keyword
MENU ▼
Read by QxMD icon Read
search

Stochastic gene regulation

keyword
https://www.readbyqxmd.com/read/28069947/first-passage-time-approach-to-controlling-noise-in-the-timing-of-intracellular-events
#1
Khem Raj Ghusinga, John J Dennehy, Abhyudai Singh
In the noisy cellular environment, gene products are subject to inherent random fluctuations in copy numbers over time. How cells ensure precision in the timing of key intracellular events despite such stochasticity is an intriguing fundamental problem. We formulate event timing as a first-passage time problem, where an event is triggered when the level of a protein crosses a critical threshold for the first time. Analytical calculations are performed for the first-passage time distribution in stochastic models of gene expression...
January 9, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28038456/dna-methylation-landscape-of-hepatoblastomas-reveals-arrest-at-early-stages-of-liver-differentiation-and-cancer-related-alterations
#2
Mariana Maschietto, Tatiane Cristina Rodrigues, André Yoshiaki Kashiwabara, Érica Sara Souza de Araujo, Talita Ferreira Marques Aguiar, Cecilia Maria Lima da Costa, Isabela Werneck da Cunha, Luciana Dos Reis Vasques, Monica Cypriano, Helena Brentani, Silvia Regina Caminada de Toledo, Peter Lees Pearson, Dirce Maria Carraro, Carla Rosenberg, Ana Cristina Victorino Krepischi
Hepatoblastomas are uncommon embryonal liver tumors accounting for approximately 80% of childhood hepatic cancer. We hypothesized that epigenetic changes, including DNA methylation, could be relevant to hepatoblastoma onset. The methylomes of eight matched hepatoblastomas and non-tumoral liver tissues were characterized, and data were validated in an independent group (11 hepatoblastomas). In comparison to differentiated livers, hepatoblastomas exhibited a widespread and non-stochastic pattern of global low-level hypomethylation...
December 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/27997556/self-organizing-global-gene-expression-regulated-through-criticality-mechanism-of-the-cell-fate-change
#3
Masa Tsuchiya, Alessandro Giuliani, Midori Hashimoto, Jekaterina Erenpreisa, Kenichi Yoshikawa
BACKGROUND: A fundamental issue in bioscience is to understand the mechanism that underlies the dynamic control of genome-wide expression through the complex temporal-spatial self-organization of the genome to regulate the change in cell fate. We address this issue by elucidating a physically motivated mechanism of self-organization. PRINCIPAL FINDINGS: Building upon transcriptome experimental data for seven distinct cell fates, including early embryonic development, we demonstrate that self-organized criticality (SOC) plays an essential role in the dynamic control of global gene expression regulation at both the population and single-cell levels...
2016: PloS One
https://www.readbyqxmd.com/read/27983596/estrogenic-endocrine-disrupting-chemicals-influencing-nrf1-regulated-gene-networks-in-the-development-of-complex-human-brain-diseases
#4
REVIEW
Mark Preciados, Changwon Yoo, Deodutta Roy
During the development of an individual from a single cell to prenatal stages to adolescence to adulthood and through the complete life span, humans are exposed to countless environmental and stochastic factors, including estrogenic endocrine disrupting chemicals. Brain cells and neural circuits are likely to be influenced by estrogenic endocrine disruptors (EEDs) because they strongly dependent on estrogens. In this review, we discuss both environmental, epidemiological, and experimental evidence on brain health with exposure to oral contraceptives, hormonal therapy, and EEDs such as bisphenol-A (BPA), polychlorinated biphenyls (PCBs), phthalates, and metalloestrogens, such as, arsenic, cadmium, and manganese...
