Epigenetic Regulators as the Gatekeepers of Hematopoiesis
Authors: Cecilia Pessoa Rodrigues, Maria Shvedunova, Asifa Akhtar
Journal: Trends in Genetics (2020)

The epigenetic landscape regulates HSC heterogeneity and hematopoietic cell fate decisions.Chromatin analyses of hematopoietic cells have led to novel insights into HSC priming and biology.Crosstalk between metabolism and chromatin is emerging as a crucial facet in regulating hematopoiesis.Epigenetic regulators are promising targets for treatment of blood disorders including leukemia. Hematopoiesis is the process by which both fetal and adult organisms derive the full repertoire of blood cells from a single multipotent progenitor cell type, the hematopoietic stem cells (HSCs). Correct enactment of this process relies on a synergistic interplay between genetically encoded differentiation programs and a host of cell-intrinsic and cell-extrinsic factors. These include the influence of the HSC niche microenvironment, action of specific transcription factors, and alterations in intracellular metabolic state. The consolidation of these inputs with the genetically encoded program into a coherent differentiation program for each lineage is thought to rely on epigenetic modifiers. Recent work has delineated the precise contributions of different classes of epigenetic modifiers to HSC self-renewal as well as lineage specification and differentiation into various cell types. Here, we bring together what is currently known about chromatin status and the development of cells in the hematopoietic system under normal and abnormal conditions. Hematopoiesis is the process by which both fetal and adult organisms derive the full repertoire of blood cells from a single multipotent progenitor cell type, the hematopoietic stem cells (HSCs). Correct enactment of this process relies on a synergistic interplay between genetically encoded differentiation programs and a host of cell-intrinsic and cell-extrinsic factors. These include the influence of the HSC niche microenvironment, action of specific transcription factors, and alterations in intracellular metabolic state. The consolidation of these inputs with the genetically encoded program into a coherent differentiation program for each lineage is thought to rely on epigenetic modifiers. Recent work has delineated the precise contributions of different classes of epigenetic modifiers to HSC self-renewal as well as lineage specification and differentiation into various cell types. Here, we bring together what is currently known about chromatin status and the development of cells in the hematopoietic system under normal and abnormal conditions. The mammalian blood system serves as an excellent paradigm to study adult stem cell renewal and cell fate commitment, since despite their tremendous diversity in terms of cell morphology, molecular features and functions – ranging from oxygen carriage to wound healing and pathogen defense – all the mature blood cells have a common progenitor: the hematopoietic stem cells (HSCs; see Glossary). These cells are a relatively rare population that sits at the apex of blood cell differentiation. Functionally, HSCs are defined by their capacity to reconstitute the entire blood system of a lethally irradiated recipient [1.Orkin S.H. Zon L.I. Hematopoiesis: an evolving paradigm for stem cell biology.Cell. 2008; 132: 631-644Abstract Full Text Full Text PDF PubMed Scopus (1409) Google Scholar,2.Cumano A. Godin I. Ontogeny of the hematopoietic system.Annu. Rev. Immunol. 2007; 25: 745-785Crossref PubMed Scopus (283) Google Scholar]. Hematopoietic differentiation or hematopoiesis is a dynamic process fine-tuned by both extrinsic and intrinsic factors [3.Seita J. Weissman I.L. Hematopoietic stem cell: self-renewal versus differentiation.Wiley Interdiscip. Rev. Syst. Biol. Med. 2010; 2: 640-653Crossref PubMed Scopus (368) Google Scholar, 4.Trompouki E. et al.Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration.Cell. 2011; 147: 577-589Abstract Full Text Full Text PDF PubMed Scopus (205) Google Scholar, 5.Chambers S.M. et al.Hematopoietic fingerprints: an expression database of stem cells and their progeny.Cell Stem Cell. 2007; 1: 578-591Abstract Full Text Full Text PDF PubMed Scopus (210) Google Scholar, 6.Zhang C.C. Lodish H.F. Cytokines regulating hematopoietic stem cell function.Curr. Opin. Hematol. 