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Your search keyword '"Akopian, Veronika"' showing total 13 results
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13 results on '"Akopian, Veronika"'

1. Global delay in nascent strand DNA methylation

Author

Charlton, Jocelyn, Downing, Timothy L., Smith, Zachary D., Gu, Hongcang, Clement, Kendell, Pop, Ramona, Akopian, Veronika, Klages, Sven, Santos, David P., Tsankov, Alexander M., Timmermann, Bernd, Ziller, Michael J., Kiskinis, Evangelos, Gnirke, Andreas, and Meissner, Alexander

Published
2018
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2. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

Author

Cacchiarelli, Davide, Trapnell, Cole, Ziller, Michael J., Soumillon, Magali, Cesana, Marcella, Karnik, Rahul, Donaghey, Julie, Smith, Zachary D., Ratanasirintrawoot, Sutheera, Zhang, Xiaolan, Ho Sui, Shannan J., Wu, Zhaoting, Akopian, Veronika, Gifford, Casey A., Doench, John, Rinn, John L., Daley, George Q., Meissner, Alexander, Lander, Eric S., and Mikkelsen, Tarjei S.

Published
2015
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3. Transcription factor binding dynamics during human ES cell differentiation

Author

Tsankov, Alexander M., Gu, Hongcang, Akopian, Veronika, Ziller, Michael J., Donaghey, Julie, Amit, Ido, Gnirke, Andreas, and Meissner, Alexander

Subjects
DNA-ligand interactions -- Physiological aspects -- Analysis, Embryonic development -- Physiological aspects -- Genetic aspects, Embryonic stem cells -- Properties, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome-wide binding data for 38 transcription factors with extensive epigenome and transcriptional data across the differentiation of human embryonic stem cells to the three germ layers. We describe core regulatory dynamics and show the lineage-specific behaviour of selected factors. In addition to the orchestrated remodelling of the chromatin landscape, we find that the binding of several transcription factors is strongly associated with specific loss of DNA methylation in one germ layer, and in many cases a reciprocal gain in the other layers. Taken together, our work shows context-dependent rewiring of transcription factor binding, downstream signalling effectors, and the epigenome during human embryonic stem cell differentiation., Human embryonic stem (ES) cells hold great promise for tissue engineering and disease modelling; yet a key challenge to deriving mature, functional cell types is understanding the molecular mechanisms that [...]

Published
2015
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4. Comparison of defined culture systems for feeder cell free propagation of human embryonic stem cells

Author

Akopian, Veronika, Andrews, Peter W., Beil, Stephen, Benvenisty, Nissim, Brehm, Jennifer, Christie, Megan, Ford, Angela, Fox, Victoria, Gokhale, Paul J., Healy, Lyn, Holm, Frida, Hovatta, Outi, Knowles, Barbara B., Ludwig, Tenneille E., McKay, Ronald D. G., Miyazaki, Takamichi, Nakatsuji, Nono, Oh, Steve K. W., Pera, Martin F., Rossant, Janet, Stacey, Glyn N., and Suemori, Hirofumi

Published
2010

6. Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression

Author

Tsankov, Alexander M., primary, Wadsworth, Marc H., additional, Akopian, Veronika, additional, Charlton, Jocelyn, additional, Allon, Samuel J., additional, Arczewska, Aleksandra, additional, Mead, Benjamin E., additional, Drake, Riley S., additional, Smith, Zachary D., additional, Mikkelsen, Tarjei S., additional, Shalek, Alex K., additional, and Meissner, Alexander, additional

Published
2019
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7. An improved ScoreCard to assess the differentiation potential of human pluripotent stem cells

Author

Tsankov, Alexander M., Akopian, Veronika, Pop, Ramona, Chetty, Sundari, Gifford, Casey A., Daheron, Laurence, Melton, Douglas A., Tsankova, Nadejda M., and Meissner, Alexander

Subjects
Pluripotent Stem Cells, Mice, Teratoma, Animals, Computational Biology, Humans, Cell Differentiation, Neoplasms, Experimental, Polymerase Chain Reaction, Article, Embryoid Bodies
Abstract

Research on human pluripotent stem cells has been hampered by the lack of a standardized, quantitative, scalable assay of pluripotency. We previously described an assay called ScoreCard that used gene expression signatures to quantify differentiation efficiency. Here we report an improved version of the assay based on qPCR that enables faster, more quantitative assessment of functional pluripotency. We provide an in-depth characterization of the revised signature panel (commercially available as the TaqMan hPSC Scorecard Assay) through embryoid body and directed differentiation experiments as well as a detailed comparison to the teratoma assay. We further show that the improved ScoreCard enables a wider range of applications, such as screening of small molecules, genetic perturbations and assessment of culture conditions. Our approach can be extended beyond stem cell applications to characterize and assess the utility of other cell types and lineages.

