Emergence of form and function during embryogenesis arises in large part through cell type- and cell state- specific variation in gene expression patterns, mediated by specialized cis-regulatory elements called enhancers. Recent large-scale epigenomic mapping revealed unexpected complexity and dynamics of enhancer utilization patterns, with 400,000 putative human enhancers annotated by the ENCODE project alone. These large-scale efforts were largely enabled through understanding that enhancers share certain stereotypical chromatin features. However, an important question still lingers: What is the functional significance of enhancer chromatin modification? Here we give an overview of enhancer-associated modifications of histones and DNA, and discuss enzymatic activities involved in their dynamic deposition and removal. We describe potential downstream effectors of these marks and propose models for exploring functions of chromatin modification in regulating enhancer activity during development.

Summary Naïve and primed pluripotency is characterized by distinct signaling requirements, transcriptomes and developmental properties, but both cellular states share key transcriptional regulators, Oct4, Sox2 and Nanog. Here we demonstrate that transition between these two pluripotent states is associated with widespread Oct4 relocalization, mirrored by global rearrangement of enhancer chromatin landscapes. Our genomic and biochemical analyses identified candidate mediators of primed state-specific Oct4 binding, including Otx2 and Zic2/3. Even when differentiation cues are blocked, premature Otx2 overexpression is sufficient to exit the naïve state, induce transcription of a substantial subset of primed pluripotency-associated genes and redirect Oct4 to previously inaccessible enhancer sites. However, ability of Otx2 to engage new enhancer regions is determined by its levels, cis-encoded properties of the sites and signaling environment. Our results illuminate regulatory mechanisms underlying pluripotency and suggest that capacity of transcription factors such as Otx2 and Oct4 to pioneer new enhancer sites is highly context-dependent.

Mutation of the RB-1 tumour suppressor occurs in one third of all human tumours and is particularly associated with retinoblastoma and osteosarcoma1. Numerous functions have been ascribed to the product of the human RB-1 gene, pRB. The best known is pRB’s ability to promote cell cycle exit through inhibition of the E2F transcription factors and the transcriptional repression of genes encoding cell cycle regulators1. In addition, pRB has been shown in vitro to regulate several transcription factors that are master differentiation inducers2. Depending on the differentiation factor and cellular context, pRB can either suppress or promote their transcriptional activity. For example, pRB binds to Runx2 and potentiates its ability to promote osteogenic differentiation program in vitro3. In contrast, pRB acts together with E2F to suppress PPARγ, the master activator of adipogenesis4,5. Since osteoblasts and adipocytes can both arise from mesenchymal stem cells, these observations suggest that pRB might play a role in the choice between these two fates. However, to date, there is no evidence for this in vivo. Here we use mouse models to address this hypothesis in the context of mesenchymal tissue development and tumorigenesis. Our data show that Rb status plays a key role in establishing fate choice between bone and brown adipose tissue in vivo.

DEAD-box RNA helicases are vital for the regulation of various aspects of the RNA life cycle1, but the molecular underpinnings of their involvement, particularly in mammalian cells, remain poorly understood. Here we show that the DEAD-box RNA helicase DDX21 can sense the transcriptional status of both RNA polymerase (Pol) I and II to control multiple steps of ribosome biogenesis in human cells. We demonstrate that DDX21 widely associates with Pol I- and Pol II-transcribed genes and with diverse species of RNA, most prominently with non-coding RNAs involved in the formation of ribo-nucleoprotein complexes, including ribosomal RNA, small nucleolar RNAs (snoRNAs) and 7SK RNA. Although broad, these molecular interactions, both at the chromatin and RNA level, exhibit remarkable specificity for the regulation of ribosomal genes. In the nucleolus, DDX21 occupies the transcribed rDNA locus, directly contacts both rRNA and snoRNAs, and promotes rRNA transcription, processing and modification. In the nucleoplasm, DDX21 binds 7SK RNA and, as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, is recruited to the promoters of Pol II-transcribed genes encoding ribosomal proteins and snoRNAs. Promoter-bound DDX21 facilitates the release of the positive transcription elongation factor b (P-TEFb) from the 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes. Our results uncover the multifaceted role of DDX21 in multiple steps of ribosome biogenesis, and provide evidence implicating a mammalian RNA helicase in RNA modification and Pol II elongation control.

Mutation of the RB-1 and p53 tumor suppressors is associated with the development of human osteosarcoma. With the goal of generating a mouse model of this disease, we used conditional and transgenic mouse strains to inactivate Rb and/or p53 specifically in osteoblast precursors. The resulting Rb;p53 double mutant (DKO) animals are viable but develop early onset osteosarcomas with complete penetrance. These tumors display many of the characteristics of human osteosarcomas, including being highly metastatic. We established cell lines from the DKO osteosarcomas to further investigate their properties. These immortalized cell lines are highly proliferative and they retain their tumorigenic potential, as judged by their ability to form metastatic tumors in immunocompromised mice. Moreover, they can be induced to differentiate and, depending on the inductive signal, will adopt either the osteogenic or adipogenic fate. Consistent with this multipotency, a significant portion of these tumor cells express Sca-1, a marker that is typically associated with stem cells/uncommitted progenitors. By assaying sorted cells in transplant assays, we demonstrate that the tumorigenicity of the osteosarcoma cell lines correlates with the presence of the Sca-1 marker. Finally, we show that loss of Rb and p53 in Sca-1-positive mesenchymal stem/progenitor cells is sufficient to yield transformed cells that can initiate osteosarcoma formation in vivo.osx-cre ͉ Sca-1 ͉ hibernoma mouse model O steosarcomas account for Ϸ30% of malignant bone tumors and 3-4% of all childhood malignancies (1, 2). They arise primarily around the knee joint, lower femur and upper tibia, which are all regions of active bone growth and repair. These tumors are predominantly osteoblastic in nature, although there is a correlation between loss of differentiation and poor prognosis. The generation of new therapeutic treatments for osteosarcoma has improved the 5-year survival rate of affected individuals. However, like other mesenchymal neoplasms, osteosarcomas are predisposed to metastasize via the hematogenous route, and thus, pulmonary metastasis is a major cause of death. Analyses of both sporadic and hereditary tumors show that inactivation of the p53 and RB-1 tumor suppressors plays a key role in the development of this tumor type (1, 2). Li-Fraumeni patients, who often carry germ-line mutations in p53, are predisposed to a variety of tumors, 12% of which are bone sarcomas (3, 4). p53 mutations are also observed in 20-60% of sporadic osteosarcomas (5-7). Similarly, patients carrying germline mutations in RB-1 have an Ϸ500-fold higher incidence of osteosarcoma than the general population (8). Moreover, RB-1 mutations are detected in 70% of all adolescent osteosarcomas (9). Finally, human osteosarcomas can carry mutations in both p53 and RB-1 (10).Mouse models have provided considerable insight into the role of p53 in bone development and tumorigenesis. Experiments from three different settings suggest that p53 plays an important role in bone development by modul...