Publications
162 results found
Liang Z, Brown KE, Carroll T, et al., 2017, A high-resolution map of transcriptional repression, ELIFE, Vol: 6, ISSN: 2050-084X
Turning genes on and off is essential for development and homeostasis, yet little is known about the sequence and causal role of chromatin state changes during the repression of active genes. This is surprising, as defective gene silencing underlies developmental abnormalities and disease. Here we delineate the sequence and functional contribution of transcriptional repression mechanisms at high temporal resolution. Inducible entry of the NuRD-interacting transcriptional regulator Ikaros into mouse pre-B cell nuclei triggered immediate binding to target gene promoters. Rapid RNAP2 eviction, transcriptional shutdown, nucleosome invasion, and reduced transcriptional activator binding required chromatin remodeling by NuRD-associated Mi2beta/CHD4, but were independent of HDAC activity. Histone deacetylation occurred after transcriptional repression. Nevertheless, HDAC activity contributed to stable gene silencing. Hence, high resolution mapping of transcriptional repression reveals complex and interdependent mechanisms that underpin rapid transitions between transcriptional states, and elucidates the temporal order, functional role and mechanistic separation of NuRD-associated enzymatic activities.
Perez MEF, Bloznelyte K, Merkenschlager M, et al., 2017, Visualizing CTCF mediated DNA looping at the single molecule level, 61st Annual Meeting of the Biophysical-Society, Publisher: Biophysical Society, Pages: 169A-170A, ISSN: 0006-3495
Van de Pette M, Abbas A, Feytout A, et al., 2017, Visualizing changes in Cdkn1c expression links early life adversity to imprint mis-regulation in adults, Cell Reports, Vol: 31, Pages: 1090-1099, ISSN: 2211-1247
Imprinted genes are regulated according to parental origin and can influence embryonic growth and metabolism and confer disease susceptibility.Here we designed sensitive allele-specific reporters to non-invasively monitor imprinted Cdkn1cexpression in mice and showed that expression was modulated by environmental factors encounteredin utero.Acute exposure to chromatin modifyingdrugs resulted in de-repression of paternally inherited (silent) Cdkn1calleles in embryos that was temporary and resolved after birth.In contrast, deprivation of maternal dietary proteinin uteroprovoked permanent de-repression of imprinted Cdkn1cexpression that was sustained into adulthood and occurred through a folate-dependent mechanism of DNA methylation loss.Given the function of imprinted genes in regulating behavior and metabolic processes in adults, these results establish imprinting deregulation as a credible mechanism linking early life adversity to later-life outcomes.Furthermore,Cdkn1c-luciferasemice offer non-invasivetools to identify factors that disrupt epigenetic processes and strategies to limit their long-term impact.
Cantone I, Dharmalingam G, Chan YW, et al., 2017, Allele-specific analysis of cell fusion-mediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation, Genome Biology, Vol: 18, ISSN: 1474-760X
BackgroundInactivation of one X chromosome is established early in female mammalian development and can be reversed in vivo and in vitro when pluripotency factors are re-expressed. The extent of reactivation along the inactive X chromosome (Xi) and the determinants of locus susceptibility are, however, poorly understood. Here we use cell fusion-mediated pluripotent reprograming to study human Xi reactivation and allele-specific single nucleotide polymorphisms (SNPs) to identify reactivated loci.ResultsWe show that a subset of human Xi genes is rapidly reactivated upon re-expression of the pluripotency network. These genes lie within the most evolutionary recent segments of the human X chromosome that are depleted of LINE1 and enriched for SINE elements, predicted to impair XIST spreading. Interestingly, this cadre of genes displays stochastic Xi expression in human fibroblasts ahead of reprograming. This stochastic variability is evident between clones, by RNA-sequencing, and at the single-cell level, by RNA-FISH, and is not attributable to differences in repressive histone H3K9me3 or H3K27me3 levels. Treatment with the DNA demethylating agent 5-deoxy-azacytidine does not increase Xi expression ahead of reprograming, but instead reveals a second cadre of genes that only become susceptible to reactivation upon induction of pluripotency.ConclusionsCollectively, these data not only underscore the multiple pathways that contribute to maintaining silencing along the human Xi chromosome but also suggest that transcriptional stochasticity among human cells could be useful for predicting and engineering epigenetic strategies to achieve locus-specific or domain-specific human Xi gene reactivation.
