scholarly journals Reconstructing an epigenetic landscape using a genetic ‘pulling’ approach

2019 ◽  
Author(s):  
Michael Assaf ◽  
Shay Be’er ◽  
Elijah Roberts
Keyword(s):  
Simulated Data ◽  
Stable Gene ◽  
Epigenetic Landscape ◽  
Developmental Pathway ◽  
Developmental Networks ◽  
Genetic Switches ◽  
Fundamental Quantity ◽  
Developmental Dynamics ◽  
Stable Gene Expression ◽  
General Method

Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an epigenetic landscape with phenotypic changes being transitions between states. Measuring these transitions is challenging because they are both very rare in the absence of appropriate signals and very fast. As such, it has proven difficult to experimentally map the epigenetic landscapes that are widely believed to underly developmental networks. Here, we introduce a new nonequilibrium perturbation method to help reconstruct a regulatory network’s epigenetic landscape. We derive the mathematical theory needed and then use the method on simulated data to reconstruct the landscapes. Our results show that with a relatively small number of perturbation experiments it is possible to recover an accurate representation of the true epigenetic landscape. We propose that our theory provides a general method by which epigenetic landscapes can be studied. Finally, our theory suggests that the total perturbation impulse required to induce a switch between metastable states is a fundamental quantity in developmental dynamics.

Electric field-mediated DNA transfer: transient and stable gene expression in human and mouse lymphoid cells

1986 ◽  
Vol 6 (2) ◽  
pp. 703-706
Author(s):  
F Toneguzzo ◽  
A C Hayday ◽  
A Keating
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Lymphoid Cell ◽  
Simian Virus 40 ◽  
Lymphoid Cells ◽  
Dna Transfer ◽  
Stable Gene ◽  
Regulatory Sequences ◽  
Stable Gene Expression ◽  
Lymphoid Cell Lines

The technique of DNA transfer by electroporation was investigated in an effort to evaluate its utility for the identification of developmentally controlled regulatory sequences. Transient and stable gene expression was detected in a variety of lymphoid cell lines subjected to electroporation. No correlation existed between the levels of chloramphenicol acetyltransferase (acetyl-CoA; chloramphenicol 3-O-acetyltransferase, EC 2.3.1.28) expression and stable transfection frequency. In all lymphoid cell lines tested, the simian virus 40 early region was a better promoter than was the Rous sarcoma virus long terminal repeat.

scholarly journals Downregulation of Prdm16 mRNA is a specific antileukemic mechanism during HOXB4-mediated HSC expansion in vivo

Blood ◽  
2014 ◽  
Vol 124 (11) ◽  
pp. 1737-1747 ◽  
Author(s):  
Hui Yu ◽  
Geoffrey Neale ◽  
Hui Zhang ◽  
Han M. Lee ◽  
Zhijun Ma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stable Gene ◽  
Self Renewal ◽  
Key Points ◽  
Stable Gene Expression

Key Points HOXB4 induces stable gene expression changes in transplanted HSCs that drive balanced self-renewal and differentiation divisions. Marked downregulation of Prdm16 occurs concurrently with HOXB4-mediated HSC expansion and functions to prevent leukemia in vivo.

scholarly journals On the utility of dreaming: A general model for how learning in artificial agents can benefit from data hallucination

2020 ◽  
pp. 105971231989648 ◽  
Author(s):  
David Windridge ◽  
Henrik Svensson ◽  
Serge Thill
Keyword(s):  
Machine Learning ◽  
Simulated Data ◽  
Training Data ◽  
Successful Implementation ◽  
Artificial Agents ◽  
Learning Context ◽  
Training Set ◽  
Convergence Point ◽  
And Training ◽  
General Method

We consider the benefits of dream mechanisms – that is, the ability to simulate new experiences based on past ones – in a machine learning context. Specifically, we are interested in learning for artificial agents that act in the world, and operationalize “dreaming” as a mechanism by which such an agent can use its own model of the learning environment to generate new hypotheses and training data. We first show that it is not necessarily a given that such a data-hallucination process is useful, since it can easily lead to a training set dominated by spurious imagined data until an ill-defined convergence point is reached. We then analyse a notably successful implementation of a machine learning-based dreaming mechanism by Ha and Schmidhuber (Ha, D., & Schmidhuber, J. (2018). World models. arXiv e-prints, arXiv:1803.10122). On that basis, we then develop a general framework by which an agent can generate simulated data to learn from in a manner that is beneficial to the agent. This, we argue, then forms a general method for an operationalized dream-like mechanism. We finish by demonstrating the general conditions under which such mechanisms can be useful in machine learning, wherein the implicit simulator inference and extrapolation involved in dreaming act without reinforcing inference error even when inference is incomplete.

scholarly journals Seasonal Stability and Dynamics of DNA Methylation in Plants in a Natural Environment

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 544 ◽  
Author(s):  
Ito ◽  
Nishio ◽  
Tarutani ◽  
Emura ◽  
Honjo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Repetitive Sequences ◽  
Epigenetic Mark ◽  
Stable Gene ◽  
Natural Environments ◽  
Arabidopsis Halleri ◽  
Genome Wide ◽  
Single Clone ◽  
Intergenic Regions ◽  
Stable Gene Expression

