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Ben Van Handel,
Amélie Montel-Hagen,
Rajkumar Sasidharan,
Haruko Nakano, Roberto Ferrari,
Cornelis J Boogerd,
Johann Schredelseker,
Yanling Wang,
Sean Hunter,
Tõnis Org,
Jian Zhou,
Xinmin Li,
Matteo Pellegrini,
Jau-Nian Chen,
Stuart H Orkin,
Siavash K Kurdistani,
Sylvia M Evans,
Atsushi Nakano,
Hanna K A Mikkola
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ABSTRACT: Endothelium in embryonic hematopoietic tissues generates hematopoietic stem/progenitor cells; however, it is unknown how its unique potential is specified. We show that transcription factor Scl/Tal1 is essential for both establishing the hematopoietic transcriptional program in hemogenic endothelium and preventing its misspecification to a cardiomyogenic fate. Scl(-/-) embryos activated a cardiac transcriptional program in yolk sac endothelium, leading to the emergence of CD31+Pdgfrα+ cardiogenic precursors that generated spontaneously beating cardiomyocytes. Ectopic cardiogenesis was also observed in Scl(-/-) hearts, where the disorganized endocardium precociously differentiated into cardiomyocytes. Induction of mosaic deletion of Scl in Scl(fl/fl)Rosa26Cre-ER(T2) embryos revealed a cell-intrinsic, temporal requirement for Scl to prevent cardiomyogenesis from endothelium. Scl(-/-) endothelium also upregulated the expression of Wnt antagonists, which promoted rapid cardiomyocyte differentiation of ectopic cardiogenic cells. These results reveal unexpected plasticity in embryonic endothelium such that loss of a single master regulator can induce ectopic cardiomyogenesis from endothelial cells.
Cell 08/2012; 150(3):590-605. · 32.40 Impact Factor
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ABSTRACT: Adenovirus small e1a oncoprotein causes ~70% reduction in cellular levels of histone H3 lysine 18 acetylation (H3K18ac). It is unclear, however, where this dramatic reduction occurs genome-wide. ChIP-sequencing revealed that by 24 h after expression, e1a erases 95% of H3K18ac peaks in normal, contact-inhibited fibroblasts and replaces them with one-third as many at new genomic locations. The H3K18ac peaks at promoters and intergenic regions of genes with fibroblast-related functions are eliminated after infection, and new H3K18ac peaks are established at promoters of highly induced genes that regulate cell cycling and at new putative enhancers. Strikingly, the regions bound by the retinoblastoma family of proteins in contact-inhibited fibroblasts gain new peaks of H3K18ac in the e1a-expressing cells, including 55% of RB1-bound loci. In contrast, over half of H3K9ac peaks are similarly distributed before and after infection, independently of RB1. The strategic redistribution of H3K18ac by e1a highlights the importance of this modification for transcriptional activation and cellular transformation as well as functional differences between the RB-family member proteins.
Genome Research 04/2012; 22(7):1212-21. · 13.61 Impact Factor
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ABSTRACT: The access of transcription factors and the replication machinery to DNA is regulated by the epigenetic state of chromatin. In eukaryotes, this complex layer of regulatory processes includes the direct methylation of DNA, as well as covalent modifications to histones. Using next-generation sequencers, it is now possible to obtain profiles of epigenetic modifications across a genome using chromatin immunoprecipitation followed by sequencing (ChIP-seq). This technique permits the detection of the binding of proteins to specific regions of the genome with high resolution. It can be used to determine the target sequences of transcription factors, as well as the positions of histones with specific modification of their N-terminal tails. Antibodies that selectively bind methylated DNA may also be used to determine the position of methylated cytosines. Here, we present a data analysis pipeline for processing ChIP-seq data, and discuss the limitations and idiosyncrasies of these approaches.
Methods in molecular biology (Clifton, N.J.) 01/2012; 802:377-87.
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ABSTRACT: The HIV-1 Trans-Activator of Transcription (Tat) protein binds to multiple host cellular factors and greatly enhances the level of transcription of the HIV genome. While Tat's control of viral transcription is well-studied, much less is known about the interaction of Tat with the human genome. Here, we report the genome-wide binding map of Tat to the human genome in Jurkat T cells using chromatin immunoprecipitation combined with next-generation sequencing. Surprisingly, we found that ~53% of the Tat target regions are within DNA repeat elements, greater than half of which are Alu sequences. The remaining target regions are located in introns and distal intergenic regions; only ~7% of Tat-bound regions are near transcription start sites (TSS) at gene promoters. Interestingly, Tat binds to promoters of genes that, in Jurkat cells, are bound by the ETS1 transcription factor, the CBP histone acetyltransferase and/or are enriched for histone H3 lysine 4 tri-methylation (H3K4me3) and H3K27me3. Tat binding is associated with genes enriched with functions in T cell biology and immune response. Our data reveal that Tat's interaction with the host genome is more extensive than previously thought, with potentially important implications for the viral life cycle.
