Changes in phosphorylation of the carboxy-terminal domain (CTD) of RNA polymerase II (RNAP) are associated with transcription initiation, elongation and termination. Sites of active transcription are generally characterized by hyperphosphorylated RNAP, particularly at Ser 2 residues, whereas inactive or poised genes may lack RNAP or may bind Ser 5-phosphorylated RNAP at promoter proximal regions. Recent studies have demonstrated that silent developmental regulator genes have an unusual histone modification profile in ES cells, being simultaneously marked with Polycomb repressor-mediated histone H3K27 methylation, and marks normally associated with gene activity. Contrary to the prevailing view, we show here that this important subset of developmental regulator genes, termed bivalent genes, assemble RNAP complexes phosphorylated on Ser 5 and are transcribed at low levels. We provide evidence that this poised RNAP configuration is enforced by Polycomb Repressor Complex (PRC)-mediated ubiquitination of H2A, as conditional deletion of Ring1A and Ring1B leads to the sequential loss of ubiquitination of H2A, release of poised RNAP, and subsequent gene de-repression. These observations provide an insight into the molecular mechanisms that allow ES cells to self-renew and yet retain the ability to generate multiple lineage outcomes.

The cis-acting elements necessary for the activity of DNA replication origins in metazoan cells are still poorly understood. Here we report a thorough characterization of the DNA sequence requirements of the origin associated with the human lamin B2 gene. A 1.2-kb DNA segment, comprising the start site of DNA replication and located within a large protein-bound region, as well as a CpG island, displays origin activity when moved to different ectopic positions. Genomic footprinting analysis of both the endogenous and the ectopic origins indicates that the large protein complex is assembled in both cases around the replication start site. Replacement of this footprinted region with an unrelated sequence, maintaining the CpG island intact, abolishes origin activity and the interaction with hORC2, a subunit of the origin recognition complex. Conversely, the replacement of 17 bp within the protected region reduces the extension of the protection without affecting the interaction with hORC2. This substitution does not abolish the origin activity but makes it more sensitive to the integration site. Finally, the nearby CpG island positively affects the efficiency of initiation. This analysis reveals the modular structure of the lamin B2 origin and supports the idea that sequence elements close to the replication start site play an important role in origin activation.In 1963 Jacob, Brenner, and Cuzin (24) proposed the replicon model to explain the control of replication of the bacterial chromosome. In this model, DNA replication starts from a specific origin sequence, the replicator, that is recognized by a positive regulatory protein, the initiator. Since then the model has been validated in numerous prokaryotic and viral systems. The organization of the eukaryotic genome in multiple replication units distributed on several chromosomes has hampered the validation of this model in eukaryotes until the identification of the autonomous replicating sequences (ARS) in Saccharomyces cerevisiae. Initially identified for their ability to support the propagation of plasmid molecules in yeast cells, most of these sequences were successively proven to correspond to chromosomal replicators. ARSs are relatively short sequence elements (100 to 200 bp) that include the start site of replication, also called the origin of bidirectional DNA replication (OBR) (11). They consist of an essential 11-bp ARS consensus sequence (ACS) and of several auxiliary B elements that contribute to initiation activity. The ACS binds the origin recognition complex (ORC), a heteromeric complex of six proteins that assists the formation of a prereplicative complex on the origin. ORC orthologs have been isolated from all the eukaryotic species analyzed so far, including humans (for a review see reference 8). The ARS sequences and the ORC can be viewed as the prototypes of the eukaryotic replicator and initiator.The major obstacle to the validation of the replicon model in metazoan cells was the failure to isolate the functional homologues of the ARS elements...

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The identification of metazoan origins of DNA replication has so far been hampered by the lack of a suitable genetic screening and by the cumbersomeness of the currently available mapping procedures. Here we describe the construction of a library of nascent DNA, representative of all cellular origin sequences, and its utilization as a screening probe for origin identification in large genomic regions. The procedure developed was successfully applied to the human 5q31.1 locus, encoding for the IL-3 and GM-CSF genes. Two novel origins were identified and subsequently characterized by competitive PCR mapping, located approximately 3.5 kb downstream of the GM-CSF gene. The two origins (GM-CSF Ori1 and Ori2) were shown to interact with different members of the DNA prereplication complex. This observation reinforces the universal paradigm that initiation of DNA replication takes place at, or in close proximity to, the binding sites of the trans-acting initiator proteins.

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