2008; 15: 307-311Crossref PubMed Scopus (113) Google Scholar]. The niche is a complex multicellular network composed of stem, progenitor and mature hematopoietic cells and nonhematopoietic cell types, and represents the most significant extrinsic cue. This microenvironment provides a variety of inputs such as exposure to cytokine or growth factor signaling, variable oxygen and pH conditions, as well as cell–cell contacts and extracellular matrix stiffness. Thereby, an intact niche provides the appropriate signals and conditions for maintaining HSC quiescence and promoting progenitor cell differentiation [7.Baccin C. et al.Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization.Nat. Cell Biol. 2020; 22: 38-48Crossref PubMed Scopus (41) Google Scholar, 8.Derecka M. et al.EBF1-deficient bone marrow stroma elicits persistent changes in HSC potential.Nat. Immunol. 2020; 21: 261-273Crossref PubMed Scopus (6) Google Scholar, 9.Pinho S. Frenette P.S. Haematopoietic stem cell activity and interactions with the niche.Nat. Rev. Mol. Cell Biol. 2019; 20: 303-320Crossref PubMed Scopus (113) Google Scholar]. Moreover, different stimulations, for example immune response against viruses, will trigger the production of type one interferons such as IFNα. This cytokine can in turn act as a signal to break HSC quiescence, triggering a specific transcription network which will lean the differentiation output towards a particular cell-type program, preferentially myeloid output in this example [10.Essers M.A.G. et al.IFNalpha activates dormant haematopoietic stem cells in vivo.Nature. 2009; 458: 904-908Crossref PubMed Scopus (807) Google Scholar,11.Xia P. et al.A Circular RNA Protects Dormant Hematopoietic Stem Cells from DNA Sensor cGAS-Mediated Exhaustion.Immunity. 2018; 48: 688-701.e7Abstract Full Text Full Text PDF PubMed Scopus (73) Google Scholar]. For intrinsic cues, it is widely accepted that lineage regulators expressed in HSCs and progenitor cells instruct fate determination, as illustrated by the balance between the PU.1 and GATA1 transcription factors (TFs), where the first one elicits the myeloid program, and the second one governs the erythroid branch. Unbalanced expression of either leads to hematopoietic lineage skewing [12.Hoppe P.S. et al.Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios.Nature. 2016; 535: 299-302Crossref PubMed Google Scholar]. Therefore, the competing influences of various extrinsic and intrinsic inputs need to be coordinated to ensure balanced hematopoiesis. The classical view of hematopoiesis has been illustrated via a branching tree consisting of a stepwise series of bifurcations signposting progressive commitment to increasingly differentiated progenitor cell populations and ultimately to terminally differentiated cell types. Single-cell RNA sequencing (scRNA-seq) and in vivo lineage tracing experiments have recently overturned several aspects of this dogma (Box 1 and Figure 1, Key Figure). While HSCs remain at the top of all hematopoietic trajectories, the rigidity and hierarchical structure of the intermediate steps in the differentiation scheme have been reconsidered. While HSCs were previously thought of as homogeneous and having a blank slate with respect to differentiation, we now know that HSCs, in fact, represent a heterogeneous population consisting of cells with existing lineage biases which make them functionally uni-, bi-, or multipotent under steady-state conditions [13.Busch K. et al.Fundamental properties of unperturbed haematopoiesis from stem cells in vivo.Nature. 2015; 518: 542-546Crossref PubMed Scopus (327) Google Scholar, 14.Rodriguez-Fraticelli A.E. et al.Clonal analysis of lineage fate in native haematopoiesis.Nature. 2018; 553: 212-216Crossref PubMed Scopus (150) Google Scholar, 15.Weinreb C. et al.Lineage tracing on transcriptional landscapes links state to fate during differentiation.Science. 2020; 367Crossref PubMed Scopus (53) Google Scholar, 16.Carrelha J. et al.Hierarchically related lineage-restricted fates of multipotent haematopoietic stem cells.Nature. 