EGR1-controlled transcriptome of T HESCs
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ABSTRACT:
PROVIDER: PRJNA508815 | ENA |
REPOSITORIES: ENA
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Project description:Sequencing of mRNA isolated from a human endometrial stromal cell line (T HESCs) following control or EGR1 siRNA-mediated knockdown.
2019-04-22 | GSE123472 | GEO
Project description:Human bone marrow stromal cells (BMSCs) are key elements of the hematopoietic environment and they play a central role in bone and bone marrow physiology. However, how key BMSC functions are regulated is largely unknown. We analyzed the role of the immediate early response transcription factor EGR1 as key BMSC regulator and found that EGR1 was highly expressed in prospectively-isolated primary BMSCs, downregulated upon culture, and lower in non-CFU-F-containing CD45neg BM cells. Furthermore, EGR1 expression was lower in proliferative regenerating adult and fetal primary cells compared to adult steady-state BMSCs. Accordingly, EGR1 overexpression markedly decreased BMSC proliferation but considerably improved hematopoietic stroma support function as indicated by an increased production of transplantable CD34+CD90+ hematopoietic stem cells in expansion co-cultures. The improvement of BMSC stroma support function was mediated by increased expression of hematopoietic supporting genes, such as VCAM1 and CCL28. On the other hand, EGR1 knockdown increased ROS-mediated BMSC proliferation, and clearly reduced BMSC hematopoietic stroma support potential. These findings thus show that EGR1 is a key BMSC transcription factor with a dual role in regulating proliferation and hematopoietic stroma support function that is controlling a genetic program to coordinate the specific functions of BMSC in their different biological contexts.
2019-06-27 | PXD011767 | Pride
Project description:Purpose: To investigate the transcriptomes of H9 human embryonic stem cells (hESCs)- and peripheral blood mononuclear cells (PBMC) originated induced pluripotent stem cells (iPSCs)-derived early stage lentoid bodies at day 24 through RNA-Seq based whole transcriptome sequencing. Methods: The PBMC obtained from a healthy donor were subjected to generate iPSCs using Sendai-virus delivery system Cytotune 2.0 whereas the H9 hESCs were obtained commercially. Both hESCs and iPSCs were differentiated into lentoid bodies using “fried egg” method with feeder-free conditions as described previously. The differentiating lentoid bodies were examined for the expression of lens-specific and pluripotency markers at days 0, 6, 10, 15 and 24 by quantitative real-time PCR (qRT-PCR). Briefly, four biological replicates for each hESCs- and iPSC-derived lentoid bodies at day 24 were used for the RNA-Seq library preparation followed by sequencing on a single lane of HiSeq 2500. The raw reads were processed and analyzed using Lasergene Genomics Suite and the expression profiles were examined for differential expression using Spotfire DecisionSite with Functional Genomics. Results: The differentiating lentoid bodies at day 24 revealed transparent lens like morphological features with an increased expression of lens-specific markers including CRYGC. A total of 193.41, and 170.00 million reads were obtained for hESCs- and iPSCs-derived lentoid bodies, respectively. Of these, >96% reads aligned to the human reference genome resulting in >200x sequence coverage for both hESCs- and iPSCs-derived lentoid bodies. Additional analysis identified expression (≥ 0.659 RPKM) of 13,991 and 14,018 genes in hESCs- and iPSCs-derived lentoid bodies, respectively, representing ~70% of the total human protein-coding transcriptome expressed in lentoid bodies. Finally, a comparative analysis of both hESCs- and iPSCs-derived lentoid bodies transcriptomes identified >96% similarity at the gene level. Conclusion: The transcriptome analysis revealed an overall similar transcriptional profile in both hESCs- and iPSCs-derived lentoid bodies during differentiation at day 24.
2019-12-17 | GSE111071 | GEO
Project description:Purpose: We previously reported the generation of corneal endothelial cells (CECs) using the human peripheral blood mononuclear cells (PBMC)-originated induced pluripotent stem cells (iPSCs). Herein, we extend our analysis through RNA-Seq based transcriptome profiling of H9 human embryonic stem cells (hESCs)- and iPSCs-derived CECs. Methods: The PBMC obtained from a healthy donor were subjected to generate iPSCs using Sendai-virus delivery system Cytotune 2.0 whereas the H9 hESCs were obtained commercially. Both hESCs and iPSCs were subjected to the 20-day procedure according to our previously published CECs generation method. The differentiated CECs were characterized by immunocytochemistry. Total RNA from hESCs- and iPSCs-derived CECs was used for the preparation of RNA-Seq libraries, which were sequenced on HiSeq 2500 system. The raw RNA-Seq reads were processed and analyzed using Lasergene Genomics Suite and the expression profiles were examined for differential expression using Spotfire DecisionSite with Functional Genomics. Results: The hESCs and iPSCs were differentiated into CECs through multipotent neural crest cells (NCCs) using a 20-day procedure. The differentiating CECs on day 20 (D20) exhibited a tightly packed hexagonal/polygonal shape, which expressed CECs-associated markers, zona occludens-1 and N-cadherin at the cell boundaries. A total of 180.18, and 179.01 million reads were obtained for hESCs- and iPSCs-derived CECs, respectively. Of these, >97% reads aligned to the human reference genome resulting in >250x sequence coverage for both hESCs- and iPSCs-derived CECs. Additional analysis identified expression (≥ 0.659 RPKM) of 13,561 and 13,551 genes in hESCs- and iPSCs-derived CECs, respectively, representing ~68% of the total human protein-coding transcriptome expressed in these CECs. Finally, a comparative analysis of both hESCs- and iPSCs-derived CECs transcriptomes identified >95% similarity at the gene level. Conclusion: These analyses reveal an overall similar transcriptional profile in both hESCs- and iPSCs-derived CECs.
