Results for 'stochastic gene expression'

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  1.  15
    Stochastic gene expression, disruption of tissue averaging effects and cancer as a disease of development.Jean-Pascal Capp - 2005 - Bioessays 27 (12):1277-1285.
    Despite the extensive literature describing the somatic genetic alterations in cancer cells, the precise origins of cancer cells remain controversial. In this article, I suggest that the etiology of cancer and the generation of genetic instability in cancer cells should be considered in the light of recent findings on both the stochastic nature of gene expression and its regulation at tissue level. By postulating that gene expression is intrinsically probabilistic and that stabilization of gene (...)
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  2.  34
    Stochastic gene expression stabilization as a new therapeutic strategy for cancer.Jean-Pascal Capp - 2012 - Bioessays 34 (3):170-173.
    Graphical AbstractCurrent differentiation therapies for cancer may not be effective because it might not be enough to only use molecules targeting chromatin remodelers. It may also be necessary to stabilize the re-expressed genes to convert malignant cells into benign ones.
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  3.  19
    Stochastic gene expression is the driving force of cancer.Jean-Pascal Capp - 2011 - Bioessays 33 (10):781-782.
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  4.  70
    Objective and Subjective Probability in Gene Expression.Joel D. Velasco - 2012 - Progress in Biophysics and Molecular Biology 110:5-10.
    In this paper I address the question of whether the probabilities that appear in models of stochastic gene expression are objective or subjective. I argue that while our best models of the phenomena in question are stochastic models, this fact should not lead us to automatically assume that the processes are inherently stochastic. After distinguishing between models and reality, I give a brief introduction to the philosophical problem of the interpretation of probability statements. I argue (...)
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  5.  10
    Mechanisms of How Random Input Controls Bursting Gene Expression.Sijia Xiao, Yan Wang, Zhigang Wang & Haohua Wang - 2022 - Complexity 2022:1-17.
    The process of gene expression is affected by many extracellular stimulus signals, and the stochasticity of these signals reshapes gene expression. To adapt the fluctuation of the extracellular environment, genes have many strategies for augmenting their survival probability, frequency modulation, and amplitude modulation. However, it is unclear how genes utilize the stochasticity of signals to regulate gene expression and which strategy will be chosen to maximize cellular function. Here, we analyze a simple mechanistic model (...)
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  6.  19
    Tissue‐disruption‐induced cellular stochasticity and epigenetic drift: Common origins of aging and cancer?Jean-Pascal Capp & Frédéric Thomas - 2021 - Bioessays 43 (1):2000140.
    Age‐related and cancer‐related epigenomic modifications have been associated with enhanced cell‐to‐cell gene expression variability that characterizes increased cellular stochasticity. Since gene expression variability appears to be highly reduced by—and epigenetic and phenotypic stability acquired through—direct or long‐range cellular interactions during cell differentiation, we propose a common origin for aging and cancer in the failure to control cellular stochasticity by cell–cell interactions. Tissue‐disruption‐induced cellular stochasticity associated with epigenetic drift would be at the origin of organ dysfunction because (...)
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  7.  13
    From developmental to atavistic bet‐hedging: How cancer cells pervert the exploitation of random single‐cell phenotypic fluctuations.Jean-Pascal Capp & Frédéric Thomas - 2022 - Bioessays 44 (9):2200048.
    Stochastic gene expression plays a leading developmental role through its contribution to cell differentiation. It is also proposed to promote phenotypic diversification in malignant cells. However, it remains unclear if these two forms of cellular bet‐hedging are identical or rather display distinct features. Here we argue that bet‐hedging phenomena in cancer cells are more similar to those occurring in unicellular organisms than to those of normal metazoan cells. We further propose that the atavistic bet‐hedging strategies in cancer (...)
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  8.  16
    Problems and paradigms: Induction mechanism of a single gene molecule: Stochastic or deterministic?Minoru S. H. Ko - 1992 - Bioessays 14 (5):341-346.
    A new field of gene expression regulation research is emerging that has previously been overlooked. This new area is concerned with distinguishing the expression of a single gene from the averaged expression of many gene copies within the cell population. This paper reviews research focused on individual genes in inducible gene expression systems. The main experimental strategy is to measure the gene expression level of a single cell containing a single (...)
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  9.  28
    Genes at work in random bouts.Alexey Golubev - 2012 - Bioessays 34 (4):311-319.