December 13, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27977665/hierarchical-post-transcriptional-regulation-of-colicin-e2-expression-in-escherichia-coli
#5
Matthias Lechner, Mathias Schwarz, Madeleine Opitz, Erwin Frey
Post-transcriptional regulation of gene expression plays a crucial role in many bacterial pathways. In particular, the translation of mRNA can be regulated by trans-acting, small, non-coding RNAs (sRNAs) or mRNA-binding proteins, each of which has been successfully treated theoretically using two-component models. An important system that includes a combination of these modes of post-transcriptional regulation is the Colicin E2 system. DNA damage, by triggering the SOS response, leads to the heterogeneous expression of the Colicin E2 operon including the cea gene encoding the toxin colicin E2, and the cel gene that codes for the induction of cell lysis and release of colicin...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27919068/capturing-pairwise-and-multi-way-chromosomal-conformations-using-chromosomal-walks
#6
Pedro Olivares-Chauvet, Zohar Mukamel, Aviezer Lifshitz, Omer Schwartzman, Noa Oded Elkayam, Yaniv Lubling, Gintaras Deikus, Robert P Sebra, Amos Tanay
Chromosomes are folded into highly compacted structures to accommodate physical constraints within nuclei and to regulate access to genomic information. Recently, global mapping of pairwise contacts showed that loops anchoring topological domains (TADs) are highly conserved between cell types and species. Whether pairwise loops synergize to form higher-order structures is still unclear. Here we develop a conformation capture assay to study higher-order organization using chromosomal walks (C-walks) that link multiple genomic loci together into proximity chains in human and mouse cells...
December 8, 2016: Nature
https://www.readbyqxmd.com/read/27911801/mechanical-bounds-to-transcriptional-noise
#7
Stuart A Sevier, David A Kessler, Herbert Levine
Over the past several decades it has been increasingly recognized that stochastic processes play a central role in transcription. Although many stochastic effects have been explained, the source of transcriptional bursting (one of the most well-known sources of stochasticity) has continued to evade understanding. Recent results have pointed to mechanical feedback as the source of transcriptional bursting, but a reconciliation of this perspective with preexisting views of transcriptional regulation is lacking...
December 6, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27893965/single-cell-and-single-molecule-analysis-of-gene-expression-regulation
#8
Maria Vera, Jeetayu Biswas, Adrien Senecal, Robert H Singer, Hye Yoon Park
Recent advancements in single-cell and single-molecule imaging technologies have resolved biological processes in time and space that are fundamental to understanding the regulation of gene expression. Observations of single-molecule events in their cellular context have revealed highly dynamic aspects of transcriptional and post-transcriptional control in eukaryotic cells. This approach can relate transcription with mRNA abundance and lifetimes. Another key aspect of single-cell analysis is the cell-to-cell variability among populations of cells...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27893768/macromolecular-crowding-regulates-the-gene-expression-profile-by-limiting-diffusion
#9
Mahdi Golkaram, Stefan Hellander, Brian Drawert, Linda R Petzold
We seek to elucidate the role of macromolecular crowding in transcription and translation. It is well known that stochasticity in gene expression can lead to differential gene expression and heterogeneity in a cell population. Recent experimental observations by Tan et al. have improved our understanding of the functional role of macromolecular crowding. It can be inferred from their observations that macromolecular crowding can lead to robustness in gene expression, resulting in a more homogeneous cell population...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27875323/estimating-intrinsic-and-extrinsic-noise-from-single-cell-gene-expression-measurements
#10
Audrey Qiuyan Fu, Lior Pachter
Gene expression is stochastic and displays variation ("noise") both within and between cells. Intracellular (intrinsic) variance can be distinguished from extracellular (extrinsic) variance by applying the law of total variance to data from two-reporter assays that probe expression of identically regulated gene pairs in single cells. We examine established formulas [Elowitz, M. B., A. J. Levine, E. D. Siggia and P. S. Swain (2002): "Stochastic gene expression in a single cell," Science, 297, 1183-1186.] for the estimation of intrinsic and extrinsic noise and provide interpretations of them in terms of a hierarchical model...
