Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage by Wamstad, Joseph A., Alexander, Jeffrey M., Truty, Rebecca M., Shrikumar, Avanti, Li, Fugen, Eilertson, Kirsten E., Ding, Huiming, Wylie, John N., Pico, Alexander R., Capra, John A., Erwin, Genevieve, Kattman, Steven J., Keller, Gordon M., Srivastava, Deepak, Levine, Stuart S., Pollard, Katherine S., Holloway, Alisha K., Boyer, Laurie, Bruneau, Benoit G.

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Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution by Gu, Hongcang, Bock, Christoph, Jäger, Natalie, Smith, Zachary D., Tomazou, Eleni, Gnirke, Andreas, Meissner, Alexander, Mikkelsen, Tarjei Sigurd, 1978-, Lander, Eric Steven

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The epigenetics of epithelial-mesenchymal plasticity in cancer by Tam, Wai Leong, Weinberg, Robert A

“…This plasticity is enabled by underlying shifts in epigenetic regulation. A small cohort of pleiotropically acting transcription factors is widely recognized to effect these shifts by controlling the expression of a constituency of key target genes. …”
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Replication-Coupled Chromatin Assembly Generates a Neuronal Bilateral Asymmetry in C. elegans by Nakano, Shunji, Stillman, Bruce, Horvitz, Howard Robert

“…Our results reveal that replication-coupled nucleosome assembly is necessary to generate a bilateral asymmetry in C. elegans neuroanatomy and suggest that left-right asymmetric epigenetic regulation can establish bilateral asymmetry in the nervous system.…”
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CpG island structure and trithorax/polycomb chromatin domains in human cells by Orlando, David A., Guenther, Matthew G., Frampton, Garrett M., Young, Richard A.

“…TrxG and PcG complexes play key roles in the epigenetic regulation of development through H3K4me3 and H3K27me3 modification at specific sites throughout the human genome, but how these sites are selected is poorly understood. …”
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Low-input chromatin profiling in Arabidopsis endosperm using CUT&RUN by Zheng, Xiao-yu, Gehring, Mary

“…During endosperm development, differential epigenetic regulation of the maternal and paternal genomes plays important roles in regulating gene expression, especially at imprinted genes. …”
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Cdk1 Controls Global Epigenetic Landscape in Embryonic Stem Cells by Michowski, Wojciech, Chick, Joel M, Chu, Chen, Kolodziejczyk, Aleksandra, Wang, Yichen, Suski, Jan M, Abraham, Brian, Anders, Lars, Day, Daniel, Dunkl, Lukas M, Li Cheong Man, Mitchell, Zhang, Tian, Laphanuwat, Phatthamon, Bacon, Nickolas A, Liu, Lijun, Fassl, Anne, Sharma, Samanta, Otto, Tobias, Jecrois, Emanuelle, Han, Richard, Sweeney, Katharine E, Marro, Samuele, Wernig, Marius, Geng, Yan, Moses, Alan, Li, Cheng, Gygi, Steven P, Young, Richard A, Sicinski, Piotr

“…Cdk1 phosphorylates many proteins involved in epigenetic regulation, including writers and erasers of all major histone marks. …”
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An Endogenously Tagged Fluorescent Fusion Protein Library in Mouse Embryonic Stem Cells by Harikumar, Arigela, Edupuganti, Raghu Ram, Sorek, Matan, Azad, Gajendra Kumar, Markoulaki, Styliani, Sehnalová, Petra, Legartová, Soňa, Bártová, Eva, Farkash-Amar, Shlomit, Jaenisch, Rudolf, Alon, Uri, Meshorer, Eran

“…Embryonic stem cells (ESCs), with their dual capacity to self-renew and differentiate, are commonly used to study differentiation, epigenetic regulation, lineage choices, and more. Using non-directed retroviral integration of a YFP/Cherry exon into mouse ESCs, we generated a library of over 200 endogenously tagged fluorescent fusion proteins and present several proof-of-concept applications of this library. …”
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Editing DNA Methylation in the Mammalian Genome by Liu, X. Shawn, Wu, Hao, Ji, Xiong, Stelzer, Yonatan, Czauderna, Szymon, Shu, Jian, Dadon, Daniel Benjamin, Jaenisch, Rudolf, Wu, Xuebing, Ph. D. Massachusetts Institute of Technology, Young, Richard A.