    Cell interdivision periods (IDP) in homogenous cell populations vary stochastically. Another aspect of probabilistic cell behavior is randomness in cell differentiation. These features are suggested to result from competing stochastic events of assembly/disassembly of the transcription pre‐initiation complex (PIC) at gene promoters. The time needed to assemble a proper PIC from different proteins, which must be numerous enough to make their combination gene specific, may be comparable to the IDP. Nascent mRNA visualization at defined genes and inferences (...)
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  10.  7
    Exploring the role of transcriptional and post‐transcriptional processes in mRNA co‐expression.Óscar García-Blay, Pieter G. A. Verhagen, Benjamin Martin & Maike M. K. Hansen - 2023 - Bioessays 45 (12):2300130.
    Co‐expression of two or more genes at the single‐cell level is usually associated with functional co‐regulation. While mRNA co‐expression—measured as the correlation in mRNA levels—can be influenced by both transcriptional and post‐transcriptional events, transcriptional regulation is typically considered dominant. We review and connect the literature describing transcriptional and post‐transcriptional regulation of co‐expression. To enhance our understanding, we integrate four datasets spanning single‐cell gene expression data, single‐cell promoter activity data and individual transcript half‐lives. Confirming expectations, we (...)
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  11.  79
    The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post‐Darwinian biology?Sui Huang - 2012 - Bioessays 34 (2):149-157.
    The Neo‐Darwinian concept of natural selection is plausible when one assumes a straightforward causation of phenotype by genotype. However, such simple 1:1 mapping must now give place to the modern concepts of gene regulatory networks and gene expression noise. Both can, in the absence of genetic mutations, jointly generate a diversity of inheritable randomly occupied phenotypic states that could also serve as a substrate for natural selection. This form of epigenetic dynamics challenges Neo‐Darwinism. It needs to incorporate (...)
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  12.  30
    Post‐Transcriptional Noise Control.Maike M. K. Hansen & Leor S. Weinberger - 2019 - Bioessays 41 (7):1900044.
    Recent evidence indicates that transcriptional bursts are intrinsically amplified by messenger RNA cytoplasmic processing to generate large stochastic fluctuations in protein levels. These fluctuations can be exploited by cells to enable probabilistic bet‐hedging decisions. But large fluctuations in gene expression can also destabilize cell‐fate commitment. Thus, it is unclear if cells temporally switch from high to low noise, and what mechanisms enable this switch. Here, the discovery of a post‐transcriptional mechanism that attenuates noise in HIV is reviewed. (...)
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  13.  10
    The dynamic role of cohesin in maintaining human genome architecture.Abhishek Agarwal, Sevastianos Korsak, Ashutosh Choudhury & Dariusz Plewczynski - 2023 - Bioessays 45 (10):2200240.
    Recent advances in genomic and imaging techniques have revealed the complex manner of organizing billions of base pairs of DNA necessary for maintaining their functionality and ensuring the proper expression of genetic information. The SMC proteins and cohesin complex primarily contribute to forming higher‐order chromatin structures, such as chromosomal territories, compartments, topologically associating domains (TADs) and chromatin loops anchored by CCCTC‐binding factor (CTCF) protein or other genome organizers. Cohesin plays a fundamental role in chromatin organization, gene expression (...)
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  14.  47
    Population transcriptomics with single‐cell resolution: A new field made possible by microfluidics.Charles Plessy, Linda Desbois, Teruo Fujii & Piero Carninci - 2013 - Bioessays 35 (2):131-140.
    Tissues contain complex populations of cells. Like countries, which are comprised of mixed populations of people, tissues are not homogeneous. Gene expression studies that analyze entire populations of cells from tissues as a mixture are blind to this diversity. Thus, critical information is lost when studying samples rich in specialized but diverse cells such as tumors, iPS colonies, or brain tissue. High throughput methods are needed to address, model and understand the constitutive and stochastic differences between individual (...)
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  15.  42
    Gravity Constraints Drive Biological Systems Toward Specific Organization Patterns.Mariano Bizzarri, Maria Grazia Masiello, Alessandro Giuliani & Alessandra Cucina - 2018 - Bioessays 40 (1):1700138.
    Different cell lineages growing in microgravity undergo a spontaneous transition leading to the emergence of two distinct phenotypes. By returning these populations in a normal gravitational field, the two phenotypes collapse, recovering their original configuration. In this review, we hypothesize that, once the gravitational constraint is removed, the system freely explores its phenotypic space, while, when in a gravitational field, cells are “constrained” to adopt only one favored configuration. We suggest that the genome allows for a wide range of “possibilities” (...)
