

Project description:Covalent modifications of RNA and DNA both regulate numerous biological processes, including development and cancer. The most abundant modification of RNA is that of N6-methyladenosine(m6A), while in the case of DNA, the CpG cytosine methylation characterizes cis-regulatory elements for spatial-temporal gene regulation. Recent studies establish a role for RNA m6A in regulating chromatin through histone modifications. However, whether there is also interplay between RNA and DNA methylation remains unknown. We address this question by studying regulation of the primate-specific transposable element (TE), LTR7/HERV-H, that is specifically activated in human embryonic stem cells (hESCs). Exploiting a novel proteomic approach, we find the RNA m6A-reader, YTHDC2, binds to LTR/HERV-H chromatin through interaction with m6A-modified HERV-H transcripts. Significantly, YTHDC2 recruits DNA demethylase, TET1, to activate LTR7/HERV-H via 5-hydroxymethycytosine(5hmC)-mediated DNA methylation. Furthermore, the YTHDC2/LTR7-axis prevents neural conversion of hESCs. Our results establish previously unknown crosstalk between RNA m6A and DNA methylation and new mechanisms controlling TE activity and hESC fate. We focused on the regulation of the primate-specific TE family, LTR7/HERV-H that is specifically active in the pluripotent human embryonic stem cells (hESCs) then silenced in differentiated lineages. We develop CARGO-BioID, a CRISPR-based TE-centric proteomics approach, to identify the proteins associated with thousands of copies of endogenous LTR7/HERV-H loci and potentially regulate their activity in hESCs. We found YTHDC2 and TET1 interact with each other and subsequently regulate m6A level on HERVH transcripts and 5hmC level on HERV-H genomic loci, which is critical for LTR7/HERV-H activities.

2023-05-12 | GSE224669 | GEO

The RNA m6A reader YTHDC2 recruits TET1 to demethylate transposable elements DNA and prevent neural fate of human pluripotent stem cells [RIP-Seq]

2023-05-12 | GSE210864 | GEO

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