“…Finally, we show that these tools can edit DNA methylation in mice, demonstrating their wide utility for functional studies of epigenetic regulation.…”
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DNA methylation dynamics of the human preimplantation embryo by Smith, Zachary D., Chan, Michelle Mei Wah, Humm, Kathryn C., Karnik, Rahul, Mekhoubad, Shila, Regev, Aviv, Eggan, Kevin, Meissner, Alexander

“…Together, our data confirm that paternal genome demethylation is a general attribute of early mammalian development that is characterized by distinct modes of epigenetic regulation.…”
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The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells by Beyaz, Semir, Kim, Ji Hyung, Pinello, Luca, Huang, Jialiang, Kerenyi, Marc A, Das, Partha P, Barnitz, R Anthony, Herault, Aurelie, Haining, W Nicholas, Passegue, Emmanuelle, Yuan, Guo-Cheng, Orkin, Stuart H, Winau, Florian, Xifaras, Michael, Dogum, Rizkullah, Yilmaz, Omer, Hu, Yu,M.C.P.Massachusetts Institute of Technology.

“…However, little is known about the epigenetic regulation of iNKT cell development. Here we found that the H3K27me3 histone demethylase UTX was an essential cell-intrinsic factor that controlled an iNKT-cell lineage-specific gene-expression program and epigenetic landscape in a demethylase-Activity-dependent manner. …”
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Renal tubular Sirt1 attenuates diabetic albuminuria by epigenetically suppressing Claudin-1 overexpression in podocytes by Hasegawa, Kazuhiro, Wakino, Shu, Simic, Petra, Sakamaki, Yusuke, Minakuchi, Hitoshi, Fujimura, Keiko, Hosoya, Kozi, Komatsu, Motoaki, Kaneko, Yuka, Kanda, Takeshi, Kubota, Eiji, Tokuyama, Hirobumi, Itoh, Hiroshi, Guarente, Leonard Pershing, Hayashi, Koichi, 1967-

“…Downregulation of Sirt1 and upregulation of the tight junction protein Claudin-1 by SIRT1-mediated epigenetic regulation in podocytes contributed to albuminuria. …”
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Conserved imprinting associated with unique epigenetic signatures in the Arabidopsis genus by Gehring, Mary, Klosinska, Maja, Picard, Colette Lafontaine

“…Thus, there appear to be at least two classes of PEGs in terms of methylation features (Fig. 3a), which may correspond to different modes of epigenetic regulation. PEGs conserved with A. thaliana are found in both classes, although the majority (12/18) are CHG hypermethylated (Supplementary Table 4).To determine if there was a quantitative relationship between gain of CHG methylation and allelic expression bias, we plotted the difference in CHG methylation between maternal alleles in the embryo and endosperm relative to the ratio of maternal to paternal allele transcripts (Fig. 3c). …”
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Molecular Control of Induced Pluripotency by Theunissen, Thorold W., Jaenisch, Rudolf

“…We examine the trajectories connecting somatic and pluripotent cells, genetic and chemical methodologies for inducing pluripotency, the role of endogenous master transcription factors in establishing the pluripotent state, and functional interactions between reprogramming factors and epigenetic regulators. Defining the crosstalk among the diverse molecular actors implicated in cellular reprogramming presents a major challenge for future inquiry.…”
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Polycomb Repressive Complex 2 Regulates Lineage Fidelity during Embryonic Stem Cell Differentiation by Levine, Stuart S., Thornton, Seraphim R., Butty, Vincent L G, Boyer, Laurie Ann

“…Moreover, while studies suggest that PRC2 prevents DNA methylation, how these two epigenetic regulators coordinate to regulate lineage programs is poorly understood. …”
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Bmi1 is required for tumorigenesis in a mouse model of intestinal cancer by Maynard, Mindy, Perret, C., Whyte, P., Ferretti, Roberta, Lees, Jacqueline, Hilgendorf, K. I.

“…The epigenetic regulator BMI1 is upregulated progressively in a wide variety of human tumors including colorectal cancer. …”
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