Transglutaminase 2 regulates terminal erythroid differentiation via cross-linking activity
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE229589 | GEO | 2023/04/23
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptome analysis of total RNA samples from FACS sorted erythroblasts To further verify the role of cytokine triggered inflammation signaling in erythropoiesis, we decided to follow the profile of gene expression in erythroblasts using DNA microarrays. To elucidated the gene expression pattern in cytokine, especially IL-6, challenged erythroblasts, in vitro IL-6 treated erythroblasts in EPO containing medium both at day 1 and day 2 were collected. We also sorted the erythroblasts at different stages (Proerythroblasts(I),Basophilic(II) and polychromatic(III) erythroblasts,Orthochromatic(IV) erythroblasts) from both DWT and DKO bone marrow cells through fluorescence activated cell sorting. Total RNA were extracted and processed to hybridize with Affymetrix mouse Clariom S microarrays.
2017-09-09 | GSE98375 | GEO
Project description:In absence of selenium, proerythroblasts exhibited delay in differentation into basophilic erythroblasts during phenylhydrazine induced stress erythropoiesis. This microarray project was aiming to explore gene expression patterns in erythroblasts in the function of selenium status.
2018-05-28 | GSE102056 | GEO
Project description:Stab2-iCreF3tg/wt Ctnnb1(Ex3)fl/wt become anemic by the age of three months. We utilzed this model to investigated effects of niche Wnt-Signaling alterations on the terminal erythroid progenitor populations PIII (polychromatic erythroblasts) and PIV (orthochromatic erythroblasts and reticulocytes) by microarray transcriptome analysis.
2021-10-13 | GSE159520 | GEO
Project description:Human erythroblasts purified from cord blood were cultured in vitro and FACS-sorted into five highly purified populations representing distinct differentiation stages: proerythroblasts, early basophilic erythroblasts, late basophilic erythroblasts, polychromatophilic erythroblasts, and orthochromatophilic erythroblasts. The methods for culture and sorting experiments are given in Hu et al. 2013. For each RNA-seq library, RNA was isolated from 1x 106 sorted human erythroblasts using RNeasy Plus Mini kits (Qiagen). Libraries were then prepared using Illumina TruSeqTM RNA kits to obtain 50 nt reads. Collaborators at the New Your Blood Center were responsible for erythroblast culture, FACS purification of erythroblast populations, and acquisition of RNA-seq data. Collaborators at U.C. Berkeley and Lawrence Berkeley National Laboratory performed data analysis and experimental validation of alternative splicing in erythroblasts. Results: Differentiating erythroblasts execute a dynamic alternative splicing program that is enriched in genes affecting cell cycle, organelle organization, chromatin function, and RNA processing. Alternative splicing plays a major role in regulating gene expression to ensure synthesis of appropriate proteome at each stage as the cells remodel in preparation for production of mature red cells. Erythroid differentiation stage-specific transcriptome analysis was performed by RNA-seq analysis of highly purified erythroblast populations
2013-12-25 | E-GEOD-53635 | biostudies-arrayexpress
Project description:Human erythroblasts purified from cord blood were cultured in vitro and FACS-sorted into five highly purified populations representing distinct differentiation stages: proerythroblasts, early basophilic erythroblasts, late basophilic erythroblasts, polychromatophilic erythroblasts, and orthochromatophilic erythroblasts. The methods for culture and sorting experiments are given in Hu et al. 2013. For each RNA-seq library, RNA was isolated from 1x 106 sorted human erythroblasts using RNeasy Plus Mini kits (Qiagen). Libraries were then prepared using Illumina TruSeqTM RNA kits to obtain 50 nt reads. Collaborators at the New Your Blood Center were responsible for erythroblast culture, FACS purification of erythroblast populations, and acquisition of RNA-seq data. Collaborators at U.C. Berkeley and Lawrence Berkeley National Laboratory performed data analysis and experimental validation of alternative splicing in erythroblasts. Results: Differentiating erythroblasts execute a dynamic alternative splicing program that is enriched in genes affecting cell cycle, organelle organization, chromatin function, and RNA processing. Alternative splicing plays a major role in regulating gene expression to ensure synthesis of appropriate proteome at each stage as the cells remodel in preparation for production of mature red cells.