December 1, 2016: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/27858532/tracking-the-evolution-of-epialleles-during-neural-differentiation-and-brain-development-d-aspartate-oxidase-as-a-model-gene
#11
Ermanno Florio, Simona Keller, Lorena Coretti, Ornella Affinito, Giovanni Scala, Francesco Errico, Annalisa Fico, Francesca Boscia, Maria Josè Sisalli, Mafalda Giovanna Reccia, Gennaro Miele, Antonella Monticelli, Antonella Scorziello, Francesca Lembo, Luca Colucci-D'Amato, Gabriella Minchiotti, Vittorio Enrico Avvedimento, Alessandro Usiello, Sergio Cocozza, Lorenzo Chiariotti
We performed ultra-deep methylation analysis at single molecule level of the promoter region of developmentally regulated D-Aspartate oxidase (Ddo), as a model gene, during brain development and embryonic stem cell neural differentiation. Single molecule methylation analysis enabled us to establish the effective epiallele composition within mixed or pure brain cell populations. In this framework, an epiallele is defined as a specific combination of methylated CpG within Ddo locus and can represent the epigenetic haplotype revealing a cell-to-cell methylation heterogeneity...
November 18, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27835978/importins-promote-high-frequency-nf-%C3%AE%C2%BAb-oscillations-increasing-information-channel-capacity
#12
Zbigniew Korwek, Karolina Tudelska, Paweł Nałęcz-Jawecki, Maciej Czerkies, Wiktor Prus, Joanna Markiewicz, Marek Kochańczyk, Tomasz Lipniacki
BACKGROUND: Importins and exportins influence gene expression by enabling nucleocytoplasmic shuttling of transcription factors. A key transcription factor of innate immunity, NF-κB, is sequestered in the cytoplasm by its inhibitor, IκBα, which masks nuclear localization sequence of NF-κB. In response to TNFα or LPS, IκBα is degraded, which allows importins to bind NF-κB and shepherd it across nuclear pores. NF-κB nuclear activity is terminated when newly synthesized IκBα enters the nucleus, binds NF-κB and exportin which directs the complex to the cytoplasm...
November 11, 2016: Biology Direct
https://www.readbyqxmd.com/read/27835699/gasdermin-c-is-upregulated-by-inactivation-of-transforming-growth-factor-%C3%AE-receptor-type-ii-in-the-presence-of-mutated-apc-promoting-colorectal-cancer-proliferation
#13
Masashi Miguchi, Takao Hinoi, Manabu Shimomura, Tomohiro Adachi, Yasufumi Saito, Hiroaki Niitsu, Masatoshi Kochi, Haruki Sada, Yusuke Sotomaru, Tsuneo Ikenoue, Kunitoshi Shigeyasu, Kohji Tanakaya, Yasuhiko Kitadai, Kazuhiro Sentani, Naohide Oue, Wataru Yasui, Hideki Ohdan
Mutations in TGFBR2, a component of the transforming growth factor (TGF)-β signaling pathway, occur in high-frequency microsatellite instability (MSI-H) colorectal cancer (CRC). In mouse models, Tgfbr2 inactivation in the intestinal epithelium accelerates the development of malignant intestinal tumors in combination with disruption of the Wnt-β-catenin pathway. However, no studies have further identified the genes influenced by TGFBR2 inactivation following disruption of the Wnt-β-catenin pathway. We previously described CDX2P-G19Cre;Apcflox/flox mice, which is stochastically null for Apc in the colon epithelium...
2016: PloS One
https://www.readbyqxmd.com/read/27832998/mathematical-aspects-of-the-regulation-of-gene-transcription-by-promoters
#14
Vladimir P Zhdanov
Although the transcriptional regulation of gene expression has been a subject of intense experimental and theoretical studies over the past several decades, the understanding of this process is still incomplete. In particular, the models focused on the function of transcription factors usually take into account only the lateral interactions between them in the ground bound state. The rates of attachment and detachment of transcription factors on the promoter sites depend, however, also on the lateral interactions in the activated state...
