Transcriptome dynamics during human erythroid differentiation and development.
Ontology highlight
ABSTRACT:
SUBMITTER: Yang Y
PROVIDER: S-EPMC4151266 | biostudies-literature | 2013 Nov-Dec
REPOSITORIES: biostudies-literature
Publications
Transcriptome dynamics during human erythroid differentiation and development.
Yang Yadong Y Wang Hai H Chang Kai-Hsin KH Qu Hongzhu H Zhang Zhaojun Z Xiong Qian Q Qi Heyuan H Cui Peng P Lin Qiang Q Ruan Xiuyan X Yang Yaran Y Li Yajuan Y Shu Chang C Li Quanzhen Q Wakeland Edward K EK Yan Jiangwei J Hu Songnian S Fang Xiangdong X
Genomics 20131008 5-6
To explore the mechanisms controlling erythroid differentiation and development, we analyzed the genome-wide transcription dynamics occurring during the differentiation of human embryonic stem cells (HESCs) into the erythroid lineage and development of embryonic to adult erythropoiesis using high throughput sequencing technology. HESCs and erythroid cells at three developmental stages: ESER (embryonic), FLER (fetal), and PBER (adult) were analyzed. Our findings revealed that the number of expres ...[more]
Similar Datasets
Project description:MicroRNAs (miRNAs) are an abundant class of small noncoding RNAs that regulate diverse cellular functions by sequence-specific inhibition of gene expression. We determined miRNA expression profile during erythroid differentiation and putative roles in erythroid differentiation.The expression profile of 295 miRNAs before and after their erythroid differentiation induction was analyzed using microarray. Fluorescein-activated cell sorting analysis was used to isolate mouse spleen erythroblasts at different differentiation stages. Human cord blood CD34+ progenitors were differentiated in vitro. Real-time reverse transcriptase polymerase chain reaction was used to confirm the results of miRNA microarray. Synthetic oligonucleotides for miR-451 overexpression or knockdown were transfected into MEL cells.More than 100 miRNAs were found to be expressed in erythroid cells. The majority of them showed changes in their expression levels with progression of erythroid differentiation. Further analysis revealed that overall miRNA expression levels are increased upon erythroid differentiation. Of the miRNAs analyzed, miR-451 was most significantly upregulated during erythroid maturation. Functional studies using gain of function and loss of function approaches showed that miR-451 is associated with erythroid maturation.Dynamic changes in miRNA expression occurred during erythroid differentiation, with an overall increase in the levels of miRNAs upon terminal differentiation of erythroid cells. MiR-451 may play a role in promoting erythroid differentiation.
| S-EPMC1955220 | biostudies-literature
Project description:We recently developed fluorescence-activated cell sorting (FACS)-based methods to purify morphologically and functionally discrete populations of cells, each representing specific stages of terminal erythroid differentiation. We used these techniques to obtain pure populations of both human and murine erythroblasts at distinct developmental stages. RNA was prepared from these cells and subjected to RNA sequencing analyses, creating unbiased, stage-specific transcriptomes. Tight clustering of transcriptomes from differing stages, even between biologically different replicates, validated the utility of the FACS-based assays. Bioinformatic analyses revealed that there were marked differences between differentiation stages, with both shared and dissimilar gene expression profiles defining each stage within transcriptional space. There were vast temporal changes in gene expression across the differentiation stages, with each stage exhibiting unique transcriptomes. Clustering and network analyses revealed that varying stage-specific patterns of expression observed across differentiation were enriched for genes of differing function. Numerous differences were present between human and murine transcriptomes, with significant variation in the global patterns of gene expression. These data provide a significant resource for studies of normal and perturbed erythropoiesis, allowing a deeper understanding of mechanisms of erythroid development in various inherited and acquired erythroid disorders.
| S-EPMC4041167 | biostudies-literature
Project description:Interplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci, but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Notably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors.