2013-12-25 | GSE53635 | GEO
Project description:SF3B1 knockdown in human CD34+ cells leads to increased apoptosis and cell cycle arrest of early-stage erythroid cells and generation of abnormally nucleated late-stage erythroblasts. RNA-seq analysis of SF3B1-knockdown erythroid progenitor CFU-E cells revealed altered splicing of an E3 ligase Makorin Ring Finger Protein 1 (MKRN1) and subsequent activation of p53 pathway.Decreased expression of genes involved in mitosis/cytokinesis pathway including polo-like kinase 1 (PLK1) was noted in SF3B1-knockdown polychromatic and orthochromatic erythroblasts comparing to control cells.
2021-04-24 | GSE173232 | GEO
Project description:It is unclear how epigenetic changes regulate the induction of erythroid-specific genes during terminal erythropoiesis. Here we use global mRNA sequencing (mRNA-seq) and chromatin immunoprecipitation coupled to high-throughput sequencing (CHIP-seq) to investigate the changes that occur in mRNA levels, RNA Polymerase II (Pol II) occupancy and multiple post-translational histone modifications when erythroid progenitors differentiate into late erythroblasts. Among genes induced during this developmental transition, there was an increase in the occupancy of Pol II, the activation marks H3K4me2, H3K4me3, H3K9Ac and H4K16Ac, and the elongation methylation mark H3K79me2. In contrast, genes that were repressed during differentiation showed relative decreases in H3K79me2 levels yet had levels of Pol II binding and active histone marks similar to those in erythroid progenitors. We also found that relative changes in histone modification levels-in particular, H3K79me2 and H4K16ac-were most predictive of gene expression patterns. Our results suggest that in terminal erythropoiesis both promoter and elongation-associated marks contribute to the induction of erythroid genes, while gene repression is marked by changes in histone modifications mediating Pol II elongation. Our data maps the epigenetic landscape of terminal erythropoiesis and suggests that control of transcription elongation regulates gene expression during terminal erythroid differentiation. Mouse fetal liver cells are double-labeled for erythroid-specific TER119 and non erythroid-specific transferrin receptor (CD71) and then sorted by flow-cytometry. E14.5 fetal livers contain at least five distinct populations of cells (R1 through R5); as they progressively differentiate they gain TER119 and then gain and subsequently lose CD71. CFU-E cells and proerythroblasts make up the R1 population; R2 consists of proerythroblasts and early basophilic erythroblasts; R3 includes early and late basophilic erythroblasts; R4 is mostly polychromatophilic and orthochromatophilic erythroblasts; and R5 is comprised of late orthochromatophilic erythroblasts and reticulocytes. We have sorted for R2-R5 cells for RNA-seq experiment.
2011-09-13 | E-GEOD-32110 | biostudies-arrayexpress
Project description:Fine-resolution differentiation trajectories of adult human hematopoietic stem cells (HSC) involved in the generation of red cells is critical for understanding dynamic developmental changes that accompany human erythropoiesis. Using Single-cell RNA sequencing (scRNA-seq) of primary human terminal erythroid cells (CD34−CD235a+) isolated directly from adult bone marrow (BM) and umbilical cord blood (UCB), we documented the transcriptome of terminally differentiated human erythroblasts at unprecedented resolution. The insights enabled us to distinguish polychromatic erythroblasts (PolyE) at the early and late stages of development as well as the different development stages of orthochromatic erythroblasts (OrthoE). We further identified a set of putative regulators of terminal erythroid differentiation and functionally validated three of the identified genes, AKAP8L, TERF2IP and RNF10, by monitoring cell differentiation and apoptosis. We documented that knockdown of AKAP8L suppressed the commitment of HSC to erythroid lineage and cell proliferation, and delayed differentiation of colony forming unit-erythroid (CFU-E) to the proerythroblast stage (ProE). In contrast, the knockdown of TERF2IP and RNF10 delayed differentiation of PolyE to OrthoE stage. Taken together, the convergence and divergence of the transcriptional continuums at single-cell resolution underscore the transcriptional regulatory networks that underlie human fetal and adult terminal erythroid differentiation.
2020-05-25 | GSE150774 | GEO
Project description:Nascent strand were purified with the BrdU methods from culture human basophilic erythroblasts and sequenced.
2015-05-19 | GSE61972 | GEO
Project description:Nascent strand were purified with either the BrdU or the lambda exonuclease methods from culture human basophilic erythroblasts and sequenced/
2014-05-01 | GSE50976 | GEO