AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesInformation Science
ChromatinErythroid CellsChromatin Assembly and DisassemblyErythropoiesisHistonesChromatin ImmunoprecipitationErythroblastsNucleosomesLeukemia, Erythroblastic, AcuteGlobinsErythropoietinGATA1 Transcription FactorErythrocytesTranscription, GeneticTranscription FactorsPromoter Regions, GeneticAcetylationErythroid-Specific DNA-Binding FactorsDNA-Binding ProteinsCell DifferentiationChromosomal Proteins, Non-HistoneMicrococcal NucleaseHematopoietic Stem CellsDNACell NucleusGene Expression RegulationK562 CellsReceptors, ErythropoietinBase SequenceNuclear ProteinsCell LineMolecular Sequence DataColony-Forming Units AssayProtein BindingDeoxyribonuclease IChromatin Assembly Factor-1Sex Chromatinbeta-GlobinsFetal HemoglobinMethylationEpigenesis, GeneticCells, CulturedHeterochromatinHematopoiesisGene SilencingRepressor ProteinsNF-E2 Transcription Factor, p45 SubunitGlycophorinBinding SitesBone Marrow Cellsgamma-GlobinsMegakaryocytesRNA, MessengerBone MarrowReticulocytesNF-E2 Transcription FactorGATA2 Transcription FactorHistone DeacetylasesHeLa CellsEnhancer Elements, GeneticHistone AcetyltransferasesChickensTranscriptional ActivationLocus Control RegionGene Expression Regulation, DevelopmentalMutationKruppel-Like Transcription FactorsFriend murine leukemia virusCell LineageSaccharomyces cerevisiae ProteinsChromosomesPolycythemia Vera5-Aminolevulinate SynthetaseSaccharomyces cerevisiaeDNA MethylationDNA ReplicationInsulator ElementsCell Cycle ProteinsLysineHistone-Lysine N-MethyltransferaseCell DivisionSpectrinAmino Acid SequenceTrans-ActivatorsAntigens, CD34Dimethyl SulfoxideLiverRNA Polymerase IIYolk SacStem Cell FactorHeminHemoglobinsEuchromatinCell CyclePolycythemiaTumor Cells, CulturedAnemiaLeukemia, ExperimentalMitosisDeoxyribonucleases
DifferentiationOpen chromatinTranscriptionalGenesCellsMaturationGata1EnhancerHematopoieticMegakaryocytesLineagesProteinsRegulatoryGenomeProgenitorHistone methyltransferaseGenomicPhenotypePromoterStructuralInteractionsPromoters and enhancersTranscription factorReplicationGene transcriptionAccessibilityVivoAcuteDrosophilaInteractionInterplayNuclearRepressiveRegulatorExpressionMolecular
Differentiation21
  • Orthologous to human TAL1 (TAL bHLH transcription factor 1, erythroid differentiation factor). (nih.gov)
  • The histone methyltransferase Setd8 alters the chromatin landscape and regulates the expression of key transcription factors during erythroid differentiation. (rochester.edu)
  • Although studies have identified several miRNAs that regulate erythroid commitment and differentiation, we do not understand the mechanism by which the crucial erythroid transcription factors, GATA-1and NF-E2 directly regulate and control differentiation via miRNA pathways. (molcells.org)
  • In this study, we identified miR-199b-5p as a key regulator of human erythropoiesis, and its expression was up-regulated during the erythroid differentiation of K562 cells. (molcells.org)
  • Taken together, our results establish a functional link among the erythroid transcription factors GATA-1/NF-E2, miR-199b-5p and c-Kit, and provide new insights into the coupling of transcription and post-transcription regulation in erythroid differentiation. (molcells.org)
  • The up-regulation of miR-199b-5p during erythroid differentiation was dependent on the binding of GATA-1 and NF-E2 to its gene locus, which activated its transcription and maintained its high expression level in mature erythroid cells. (molcells.org)
  • lab: PSU-m lab description: Hardison - Penn State University datatype: ChipSeq datatype description: Chromatin IP Sequencing cell: G1E-ER4 cell organism: mouse cell description: Gata1 restored erythroid cells, differentiation induced by estradiol (E2) cell sex: M antibody: Input antibody description: Control signal which may be subtracted from experimental raw signal before peaks are called. (nih.gov)
  • With the advent of new genomics technologies and improved biological in vitro differentiation systems, time series ChIP-seq data sets have been generated that allow for investigating chromatin states across multiple time points. (biomedcentral.com)
