Many genes determining cell identity are regulated by clusters of mediator-bound enhancer elements collectively referred to as super-enhancers. These have been proposed to manifest higher-order properties important in development and disease. Here, we report a comprehensive functional dissection of one of the strongest putative super-enhancers in erythroid cells. By generating a series of mouse models, deleting each of the five regulatory elements of the α-globin super-enhancer singly and in informative combinations, we demonstrate that each constituent enhancer appears to act independently and in an additive fashion with respect to hematologic phenotype, gene expression, chromatin structure and chromosome conformation, without clear evidence of synergistic or higher-order effects. Our study highlights the importance of functional genetic analyses for the identification of new concepts in transcriptional regulation.

The mutagenic effect of hepatitis B (HBV) integration in predisposing risk to hepatocellular carcinoma (HCC) remains elusive. In this study, we performed transcriptome sequencing of HBV-positive HCC cell lines and showed transcription of viral-human gene fusions from the site of genome integrations. We discovered tumor-promoting properties of a chimeric HBx-LINE1 that, intriguingly, functions as a hybrid RNA. HBx-LINE1 can be detected in 23.3% of HBV-associated HCC tumors and correlates with poorer patient survival. HBx-LINE1 transgenic mice showed heightened susceptibility to diethylnitrosamine-induced tumor formation. We further show that HBx-LINE1 expression affects β-catenin transactivity, which underlines a role in activating Wnt signaling. Thus, this study identifies a viral-human chimeric fusion transcript that functions like a long noncoding RNA to promote HCC.

The transcription factor Runx1/AML1 is an important regulator of hematopoiesis and is critically required for the generation of the first definitive hematopoietic stem cells (HSCs) in the major vasculature of the mouse embryo. As a pivotal factor in HSC ontogeny, its transcriptional regulation is of high interest but is largely undefined. In this study, we used a combination of comparative genomics and chromatin analysis to identify a highly conserved 531-bp enhancer located at position ؉ 23.5 in the first intron of the 224-kb mouse Runx1 gene. We show that this enhancer contributes to the early hematopoietic expression of Runx1. Transcription factor binding in vivo and analysis of the mutated enhancer in transient transgenic mouse embryos implicate Gata2 and Ets proteins as critical factors for its function. We also show that the SCL/Lmo2/Ldb-1 complex is recruited to the enhancer in vivo. Importantly, transplantation experiments demonstrate that the intronic Runx1 enhancer targets all definitive HSCs in the mouse embryo, suggesting that it functions as a crucial cis-regulatory element that integrates the Gata, Ets, and SCL transcriptional networks to initiate HSC generation. IntroductionThe interest in stem cell-based therapies has emphasized the importance of understanding the molecular mechanisms by which cells choose their fate and mature along a particular lineage. The hematopoietic system has been particularly amenable for these type of studies, and preliminary gene regulatory networks have been generated to summarize and model the data obtained from a variety of in vitro and in vivo studies. 1,2 However, few studies have directly addressed the transcriptional regulation of critical hematopoietic regulators at the stages at which they are active (ie, during hematopoietic stem cell [HSC] formation in embryonic development). The transcription factor (TF) Runx1 (also known as AML1, Cbfa2, or Pebp2␣) is arguably the most critical regulator of definitive HSC formation and is a frequent target of chromosomal translocations in leukemia (reviewed in de Bruijn and Speck 3 ; Jaffredo et al 4 ; and Speck and Gilliland 5 ). To advance our understanding of the molecular mechanisms involved in the process of HSC specification, it is thus of great interest to determine how Runx1 expression is regulated, particularly in HSC fated precursor cells. Very little is known concerning the transcriptional regulation of Runx1. Although several signaling pathways and TFs have been reported to act upstream of Runx1 in the development of the hematopoietic system (reviewed in Levanon and Groner 6 ), [7][8][9][10][11][12][13][14][15] no cis-regulatory elements have been identified. In the present study, we set out to identify and functionally characterize Runx1 cis-elements that are sufficient to drive reporter gene expression specifically to the sites of HSC emergence in a Runx1-specific pattern. Identification of such element(s) is a prerequisite to place the master regulator Runx1 firmly in the transcriptional network governing H...