2018; 554: 106-111Crossref PubMed Scopus (103) Google Scholar, 17.Pei W. et al.Polylox barcoding reveals haematopoietic stem cell fates realized in vivo.Nature. 2017; 548: 456-460Crossref PubMed Scopus (148) Google Scholar, 18.Velten L. et al.Human haematopoietic stem cell lineage commitment is a continuous process.Nat. Cell Biol. 2017; 19: 271-281Crossref PubMed Scopus (261) Google Scholar]. It has been hypothesized that these lineage biases are established through epigenetic priming during hematopoiesis [19.Rybtsov S. et al.Tracing the origin of the HSC hierarchy reveals an SCF-dependent, IL-3-independent CD43(-) embryonic precursor.Stem Cell Rep. 2014; 3: 489-501Abstract Full Text Full Text PDF PubMed Scopus (66) Google Scholar,20.Yu V.W.C. et al.Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells.Cell. 2016; 167: 1310-1322.e17Abstract Full Text Full Text PDF PubMed Scopus (90) Google Scholar]. Remarkably, single HSCs show a stereotypical behavior upon transplantation, in which the future lineage trajectory or fate of an individual HSC clone appears to be established prior to young adulthood and persistently manifests under various conditions. Furthermore, while the transcriptome is not consistently correlated with future trajectory, epigenetic features such as DNA methylation and chromatin accessibility reveal a confident association with the subsequent function of specific clones [20.Yu V.W.C. et al.Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells.Cell. 2016; 167: 1310-1322.e17Abstract Full Text Full Text PDF PubMed Scopus (90) Google Scholar]. In agreement with this finding, short-term exposure to an immune threat such as bacteria can induce C/EBPβ-dependent changes in chromatin accessibility, which in turn prime the HSCs towards the myeloid compartment upon secondary infections [21.de Laval B. et al.C/EBPβ-Dependent Epigenetic Memory Induces Trained Immunity in Hematopoietic Stem Cells.Cell Stem Cell. 2020; 26: 793Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar]. Also, changes in the niche compartment have been shown to imprint a lasting influence on HSC chromatin accessibility that persists even following transplantation [8.Derecka M. et al.EBF1-deficient bone marrow stroma elicits persistent changes in HSC potential.Nat. Immunol. 2020; 21: 261-273Crossref PubMed Scopus (6) Google Scholar]. These data suggest that epigenetic memory represents an important factor in guiding HSC fate decisions.Box 1scRNA-seq and In Vivo Lineage Tracing Have Transformed Our View of HematopoiesisEven though the first observation of the HSCs' remarkable ability to restore the entire hematopoietic system was >50 years [159.Till J.E. McCULLOCH E.A. A direct measurement of the radiation sensitivity of normal mouse bone marrow cells.Radiat. Res. 1961; 14: 213-222Crossref PubMed Google Scholar], the understanding of how – in terms of trajectory – they do so remains a fascinating question to this day. The classical dogma states that hematopoiesis consists of a stepwise differentiation, where asymmetric division of HSCs gives rise to one daughter cell which retains HSC characteristics and a second daughter cell which loses the self-renewal capacity but retains multipotent differentiation ability, known as a multipotent progenitor cell (MPP; see Figure 1 in main text). According to the classical model, MPPs will participate in sequential binary decisions [160.Akashi K. et al.A clonogenic common myeloid progenitor that gives rise to all myeloid lineages.Nature. 2000; 404: 193-197Crossref PubMed Scopus (1765) Google Scholar,161.Kondo M. et al.Identification of clonogenic common lymphoid progenitors in mouse bone marrow.Cell. 1997; 91: 661-672Abstract Full Text Full Text PDF PubMed Google Scholar] until they reach a fully differentiated mature blood cell type. The classical model has been predominantly derived from studies employing transplantation assays. Although transplants are valuable for their ability to determine self-renewal and lineage potential of HSCs, their reliance on surface markers to identify HSCs may mean that they miss the full scope of HSC heterogeneity.The combination of next-generation techniques such as scRNA-seq with unperturbed in vivo tracking experiments and single-cell transplantations have challenged the classical hierarchical view of hematopoiesis. Recent work has uncovered new hematopoietic cell populations and unprecedented branching points that give rise to the notion that hematopoiesis is better represented as a continuum [13.Busch K. et al.Fundamental properties of unperturbed haematopoiesis from stem cells in vivo.Nature. 