  • Recent advances deeply increase our understanding of erythropoiesis control and its deregulation in pathological conditions thanks to the studies of chromatin organization and post-transcriptional regulatory mechanisms occurring during erythroid cell differentiation. (esh.org)
  • This identified IOX1, a pan-histone demethylase inhibitor, which selectively downregulates α-globin expression without perturbing erythroid differentiation or general gene expression, more specifically β-like globin expression. (haematologica.org)
  • We first optimized a serum-free, miniature erythroid differentiation system starting from primary human CD34 cells, the exact type of cells we would ultimately like to target in vivo ( Figure 1 ). (haematologica.org)
  • Characterization and validation of the small scale erythroid differentiation system used for small molecule screen. (haematologica.org)
  • An essential step for understanding gene regulatory pathways at key differentiation time points, therefore, should lie in characterizing the enzymes responsible for reorganizing and potentiating particular chromatin domains. (biomedcentral.com)
  • Another large gap in our understanding of osteoclastogenic transcription program is the identification of chromatin factors that have the potential to link specific aspects of chromatin function to osteoclast differentiation processes. (biomedcentral.com)
  • This system will enable us to visualise promoter/enhancer dynamics throughout erythroid differentiation and correlate chromatin movements with gene transcription. (ox.ac.uk)
  • We use this approach to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. (umassmed.edu)
  • Integrated analysis of chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation. (umassmed.edu)
  • Cohesin binding increases at active regulatory elements only during erythroid differentiation. (ox.ac.uk)
  • Depletion of Cohesin severely impairs erythroid differentiation, particularly at Etv6-pre-bound loci, but augments self-renewal programmes. (ox.ac.uk)
  • Together with corroborative findings in acute myeloid leukemia and myelodysplastic syndrome patient samples, these data suggest Cohesin-mediated alleviation of Etv6 repression is required for dynamic expression at critical erythroid genes during differentiation and how this may be perturbed in myeloid malignancies. (ox.ac.uk)
  • Ectopic expression of these factors in murine erythroid progenitors blocked in vitro erythroid differentiation and led to immortalization associated with decreased chromatin accessibility at GATA1-binding sites and functional interference with GATA1 activity. (ox.ac.uk)
Open chromatin4
  • We utilize time series ATAC-seq data measuring open chromatin to define promoters and enhancer candidates. (biomedcentral.com)
  • ACSs and DNaseI HSs were distributed between both expressed and nonexpressed genes, suggesting that a large proportion of genes reside within open chromatin domains. (uea.ac.uk)
  • We investigated the presence of transposable elements (TEs) in open chromatin regions across all tissues, these included identifications of porcine endogenous retroviruses (PERVs) exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements. (biomedcentral.com)
  • Erythroblasts are mildly increased in size with bizarre nuclear abnormalities including multilobulated nuclei, open chromatin pattern simulating megaloblastic appearance. (mhmedical.com)
Transcriptional6
  • The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. (elifesciences.org)
  • GATA-1 and PU.1 then initiate the presumed cascade of It governs the erythroid - myeloid lineages and demonstrates both transcriptional changes that culminate in the specification of the commitment as well as priming features [6,7]. (lu.se)
  • Focal alteration in chromatin structure in vivo, detectable through hypersensitivity to DNaseI and other nucleases, is the sine qua non of a diverse cast of transcriptional regulatory elements including enhancers, promoters, insulators, and locus control regions. (uea.ac.uk)
  • Fig. 3: eRNAs modulate the chromatin interactions of transcriptional regulators. (nature.com)
  • Chromatin insulators are DNA-protein complexes that influence gene expression by establishing chromatin domains subject to distinct transcriptional controls, likely through alteration of their spatial organization. (nih.gov)
