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A bivalent chromatin structure marks key developmental genes in embryonic stem cells, Cell 125
, 2006
"... The most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within regions enriched for genes encoding developmentally important transcription factors (TFs). This suggests that HCNE-rich regions may contain key regulatory controls involved in development. We explored this by ex ..."
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The most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within regions enriched for genes encoding developmentally important transcription factors (TFs). This suggests that HCNE-rich regions may contain key regulatory controls involved in development. We explored this by examining histone methylation in mouse embryonic stem (ES) cells across 56 large HCNE-rich loci. We identified a specific modification pattern, termed ‘‘bivalent domains,’ ’ consisting of large regions of H3 lysine 27 methylation harboring smaller regions of H3 lysine 4 methylation. Bivalent domains tend to coincide with TF genes expressed at low levels. We propose that bivalent domains silence developmental genes in ES cells while keeping them poised for activation. We also found striking correspondences between genome sequence and histone methylation in ES cells, which become notably weaker in differentiated cells. These results highlight the importance of DNA sequence in defining the initial epigenetic landscape and suggest a novel chromatin-based mechanism for maintaining pluripotency.
Polycomb mediated epigenetic silencing and replication timing at the INK4a/ARF locus during senescence. PLoS One 4
, 2009
"... Background: The INK4/ARF locus encodes three tumor suppressor genes (p15Ink4b, Arf and p16Ink4a) and is frequently inactivated in a large number of human cancers. Mechanisms regulating INK4/ARF expression are not fully characterized. Principal Findings: Here we show that in young proliferating embry ..."
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Background: The INK4/ARF locus encodes three tumor suppressor genes (p15Ink4b, Arf and p16Ink4a) and is frequently inactivated in a large number of human cancers. Mechanisms regulating INK4/ARF expression are not fully characterized. Principal Findings: Here we show that in young proliferating embryonic fibroblasts (MEFs) the Polycomb Repressive Complex 2 (PRC2) member EZH2 together with PRC1 members BMI1 and M33 are strongly expressed and localized at the INK4/ARF regulatory domain (RD) identified as a DNA replication origin. When cells enter senescence the binding to RD of both PRC1 and PRC2 complexes is lost leading to a decreased level of histone H3K27 trimethylation (H3K27me3). This loss is accompanied with an increased expression of the histone demethylase Jmjd3 and with the recruitment of the MLL1 protein, and correlates with the expression of the Ink4a/Arf genes. Moreover, we show that the Polycomb protein BMI1 interacts with CDC6, an essential regulator of DNA replication in eukaryotic cells. Finally, we demonstrate that Polycomb proteins and associated epigenetic marks are crucial for the control of the replication timing of the INK4a/ARF locus during senescence. Conclusions: We identified the replication licencing factor CDC6 as a new partner of the Polycomb group member BMI1. Our results suggest that in young cells Polycomb proteins are recruited to the INK4/ARF locus through CDC6 and the resulting silent locus is replicated during late S-phase. Upon senescence, Jmjd3 is overexpressed and the MLL1 protein is recruited to the locus provoking the dissociation of Polycomb from the INK4/ARF locus, its transcriptional activation and its
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, 2009
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Pou5f1 Post-translational Modifications Modulate Gene Expression and Cell Fate
"... e533. All works published in PloSOne are open access, licensed under the Creative Commons Attribution License. Everything is immediately available without cost to anyone, anywhere-to read, download, redistribute, include in databases, and otherwise use-provided that the original author and source ar ..."
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e533. All works published in PloSOne are open access, licensed under the Creative Commons Attribution License. Everything is immediately available without cost to anyone, anywhere-to read, download, redistribute, include in databases, and otherwise use-provided that the original author and source are credited. Copyright is retained by the author. iii Embryonic stem cells (ESCs) are characterized by their unlimited capacity for self-renewal and the ability to contribute to every lineage of the developing embryo. The promoters of developmentally regulated loci within these cells are marked by coincident epigenetic modifications of gene activation and repression, termed bivalent domains. Trithorax group (TrxG) and Polycomb Group (PcG) proteins respectively place these epigenetic marks on chromatin and extensively colocalize with Oct4 in ESCs. Although it appears that these cells are poised and ready for differentiation, the switch that permits this transition is critically held in check. The derepression of bivalent domains upon knockdown
Mol. Hum. Reprod. Advance Access published August 20, 2008 1 NEW RESEARCH HORIZON Understanding pluripotency- how embryonic
"... stem cells keep their options open ..."
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12 Reviews on Recent Clinical Trials, 2009, 4, 12-26 Molecular Pathology of Sarcomas
"... Abstract: Bone and soft tissue sarcomas are an infrequent group of tumours with a prevalence of 4 in 100000 people/year. Sarcomas, such as synovial sarcoma, Ewing’s sarcoma and osteosarcoma, are more usual in adolescents or in young adults. Neoplasias such as leiomyosarcoma or liposarcoma are more f ..."
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Abstract: Bone and soft tissue sarcomas are an infrequent group of tumours with a prevalence of 4 in 100000 people/year. Sarcomas, such as synovial sarcoma, Ewing’s sarcoma and osteosarcoma, are more usual in adolescents or in young adults. Neoplasias such as leiomyosarcoma or liposarcoma are more frequent in patients over 55 years. One relevant topic is related to sarcomagenesis elucidation, a key for discovering the early molecular mechanisms involved in the development of sarcomas as well as the identification of reliable molecular markers and possible therapeutic targets. Today, it is known that the cellular context contributes to the phenotype. Analysis of gene expression profiling of human sarcomas revealed tightly clustered groups and could denote the existence of common signalling pathways for each branch. From the molecular point of view, these neoplasias are grouped into two main types: (a) sarcomas showing specific genetic alterations and relatively simple karyotypes, and translocations which originate gene fusions (e.g., EWS-FLI1 in Ewing’s sarcoma); or specific genetic mutations (e.g., c-kit in the gastrointestinal stromal tumour), and (b) sarcomas showing unspecific gene alterations and very complex karyotypes, and very numerous gains and losses. This review points out the clinical projection of sarcomagenesis elucidation and knowledge of diverse types of molecular alterations.
PLoS BIOLOGY Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation
"... DNA replication in mammals is regulated via the coordinate firing of clusters of replicons that duplicate megabasesized chromosome segments at specific times during S-phase. Cytogenetic studies show that these ‘‘replicon clusters’’ coalesce as subchromosomal units that persist through multiple cell ..."
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DNA replication in mammals is regulated via the coordinate firing of clusters of replicons that duplicate megabasesized chromosome segments at specific times during S-phase. Cytogenetic studies show that these ‘‘replicon clusters’’ coalesce as subchromosomal units that persist through multiple cell generations, but the molecular boundaries of such units have remained elusive. Moreover, the extent to which changes in replication timing occur during differentiation and their relationship to transcription changes has not been rigorously investigated. We have constructed highresolution replication-timing profiles in mouse embryonic stem cells (mESCs) before and after differentiation to neural precursor cells. We demonstrate that chromosomes can be segmented into multimegabase domains of coordinate replication, which we call ‘‘replication domains,’ ’ separated by transition regions whose replication kinetics are consistent with large originless segments. The molecular boundaries of replication domains are remarkably well conserved between distantly related ESC lines and induced pluripotent stem cells. Unexpectedly, ESC differentiation was accompanied by the consolidation of smaller differentially replicating domains into larger coordinately replicated units whose replication time was more aligned to isochore GC content and the density of LINE-1 transposable elements, but not gene density. Replication-timing changes were coordinated with transcription changes for weak promoters more than strong promoters, and were accompanied by rearrangements in subnuclear position. We