January 2017: Mathematical Biosciences
https://www.readbyqxmd.com/read/27773987/how-genes-modulate-patterns-of-aging-related-changes-on-the-way-to-100-biodemographic-models-and-methods-in-genetic-analyses-of-longitudinal-data
#15
Anatoliy I Yashin, Konstantin G Arbeev, Deqing Wu, Liubov Arbeeva, Alexander Kulminski, Irina Kulminskaya, Igor Akushevich, Svetlana V Ukraintseva
BACKGROUND AND OBJECTIVE: To clarify mechanisms of genetic regulation of human aging and longevity traits, a number of genome-wide association studies (GWAS) of these traits have been performed. However, the results of these analyses did not meet expectations of the researchers. Most detected genetic associations have not reached a genome-wide level of statistical significance, and suffered from the lack of replication in the studies of independent populations. The reasons for slow progress in this research area include low efficiency of statistical methods used in data analyses, genetic heterogeneity of aging and longevity related traits, possibility of pleiotropic (e...
2016: North American Actuarial Journal: NAAJ
https://www.readbyqxmd.com/read/27771899/determining-the-roles-of-inositol-trisphosphate-receptors-in-neurodegeneration-interdisciplinary-perspectives-on-a-complex-topic
#16
Silvia Honda Takada, Juliane Midori Ikebara, Erica de Sousa, Débora Sterzeck Cardoso, Rodrigo Ribeiro Resende, Henning Ulrich, Martin Rückl, Sten Rüdiger, Alexandre Hiroaki Kihara
It is well known that calcium (Ca(2+)) is involved in the triggering of neuronal death. Ca(2+) cytosolic levels are regulated by Ca(2+) release from internal stores located in organelles, such as the endoplasmic reticulum. Indeed, Ca(2+) transit from distinct cell compartments follows complex dynamics that are mediated by specific receptors, notably inositol trisphosphate receptors (IP3Rs). Ca(2+) release by IP3Rs plays essential roles in several neurological disorders; however, details of these processes are poorly understood...
October 22, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27711197/a-multistate-toggle-switch-defines-fungal-cell-fates-and-is-regulated-by-synergistic-genetic-cues
#17
Matthew Z Anderson, Allison M Porman, Na Wang, Eugenio Mancera, Denis Huang, Christina A Cuomo, Richard J Bennett
Heritable epigenetic changes underlie the ability of cells to differentiate into distinct cell types. Here, we demonstrate that the fungal pathogen Candida tropicalis exhibits multipotency, undergoing stochastic and reversible switching between three cellular states. The three cell states exhibit unique cellular morphologies, growth rates, and global gene expression profiles. Genetic analysis identified six transcription factors that play key roles in regulating cell differentiation. In particular, we show that forced expression of Wor1 or Efg1 transcription factors can be used to manipulate transitions between all three cell states...
October 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27672159/hypothesis-type-i-toxin-antitoxin-genes-enter-the-persistence-field-a-feedback-mechanism-explaining-membrane-homoeostasis
#18
REVIEW
Kenn Gerdes
Bacteria form persisters, cells that are tolerant to multiple antibiotics and other types of environmental stress. Persister formation can be induced either stochastically in single cells of a growing bacterial ensemble, or by environmental stresses, such as nutrient starvation, in a subpopulation of cells. In many cases, the molecular mechanisms underlying persistence are still unknown. However, there is growing evidence that, in enterobacteria, both stochastically and environmentally induced persistence are controlled by the second messenger (p)ppGpp...
November 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27665109/gene-expression-noise-is-affected-differentially-by-feedback-in-burst-frequency-and-burst-size
#19
Pavol Bokes, Abhyudai Singh
Inside individual cells, expression of genes is stochastic across organisms ranging from bacterial to human cells. A ubiquitous feature of stochastic expression is burst-like synthesis of gene products, which drives considerable intercellular variability in protein levels across an isogenic cell population. One common mechanism by which cells control such stochasticity is negative feedback regulation, where a protein inhibits its own synthesis. For a single gene that is expressed in bursts, negative feedback can affect the burst frequency or the burst size...
September 24, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27658712/the-molecular-choreography-of-protein-synthesis-translational-control-regulation-and-pathways
#20
Jin Chen, Junhong Choi, Seán E O'Leary, Arjun Prabhakar, Alexey Petrov, Rosslyn Grosely, Elisabetta Viani Puglisi, Joseph D Puglisi
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints...
January 2016: Quarterly Reviews of Biophysics
keyword
keyword
79106
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"