| S-EPMC3202283 | biostudies-literature
Project description:To explore the mechanisms controlling erythroid differentiation and development in human, we analyzed the genome-wide transcription dynamics that occurs during the differentiation of HESCs into the erythroid lineage and development of embryonic to adult erythropoiesis using high throughput sequencing technology. Undifferentiated HESCs as well as erythroid cells at three developmental stages-ESER (embryonic stage), FLER (fetal stage) and PBER (adult stage)-were analyzed. Our findings revealed that the number of expressed genes decreased during the differentiation, while the total expression intensity increased. At the 3 transitions (HESC-ESER, ESER-FLER and FLER-PBER), differential expression of many types of genes was observed at every transition. These differentially expressed genes were involved in maintaining the pluripotency of stem cells, early erythroid specification, rapid cell growth and enucleation potential. In addition, differentially expressed genes were found to constitute networks and central nodes at each transition. Clusters of genes in some chromosomal regions switched between expression and silence. We also discovered that differentially expressed genes constituted networks and central nodes of them in each transition. Our studies provide a fundamental basis for further investigation of erythroid differentiation and development. Compare the transcriptome of embryonic stem cells and three erythroid cell types at different developmental stages
2013-10-31 | E-GEOD-32991 | biostudies-arrayexpress
Project description:To explore the mechanisms controlling erythroid differentiation and development in human, we analyzed the genome-wide transcription dynamics that occurs during the differentiation of HESCs into the erythroid lineage and development of embryonic to adult erythropoiesis using high throughput sequencing technology. Undifferentiated HESCs as well as erythroid cells at three developmental stages-ESER (embryonic stage), FLER (fetal stage) and PBER (adult stage)-were analyzed. Our findings revealed that the number of expressed genes decreased during the differentiation, while the total expression intensity increased. At the 3 transitions (HESC-ESER, ESER-FLER and FLER-PBER), differential expression of many types of genes was observed at every transition. These differentially expressed genes were involved in maintaining the pluripotency of stem cells, early erythroid specification, rapid cell growth and enucleation potential. In addition, differentially expressed genes were found to constitute networks and central nodes at each transition. Clusters of genes in some chromosomal regions switched between expression and silence. We also discovered that differentially expressed genes constituted networks and central nodes of them in each transition. Our studies provide a fundamental basis for further investigation of erythroid differentiation and development.
2013-10-31 | GSE32991 | GEO
Project description:There is an imbalance between the supply and demand of functional red blood cells (RBCs) in clinical applications. This imbalance can be addressed by regenerating RBCs using several in vitro methods. Induced pluripotent stem cells (iPSCs) can handle the low supply of cord blood and the ethical issues in embryonic stem cell research, and provide a promising strategy to eliminate immune rejection. However, no complete single-cell level differentiation pathway exists for the iPSC-derived erythroid differentiation system. In this study, we used iPSC line BC1 to establish a RBC regeneration system. The 10X Genomics single-cell transcriptome platform was used to map the cell lineage and differentiation trajectory on day 14 of the regeneration system. We observed that iPSC differentiation was not synchronized during embryoid body (EB) culture. The cells (on day 14) mainly consisted of mesodermal and various blood cells, similar to the yolk sac hematopoiesis. We identified six cell classifications and characterized the regulatory transcription factor (TF) networks and cell-cell contacts underlying the system. iPSCs undergo two transformations during the differentiation trajectory, accompanied by the dynamic expression of cell adhesion molecules and estrogen-responsive genes. We identified erythroid cells at different stages, such as burst-forming unit erythroid (BFU-E) and orthochromatic erythroblast (ortho-E) cells, and found that the regulation of TFs (e.g., TFDP1 and FOXO3) is erythroid-stage specific. Immune erythroid cells were identified in our system. This study provides systematic theoretical guidance for optimizing the iPSC-derived erythroid differentiation system, and this system is a useful model for simulating in vivo hematopoietic development and differentiation.
| S-EPMC8864192 | biostudies-literature
Project description:The endosperm is a major organ of the seed that plays vital roles in determining seed weight and quality. However, genome-wide transcriptome patterns throughout maize endosperm development have not been comprehensively investigated to date. Accordingly, we performed a high-throughput RNA sequencing (RNA-seq) analysis of the maize endosperm transcriptome at 5, 10, 15 and 20 days after pollination (DAP). We found that more than 11,000 protein-coding genes underwent alternative splicing (AS) events during the four developmental stages studied. These genes were mainly involved in intracellular protein transport, signal transmission, cellular carbohydrate metabolism, cellular lipid metabolism, lipid biosynthesis, protein modification, histone modification, cellular amino acid metabolism, and DNA repair. Additionally, 7,633 genes, including 473 transcription factors (TFs), were differentially expressed among the four developmental stages. The differentially expressed TFs were from 50 families, including the bZIP, WRKY, GeBP and ARF families. Further analysis of the stage-specific TFs showed that binding, nucleus and ligand-dependent nuclear receptor activities might be important at 5 DAP, that immune responses, signalling, binding and lumen development are involved at 10 DAP, that protein metabolic processes and the cytoplasm might be important at 15 DAP, and that the responses to various stimuli are different at 20 DAP compared with the other developmental stages. This RNA-seq analysis provides novel, comprehensive insights into the transcriptome dynamics during early endosperm development in maize.