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  16.  26
    Gene expression in the twilight of death.Alexander E. Pozhitkov & Peter A. Noble - 2017 - Bioessays 39 (9):1700066.
    After a vertebrate dies, many of its organ systems, tissues, and cells remain functional while its body no longer works as a whole. We define this state as the “twilight of death” − the transition from a living body to a decomposed corpse. We claim that the study of the twilight of death is important to ethical, legal and medical science. We examined gene expression at the twilight of death in the zebrafish and mouse reaching the conclusion that (...)
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  17. Behavior genetics and postgenomics.Evan Charney - 2012 - Behavioral and Brain Sciences 35 (5):331-358.
    The science of genetics is undergoing a paradigm shift. Recent discoveries, including the activity of retrotransposons, the extent of copy number variations, somatic and chromosomal mosaicism, and the nature of the epigenome as a regulator of DNA expressivity, are challenging a series of dogmas concerning the nature of the genome and the relationship between genotype and phenotype. According to three widely held dogmas, DNA is the unchanging template of heredity, is identical in all the cells and tissues of the body, (...)
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  18.  14
    Defining heterogeneity within bacterial populations via single cell approaches.Kimberly M. Davis & Ralph R. Isberg - 2016 - Bioessays 38 (8):782-790.
    Bacterial populations are heterogeneous, which in many cases can provide a selective advantage during changes in environmental conditions. In some instances, heterogeneity exists at the genetic level, in which significant allelic variation occurs within a population seeded by a single cell. In other cases, heterogeneity exists due to phenotypic differences within a clonal, genetically identical population. A variety of mechanisms can drive this latter strategy. Stochastic fluctuations can drive differential gene expression, but heterogeneity in gene (...) can also be driven by environmental changes sensed by individual cells residing in distinct locales. Utilizing multiple single cell approaches, workers have started to uncover the extent of heterogeneity within bacterial populations. This review will first describe several examples of phenotypic and genetic heterogeneity, and then discuss many single cell approaches that have recently been applied to define heterogeneity within bacterial populations. (shrink)
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  19.  27
    Serial analysis of gene expression: ESTs get smaller.Mark D. Adams - 1996 - Bioessays 18 (4):261-262.
    Measuring gene expression on a global scale has been one of the vexing problems of cell biology. Velculescu et al.(1) recently proposed a system for identifying gene expression levels based on very short sequence tags – about nine base pairs – located at a specific site within a gene transcript. By coupling the strategy to current automated sequencing machines and the large expressed sequence tag databases, it should be possible to follow changes in gene (...)
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  20.  21
    Monoallelic gene expression and mammalian evolution.Barry Keverne - 2009 - Bioessays 31 (12):1318-1326.
    Monoallelic gene expression has played a significant role in the evolution of mammals enabling the expansion of a vast repertoire of olfactory receptor types and providing increased sensitivity and diversity. Monoallelic expression of immune receptor genes has also increased diversity for antigen recognition, while the same mechanism that marks a single allele for preferential rearrangement also provides a distinguishing feature for directing hypermutations. Random monoallelic expression of the X chromosome is necessary to balance gene dosage (...)
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  21.  17
    How gene expression in fast‐proliferating cells keeps pace.Rui G. Martinho, Leonardo G. Guilgur & Pedro Prudêncio - 2015 - Bioessays 37 (5):514-524.
    The development of living organisms requires a precise coordination of all basic cellular processes, in space and time. Early embryogenesis of most species with externally deposited eggs starts with a series of extremely fast cleavage cycles. These divisions have a strong influence on gene expression as mitosis represses transcription and pre‐mRNA processing. In this review, we will describe the distinct adaptations for efficient gene expression and discuss the emerging role of the multifunctional NineTeen Complex (NTC) in (...)
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  22. Gene expression patterns in a novel animal appendage: The sea urchin pluteus arm.A. C. Love, M. E. Lee & R. A. Raff - 2007 - Evolution & Development 9:51–68.
    The larval arms of echinoid plutei are used for locomotion and feeding. They are composed of internal calcite skeletal rods covered by an ectoderm layer bearing a ciliary band. Skeletogenesis includes an autonomous molecular differentiation program in primary mesenchyme cells (PMCs), initiated when PMCs leave the vegetal plate for the blastocoel, and a patterning of the differentiated skeletal units that requires molecular cues from the overlaying ectoderm. The arms represent a larval feature that arose in the echinoid lineage during the (...)
