Chromatin modifications in hematopoietic multipotent and committed progenitors are independent of gene subnuclear positioning relative to repressive compartments

Epigenetic Factors That Control Pericentric Heterochromatin Organization in Mammals

Pericentric heterochromatin (PCH) is a particular form of constitutive heterochromatin that is localized to both sides of centromeres and that forms silent compartments enriched in repressive marks. These genomic regions contain species-specific repetitive satellite DNA that differs in terms of nucleotide sequences and repeat lengths. In spite of this sequence diversity, PCH is involved in many biological phenomena that are conserved among species, including centromere function, the preservation of genome integrity, the suppression of spurious recombination during meiosis, and the organization of genomic silent compartments in the nucleus. PCH organization and maintenance of its repressive state is tightly regulated by a plethora of factors, including enzymes (e.g., DNA methyltransferases, histone deacetylases, and histone methyltransferases), DNA and histone methylation binding factors (e.g., MECP2 and HP1), chromatin remodeling proteins (e.g., ATRX and DAXX), and non-coding RNAs. This evidence helps us to understand how PCH organization is crucial for genome integrity. It then follows that alterations to the molecular signature of PCH might contribute to the onset of many genetic pathologies and to cancer progression. Here, we describe the most recent updates on the molecular mechanisms known to underlie PCH organization and function.

Gene expression profiles associated with pediatric relapsed AML

Development of relapse remains a problem for further improvements in the survival of pediatric AML patients. While virtually all patients show a good response to initial treatment, more patients respond poorly when treated at relapse. The cellular characteristics of leukemic blast cells that allow survival of initial treatment, relapse development and subsequent resistance to salvage treatment remain largely elusive. Therefore, we studied if leukemic blasts at relapse biologically resemble their initial diagnosis counterparts. We performed microarray gene expression profiling on paired initial and relapse samples of 23 pediatric AML patients. In 11 out of 23 patients, gene expression profiles of initial and corresponding relapse samples end up in different clusters in unsupervised analysis, indicating altered gene expression profiles. In addition, shifts in type I/II mutational status were found in 5 of these 11 patients, while shifts were found in 3 of the remaining 12 patients. Although differentially expressed genes varied between patients, they were commonly related to hematopoietic differentiation, encompassed genes involved in chromatin remodeling and showed associations with similar transcription factors. The top five were CEBPA, GFI1, SATB1, KLF2 and TBP. In conclusion, the leukemic blasts at relapse are biologically different from their diagnosis counterparts. These differences may be exploited for further development of novel treatment strategies.

Characterization of combinatorial histone modifications on lineage-affiliated genes during hematopoietic stem cell myeloid commitment

Hematopoietic stem cells (HSCs) are multipotent stem cells capable of self-renewal and multilineage differentiation. Mechanisms regulating the maintenance of HSCs' multipotency and differentiation are still unclear. In this study, we observed the role of combinatorial histone modification pattern in the maintenance of HSCs' pluripotency and differentiation. HSCs (CD34(+)CD38(low)) were collected from human umbilical cord blood and induced to differentiate to committed cells in vitro. The histone modifications on lineage-specific transcription factors/genes in multipotent HSCs and differentiated progenies, including megakaryocytes, granulocytes, and erythrocytes, were analyzed by chromatin immunoprecipitation-quantitative polymerase chain reaction. Our results showed that a certain level of acH4 and acH3 together with high level of H3K4me2, low level of H3K4me3, and a certain level of H3K9me3 and H3K27me3 were present in lineage-specific genes in CD34(+)CD38(low) HSCs. As CD34(+)CD38(low) cells differentiated into granulocytes, erythroid cells, and megakaryocytes, the modification levels of acH3, acH4, and H3K4me2 on lineage-specific genes remained the same or elevated, while H3K4me3 level was increased greatly. At the same time, H3K9me3 and H3K27me3 modification levels became lower. In non-lineage-specific genes, the acH3 and acH4 levels were decreased, and H3K4me3 level remained at low level, while H3K9me3 and H3K27me3 levels were increased drastically. Our data suggest that combinatorial histone modification patterns have implicated function in maintaining the multipotency of HSCs and keeping the accuracy of gene expression program during HSC differentiation.

Role of nuclear architecture in epigenetic alterations in cancer

It is widely accepted that cancer results from an array of epigenetic and genetic alterations, particularly aberrant epigenetic patterns that are a hallmark of every cancer type studied. Another well-known feature of cancer cells is the array of abnormalities in their nuclear structure. Although it is known that nuclear structure has an important role in the regulation of gene expression, we know little about the direct relationship between nuclear structural alterations and aberrant epigenetic patterns in cancer. Here, we discuss some of the recent studies from our lab and others to understand the relationship between alterations of nuclear architecture and aberrant epigenetic patterns in cancer cells. Although the precise relationship remains elusive, we suggest that changes in nuclear structure and composition could alter long-range genomic interactions and cause global epigenetic changes during tumorigenesis. We emphasize the need for further studies to elucidate the direct relationship between nuclear structure alterations and aberrant epigenetic patterns in cancers.