| S-EPMC5047526 | biostudies-literature
Project description:The K-Cl cotransporter (KCC) regulates red blood cell (RBC) volume, especially in reticulocytes. Western blot analysis of RBC membranes revealed KCC1, KCC3, and KCC4 proteins in mouse and human cells, with higher levels in reticulocytes. KCC content was higher in sickle versus normal RBC, but the correlation with reticulocyte count was poor, with inter-individual variability in KCC isoform ratios. Messenger RNA for each isoform was measured by real time RT-quantitative PCR. In human reticulocytes, KCC3a mRNA levels were consistently the highest, 1-7-fold higher than KCC4, the second most abundant species. Message levels for KCC1 and KCC3b were low. The ratios of KCC RNA levels varied among individuals but were similar in sickle and normal RBC. During in vivo maturation of human erythroblasts, KCC3a RNA was expressed consistently, whereas KCC1 and KCC3b levels declined, and KCC4 message first increased and then decreased. In mouse erythroblasts, a similar pattern for KCC3 and KCC1 expression during in vivo differentiation was observed, with low KCC4 RNA throughout despite the presence of KCC4 protein in mature RBC. During differentiation of mouse erythroleukemia cells, protein levels of KCCs paralleled increasing mRNA levels. Functional properties of KCCs expressed in HEK293 cells were similar to each other and to those in human RBC. However, the anion dependence of KCC in RBC resembled most closely that of KCC3. The results suggest that KCC3 is the dominant isoform in erythrocytes, with variable expression of KCC1 and KCC4 among individuals that could result in modulation of KCC activity.
| S-EPMC3162409 | biostudies-literature
Project description:BackgroundHuman globin gene expression is precisely regulated by a complicated network of transcription factors and chromatin modifying activities during development and erythropoiesis. Eos (Ikaros family zinc finger 4, IKZF4), a member of the zinc finger transcription factor Ikaros family, plays a pivotal role as a repressor of gene expression. The aim of this study was to examine the role of Eos in globin gene regulation.Methodology/principal findingsWestern blot and quantitative real-time PCR detected a gradual decrease in Eos expression during erythroid differentiation of hemin-induced K562 cells and Epo-induced CD34+ hematopoietic stem/progenitor cells (HPCs). DNA transfection and lentivirus-mediated gene transfer demonstrated that the enforced expression of Eos significantly represses the expression of γ-globin, but not other globin genes, in K562 cells and CD34+ HPCs. Consistent with a direct role of Eos in globin gene regulation, chromatin immunoprecipitaion and dual-luciferase reporter assays identified three discrete sites located in the DNase I hypersensitivity site 3 (HS3) of the β-globin locus control region (LCR), the promoter regions of the Gγ- and Aγ- globin genes, as functional binding sites of Eos protein. A chromosome conformation capture (3C) assay indicated that Eos may repress the interaction between the LCR and the γ-globin gene promoter. In addition, erythroid differentiation was inhibited by enforced expression of Eos in K562 cells and CD34+ HPCs.Conclusions/significanceOur results demonstrate that Eos plays an important role in the transcriptional regulation of the γ-globin gene during erythroid differentiation.
| S-EPMC3145782 | biostudies-literature
Project description:The aim of the present study has been to establish serum-free culture conditions for ex vivo expansion and differentiation of human CD34(+) cells into erythroid lineage and to study the chromatin structure, gene expression, and transcription factor recruitment at the alpha-globin locus in the developing erythron.A basal Iscove's modified Dulbecco's medium cell culture medium with 1% bovine serum albumin as a serum replacement and a combination of cytokines and growth factors was used for expansion and differentiation of the CD34(+) cells. Expression patterns of the alpha- and beta-like genes at various stages of erythropoiesis was studied by reverse transcriptase quantitative polymerase chain reaction analysis, profile of key erythroid transcription factors was investigated by Western blotting, and the chromatin structure and transcription factor recruitment at the alpha-globin locus was investigated by chromatin immunoprecipitation quantitative polymerase chain reaction analysis.Human CD34(+) cells in the serum-free medium undergo near synchronous erythroid differentiation to yield large amount of cells at different differentiation stages. We observe distinct patterns of the histone modifications and transcription factor binding at the alpha-globin locus during erythroid differentiation of CD34(+) cells. Nuclear factor erythroid-derived 2 (NF-E2) was present at upstream activator sites even before addition of erythropoietin (EPO), while bound GATA-1 was only detectable after EPO treatment. After 7 days of EPO treatment, H3K4Me2 modification uniformly increases throughout the alpha-globin locus. Acetylation at H3K9 and binding of Pol II, NF-E2, and GATA-1 were restricted to certain hypersensitive sites of the enhancer and theta gene, and were conspicuously low at the alpha-like globin promoters. Rearrangement of the insulator binding factor CTCF took place at and around the alpha-globin locus as CD34(+) cells differentiated into erythroid pathway.Our results indicate that remodeling of the upstream elements may be the primary event in activation of alpha-globin gene expression. Activation of alpha-globin genes upon EPO treatment involves initial binding of Pol II, downregulation of pre-existing factors like NF-E2, removal of CTCF from the locus, then rebinding of CTCF in an altered pattern, and concurrent or subsequent binding of transcription factors like GATA-1.
| S-EPMC2997688 | biostudies-literature