     
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  23.  26
    New genes expressed in human brains: Implications for annotating evolving genomes.Yong E. Zhang, Patrick Landback, Maria Vibranovski & Manyuan Long - 2012 - Bioessays 34 (11):982-991.
    New genes have frequently formed and spread to fixation in a wide variety of organisms, constituting abundant sets of lineage‐specific genes. It was recently reported that an excess of primate‐specific and human‐specific genes were upregulated in the brains of fetuses and infants, and especially in the prefrontal cortex, which is involved in cognition. These findings reveal the prevalent addition of new genetic components to the transcriptome of the human brain. More generally, these findings suggest that genomes are continually evolving in (...)
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  24.  22
    Gene expression and the evolution of insect polyphenisms.Jay D. Evans & Diana E. Wheeler - 2001 - Bioessays 23 (1):62-68.
    Polyphenic differences between individuals arise not through differences at the genome level but as a result of specific cues received during development. Polyphenisms often involve entire suites of characters, as shown dramatically by the polyphenic castes found in many social insect colonies. An understanding of the genetic architecture behind polyphenisms provides a novel means of studying the interplay between genomes, gene expression and phenotypes. Here we discuss polyphenisms and molecular genetic tools now available to unravel their developmental bases (...)
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  25.  14
    Gene expression and the evolution of insect polyphenisms†.Jay D. Evans & Diana E. Wheeler - 2001 - Bioessays 23 (1):62-68.
    Polyphenic differences between individuals arise not through differences at the genome level but as a result of specific cues received during development. Polyphenisms often involve entire suites of characters, as shown dramatically by the polyphenic castes found in many social insect colonies. An understanding of the genetic architecture behind polyphenisms provides a novel means of studying the interplay between genomes, gene expression and phenotypes. Here we discuss polyphenisms and molecular genetic tools now available to unravel their developmental bases (...)
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  26.  24
    Temperature‐controlled Rhythmic Gene Expression in Endothermic Mammals: All Diurnal Rhythms are Equal, but Some are Circadian.Marco Preußner & Florian Heyd - 2018 - Bioessays 40 (7):1700216.
    The circadian clock is a cell autonomous oscillator that controls many aspects of physiology through generating rhythmic gene expression in a time of day dependent manner. In addition, in endothermic mammals body temperature cycles contribute to rhythmic gene expression. These body temperature‐controlled rhythms are hard to distinguish from classic circadian rhythms if analyzed in vivo in endothermic organisms. However, they do not fulfill all criteria of being circadian if analyzed in cell culture or in conditions where (...)
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  27.  76
    Gene expression and the concept of the phenotype.Ohad Nachtomy, Ayelet Shavit & Zohar Yakhini - 2007 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 38 (1):238-254.
    While the definition of the ‘genotype’ has undergone dramatic changes in the transition from classical to molecular genetics, the definition of the ‘phenotype’ has remained for a long time within the classical framework. In addition, while the notion of the genotype has received significant attention from philosophers of biology, the notion of the phenotype has not. Recent developments in the technology of measuring gene-expression levels have made it possible to conceive of phenotypic traits in terms of levels of (...)
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  28.  20
    Gene expression and the concept of the phenotype.Ohad Nachtomy, Ayelet Shavit & Zohar Yakhini - 2005 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 38 (1):238-254.
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  29.  12
    Gene expression, cellular diversification and tumor progression to the metastatic phenotype.Garth L. Nicolson - 1991 - Bioessays 13 (7):337-342.
    Alterations in the expression of certain genes or in their products can render benign tumor cells metastatic. Experimentally this has been quickly performed by transferring dominantly acting oncogenes such as c‐H‐rasEJ into susceptible cells, but in vivo such a rapid qualitative change in a dominantly acting oncogene occurs only rarely, and progression to highly metastatic phenotypes is thought to occur through a slow stepwise process. Such slow changes can be reversible and need not involve known dominantly acting oncogenes, consistent (...)
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  30.  16
    Genome analysis with gene expression microarrays.Mark Schena - 1996 - Bioessays 18 (5):427-431.
    Advances in biochemistry, chemistry and engineering have enabled the development of a new gene expression assay. This ‘chip‐based’ approach utilizes microscopic arrays of cDNAs printed on glass as high‐density hybridization targets. Fluorescent probe mixtures derived from total cellular messenger RNA (mRNA) hybridize to cognate elements on the array, allowing accurate measurement of the expression of the corresponding genes. Array densities of >1,000 cDNAs per cm2 enable quantitative expression monitoring of a large number of genes in a (...)