[Heterochromatin compartments and gene silencing: human hematopoietic differentiation as a model study]

In order to accomplish its differentiation program, the nucleus of a multipotent cell must be sequentially reprogrammed to acquire and maintain new gene expression patterns. When a stem cell is committed to differentiate towards a given lineage, global genome reprogramming involves both repression of non-affiliated genes and selective activation of genes involved in the establishment of the lineage. Accumulating evidence indicates that lineage specific gene expression is determined not only by the availability of specific transcription factors, but also by epigenetic modifications including both local modifications of DNA and chromatin structure, as well as global topological changes in chromosomes and genes positioning in the nucleus. Combined, these different levels of gene regulation allow for fine controls that integrate environmental and intracellular signals to establish appropriate gene expression programs, and hence ultimately determine the identity of the cell. Therefore, epigenetic modifications most likely precede gene activation and play a critical role in the choices of a stem cell to continue to self-renew or to differentiate. However, the cause-effect relationship between chromatin structure, nuclear architecture and cell-fate decisions is still a matter of debate. The pericentromeric heterochromatin compartment will be presented as one of the best studied examples to understand the impact of and positioning of a gene on its transcription. We will set the influence of heterochromatin compartments in the context of hematopoietic differentiation of human multipotent progenitors.

Epigenetic modifications in 3D: nuclear organization of the differentiating mammary epithelial cell

During the development of tissues, complex programs take place to reach terminally differentiated states with specific gene expression profiles. Epigenetic regulations such as histone modifications and chromatin condensation have been implicated in the short and long-term control of transcription. It has recently been shown that the 3D spatial organization of chromosomes in the nucleus also plays a role in genome function. Indeed, the eukaryotic interphase nucleus contains sub-domains that are characterized by their enrichment in specific factors such as RNA Polymerase II, splicing machineries or heterochromatin proteins which render portions of the genome differentially permissive to gene expression. The positioning of individual genes relative to these sub-domains is thought to participate in the control of gene expression as an epigenetic mechanism acting in the nuclear space. Here, we review what is known about the sub-nuclear organization of mammary epithelial cells in connection with gene expression and epigenetics. Throughout differentiation, global changes in nuclear architecture occur, notably with respect to heterochromatin distribution. The positions of mammary-specific genes relative to nuclear sub-compartments varies in response to hormonal stimulation. The contribution of tissue architecture to cell differentiation in the mammary gland is also seen at the level of nuclear organization, which is sensitive to microenvironmental stimuli such as extracellular matrix signaling. In addition, alterations in nuclear organization are concomitant with immortalization and carcinogenesis. Thus, the fate of cells appears to be controlled by complex pathways connecting external signal integration, gene expression, epigenetic modifications and chromatin organization in the nucleus.

Gfi-1B promoter remains associated with active chromatin marks throughout erythroid differentiation of human primary progenitor cells

Growth Factor Independent-1B (Gfi-1B) is a transcriptional repressor that plays critical roles in the control of erythropoiesis and megakaryopoiesis. Gfi-1B expression was described to be repressed by an autoregulatory feedback control loop. Here, we show that Gfi-1 transcription is positively regulated early after induction of erythroid differentiation and remains highly active to late erythroblasts. Using chromatin immunoprecipitation assays in CD34⁺ cells from human cord blood, we found that Gfi-1 and GATA-2 in immature progenitors and then Gfi-1B and GATA-1 in erythroblasts are bound to the Gfi-1B promoter as well as to the promoter of c-myc, a known Gfi-1B target gene. Surprisingly, this Gfi-1/GATA-2–Gfi-1B/GATA-1 switch observed at erythroblast stages is associated to an increase in the Gfi-1B transcription whereas it triggers repression of c-myc transcription. Accordingly, analysis of chromatin modification patterns shows that HDAC, CoREST, and LSD1 are recruited to the c-myc promoter leading to appearance of repressive chromatin marks. In contrast, the Gfi-1B promoter remains associated with a transcriptionally active chromatin configuration as highlighted by an increase in histone H3 acetylation and concomitant release of the LSD1 and CoREST corepressors. The repressive function of Gfi-1B therefore depends on the nature of the proteins recruited to the target gene promoters and on chromatin modifications. We conclude that Gfi-1B behaves as a lineage-affiliated gene with an open chromatin configuration in multipotent progenitors and sustained activation as cells progress throughout erythroid differentiation.