PLoS ONE 01/2011; 6(11):e26894. · 4.09 Impact Factor
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ABSTRACT: The cancerous cellular state is associated with multiple epigenetic alterations, but elucidating the precise order of such alterations during tumorigenic progression and their contributions to the transformed phenotype remains a significant challenge in cancer biology. Here we discuss recent findings on how viral oncoproteins exploit specific epigenetic processes to coerce normal cells to replicate when they should remain quiescent - a hallmark of cancer. These findings may highlight roles of epigenetic processes in normal biology and shed light on epigenetic events occurring along the path of non-viral neoplastic transformation.
Nature Reviews Genetics 04/2009; 10(5):290-4. · 38.08 Impact Factor
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Christos Gekas,
Katrin E Rhodes,
Laurraine M Gereige,
Hildur Helgadottir, Roberto Ferrari,
Siavash K Kurdistani,
Encarnación Montecino-Rodriguez,
Rhonda Bassel-Duby,
Eric Olson,
Andrei V Krivtsov,
Scott Armstrong,
Stuart H Orkin,
Matteo Pellegrini,
Hanna K A Mikkola
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ABSTRACT: The basic helix-loop-helix transcription factor stem cell leukemia gene (Scl) is a master regulator for hematopoiesis essential for hematopoietic specification and proper differentiation of the erythroid and megakaryocyte lineages. However, the critical downstream targets of Scl remain undefined. Here, we identified a novel Scl target gene, transcription factor myocyte enhancer factor 2 C (Mef2C) from Scl(fl/fl) fetal liver progenitor cell lines. Analysis of Mef2C(-/-) embryos showed that Mef2C, in contrast to Scl, is not essential for specification into primitive or definitive hematopoietic lineages. However, adult VavCre(+)Mef2C(fl/fl) mice exhibited platelet defects similar to those observed in Scl-deficient mice. The platelet counts were reduced, whereas platelet size was increased and the platelet shape and granularity were altered. Furthermore, megakaryopoiesis was severely impaired in vitro. Chromatin immunoprecipitation microarray hybridization analysis revealed that Mef2C is directly regulated by Scl in megakaryocytic cells, but not in erythroid cells. In addition, an Scl-independent requirement for Mef2C in B-lymphoid homeostasis was observed in Mef2C-deficient mice, characterized as severe age-dependent reduction of specific B-cell progenitor populations reminiscent of premature aging. In summary, this work identifies Mef2C as an integral member of hematopoietic transcription factors with distinct upstream regulatory mechanisms and functional requirements in megakaryocyte and B-lymphoid lineages.
Blood 03/2009; 113(15):3461-71. · 9.90 Impact Factor
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ABSTRACT: Adenovirus e1a induces quiescent human cells to replicate. We found that e1a causes global relocalization of the RB (retinoblastoma) proteins (RB, p130, and p107) and p300/CBP histone acetyltransferases on promoters, the effect of which is to restrict the acetylation of histone 3 lysine-18 (H3K18ac) to a limited set of genes, thereby stimulating cell cycling and inhibiting antiviral responses and cellular differentiation. Soon after expression, e1a binds transiently to promoters of cell cycle and growth genes, causing enrichment of p300/CBP, PCAF (p300/CBP-associated factor), and H3K18ac; depletion of RB proteins; and transcriptional activation. e1a also associates transiently with promoters of antiviral genes, causing enrichment for RB, p130, and H4K16ac; increased nucleosome density; and transcriptional repression. At later times, e1a and p107 bind mainly to promoters of development and differentiation genes, repressing transcription. The temporal order of e1a binding requires its interactions with p300/CBP and RB proteins. Our data uncover a defined epigenetic reprogramming leading to cellular transformation.
Science 09/2008; 321(5892):1086-8. · 31.20 Impact Factor
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ABSTRACT: Acetylation of histones plays an important role in regulating transcription. Histone acetylation is mediated partly by the recruitment of specific histone acetyltransferases (HATs) and deacetylases (HDACs) to genomic loci by transcription factors, resulting in modulation of gene expression. Although several specific interactions between transcription factors and HATs and HDACs have been elaborated in Saccharomyces cerevisiae, the full regulatory network remains uncharacterized. We have utilized a linear regression of optimized sigmoidal functions to correlate transcription factor binding patterns to the acetylation profiles of 11 lysines in the four core histones measured at all S. cerevisiae promoters. The resulting associations are combined with large-scale protein-protein interaction data sets to generate a comprehensive model that relates recruitment of specific HDACs and HATs to transcription factors and their target genes and the resulting effects on individual lysines. This model provides a broad and detailed view of the regulatory network, describing which transcription factors are most significant in regulating acetylation of specific lysines at defined promoters. We validate the model, both computationally and experimentally, to demonstrate that it yields accurate predictions of these regulatory mechanisms.
Molecular Systems Biology 02/2007; 3:153. · 8.63 Impact Factor