2020-02-16 | GSE110872 | GEO
Project description:With anti-EGR1 immunoprecipitated chromatin from mouse prefrontal cortices, we generated EGR1 binding maps with 12, 014 high-confidence peaks. Approximately 81% of EGR1 peaks were within genic regions or nearby promoters, and over 45% EGR1 peaks were in the proximal promoter regions within 1 kb from transcription starting sites.
2019-07-31 | GSE67482 | GEO
Project description:In this study we used CRISPR/Cas9 to generate KO clones of the HEK-RAF-ER cell line that lack expression of EGR1, FOS and profiled the transcriptome after inducing RAF/MAPK signaling.
2024-01-13 | GSE250532 | GEO
Project description:We performed transcriptome profiling for frontal cortex tissues derived from 6~8 week old Egr1-/- and Tet1-/- mice.
2019-07-25 | GSE108750 | GEO
Project description:To gain insight into the function of DNA-PKcs within immune cells, we performed a quantitative phosphoproteomic screen in T cells to identify first order phosphorylation targets of DNA-PKcs. Results indicate that DNA-PKcs phosphorylates the transcription factor Egr1 (early growth response protein 1) at S301. Expression of Egr1 is induced early upon T cell activation and dictates T cell response by modulating expression of cytokines and key costimulatory molecules. Mutation of serine 301 to alanine via CRISPR-Cas9 resulted in increased proteasomal degradation of Egr1 and a decrease in Egr1-dependent transcription of IL2 (interleukin-2) in activated T cells. Our findings identify DNA-PKcs as a critical intermediary link between T cell activation and T cell fate and a novel phosphosite involved in regulating Egr1 activity.
2021-12-21 | PXD026352 | Pride
Project description:Histones modulate gene expression by chromatin compaction, regulating numerous processes such as differentiation. However, the mechanisms underlying histone degradation remain elusive. When compared with their differentiated counterparts, immortal human embryonic stem cells (hESCs) have a unique chromatin architecture and low levels of trimethylated histone H3 at lysine 9 (H3K9me3), a heterochromatin-associated modification. Here we assess a link between the intrinsic epigenetic landscape and ubiquitin-proteasome system of hESCs. We find that hESCs exhibit high expression of UBE2K, a ubiquitin-conjugating enzyme. Loss of UBE2K increases the levels of H3K9 trimethyltransferase SETDB1, resulting in H3K9 trimethylation and repression of neurogenic genes during differentiation. Concomitantly, loss of UBE2K impairs the ability of hESCs to differentiate into neural progenitors with neurogenic properties. Besides H3K9 trimethylation, we find that UBE2K binds histone H3 to induce its polyubiquitination and degradation by the proteasome. Notably, ubc-20, the worm orthologue of UBE2K, also regulates both histone H3 levels and H3K9 trimethylation in C. elegans germline. Thus, our results indicate that UBE2K crosses evolutionary boundaries to promote histone H3 degradation and reduce H3K9me3 repressive marks in immortal cells.
2020-06-01 | PXD018625 | Pride
Project description:Early growth response gene 1 (EGR1) has been implicated in megakaryocyte differentiation induced by PMA (phorbol 12-myristate 13-acetate). The identification of direct EGR1 target genes in global scale is critical for our understanding of how EGR1 contributes to this process. In this study, we provide a global survey on the binding location of EGR1 in the K562 cell treated by PMA using chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq). K562 is a human erythroleukemia cell line, which is situated in the common progenitor stage of megakaryocytic and erythroid lineages of the hematopoietic stem cell differentiation and its normally following differentiation is blockaded. Upon exposure to PMA stimuli, K562 cell can be induced into megakaryocytic cell, which provides a model for the study of transcriptional control networks. Over 14 000 highly confident in vivo EGR1 binding sites were identified in PMA treated K562 cell. More than 70% of these genomic sites associated with EGR1 binding were located around annotated gene regions. This whole genome study on the EGR1 targets may help a better understanding of the EGR1 regulated genes and the downstream pathway in megakaryocyte differentiation. The in vivo binding locations of EGR1 in K562 cell treated with PMA (phorbol 12-myristate 13-acetate, 10 ng/ml for 2 hours) were identified using chromatin immunoprecipitation combing with massively parallel sequencing (ChIP-Seq) based on AB SOLiD System 2.0.
2010-09-08 | E-GEOD-21665 | biostudies-arrayexpress