: DNA methylation has been considered a stable epigenetic mark but may respond to fluctuating environments. However, it is unclear how they behave in natural environments. Here, we analyzed seasonal patterns of genome-wide DNA methylation in a single clone from a natural population of the perennial Arabidopsis halleri. The genome-wide pattern of DNA methylation was primarily stable, and most of the repetitive regions were methylated across the year. Although the proportion was small, we detected seasonally methylated cytosines (SeMCs) in the genome. SeMCs in the CHH context were detected predominantly at repetitive sequences in intergenic regions. In contrast, gene-body CG methylation (gbM) itself was generally stable across seasons, but the levels of gbM were positively associated with seasonal stability of RNA expression of the genes. These results suggest the existence of two distinct aspects of DNA methylation in natural environments: sources of epigenetic variation and epigenetic marks for stable gene expression.

Stable Gene Transfer and Expression in Human Primary T-Cells by the Sleeping Beauty Transposon System.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 5539-5539
Author(s):  
Xianzheng Zhou ◽  
Xin Huang ◽  
Andrew C. Wilber ◽  
Lei Bao ◽  
Dong Tuong ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
Gene Transfer ◽  
Transgene Expression ◽  
Sleeping Beauty ◽  
Stable Gene ◽  
Cell Clones ◽  
Stable Gene Expression

Abstract The Sleeping Beauty (SB) transposon system is a non-viral DNA delivery system in which a transposase directs integration of an SB transposon into TA-dinucleotide sites in the genome. To determine whether the SB transposon system can mediate integration and long-term transgene expression in human primary T-cells, freshly isolated peripheral blood lymphocytes (PBLs) without prior activation were nucleofected with SB vectors carrying a DsRed reporter gene. Plasmids containing the SB transposase on the same (cis) (n=10) or separate molecule (trans) (n=8) as the SB transposon mediated long-term and stable reporter gene expression in human primary T-cells. We observed that delivery of SB transposase-encoding plasmid in trans effectively mediated stable gene expression in primary T-cells, exhibiting about a 3-fold increase (11% vs. 3% with 10 microgram plasmid on day 21) in potency in comparison with the cis vector (p<0.0001). In addition, a transposase mutant construct was incapable of mediating stable gene expression in human PBLs (n=6, p<0.0001), confirming that catalytic DDE domain is necessary for transposition in human primary T-cells. Immunophenotyping analysis in transposed T-cells showed that both CD4 and CD8 T-cells were transgene positive. SB-mediated high level of transgene expression in human T-cells was maintained in culture for at least 4 months without losing observable expression. Southern hybridization analysis showed a variety of transposon integrants among the 6 DsRed positive T-cell clones and no transposon sequences identifiable in the 2 DsRed negative clones. Sequencing of transposon:chromosome junctions in 5 out of 6 transposed T-cell clones confirmed that stable gene expression was due to SB-mediated transposition. In other studies, PBLs were successfully transfected using the SB transposon system and shown to stably and functionally express a fusion protein consisting of a surface receptor useful for positive T-cell selection and a “suicide” gene useful for elimination of transfected T-cells after chemotherapy. This study is the first report demonstrating that the SB transposon system can mediate stable gene transfer in human primary PBLs, which may be more advantageous for T-cell based gene therapies over widely used virus-based or conventional mammalian DNA vectors in terms of simplicity, stability, efficiency and safety.

scholarly journals FACT sets a barrier for cell fate reprogramming inC. elegansand Human

2017 ◽  
Author(s):  
Ena Kolundzic ◽  
Andreas Ofenbauer ◽  
Bora Uyar ◽  
Anne Sommermeier ◽  
Stefanie Seelk ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Fate ◽  
Chromatin Accessibility ◽  
Genetic Screen ◽  
Cellular Reprogramming ◽  
Stable Gene ◽  
C Elegans ◽  
Chromatin Regulator ◽  
Evolutionarily Conserved ◽  
Stable Gene Expression

The chromatin regulator FACT (Facilitates Chromatin Transcription) is essential for ensuring stable gene expression by promoting transcription. In a genetic screen usingC. eleganswe identified that FACT maintains cell identities and acts as a barrier for transcription factor-mediated cell fate reprogramming. Strikingly, FACTs role as a reprogramming barrier is conserved in humans as we show that FACT depletion enhances reprogramming of fibroblasts into stem cells and neurons. Such activity of FACT is unexpected since known reprogramming barriers typically repress gene expression by silencing chromatin. In contrast, FACT is a positive regulator of gene expression suggesting an unprecedented link of cell fate maintenance with counteracting alternative cell identities. This notion is supported by ATAC-seq analysis showing that FACT depletion results in decreased but also increased chromatin accessibility for transcription factors. Our findings identify FACT as a cellular reprogramming barrier inC. elegansand in Human, revealing an evolutionarily conserved mechanism for cell fate protection.

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