Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus

Enhancer requirement for histone methylation linked with gene activation

Enhancers cause a high level of transcription and activation of chromatin structure at target genes. Hyperacetylation of histones H3 and H4, a mark of active chromatin, is established broadly across target loci by enhancers that function over long distances. In the present study, we studied the role of an enhancer in methylation of various lysine residues on H3 by comparing a model gene locus having an active enhancer with one in which the enhancer has been inactivated within the context of minichromosomes. The intact enhancer affected histone methylation at K4, K9 and K36 in distinct ways depending on the methylation level and the location in the locus. All three lysine residues were highly tri-methylated in the coding region of the gene linked to the active enhancer but not the inactive enhancer. However di-methylation of K9 and K36 was not affected by the enhancer. The enhancer region itself was marked by mono-methylation at K4 and K9, distinguishing it from the methyl marks in the gene coding region. These results indicate that an enhancer has roles in establishing active histone methylation patterns linked with gene transcription rather than removing methylation linked with gene inactivation.

Alterations of the CxxC domain preclude oncogenic activation of mixed-lineage leukemia 2

The mixed-lineage leukemia (MLL) family of histone methyltransferases has become notorious for the participation of the founding member, MLL, in fusion proteins that cause acute leukemia. Despite structural conservation, no other MLL homolog has so far been found in a similar arrangement. Here, we show that fusion proteins based on Mll2, the closest relative of MLL, are incapable of transforming hematopoietic cells. Elaborate swap experiments identified the small CxxC zinc-binding region of Mll2 and an adjacent 'post-CxxC' stretch of basic amino acids as the essential determinants for the observed difference. Gel shift experiments indicated that the combined CxxC and post-CxxC domains of MLL and Mll2 possess almost indistinguishable DNA-binding properties in vitro. Within the cellular environment, however, these motifs guided MLL and Mll2 to a largely nonoverlapping target gene repertoire, as evidenced by nuclear localization, reporter assays, and measurements of homeobox gene levels in primary cells expressing MLL and Mll2 fusion proteins. Therefore, the CxxC domain appears to be a promising target for therapies aimed at MLL fusion proteins without affecting the general function of other MLL family members.

Locus control region mediated regulation of adult beta-globin gene expression

Many genes residing in gene clusters and expressed in a differentiation or developmental-stage specific manner are regulated by locus control regions (LCRs). These complex genetic regulatory elements are often composed of several DNAse I hypersensitive sites (HS sites) that function together to regulate the expression of several cis-linked genes. Particularly well characterized is the LCR associated with the beta-globin gene locus. The beta-globin LCR consists of five HS sites that are located upstream of the beta-like globin genes. Recent data demonstrate that the LCR is required for the association of the beta-globin gene locus with transcription foci or factories. The observation that RNA polymerase II associates with the LCR in erythroid progenitor or hematopoietic stem cells which do not express the globin genes suggests that the LCR is always in an accessible chromatin configuration during differentiation of erythroid cells. We propose that erythroid specific factors together with ubiquitous proteins mediate a change in chromatin configuration that juxtaposes the globin genes and the LCR. The proximity then facilitates the transfer of activities from the LCR to the globin genes. In this article we will discuss recent observations regarding beta-globin locus activation with a particular emphasis on LCR mediated activation of adult beta-globin gene expression.

Epigenetics of beta-globin gene regulation

It is widely recognized that the next great challenge in the post-genomic period is to understand how the genome establishes the cell and tissue specific patterns of gene expression that underlie development. The beta-globin genes are among the most extensively studied tissue specific and developmentally regulated genes. The onset of erythropoiesis in precursor cells and the progressive expression of different members of the beta-globin family during development are accompanied by dramatic epigenetic changes in the locus. In this review, we will consider the relationship between histone and DNA modifications and the transcriptional activity of the beta-globin genes, the dynamic changes in epigenetic modifications observed during erythroid development, and the potential these changes hold as new targets for therapy in human disease.