  • Transcriptional environment and chromatin architecture interplay dictates globin expression patterns of heterospecific hybrids derived from undifferentiated human embryonic stem cells or from their erythroid progeny. (uci.edu)
Genes7
  • We develop a computational model for the hematopoietic erythroid-myeloid lineage decision, which is determined by a genetic switch involving the genes PU.1 and GATA-1. (lu.se)
  • However, prior to commitment, it has been cells, it is evident that GATA-1 and PU.1 are able to specify observed that many genes are expressed at intermediate or basal erythroid and myeloid cell fates (see [16] and references therein). (lu.se)
  • MMP-9 plays a direct role in the activation of pro-osteoclastogenic genes by cleaving histone H3N-terminal tail (H3NT) and altering chromatin architecture. (biomedcentral.com)
  • The analysis of genomic expression during human myelopoiesis using an integrative computational approach allowed discovering important relationships between genomic position, biological function and expression patterns and highlighting chromatin domains, including genes with coordinated expression and lineage-specific functions. (biomedcentral.com)
  • The HS-40 enhancer is the major cis-acting regulatory element responsible for the developmental stage- and erythroid lineage-specific expression of the human α-like globin genes, the embryonic ζ and the adult α2/α/1. (tmu.edu.tw)
  • Examples include metazoan Hox genes, master regulators of body segmentation, and the vertebrate beta-globin locus, which changes in expression during erythroid development. (nih.gov)
  • The last 2 CDA types are caused by mutations in the erythroid transcription factor genes KLF1 (19p13.2) and GATA1 (Xp11.23). (orpha.net)
Cells19
  • Codanin-1 Mutations Engineered in Human Erythroid Cells Demonstrate Role of CDAN1 in Terminal Erythroid Maturation. (rochester.edu)
  • Furthermore, the increase of miR-199b-5p in erythroid cells occurred in a GATA-1- and NF-E2-dependent manner during erythrocyte maturation. (molcells.org)
  • Forced expression of miRNA-199b-5p in K562 cells affected erythroid cell proliferation and maturation. (molcells.org)
  • Moreover, we identified c-Kit as a direct target of miR-199b-5p in erythroid cells. (molcells.org)
  • Our data show that selective silencing of α-globin expression in erythroid cells is pharmacologically feasible, and IOX1 is a lead compound to developing new therapy to treat β-thalassemia through the novel pathway of downregulating α-globin expression. (haematologica.org)
  • In embryonic stem cells, SMAD2/3-TIF1γ recognizes specific chromatin marks, promoting access of SMAD2/3-SMAD4 to otherwise repressed targets. (shu.edu)
  • First, human erythroid K562 cells stably integrated with various HS-40 mutants cis linked to a human α-globin promoter-growth hormone hybrid gene were analyzed by genomic footprinting and expression analysis. (tmu.edu.tw)
  • Second, a specific 1- bp, GC→TA mutation in the 3'-NA motif of HS-40, 3'-NA(II), has been shown previously to cause significant derepression of the embryonic ζ-globin promoter activity in erythroid cells. (tmu.edu.tw)
  • Finally, we show by chromatin immunoprecipitation experiments that only binding of NF- E2, not AP1, could be detected in vivo in K562 cells around the HS-40 region. (tmu.edu.tw)
  • These data exclude a role for AP1 in the developmental regulation of the human α-globin locus via the 3'-NA motif of HS-40 in embryonic/fetal erythroid cells. (tmu.edu.tw)
  • 61,000 ACSs derived from erythroid cells. (uea.ac.uk)
  • Our study implicates SPOP and the CUL3 ubiquitin ligase system in controlling HbF production in human erythroid cells and may offer new therapeutic strategies for the treatment of b-hemoglobinopathies. (wustl.edu)
  • CRISPR/Cas9-mediated TPM1 knockout in human induced pluripotent stem cells (iPSCs) enhanced hematopoietic progenitor development, increasing total megakaryocyte and erythroid cell yields. (biomedcentral.com)
  • The histone H3K4 demethylase JARID1A directly interacts with haematopoietic transcription factor GATA1 in erythroid cells through its second PHD domain. (ox.ac.uk)
  • The vacuoles usually occur in early erythroid cells as seen here and very occasionally in myeloid cells. (mhmedical.com)
  • Most of the red pulp is composed of erythroid islands, myeloid precursor cells and megakaryocytes. (cap.org)