Published
2015

8. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

Author

Massachusetts Institute of Technology. Department of Biology, Lander, Eric Steven, Cacchiarelli, Davide, Trapnell, Cole, Ziller, Michael J., Soumillon, Magali, Cesana, Marcella, Karnik, Rahul, Donaghey, Julie, Smith, Zachary D., Ratanasirintrawoot, Sutheera, Zhang, Xiaolan, Ho Sui, Shannan J., Wu, Zhaoting, Akopian, Veronika, Gifford, Casey A., Doench, John, Rinn, John L., Daley, George Q., Meissner, Alexander, Mikkelsen, Tarjei S., Massachusetts Institute of Technology. Department of Biology, Lander, Eric Steven, Cacchiarelli, Davide, Trapnell, Cole, Ziller, Michael J., Soumillon, Magali, Cesana, Marcella, Karnik, Rahul, Donaghey, Julie, Smith, Zachary D., Ratanasirintrawoot, Sutheera, Zhang, Xiaolan, Ho Sui, Shannan J., Wu, Zhaoting, Akopian, Veronika, Gifford, Casey A., Doench, John, Rinn, John L., Daley, George Q., Meissner, Alexander, and Mikkelsen, Tarjei S.

Abstract

Induced pluripotency is a promising avenue for disease modeling and therapy, but the molecular principles underlying this process, particularly in human cells, remain poorly understood due to donor-to-donor variability and intercellular heterogeneity. Here, we constructed and characterized a clonal, inducible human reprogramming system that provides a reliable source of cells at any stage of the process. This system enabled integrative transcriptional and epigenomic analysis across the human reprogramming timeline at high resolution. We observed distinct waves of gene network activation, including the ordered re-activation of broad developmental regulators followed by early embryonic patterning genes and culminating in the emergence of a signature reminiscent of pre-implantation stages. Moreover, complementary functional analyses allowed us to identify and validate novel regulators of the reprogramming process. Altogether, this study sheds light on the molecular underpinnings of induced pluripotency in human cells and provides a robust cell platform for further studies.

Published
2017

10. Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells

Author

Liao, Jing, primary, Karnik, Rahul, additional, Gu, Hongcang, additional, Ziller, Michael J, additional, Clement, Kendell, additional, Tsankov, Alexander M, additional, Akopian, Veronika, additional, Gifford, Casey A, additional, Donaghey, Julie, additional, Galonska, Christina, additional, Pop, Ramona, additional, Reyon, Deepak, additional, Tsai, Shengdar Q, additional, Mallard, William, additional, Joung, J Keith, additional, Rinn, John L, additional, Gnirke, Andreas, additional, and Meissner, Alexander, additional

Published
2015
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11. The GCTM-5 Epitope Associated with the Mucin-Like Glycoprotein FCGBP Marks Progenitor Cells in Tissues of Endodermal Origin

Author

Stamp, Lincon A., primary, Braxton, David R., additional, Wu, Jun, additional, Akopian, Veronika, additional, Hasegawa, Kouichi, additional, Chandrasoma, Parakrama T., additional, Hawes, Susan M., additional, McLean, Catriona, additional, Petrovic, Lydia M., additional, Wang, Kasper, additional, and Pera, Martin F., additional

Published
2012
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12. Epigenomics and chromatin dynamics

Author

Akopian, Veronika, primary, Chan, Michelle M, additional, Clement, Kendell, additional, Galonska, Christina, additional, Gifford, Casey A, additional, Lehtola, Elizabeth, additional, Liao, Jing, additional, Samavarchi-Tehrani, Payman, additional, Sindhu, Camille, additional, Smith, Zachary D, additional, Tsankov, Alexander M, additional, Webster, Jamie, additional, Zhang, Yingying, additional, Ziller, Michael J, additional, and Meissner, Alexander, additional

Published
2012
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13. Epigenomics and Chromatin Dynamics

Author

Akopian, Veronika, Chan, Michelle, Clement, Kendell, Galonska, Christina, Gifford, Casey, Lehtola, Elizabeth, Liao, Jing, Samavarchi-Tehrani, Payman, Sindhu, Camille, Smith, Zachary D, Tsankov, Alexander, Webster, Jamie Orme, Zhang, Yingying, Ziller, Michael Johannes, and Meissner, Alexander

Abstract

A report of the 'Joint Keystone Symposium on Epigenomics and Chromatin Dynamics', Keystone, Colorado, 17-22 January 2012. This year's Joint Keystone Symposium on Epigenomics and Chromatin Dynamics was one of the largest Keystone meetings to date, reflecting the excitement and many developments in this area. Richard Young opened the meeting by giving a historic overview before sharing more detailed insights from his recent work in describing the role of the lysine demethylase Lsd1 in mouse embryonic stem (ES) cell differentiation. He also set the broader stage and highlighted the excitement concerning recent advances in epigenetic drugs such as the new bromodomain inhibitors., Stem Cell and Regenerative Biology

Published
2012
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