Gupta P, Lavagnolli T, Mira-Bontenbal H, et al., 2016, Analysis of Cohesin Function in Gene Regulation and Chromatin Organization in Interphase., Methods Mol Biol, Vol: 1515, Pages: 197-216
Cohesin is essential for the maintenance of chromosomes through the cell cycle. In addition, cohesin contributes to the regulation of gene expression and the organization of chromatin in interphase cells. To study cohesin's role in gene expression and chromatin organization, it is necessary to avoid secondary effects due to disruption of vital cohesin functions in the cell cycle. Here we describe experimental approaches to achieve this and the methods applied to define cohesin's role in interphase.
Merkenschlager M, Nora EP, 2016, CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation, Annual Review of Genomics and Human Genetics, Vol: 17, ISSN: 1545-293X
Genome function, replication, integrity, and propagation rely on the dynamic structural organization of chromosomes during the cell cycle.Genome folding in interphase provides regulatory segmentation for appropriate transcriptional control, facilitates ordered genome replication, and contributes to genome integrity by limiting illegitimate recombination. Here, we review recent high-resolution chromosome conformation capture and functional studies that have informed models of the spatial and regulatory compartmentalization of mammalian genomes, and discuss mechanistic models for how CTCF and cohesin control the functional architecture of mammalian chromosomes. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 17 is August 31, 2016. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.
Bond J, Domaschenz R, Roman-Trufero M, et al., 2016, Direct interaction of Ikaros and Foxp1 modulates expression of the G protein-coupled receptor G2A in B-lymphocytes and acute lymphoblastic leukemia, Oncotarget, Vol: 7, Pages: 65923-65936, ISSN: 1949-2553
Ikaros and Foxp1 are transcription factors that play key roles in normal lymphopoiesis and lymphoid malignancies. We describe a novel physical and functional interaction between the proteins, which requires the central zinc finger domain of Ikaros. The Ikaros-Foxp1 interaction is abolished by deletion of this region, which corresponds to the IK6 isoform that is commonly associated with high-risk acute lymphoblastic leukemia (ALL). We also identify the Gpr132 gene, which encodes the orphan G protein-coupled receptor G2A, as a novel target for Foxp1. Increased expression of Foxp1 enhanced Gpr132 transcription and caused cell cycle changes, including G2 arrest. Co-expression of wild-type Ikaros, but not IK6, displaced Foxp1 binding from the Gpr132 gene, reversed the increase in Gpr132 expression and inhibited G2 arrest. Analysis of primary ALL samples revealed a significant increase in GPR132 expression in IKZF1-deleted BCR-ABL negative patients, suggesting that levels of wild-type Ikaros may influence the regulation of G2A in B-ALL. Our results reveal a novel effect of Ikaros haploinsufficiency on Foxp1 functioning, and identify G2A as a potential modulator of the cell cycle in Ikaros-deleted B-ALL.
Fisher AG, 2016, Ordered chromatin changes and human X chromosome reactivation by cell fusion-mediated pluripotent reprogramming, Nature Communications, Vol: 7, ISSN: 2041-1723
Erasure of epigenetic memory is required to convert somatic cells towards pluripotency. Reactivation of the inactive X chromosome (Xi) has been used to model epigenetic reprogramming in mouse, but human studies are hampered by Xi epigenetic instability and difficulties in tracking partially reprogrammed iPSCs. Here we use cell fusion to examine the earliest events in the reprogramming-induced Xi reactivation of human female fibroblasts. We show that a rapid and widespread loss of Xi-associated H3K27me3 and XIST occurs in fused cells and precedes the bi-allelic expression of selected Xi-genes by many heterokaryons (30–50%). After cell division, RNA-FISH and RNA-seq analyses confirm that Xi reactivation remains partial and that induction of human pluripotency-specific XACT transcripts is rare (1%). These data effectively separate pre- and post-mitotic events in reprogramming-induced Xi reactivation and reveal a complex hierarchy of epigenetic changes that are required to reactivate the genes on the human Xi chromosome.