  • Large cell lymphoma and leukemia cells tend to have large size nuclei, less mature chromatin, and visible nucleoli with and without cytoplasmic vacuoles. (cytojournal.com)
  • Collectively, our data indicate that AEL is a molecularly heterogeneous disease with an erythroid identity that results in part from the aberrant activity of key erythroid transcription factors in hematopoietic stem or progenitor cells. (ox.ac.uk)
  • Globin phenotype of erythroid cells derived from human induced pluripotent stem cells. (uci.edu)
Maturation4
  • The Steiner laboratory utilizes genomics techniques to study the molecular mechanisms underlying erythroid maturation and development. (rochester.edu)
  • Regulation of RNA Polymerase II Activity is Essential for Terminal Erythroid Maturation. (rochester.edu)
  • Depletion of SPOP or overexpression of a dominant negative version significantly raised fetal globin messenger RNA and protein levels with minimal detrimental effects on normal erythroid maturation, as determined by transcriptome and proteome analyses. (wustl.edu)
  • The erythroid islands show normoblastic maturation. (cap.org)
Gata11
  • SATB1 Chromatin Loops Regulate Megakaryocyte/Erythroid Progenitor Expansion by Facilitating HSP70 and GATA1 Induction. (ucla.edu)
Enhancer6
  • Co-localized combinations of histone modifications ("chromatin states") have been shown to correlate with promoter and enhancer activity. (biomedcentral.com)
  • With the advent of time series Hi-C data it is now possible to connect promoters and enhancers and to analyze chromatin state trajectories at promoter-enhancer pairs. (biomedcentral.com)
  • We present TimelessFlex, a framework for investigating chromatin state trajectories at promoters and enhancers and at promoter-enhancer pairs based on Hi-C information. (biomedcentral.com)
  • TimelessFlex clusters time series histone modifications at promoter-enhancer pairs based on Hi-C and it can identify distinct chromatin states at promoter and enhancer feature regions and their changes over time. (biomedcentral.com)
  • Fig. 2: eRNA regulation of enhancer-promoter interactions and the epigenetic state of chromatin. (nature.com)
  • I am developing a live-cell model in which chromatin at the alpha globin promoter and enhancer sequences is bound by fluorescently labelled proteins. (ox.ac.uk)
Hematopoietic1
  • Citation: Chickarmane V, Enver T, Peterson C (2009) Computational Modeling of the Hematopoietic Erythroid-Myeloid Switch Reveals Insights into Cooperativity, Priming, and Irreversibility. (lu.se)
Megakaryocytes1
Lineages1
  • [ 3 , 4 ] as a type of MDS with one or more cytopenias and dysplastic changes in two or more of the myeloid lineages (erythroid, granulocytic, or megakaryocytic). (medscape.com)
Proteins2
  • The laboratory is particularly interested in studying how specific DNA sequences, DNA binding proteins, and chromatin. (rochester.edu)
  • To identify new HbF regulators that might be amenable to pharmacologic control, we screened a protein domain-focused CRISPR-Cas9 library targeting chromatin regulators, including BTB domain-containing proteins. (wustl.edu)
Regulatory4
  • A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits. (biomedcentral.com)
  • Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq, and identified 557,273 merged peaks, which greatly expanded the pig regulatory element repository. (biomedcentral.com)
  • Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions, as well as regulatory variants of loci associated with complex traits in pigs. (biomedcentral.com)
  • The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. (umassmed.edu)
Genome3
  • Chromatin states have initially been annotated in a spatial manner genome-wide, by segmenting the genome into distinct states based on histone modification ChIP-seq data from, for instance, one cell line, which represents an unsupervised learning problem. (biomedcentral.com)
  • We developed an approach for genome-scale identification of DNaseI hypersensitive sites (HSs) via isolation and cloning of in vivo DNaseI cleavage sites to create libraries of active chromatin sequences (ACSs). (uea.ac.uk)
  • However, the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs. (biomedcentral.com)
Progenitor1