EKLF restricts megakaryocytic differentiation at the benefit of erythrocytic differentiation

Previous observations suggested that functional antagonism between FLI-1 and EKLF might be involved in the commitment toward erythrocytic or megakaryocytic differentiation. We show here, using inducible shRNA expression, that EKLF knockdown in mouse erythroleukemia (MEL) cells decreases erythrocytic and increases megakaryocytic as well as Fli-1 gene expression. Chromatin immunoprecipitation analyses revealed that the increase in megakaryocytic gene expression is associated with a marked increase in RNA pol II and FLI-1 occupancy at their promoters, albeit FLI-1 protein levels are only minimally affected. Similarly, we show that human CD34+ progenitors infected with shRNA lentivirus allowing EKLF knockdown generate an increased number of differentiated megakaryocytic cells associated with increased levels of megakaryocytic and Fli-1 gene transcripts. Single-cell progeny analysis of a cell population enriched in bipotent progenitors revealed that EKLF knockdown increases the number of megakaryocytic at the expense of erythrocytic colonies. Taken together, these data indicate that EKLF restricts megakaryocytic differentiation to the benefit of erythrocytic differentiation and suggest that this might be at least partially mediated by the inhibition of FLI-1 recruitment to megakaryocytic and Fli-1 gene promoters.

Ultrasensitive gene regulation by positive feedback loops in nucleosome modification

Eukaryotic transcription involves the synergistic interaction of many different proteins. However, the question remains how eukaryotic promoters achieve ultrasensitive or threshold responses to changes in the concentration or activity of a single transcription factor (TF). We show theoretically that by recruiting a histone-modifying enzyme, a TF binding non-cooperatively to a single site can change the balance between opposing positive feedback loops in histone modification to produce a large change in gene expression in response to a small change in concentration of the TF. This mechanism can also generate bistable promoter responses, allowing a gene to be on in some cells and off in others, despite the cells being in identical conditions. In addition, the system provides a simple means by which the activities of many TFs could be integrated at a promoter.

NFAT is well placed to direct both enhancer looping and domain-wide models of enhancer function

Nuclear factor of activated T cells (NFAT) plays a central role in activating gene expression at the level of chromatin structure. A study now reveals that NFAT may also help to organize chromatin domains and enable enhancer-promoter communication. In activated T cells, inducible intrachromosomal looping occurs between the tumor necrosis factor-alpha (TNF-alpha) gene promoter and two NFAT-dependent enhancers located at -9 kb and +3 kb. This topology places the TNF-alpha gene and the adjacent lymphotoxin (LT) genes in separate loops, thereby allowing independent regulation of the TNF-alpha gene within a multigene locus. These findings build on other studies that indicate that NFAT is intimately associated with activities that disrupt nucleosomes within enhancers and mobilize nucleosomes across extensive chromatin domains linking enhancers and promoters. Taken together, these studies highlight NFAT as a factor that creates a chromatin environment that is permissive for both the recruitment and the clustering of factors that control transcription at promoters and enhancers.

Transcription and chromatin organization of a housekeeping gene cluster containing an integrated beta-globin locus control region

The activity of locus control regions (LCR) has been correlated with chromatin decondensation, spreading of active chromatin marks, locus repositioning away from its chromosome territory (CT), increased association with transcription factories, and long-range interactions via chromatin looping. To investigate the relative importance of these events in the regulation of gene expression, we targeted the human β-globin LCR in two opposite orientations to a gene-dense region in the mouse genome containing mostly housekeeping genes. We found that each oppositely oriented LCR influenced gene expression on both sides of the integration site and over a maximum distance of 150 kilobases. A subset of genes was transcriptionally enhanced, some of which in an LCR orientation-dependent manner. The locus resides mostly at the edge of its CT and integration of the LCR in either orientation caused a more frequent positioning of the locus away from its CT. Locus association with transcription factories increased moderately, both for loci at the edge and outside of the CT. These results show that nuclear repositioning is not sufficient to increase transcription of any given gene in this region. We identified long-range interactions between the LCR and two upregulated genes and propose that LCR-gene contacts via chromatin looping determine which genes are transcriptionally enhanced.

Hematopoiesis: an evolving paradigm for stem cell biology

Establishment and maintenance of the blood system relies on self-renewing hematopoietic stem cells (HSCs) that normally reside in small numbers in the bone marrow niche of adult mammals. This Review describes the developmental origins of HSCs and the molecular mechanisms that regulate lineage-specific differentiation. Studies of hematopoiesis provide critical insights of general relevance to other areas of stem cell biology including the role of cellular interactions in development and tissue homeostasis, lineage programming and reprogramming by transcription factors, and stage- and age-specific differences in cellular phenotypes.