Graham B, Marcais A, Dharmalingam G, et al., 2016, MicroRNAs of the miR-290-295 Family Maintain Bivalency in Mouse Embryonic Stem Cells., Stem Cell Reports, Vol: 6, Pages: 635-642, ISSN: 2213-6711
Numerous developmentally regulated genes in mouse embryonic stem cells (ESCs) are marked by both active (H3K4me3)- and polycomb group (PcG)-mediated repressive (H3K27me3) histone modifications. This bivalent state is thought to be important for transcriptional poising, but the mechanisms that regulate bivalent genes and the bivalent state remain incompletely understood. Examining the contribution of microRNAs (miRNAs) to the regulation of bivalent genes, we found that the miRNA biogenesis enzyme DICER was required for the binding of the PRC2 core components EZH2 and SUZ12, and for the presence of the PRC2-mediated histone modification H3K27me3 at many bivalent genes. Genes that lost bivalency were preferentially upregulated at the mRNA and protein levels. Finally, reconstituting Dicer-deficient ESCs with ESC miRNAs restored bivalent gene repression and PRC2 binding at formerly bivalent genes. Therefore, miRNAs regulate bivalent genes and the bivalent state itself.
Ing-Simmons E, Merkenschlager M, 2016, Oncometabolite Tinkers with Genome Folding, Boosting Oncogene Expression., Trends in Molecular Medicine, Vol: 22, Pages: 185-187, ISSN: 1471-4914
A recent article makes a compelling case for a new mechanism by which heterozygous mutations in isocitrate dehydrogenases (IDH1/2) - implicated in cancer - undermine gene regulation. 2-Hydroxyglutarate (2HG) produced by mutant IDH alters the binding of the chromosomal organizer protein CTCF, disrupting the spatial and regulatory organization of the genome.
Gupta P, Lavagnolli T, Mira-Bontenbal H, et al., 2015, Cohesin's role in pluripotency and reprogramming., Cell Cycle, Vol: 15, Pages: 324-330, ISSN: 1551-4005
Cohesin is required for ES cell self-renewal and iPS-mediated reprogramming of somatic cells. This may indicate a special role for cohesin in the regulation of pluripotency genes, perhaps by mediating long-range chromosomal interactions between gene regulatory elements. However, cohesin is also essential for genome integrity, and its depletion from cycling cells induces DNA damage responses. Hence, the failure of cohesin-depleted cells to establish or maintain pluripotency gene expression could be explained by a loss of long-range interactions or by DNA damage responses that undermine pluripotency gene expression. In recent work we began to disentangle these possibilities by analyzing reprogramming in the absence of cell division. These experiments showed that cohesin was not specifically required for reprogramming, and that the expression of most pluripotency genes was maintained when ES cells were acutely depleted of cohesin. Here we take this analysis to its logical conclusion by demonstrating that deliberately inflicted DNA damage - and the DNA damage that results from proliferation in the absence of cohesin - can directly interfere with pluripotency and reprogramming. The role of cohesin in pluripotency and reprogramming may therefore be best explained by essential cohesin functions in the cell cycle.
Merkenschlager M, Marcais A, 2015, microRNAs calibrate T cell responses by regulating mTOR., Oncotarget, Vol: 6, Pages: 34059-34060, ISSN: 1949-2553
Landeira D, Bagci H, Malinowski AR, et al., 2015, Jarid2 coordinates nanog expression and PCP/Wnt signaling required for efficient ESC differentiation and early embryo development, Cell Reports, Vol: 12, Pages: 573-586, ISSN: 2211-1247
Jarid2 is part of the Polycomb Repressor complex 2 (PRC2) responsible for genome-wide H3K27me3 deposition. Unlike other PRC2-deficient embryonic stem cells (ESCs), however, Jarid2-deficient ESCs show a severe differentiation block, altered colony morphology, and distinctive patterns of deregulated gene expression. Here, we show that Jarid2−/− ESCs express constitutively high levels of Nanog but reduced PCP signaling components Wnt9a, Prickle1, and Fzd2 and lowered β-catenin activity. Depletion of Wnt9a/Prickle1/Fzd2 from wild-type ESCs or overexpression of Nanog largely phenocopies these cellular defects. Co-culture of Jarid2−/− with wild-type ESCs restores variable Nanog expression and β-catenin activity and can partially rescue the differentiation block of mutant cells. In addition, we show that ESCs lacking Jarid2 or Wnt9a/Prickle1/Fzd2 or overexpressing Nanog induce multiple ICM formation when injected into normal E3.5 blastocysts. These data describe a previously unrecognized role for Jarid2 in regulating a core pluripotency and Wnt/PCP signaling circuit that is important for ESC differentiation and for pre-implantation development.
