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Chromatin Modifications (chromatin + modifications)
Selected AbstractsEpigenetic reprogramming: Enforcer or enabler of developmental fate?DEVELOPMENT GROWTH & DIFFERENTIATION, Issue 6 2010Alexander N. Combes A single fertilized egg is programmed to differentiate into a multitude of distinct cell types that comprise a multicellular organism. Epigenetic mechanisms such as DNA methylation and histone modifications are intricately involved in regulating developmental potential and cellular identity by establishing permissive or repressive chromatin states that are mitotically heritable. Here, we review the dynamics of major epigenetic marks during early mammalian development, and explore the question of whether DNA methylation and chromatin modifications enable or enforce changes that lead to the first cell fate decision. [source] Regulation of IL-4 production in mast cells: a paradigm for cell-type-specific gene expressionIMMUNOLOGICAL REVIEWS, Issue 1 2001Deborah L. Weiss Summary: The role of interleukin (IL)-4 as an important immunomodulatory cytokine is well established. IL-4 exhibits a highly restricted pattern of expression by cells of distinct lineages. The cell types that produce IL-4 are located in anatomically distinct locations (e.g. circulating T cells vs. fixed tissue mast cells) and thus have access to different IL-4-responsive target cells. In addition, these cells appear to regulate IL-4 expression in cell-type-specific ways. These findings suggest that an understanding of IL-4 gene regulation in T and mast cells could provide the means to specifically control IL-4 release in a lineage- and site-specific manner. In this article we review the current knowledge regarding the cell-type specific regulation of IL-4 gene expression in mast cells and compare this to what has been defined in T cells. We show that there are distinct yet parallel events that control developmentally determined chromatin modifications, allowing accessibility of the locus, and provide the potential for transcription. In differentiated cells, a subset of unique cell activation signals initiates the cascade of events that lead to transcriptional activation of the IL-4 gene. This work was supported by the National Science Foundation (DLW), the National Institutes of Health and the Multiple Sclerosis Society (MAB). We appreciate the technical and intellectual contributions of many colleagues including Doris Powell, John Hural, Tammy Nachman, Ben Hock, David Tara, Greg Henkel, Susan Lee, Millie Kwan, Melanie Sherman and Ginny Secor. [source] Dynamic assembly of chromatin complexes during cellular senescence: implications for the growth arrest of human melanocytic neviAGING CELL, Issue 4 2007Debdutta Bandyopadhyay Summary The retinoblastoma (RB)/p16INK4a pathway regulates senescence of human melanocytes in culture and oncogene-induced senescence of melanocytic nevi in vivo. This senescence response is likely due to chromatin modifications because RB complexes from senescent melanocytes contain increased levels of histone deacetylase (HDAC) activity and tethered HDAC1. Here we show that HDAC1 is prominently detected in p16INK4a -positive, senescent intradermal melanocytic nevi but not in proliferating, recurrent nevus cells that localize to the epidermal/dermal junction. To assess the role of HDAC1 in the senescence of melanocytes and nevi, we used tetracycline-based inducible expression systems in cultured melanocytic cells. We found that HDAC1 drives a sequential and cooperative activity of chromatin remodeling effectors, including transient recruitment of Brahma (Brm1) into RB/HDAC1 mega-complexes, formation of heterochromatin protein 1, (HP1,)/SUV39H1 foci, methylation of H3-K9, stable association of RB with chromatin and significant global heterochromatinization. These chromatin changes coincide with expression of typical markers of senescence, including the senescent-associated ,-galactosidase marker. Notably, formation of RB/HP1, foci and early tethering of RB to chromatin depends on intact Brm1 ATPase activity. As cells reached senescence, ejection of Brm1 from chromatin coincided with its dissociation from HP1,/RB and relocalization to protein complexes of lower molecular weight. These results provide new insights into the role of the RB pathway in regulating cellular senescence and implicate HDAC1 as a likely mediator of early chromatin remodeling events. [source] How Epigenomics Contributes to the Understanding of Gene Regulation in Toxoplasma gondii,THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 6 2008MATHIEU GISSOT ABSTRACT. How apicomplexan parasites regulate their gene expression is poorly understood. The complex life cycle of these parasites implies tight control of gene expression to orchestrate the appropriate expression pattern at the right moment. Recently, several studies have demonstrated the role of epigenetic mechanisms for control of coordinated expression of genes. In this review, we discuss the contribution of epigenomics to the understanding of gene regulation in Toxoplasma gondii. Studying the distribution of modified histones on the genome links chromatin modifications to gene expression or gene repression. In particular, coincident trimethylated lysine 4 on histone H3 (H3K4me3), acetylated lysine 9 on histone H3 (H3K9ac), and acetylated histone H4 (H4ac) mark promoters of actively transcribed genes. However, the presence of these modified histones at some non-expressed genes and other histone modifications at only a subset of active promoters implies the presence of other layers of regulation of chromatin structure in T. gondii. Epigenomics analysis provides a powerful tool to characterize the activation state of genomic loci of T. gondii and possibly of other Apicomplexa including Plasmodium or Cryptosporidium. Further, integration of epigenetic data with expression data and other genome-wide datasets facilitates refinement of genome annotation based upon experimental data. [source] Global analysis of siRNA-mediated transcriptional gene silencingBIOESSAYS, Issue 12 2005Harsh H. Kavi The RNAi machinery is not only involved with post-transcriptional degradation of messenger RNAs, but also used for targeting of chromatin changes associated with transcriptional silencing. Two recent papers determine the global patterns of gene expression and chromatin modifications produced by the RNAi machinery in fission yeast.(9, 10) The major sites include the outer centromere repeats, the mating-type locus and subtelomeric regions. By comparison, studies of Arabidopsis heterochromatin also implicate transposons as a major target for silencing. Analyses of siRNA libraries from Drosophila, nematodes and Arabidopsis indicate that major repeats at centromeres, telomeres and transposable elements are likely targets of RNAi. Also, intergenic regions are implicated as targets in Arabidopsis. BioEssays 27:1209,1212, 2005. © 2005 Wiley Periodicals, Inc. [source] Neural stem cells: Mechanisms of fate specification and nuclear reprogramming in regenerative medicineBIOTECHNOLOGY JOURNAL, Issue 12 2008Carsten W. Lederer Abstract Recently, intense interest in the potential use of neural stem cells (NSC) in the clinical therapy of brain disease and injury has resulted in rapid progress in research on the properties of NSC, their innate and directed differentiation potential and the induced reprogramming of differentiated somatic cells to revert to a pluripotent NSC-like state. The aim of this review is to give an overview of our current operational definitions of the NSC lineage, the growing understanding of extrinsic and intrinsic mechanisms, including heritable but reversible epigenetic chromatin modifications that regulate the maintenance and differentiation of NSC in vivo, and to emphasize ground-breaking efforts of cellular reprogramming with the view to generating patient-specific stem cells for cell replacement therapy. This is set against a summary of current practical procedures for the isolation, research and application of NSC, and of the state of the art in NSC-based regenerative medicine of the nervous system. Both provide the backdrop for the translation of recent findings into innovative clinical applications, with the hope of increasing the safety, efficiency and ethical acceptability of NSC-based therapies in the near future. [source] | ||||||||||