Hippo signaling controls organ size and tissue regeneration in many organs, but its roles in chondrocyte differentiation and bone repair remain elusive. Here, we demonstrate that Yap1, an effector of Hippo pathway inhibits skeletal development, postnatal growth, and bone repair. We show that Yap1 regulates chondrocyte differentiation at multiple steps in which it promotes early chondrocyte proliferation but inhibits subsequent chondrocyte maturation both in vitro and in vivo. Mechanistically, we find that Yap1 requires Teads binding for direct regulation of Sox6 expression to promote chondrocyte proliferation. In contrast, Yap1 inhibits chondrocyte maturation by suppression of Col10a1 expression through interaction with Runx2. In addition, Yap1 also governs the initiation of fracture repair by inhibition of cartilaginous callus tissue formation. Taken together, our work provides insights into the mechanism by which Yap1 regulates endochondral ossification, which may help the development of therapeutic treatment for bone regeneration.

The transcription factor Runx1 is a pivotal regulator of definitive hematopoiesis in mouse ontogeny. Vertebrate Runx1 is transcribed from 2 promoters, the distal P1 and proximal P2, which provide a paradigm of the complex transcriptional and translational control of Runx1 function. However, very little is known about the biologic relevance of alternative Runx1 promoter usage in definitive hematopoietic cell emergence. Here we report that both promoters are active at the very onset of definitive hematopoiesis, with a skewing toward the P2. Moreover, functional and morphologic analysis of a novel P1-null and an attenuated P2 mouse model revealed that although both promoters play important nonredundant roles in the emergence of definitive hematopoietic cells, the proximal P2 was most critically required for this. The nature of the observed phenotypes is indicative of a differential contribution of the P1 and P2 promoters to the control of overall Runx1 levels, where and when this is most critically required. In addition, the dynamic expression of P1-Runx1 and P2-Runx1 points at a requirement for Runx1 early in development, when the P2 is still the prevalent promoter in the emerging hemogenic endothelium and/or first committed hematopoietic cells. (Blood. 2010;115(15): 3042-3050) IntroductionThe generation of the definitive hematopoietic system during embryogenesis critically depends on the transcription factor Runx1. In mice, homozygous loss of Runx1 function results in embryonic lethality attributable to a complete lack of functional definitive hematopoietic stem cells (HSCs) and progenitor cells and hemorrhages in the central nervous system. 1-3 Runx1 belongs to the family of runt-domain transcription factors. The 3 mammalian members of this family, Runx1, 2, and 3, all are important developmental regulators and bind to the same DNA motif. 4 Although both Runx2 and Runx3 have been implicated in hematopoiesis, only Runx1 has a role in the emergence of definitive hematopoietic cells, 5 reflecting its specific expression at hemogenic sites. 6,7 Recently, it was shown that Runx1 is required in VE-cadherin ϩ cells of the embryo, within the developmental window that starts with the initiation of Runx1 expression in these cells and ends when/before definitive HSCs reach the embryonic day (E) 11 fetal liver (FL). 8 Although the precise developmental stage(s) at which Runx1 is required within this window remains to be determined, it is generally believed to be at the transition of hemogenic endothelium to definitive hematopoietic cells. 6,[8][9][10] In the adult, Runx1 is no longer critically required in HSCs, although it still plays important roles in maintaining hematopoietic homeostasis and in the generation of specific hematopoietic cells/lineages. [11][12][13] Not only the expression pattern of Runx1 but also its levels need to be tightly controlled for the normal emergence of HSCs in the embryo. 3 To gain insight into how this is achieved, we have initiated studies into the transcriptional regulation of Runx1. 14,15...

