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Transcriptome analysis of PRMT6 knock-out in NT2/D1 cells

ABSTRACT: Transcriptome analysis of PRMT6 knock-out in NT2/D1 cells

PROVIDER: PRJNA420764 | ENA |

REPOSITORIES: ENA

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Transcriptome analysis of PRMT6 knock-out in NT2/D1 cells

Project description:Whole transcriptome for PRMT6 knock-out and control NT2/D1 cells with and without ATRA (all-trans retinoic acid) was sequenced. These samples were compared to each other to find differentially regulated genes and PRMT6-dependent transcriptome in pluripotency and differentiating cells.

2018-09-27 | GSE107611 | GEO

Repressive mark H3K27me3 in PRMT6 KO NT2/D1 cells

Project description:Repressive mark H3K27me3 in PRMT6 KO NT2/D1 cells

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Repressive mark H3K27me3 in PRMT6 KO NT2/D1 cells

Project description:Protein arginine methyltransferase 6 (PRMT6) is an epigenetic regulator of fundamental cellular processes, such as gene expression and DNA repair. Asymmetric dimethylation of histone H3 at arginine 2 (H3R2me2a) is the major histone modification catalyzed by PRMT6. To identify the genome-wide deposition and transcriptional impact of H3R2me2a, we established PRMT6 deletion in a human cell model of neural differentiation. These knockout cells show severe neural differentiation defects. ChIP-seq profiling reveals that H3R2me2a is present at promoter as well as non-promoter sites in a PRMT6-dependent manner. Loss of H3R2me2a causes enhanced H3K4me3 deposition and target gene transcription supporting a genome-wide repressive nature of H3R2me2a. Intriguingly, the non-promoter H3R2me2a peaks co-localize with active enhancer marks, such as H3K4me1 and H3K27ac.

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Human NTERA2 (NT2/D1) cells lines

Project description:This SuperSeries is composed of the following subset Series: GSE16858: Human NTERA2 (NT2/D1) cells lines: shZRF1 vs. shRandom during Retinoic Acid (RA) administration GSE16878: Human NTERA2 (NT2/D1) cells lines: Genomewide distribution of ZRF1 at gene promoters during RA administration Refer to individual Series

2010-12-24 | E-GEOD-16891 | biostudies-arrayexpress

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Project description:To identify novel downstream target genes of SOX9, transcriptome analysis of SOX9 transfected human embryonic testicular cell line, NT2/D1, was carried out.

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Differentially expressed genes in human hippocampus and Tera-1 cell line versus HepG2, A549, NT2/D1 and NGP127 cells.

Project description:We discovered a new tissue specific enhancer originated from the human spesific endogenous retrovirus (hsERV). This enhancer displayed its activity in hippocampus and Tera-1 cell line as opposed to HepG2, A549, NT2/D1 and NGP127 cells. The aim of this study was to find transcription factors responsible for the hsERV enhancer activity. So we attempted to identify a fraction of transcription factor genes that were upregulated in enhancer-positive cells. Total RNA obtained from human hippocampus and Tera-1, HepG2, A549, NT2/D1 and NGP127 cell lines.

2013-01-26 | E-GEOD-43773 | biostudies-arrayexpress

Differentially expressed genes in human hippocampus and Tera-1 cell line versus HepG2, A549, NT2/D1 and NGP127 cells.

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Distribution of macroH2A1 and macroH2A2 at gene promoters in NT2/D1 cells

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ARRDC4 knock out Mouse Heart Analysis

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Identification of interaction partners of PRMT6

Project description:To identify transcription factors of PRMT6 which could recruit PRMT6 to target genes, we used affinity purification of avi-tagged PRMT6 in combination with stable isotope labeling of amino acids in cell culture (SILAC) based mass spectrometry. For this, K562 cells were transduced with a lentiviral co expression vector for the BirA-ligase and avi-PRMT6 with a 21 amino acid taq, which is biotinylated in the cells. Cells expressing the BirA-ligase only served as a control. Avi-PRMT6 cells were grown in heavy SILAC medium and control cells in light SILAC medium for seven passages. Nuclear extracts were prepared from 1x108 cells and subjected to avi-PRMT6 affinity purification using magnetic streptavidin beads. Subsequently, the proteins were eluted from the beads. The eluates from the avi-PRMT6 and the control were mixed in a one to one ratio. Subsequently, we performed quantitative mass spectrometry (MS)-based analysis of the PRMT6 interactome.

2021-09-09 | PXD021804 | Pride

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