2015; 518: 542-546Crossref PubMed Scopus (327) Google Scholar,162.Sun J. et al.Clonal dynamics of native haematopoiesis.Nature. 2014; 514: 322-327Crossref PubMed Scopus (415) Google Scholar, 163.Jacobsen S.E.W. Nerlov C. Haematopoiesis in the era of advanced single-cell technologies.Nat. Cell Biol. 2019; 21: 2-8Crossref PubMed Scopus (30) Google Scholar, 164.Drissen R. et al.Distinct myeloid progenitor-differentiation pathways identified through single-cell RNA sequencing.Nat. Immunol. 2016; 17: 666-676Crossref PubMed Scopus (116) Google Scholar, 165.Adolfsson J. et al.Identification of Flt3+ lympho-myeloid stem cells lacking erythro-megakaryocytic potential a revised road map for adult blood lineage commitment.Cell. 2005; 121: 295-306Abstract Full Text Full Text PDF PubMed Scopus (828) Google Scholar, 166.Notta F. et al.Distinct routes of lineage development reshape the human blood hierarchy across ontogeny.Science. 2016; 351aab2116Crossref PubMed Scopus (324) Google Scholar, 167.Karamitros D. et al.Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells.Nat. Immunol. 2018; 19: 85-97Crossref PubMed Scopus (63) Google Scholar, 168.Nestorowa S. et al.A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation.Blood. 2016; 128e20-31Crossref PubMed Google Scholar, 169.Bowling S. et al.An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells.Cell. 2020; 181: 1410-1422.e27Abstract Full Text Full Text PDF PubMed Scopus (18) Google Scholar, 170.Wilson N.K. et al.Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations.Cell Stem Cell. 2015; 16: 712-724Abstract Full Text Full Text PDF PubMed Google Scholar, 171.Laurenti E. Göttgens B. From haematopoietic stem cells to complex differentiation landscapes.Nature. 2018; 553: 418-426Crossref PubMed Scopus (151) Google Scholar]. Nonetheless, despite the considerable advances promoted by those single-cell techniques they also have limitations and technical challenges that need to be considered. Barcode-based techniques are not able to fully assess rare HSC clones due to their exclusion by thresholding. Also, several lineage-tracing techniques rely on Cre lines, with all the associated caveats of specificity and selectivity. Researchers labelling HSCs with Pdzk1ip1-driven Cre showed that at steady state, blood lineage replenishment is highly dependent on HSCs [172.Sawai C.M. et al.Hematopoietic Stem Cells Are the Major Source of Multilineage Hematopoiesis in Adult Animals.Immunity. 2016; 45: 597-609Abstract Full Text Full Text PDF PubMed Scopus (166) Google Scholar]. In sharp contrast, researchers using the Tie2-Cre for the same purpose found that mature hematopoietic replenishment is not dependent on HSCs [13.Busch K. et al.Fundamental properties of unperturbed haematopoiesis from stem cells in vivo.Nature. 2015; 518: 542-546Crossref PubMed Scopus (327) Google Scholar]. This discrepancy could only be resolved by engagement of independent techniques. Sleeping Beauty transposon-based tagging experiments and polylox barcoding supported the idea that, with the exception of megakaryocyte fate, MPPs likely represent the actual active differentiation compartment and are responsible for the replenishment of most of the mature blood cells at status quo [14.Rodriguez-Fraticelli A.E. et al.Clonal analysis of lineage fate in native haematopoiesis.Nature. 2018; 553: 212-216Crossref PubMed Scopus (150) Google Scholar,17.Pei W. et al.Polylox barcoding reveals haematopoietic stem cell fates realized in vivo.Nature. 2017; 548: 456-460Crossref PubMed Scopus (148) Google Scholar,162.Sun J. et al.Clonal dynamics of native haematopoiesis.Nature. 