  • Phenotypic and proteomic characterization of the human erythroid progenitor continuum reveal dynamic changes in cell cycle and in metabolic pathways. (rochester.edu)
Histone methyltransferase1
  • We show that Bonus associates with the histone methyltransferase SetDB1 and the chromatin remodeler NuRD and depletion of either component releases Bonus-induced repression. (elifesciences.org)
Genomic1
Phenotype1
  • To better define the underlying molecular mechanisms driving the erythroid phenotype, we studied a series of 33 AEL samples representing 3 genetic AEL subgroups including TP53-mutated, epigenetic regulator-mutated (eg, DNMT3A, TET2, or IDH2), and undefined cases with low mutational burden. (ox.ac.uk)
Promoter1
  • Changes in chromatin states over multiple time points ("chromatin state trajectories") have previously been analyzed at promoter and enhancers separately. (biomedcentral.com)
Structural2
Interactions1
  • We developed an expectation-maximization algorithm to assign promoters and enhancers to each other based on Hi-C interactions and jointly cluster their feature regions into paired chromatin state trajectories. (biomedcentral.com)
Promoters and enhancers1
  • It has been shown by chromatin conformation capture techniques that gene promoters and enhancers interact in three-dimensional space to boost transcription. (ox.ac.uk)
Transcription factor1
  • Prior binding of the repressive Ets transcription factor Etv6 predicts Cohesin binding at these elements and Etv6 interacts with Cohesin at chromatin. (ox.ac.uk)
Replication2
  • We are building on evidence that Codanin-1 and C15ORF41 interact and play a role in a novel pathway affecting DNA replication or chromatin assembly. (ox.ac.uk)
  • CDA I is due to mutations in the CDAN1 gene (15q15.2), coding for a histone chaperone interacting protein, or in the C15ORF41 gene (15q14), coding for a predicted endonuclease putatively involved in DNA replication and/or chromatin assembly. (orpha.net)
Gene transcription2
  • Not much progress has been made in supporting this idea, but there is some indirect evidence functionally linking chromatin modification to osteoclastogenic gene transcription. (biomedcentral.com)
  • Nonetheless, which factors are mainly responsible for establishing transcriptionally competent chromatin states and exactly how altered chromatin states trigger osteoclastogenic gene transcription remain poorly understood. (biomedcentral.com)
Accessibility1
  • Over the past decades, several chromatin accessibility profiling methods including DNase I hypersensitive site sequencing (DNase-seq), micrococcal nuclease sequencing (MNase-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) have been developed. (biomedcentral.com)
Vivo1
  • In vivo models showed development of lethal erythroid, mixed erythroid/myeloid, or other malignancies depending on the cell population in which AEL-associated alterations were expressed. (ox.ac.uk)
Acute2
  • Moreover, recent studies have shown that loss of insulator activity in IDH1 mutant gliomas and T cell acute lymphoblastic leukemias leads to disruption of boundaries between chromatin domains and subsequent oncogene activation. (nih.gov)
  • Acute erythroid leukemia. (oncohemakey.com)
Drosophila1
  • Drosophila harbors the largest diversity of known chromatin insulator complexes. (nih.gov)
Interaction2
  • Recruitment of 53BP1 to chromatin flanking double strand breaks (DSBs) requires γH2AX/MDC1/RNF8-dependent ubiquitination of chromatin and interaction of 53BP1 with histone H4 methylated on lysine 20 (H4K20me). (cipsm.de)
  • SUMOylation influences Bonus's subnuclear localization, its association with chromatin and interaction with SetDB1. (elifesciences.org)
Interplay1
Nuclear1
Repressive1
  • Recruitment of Bonus to chromatin leads to silencing associated with accumulation of the repressive H3K9me3 mark. (elifesciences.org)
Regulator1
  • In the present study, we identified miR-199b-5p as a positive erythroid regulator, that was regulated by the key erythroid transcription factors GATA-1 and NF-E2. (molcells.org)
Expression2
Molecular1
  • We established an erythroid vs myeloid transcriptome-based space in which, independently of the molecular subgroup, the majority of the AEL samples exhibited a unique mapping different from both non-M6 AML and myelodysplastic syndrome samples. (ox.ac.uk)