The transcription factor Runx1 plays a pivotal role in hematopoietic stem cell (HSC) emergence, and studies into its transcriptional regulation should give insight into the critical steps of HSC specification. Recently, we identified the Runx1 ؉23 enhancer that targets reporter gene expression to the first emerging HSCs of the mouse embryo when linked to the heterologous hsp68 promoter. Endogenous Runx1 is transcribed from 2 alternative promoters, P1 and P2. Here, we examined the in vivo cis-regulatory potential of these alternative promoters and asked whether they act with and contribute to the spatiotemporal specific expression of the Runx1 ؉23 enhancer. Our results firmly establish that, in contrast to zebrafish runx1, mouse Runx1 promoter sequences do not confer any hematopoietic specificity in transgenic embryos. Yet, both mouse promoters act with the ؉23 enhancer to drive reporter gene expression to sites of HSC emergence and colonization, in a ؉23-specific pattern. (Blood. 2009;113:5121-5124) IntroductionThe transcription factor RUNX1 is a critical regulator of definitive hematopoiesis, and genomic aberrations of the gene encoding RUNX1 are frequently found in human acute leukemia. 1 In the mouse, Runx1 null mutations result in the absence of functional hematopoietic stem cells (HSCs) and definitive progenitors, leading to embryonic lethality. [2][3][4][5][6] During development, Runx1 is first expressed in the emerging hematopoietic system, including definitive HSCs. 7,8 Its highly regulated spatiotemporal expression pattern and pivotal role in HSC emergence prompted us to study its transcriptional regulation, to obtain insight into the molecular mechanisms underlying de novo HSC generation. We recently identified the Runx1 ϩ23 hematopoietic enhancer, located 23.5 kb downstream of the ATG in exon 1. 9 We showed that this ϩ23 enhancer targets reporter gene expression, from a heterologous hsp68 core promoter, to the emerging HSCs and putative HSCfated cells in the mouse embryo, and acts directly downstream of Gata2, SCL, and Ets transcription factors. Whether the ϩ23 enhancer is equally active with the endogenous Runx1 promoters has not been assessed.Runx1 is transcribed from 2 alternative promoters ( Figure 1A), a distal P1 and proximal P2, with the P1 being specific to vertebrates. [10][11][12][13] Both the P1 and P2 promoters were reported to be transcriptionally active in the emerging hematopoietic system of the mouse embryo, at the stages of yolk sac (YS), aortagonad-mesonephros (AGM), and fetal liver (FL) hematopoiesis, with P1-derived transcripts particularly prevalent among enriched FL HSCs. 11,14,15 The P2 promoter was shown to be active in HSC-fated cells 16 and to be critically required for FL hematopoiesis. 17 In vitro transfection assays suggested that neither P1 nor P2 RUNX1 promoter elements harbored tissue-specific cis-regulatory elements. 10 However, in vivo mouse promoter assays have not been reported, and it is therefore not clear to what extent cis-elements elsewhere in the locus are req...

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The Congenital Dyseyrthropoetic Anemias (CDA) are a heterogeneous group of inborn defects characterized by anemia of varying severity and morphological abnormalities of bone marrow erythroblasts. Studying their pathology has the potential to contribute to the understanding of the normal process of erythropoiesis. In CDA type I, the phenotype is largely limited to the red cell lineage with erythroblasts showing characteristic spongy nuclear chromatin on electron microscopy. Its genetic basis is due to missense mutations in the CDAN1 gene (chromosome 15q15), but the biological function of the highly conserved and non-redundant codanin-1 protein remains entirely unknown. We have produced a mouse model for CDA type I by generating transgenic mice from an ES cell line carrying a gene-trap (splice acceptor/β-galactosidase gene/neomycin resistance gene) in intron 25 of the murine CDAN1 gene. Blood and bone marrow from CDAN1gt/wt heterozygotes is morphologically and quantitatively indistinguishable from wild type animals. Northern blot analysis and RT-qPCR of codanin-1 RNA expression confirms a broad pattern of expression with the highest levels seen in erythroid tissue. Flow-cytometric analysis of β-galactosidase activity in erythroid cells from phenylhydrazine treated adult spleens shows the highest levels in the CD71high/Ter119low early erythroblasts, declining with further erythroid maturation. Furthermore, indirect immunofluorescence localizes the codanin-1/β-galactosidase fusion product in the nucleus of the CD71high/Ter119low early erythroblasts, particularly at the interface between euchromatin and heterochromatin. The presence of an in-frame β-gal in the gene trap insert, therefore, provides a method to analyze gene and protein expression from the CDAN1 promoter, and additional distribution data from heterozygous embryos and adults will be presented. Heterozygote crosses produced no homozygotes among liveborn progeny, suggesting embryonic lethality of this state. Analysis of embryos at different stages suggests development of homozygotes ceased at ~6.5d of gestation, prior to the onset of erythropoiesis. These results from the first transgenic mouse model for CDA type I, highlight a non-erythroid role for codanin-1 in early embryonic development, in addition to its role in adult human erythropoiesis. The embryonic lethality of the mouse model is consistent with the absence of homozygote null mutations in the CDAN1 genes analyzed so far in human patients. Creation of mice with the CDA type I phenotype may have to await a knock-in transgenic containing a human mutation, which is currently in preparation. The model described here should be valuable for further studies of the intracellular localization of codanin-1 and the identification of any relevant protein binding partners.