2014; 514: 322-327Crossref PubMed Scopus (415) Google Scholar]. This controversy emphasizes the need for the development and application of new approaches, models, and software to accurately deconvolute HSC fate in vivo. Even though the first observation of the HSCs' remarkable ability to restore the entire hematopoietic system was >50 years [159.Till J.E. McCULLOCH E.A. A direct measurement of the radiation sensitivity of normal mouse bone marrow cells.Radiat. Res. 1961; 14: 213-222Crossref PubMed Google Scholar], the understanding of how – in terms of trajectory – they do so remains a fascinating question to this day. The classical dogma states that hematopoiesis consists of a stepwise differentiation, where asymmetric division of HSCs gives rise to one daughter cell which retains HSC characteristics and a second daughter cell which loses the self-renewal capacity but retains multipotent differentiation ability, known as a multipotent progenitor cell (MPP; see Figure 1 in main text). According to the classical model, MPPs will participate in sequential binary decisions [160.Akashi K. et al.A clonogenic common myeloid progenitor that gives rise to all myeloid lineages.Nature. 2000; 404: 193-197Crossref PubMed Scopus (1765) Google Scholar,161.Kondo M. et al.Identification of clonogenic common lymphoid progenitors in mouse bone marrow.Cell. 1997; 91: 661-672Abstract Full Text Full Text PDF PubMed Google Scholar] until they reach a fully differentiated mature blood cell type. The classical model has been predominantly derived from studies employing transplantation assays. Although transplants are valuable for their ability to determine self-renewal and lineage potential of HSCs, their reliance on surface markers to identify HSCs may mean that they miss the full scope of HSC heterogeneity. The combination of next-generation techniques such as scRNA-seq with unperturbed in vivo tracking experiments and single-cell transplantations have challenged the classical hierarchical view of hematopoiesis. Recent work has uncovered new hematopoietic cell populations and unprecedented branching points that give rise to the notion that hematopoiesis is better represented as a continuum [13.Busch K. et al.Fundamental properties of unperturbed haematopoiesis from stem cells in vivo.Nature. 2015; 518: 542-546Crossref PubMed Scopus (327) Google Scholar,162.Sun J. et al.Clonal dynamics of native haematopoiesis.Nature. 2014; 514: 322-327Crossref PubMed Scopus (415) Google Scholar, 163.Jacobsen S.E.W. Nerlov C. Haematopoiesis in the era of advanced single-cell technologies.Nat. Cell Biol. 2019; 21: 2-8Crossref PubMed Scopus (30) Google Scholar, 164.Drissen R. et al.Distinct myeloid progenitor-differentiation pathways identified through single-cell RNA sequencing.Nat. Immunol. 2016; 17: 666-676Crossref PubMed Scopus (116) Google Scholar, 165.Adolfsson J. et al.Identification of Flt3+ lympho-myeloid stem cells lacking erythro-megakaryocytic potential a revised road map for adult blood lineage commitment.Cell. 2005; 121: 295-306Abstract Full Text Full Text PDF PubMed Scopus (828) Google Scholar, 166.Notta F. et al.Distinct routes of lineage development reshape the human blood hierarchy across ontogeny.Science. 2016; 351aab2116Crossref PubMed Scopus (324) Google Scholar, 167.Karamitros D. et al.Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells.Nat. Immunol. 2018; 19: 85-97Crossref PubMed Scopus (63) Google Scholar, 168.Nestorowa S. et al.A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation.Blood. 2016; 128e20-31Crossref PubMed Google Scholar, 169.Bowling S. et al.An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells.Cell. 2020; 181: 1410-1422.e27Abstract Full Text Full Text PDF PubMed Scopus (18) Google Scholar, 170.Wilson N.K. et al.Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations.Cell Stem Cell. 2015; 16: 712-724Abstract Full Text Full Text PDF PubMed Google Scholar, 171.Laurenti E. Göttgens B. From haematopoietic stem cells to complex differentiation landscapes.Nature. 