Tan JY, Sirey T, Honti F, et al., 2015, Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells, GENOME RESEARCH, Vol: 25, Pages: 655-666, ISSN: 1088-9051
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- Citations: 74
Blevins R, Bruno L, Carroll T, et al., 2015, microRNAs regulate cell-to-cell variability of endogenous target gene expression in developing mouse thymocytes, Plos Genetics, Vol: 11, Pages: 1-19, ISSN: 1553-7404
The development and homeostasis of multicellular organisms relies on gene regulationwithin individual constituent cells. Gene regulatory circuits that increase the robustness ofgene expression frequently incorporate microRNAs as post-transcriptional regulators.Computational approaches, synthetic gene circuits and observations in model organismspredict that the co-regulation of microRNAs and their target mRNAs can reduce cell-to-cellvariability in the expression of target genes. However, whether microRNAs directly regulatevariability of endogenous gene expression remains to be tested in mammalian cells. Herewe use quantitative flow cytometry to show that microRNAs impact on cell-to-cell variabilityof protein expression in developing mouse thymocytes. We find two distinct mechanismsthat control variation in the activation-induced expression of the microRNA target CD69.First, the expression of miR-17 and miR-20a, two members of the miR-17-92 cluster, is coregulatedwith the target mRNA Cd69 to form an activation-induced incoherent feed-forwardloop. Another microRNA, miR-181a, acts at least in part upstream of the target mRNA Cd69to modulate cellular responses to activation. The ability of microRNAs to render gene expressionmore uniform across mammalian cell populations may be important for normal developmentand for disease.
Ing-Simmons E, Seitan VC, Faure AJ, et al., 2015, Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin, Genome Research, Vol: 25, Pages: 504-513, ISSN: 1054-9803
In addition to mediating sister chromatid cohesion during the cell cycle, the cohesin complex associates with CTCF and with active gene regulatory elements to form long-range interactions between its binding sites. Genome-wide chromosome conformation capture had shown that cohesin's main role in interphase genome organization is in mediating interactions within architectural chromosome compartments, rather than specifying compartments per se. However, it remains unclear how cohesin-mediated interactions contribute to the regulation of gene expression. We have found that the binding of CTCF and cohesin is highly enriched at enhancers and in particular at enhancer arrays or “super-enhancers” in mouse thymocytes. Using local and global chromosome conformation capture, we demonstrate that enhancer elements associate not just in linear sequence, but also in 3D, and that spatial enhancer clustering is facilitated by cohesin. The conditional deletion of cohesin from noncycling thymocytes preserved enhancer position, H3K27ac, H4K4me1, and enhancer transcription, but weakened interactions between enhancers. Interestingly, ∼50% of deregulated genes reside in the vicinity of enhancer elements, suggesting that cohesin regulates gene expression through spatial clustering of enhancer elements. We propose a model for cohesin-dependent gene regulation in which spatial clustering of enhancer elements acts as a unified mechanism for both enhancer-promoter “connections” and “insulation.”
Lavagnolli T, Gupta P, Hoermanseder E, et al., 2015, Initiation and maintenance of pluripotency gene expression in the absence of cohesin, GENES & DEVELOPMENT, Vol: 29, Pages: 23-38, ISSN: 0890-9369
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- Citations: 25
Marcais A, Blevins R, Graumann J, et al., 2014, microRNA-mediated regulation of mTOR complex components facilitates discrimination between activation and anergy in CD4 T cells, Journal of Experimental Medicine, Vol: 211, Pages: 2281-2295, ISSN: 0022-1007
T cell receptor (TCR) signals can elicit full activation with acquisition of effector functions or a state of anergy. Here, we ask whether microRNAs affect the interpretation of TCR signaling. We find that Dicer-deficient CD4 T cells fail to correctly discriminate between activating and anergy-inducing stimuli and produce IL-2 in the absence of co-stimulation. Excess IL-2 production by Dicer-deficient CD4 T cells was sufficient to override anergy induction in WT T cells and to restore inducible Foxp3 expression in Il2-deficient CD4 T cells. Phosphorylation of Akt on S473 and of S6 ribosomal protein was increased and sustained in Dicer-deficient CD4 T cells, indicating elevated mTOR activity. The mTOR components Mtor and Rictor were posttranscriptionally deregulated, and the microRNAs Let-7 and miR-16 targeted the Mtor and Rictor mRNAs. Remarkably, returning Mtor and Rictor to normal levels by deleting one allele of Mtor and one allele of Rictor was sufficient to reduce Akt S473 phosphorylation and to reduce co-stimulation–independent IL-2 production in Dicer-deficient CD4 T cells. These results show that microRNAs regulate the expression of mTOR components in T cells, and that this regulation is critical for the modulation of mTOR activity. Hence, microRNAs contribute to the discrimination between T cell activation and anergy.