2018; 553: 418-426Crossref PubMed Scopus (151) Google Scholar]. Nonetheless, despite the considerable advances promoted by those single-cell techniques they also have limitations and technical challenges that need to be considered. Barcode-based techniques are not able to fully assess rare HSC clones due to their exclusion by thresholding. Also, several lineage-tracing techniques rely on Cre lines, with all the associated caveats of specificity and selectivity. Researchers labelling HSCs with Pdzk1ip1-driven Cre showed that at steady state, blood lineage replenishment is highly dependent on HSCs [172.Sawai C.M. et al.Hematopoietic Stem Cells Are the Major Source of Multilineage Hematopoiesis in Adult Animals.Immunity. 2016; 45: 597-609Abstract Full Text Full Text PDF PubMed Scopus (166) Google Scholar]. In sharp contrast, researchers using the Tie2-Cre for the same purpose found that mature hematopoietic replenishment is not dependent on HSCs [13.Busch K. et al.Fundamental properties of unperturbed haematopoiesis from stem cells in vivo.Nature. 2015; 518: 542-546Crossref PubMed Scopus (327) Google Scholar]. This discrepancy could only be resolved by engagement of independent techniques. Sleeping Beauty transposon-based tagging experiments and polylox barcoding supported the idea that, with the exception of megakaryocyte fate, MPPs likely represent the actual active differentiation compartment and are responsible for the replenishment of most of the mature blood cells at status quo [14.Rodriguez-Fraticelli A.E. et al.Clonal analysis of lineage fate in native haematopoiesis.Nature. 2018; 553: 212-216Crossref PubMed Scopus (150) Google Scholar,17.Pei W. et al.Polylox barcoding reveals haematopoietic stem cell fates realized in vivo.Nature. 2017; 548: 456-460Crossref PubMed Scopus (148) Google Scholar,162.Sun J. et al.Clonal dynamics of native haematopoiesis.Nature. 2014; 514: 322-327Crossref PubMed Scopus (415) Google Scholar]. This controversy emphasizes the need for the development and application of new approaches, models, and software to accurately deconvolute HSC fate in vivo. Factors capable of modulating the structure or function of chromatin are known as chromatin regulators. Chromatin or epigenetic factors can alter a cell's transcriptional output without eliciting changes in the underlying genetic sequence. Mechanisms of chromatin regulation involving direct modification of chromatin include DNA methylation, covalent histone modifications, and nucleosome remodeling. These can be further influenced by miRNA, long noncoding RNA (lncRNA), specialized histone variants, and 3D chromatin conformation [22.Luo M. et al.Long non-coding RNAs control hematopoietic stem cell function.Cell Stem Cell. 2015; 16: 426-438Abstract Full Text Full Text PDF PubMed Google Scholar,23.Roden C. Lu J. MicroRNAs in Control of Stem Cells in Normal and Malignant Hematopoiesis.Curr. Stem Cell Rep. 2016; 2: 183-196Crossref PubMed Scopus (12) Google Scholar]. The concerted chromatin environment produced by the sum of these modifications and factors is known as the chromatin or epigenetic landscape. In general terms, chromatin modifiers elicit local chromatin alterations, which in turn either promote or repress transcription. The chromatin landscape plays a decisive role from the start of the hematopoietic process. Multiple epigenetic factors collaborate to ensure the maintenance of the HSC pool by instructing these cells on which transcription program should be active or suppressed in order to maintain their stemness [24.Avgustinova A. Benitah S.A. Epigenetic control of adult stem cell function.Nat. Rev. Mol. Cell Biol. 2016; 17: 643-658Crossref PubMed Scopus (85) Google Scholar,25.Goodell M.A. et al.Somatic stem cell heterogeneity: diversity in the blood, skin and intestinal stem cell compartments.Nat. Rev. Mol. Cell Biol. 2015; 16: 299-309Crossref PubMed Scopus (81) Google Scholar]. Dynamic chromatin reorganization is responsible for lineage priming by ensuring that the transcription network of a determinate cell type will be facilitated, while programs associated with an alternative fate will be prevented. In this regard, epigenetic modifiers exert a strong influence on lineage commitment decisions [26.Goode D.K. et al.Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation.Dev. Cell. 2016; 36: 572-587Abstract Full Text Full Text PDF PubMed Google Scholar,27.Lara-Astiaso D. et al.Immunogenetics. Chromatin state dynamics during blood formation.Science. 2014; 345: 943-949Crossref PubMed Scopus (418) Google Scholar]. Unsurprisingly, chromatin deregulation also contributes to impaired hematopoiesis and leukemia [28.Hu D. Shilatifard A. Epigenetics of hematopoiesis and hematological malignancies.Genes Dev. 2016; 30: 2021-2041Crossref PubMed Google Scholar,29.Ntziachristos P. et al.Emerging concepts of epigenetic dysregulation in hematological malignancies.Nat. Immunol. 2016; 17: 1016-1024Crossref PubMed Google Scholar]. Mouse knockouts of enzymes responsible for DNA methylation or post-translational histone modifications frequently show hematopoietic defects ranging from bone marrow failure to leukemia [29.Ntziachristos P. et al.Emerging concepts of epigenetic dysregulation in hematological malignancies.Nat. Immunol. 2016; 17: 1016-1024Crossref PubMed Google Scholar,30.Cui K. et al.Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation.Cell Stem Cell. 2009; 4: 80-93Abstract Full Text Full Text PDF PubMed Scopus (451) Google Scholar]. Nucleosomal position and density have a remarkable influence on chromatin accessibility and regulatory function by licensing the availability of binding sites to TFs and the transcription machinery [31.Buck M.J. Lieb J.D. A chromatin-mediated mechanism for specification of conditional transcription factor targets.Nat. Genet. 2006; 38: 1446-1451Crossref PubMed Scopus (70) Google Scholar,32.Boyle A.P. et al.High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.Genome Res. 2011; 21: 456-464Crossref PubMed Scopus (0) Google Scholar] (Box 2). Accurate nucleosome phasing, density and assembly are therefore required to enable transcription at appropriate gene loci and time points. Local nucleosome occupancy and composition are finely tailored by a group of ATP-dependent enzymes termed nucleosome remodelers. They are subdivided into four major subfamilies named imitation switch (ISWI), chromodomain helicase DNA-binding (CHD/NuRD/Mi-2), switch/sucrose non-fermentable (SWI/SNF), and INO80. Mechanistically, ISWI and CHD have been shown to modulate nucleosome assembly and organization following DNA replication by regulating the maturation of nucleosomes and generating canonical nucleosomal spacing (Figure 2). The INO80 subfamily is mainly associated with the removal and replacement of a given histone by canonical or related variants. The SWI/SNF subfamily emerges as the primary remodeler responsible for regulating sliding of nucleosomes along the DNA or even releasing full nucleosomes from the chromatin. Hence, the SWI/SNF subfamily of nucleosome remodelers is essential to the regulation of nucleosome density or phasing: a process that is not only intricately linked with chromatin dynamics, but also with transcription, since nucleosomal packing hinders TF binding to motifs located in that region, while nucleosome-free regions permit rapid access to TFs [33.Clapier C.R. et al.Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes.Nat. Rev. Mol. Cell Biol. 2017; 18: 407-422Crossref PubMed Scopus (228) Google Scholar]).Box 2Interplay between TFs, Nucleosome Remodelers and Chromatin DynamicsNucleosome positioning, density and occupancy time (turnover) along the DNA can impose a physical barrier which attenuates chromatin accessibility and transcription. Nucleosome positioning is therefore intimately linked to gene expression. Strong promoters preferentially occur at regions displaying increased nucleosome turnover and low density, whereas weak promoters, despite having a high nucleosome turnover, show an increased nucleosome occupancy. Accordingly, facultative heterochromatin is characterized by low nucleosome turnover and occupancy. How do increased nucleosome turnover and reduced nucleosome occupancy translate into increased expression? TFs are proteins with specificity towards specific DNA sequences or motifs. Most TFs show affinity towards naked DNA, but are excluded from nucleosome-dense regions. One mechanistic model proposed for how TFs may gain access to histone-bound DNA is by exploiting nucleosome turnover; this model is kn