Merkenschlager M, 2014, Jarid2 Links MicroRNA and Chromatin in Th17 Cells, IMMUNITY, Vol: 40, Pages: 855-856, ISSN: 1074-7613
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- Citations: 7
Volvert M-L, Prevot P-P, Close P, et al., 2014, MicroRNA Targeting of CoREST Controls Polarization of Migrating Cortical Neurons, CELL REPORTS, Vol: 7, Pages: 1168-1183, ISSN: 2211-1247
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- Citations: 52
Gomez-Cabrero D, Abugessaisa I, Maier D, et al., 2014, Data integration in the era of omics: current and future challenges, BMC Systems Biology, Vol: 8, ISSN: 1752-0509
To integrate heterogeneous and large omics data constitutes not only a conceptual challenge but a practical hurdle in the daily analysis of omics data. With the rise of novel omics technologies and through large-scale consortia projects, biological systems are being further investigated at an unprecedented scale generating heterogeneous and often large data sets. These data-sets encourage researchers to develop novel data integration methodologies. In this introduction we review the definition and characterize current efforts on data integration in the life sciences. We have used a web-survey to assess current research projects on data-integration to tap into the views, needs and challenges as currently perceived by parts of the research community.
Seitan VC, Faure AJ, Zhan Y, et al., 2013, Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments, GENOME RESEARCH, Vol: 23, Pages: 2066-2077, ISSN: 1088-9051
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- Citations: 234
Wilson N, Butter F, Calero-Nieto F, et al., 2013, INTERROGATING THE RELATIONSHIP BETWEEN TRANSCRIPTION FACTOR COMPLEX BINDING AND TRANSCRIPTIONAL ACTIVATION, 42nd Annual Scientific Meeting of the International-Society-for-Experimental-Hematology-and-Stem-Cells (ISEH), Publisher: ELSEVIER SCIENCE INC, Pages: S19-S19, ISSN: 0301-472X
Merkenschlager M, 2013, Focus on epigenetic control of host defence: editorial, IMMUNOLOGY, Vol: 139, Pages: 275-276, ISSN: 0019-2805
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- Citations: 1
Dorsett D, Merkenschlager M, 2013, Cohesin at active genes: a unifying theme for cohesin and gene expression from model organisms to humans, CURRENT OPINION IN CELL BIOLOGY, Vol: 25, Pages: 327-333, ISSN: 0955-0674
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- Citations: 94
Coelho MB, Lopes LM, Graham B, et al., 2013, microRNA regulates mesenchymal stromal cell-mediated anti-inflammatory activity in vitro and in vivo, 39th Annual Meeting of the European-Group-for-Blood-and-Marrow-Transplantation (EBMT), Publisher: NATURE PUBLISHING GROUP, Pages: S39-S39, ISSN: 0268-3369
Aragon L, Martinez-Perez E, Merkenschlager M, 2013, Condensin, cohesin and the control of chromatin states, CURRENT OPINION IN GENETICS & DEVELOPMENT, Vol: 23, Pages: 204-211, ISSN: 0959-437X
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- Citations: 35
Piccolo FM, Bagci H, Brown KE, et al., 2013, Different Roles for Tet1 and Tet2 Proteins in Reprogramming-Mediated Erasure of Imprints Induced by EGC Fusion, MOLECULAR CELL, Vol: 49, Pages: 1023-1033, ISSN: 1097-2765
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- Citations: 81
Piccolo FM, Bagci H, Brown KE, et al., 2013, Different Roles for Tet1 and Tet2 Proteins in Reprogramming-Mediated Erasure of Imprints Induced by EGC Fusion (vol 49, pg 1023, 2013), MOLECULAR CELL, Vol: 49, Pages: 1176-1176, ISSN: 1097-2765
Merkenschlager M, Odom DT, 2013, CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets, CELL, Vol: 152, Pages: 1285-1297, ISSN: 0092-8674
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- Citations: 264
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