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  31.  15
    White gene expression, repressive chromatin domains and homeotic gene regulation in Drosophila.Vincenzo Pirrotta & Luca Rastelli - 1994 - Bioessays 16 (8):549-556.
    The use of Drosophila chromosomal rearrangements and transposon constructs involving the white gene reveals the existence of repressive chromatin domains that can spread over considerable genomic distances. One such type of domain is found in heterochromatin and is responsible for classical position‐effect variegation. Another type of repressive domain is established, beginning at specific sequences, by complexes of Polycomb Group proteins. Such complexes, which normally regulate the expression of many genes, including the homeotic loci, are responsible for silencing, white (...)
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  32.  14
    Idiomatic (gene) expressions.Matthew V. Rockman - 2003 - Bioessays 25 (5):421-424.
    Hidden among the myriad nucleotide variants that constitute each species' gene pool are a few variants that contribute to phenotypic variation. Many of these differences that make a difference are non‐coding cis‐regulatory variants, which, unlike coding variants, can only be identified through laborious experimental analysis. Recently, Cowles et al.1 described a screening method that does an end‐run around this problem by searching for genes whose cis regulation varies without having to find the polymorphic nucleotides that influence transcription. While we (...)
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  33.  20
    Gene expression during metamorphosis: An ideal model for post‐embryonic development.Jamshed R. Tata - 1993 - Bioessays 15 (4):239-248.
    The precocious induction in vivo and in culture of insect and amphibian metamorphosis by exogenous ecdysteroids and thyroid hormones, and its retardation or inhibition by juvenile hormone and prolactin, respectively, has allowed the analysis of such diverse processes of post‐embryonic development as morphogenesis, tissue remodelling, functional reorganization, and programmed cell death. Metamorphosis in vertebrates also shares many similarities with mammalian development in the late foetal and perinatal period. This review describes the regulation of expression of some of the ‘adult’ (...)
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  34.  22
    DNA Conformation Regulates Gene Expression: The MYC Promoter and Beyond.Olga Zaytseva & Leonie M. Quinn - 2018 - Bioessays 40 (4):1700235.
    Emerging evidence suggests that DNA topology plays an instructive role in cell fate control through regulation of gene expression. Transcription produces torsional stress, and the resultant supercoiling of the DNA molecule generates an array of secondary structures. In turn, local DNA architecture is harnessed by the cell, acting within sensory feedback mechanisms to mediate transcriptional output. MYC is a potent oncogene, which is upregulated in the majority of cancers; thus numerous studies have focused on detailed understanding of its (...)
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  35.  57
    Gene Expression in the Hippocampus in a Rat Model of Premenstrual Dysphoric Disorder After Treatment With Baixiangdan Capsules.Sheng Wei, Peng Sun, Yinghui Guo, Jingxuan Chen, Jieqiong Wang, Chunhong Song, Zifa Li, Ling Xue & Mingqi Qiao - 2018 - Frontiers in Psychology 9.
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  36.  10
    Regulation of mammalian gene expression by retroelements and non‐coding tandem repeats.Nikolai V. Tomilin - 2008 - Bioessays 30 (4):338-348.
    Genomes of higher eukaryotes contain abundant non‐coding repeated sequences whose overall biological impact is unclear. They comprise two categories. The first consists of retrotransposon‐derived elements. These are three major families of retroelements (LINEs, SINEs and LTRs). SINEs are clustered in gene‐rich regions and are found in promoters of genes while LINEs are concentrated in gene‐poor regions and are depleted from promoters. The second class consists of non‐coding tandem repeats (satellite DNAs and TTAGGG arrays), which are associated with mammalian (...)
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  37.  6
    X‐linked gene expression and sex determination in Caenorhabditis elegans.Philip M. Meneely - 1990 - Bioessays 12 (11):513-518.
    The signal for sex determination in the nematode Caenorhabditis elegans is the ratio between the number of × chromosomes and the number of sets of autosomes (the X/A ratio). Animals with an X/A ratio of 0.67 (a triploid with two × chromosomes) or less are males. Animals with an X/A ratio of 0.75 or more are hermaphrodites. Thus, diploid males have one × chromosome and diploid hermaphrodites have two × chromosomes. However, the difference in X‐chromosome number between the sexes is (...)
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  38.  13
    Functional gene expression domains: defining the functional unit of eukaryotic gene regulation.Niall Dillon & Pierangela Sabbattini - 2000 - Bioessays 22 (7):657-665.
    The term functional domain is often used to describe the region containing the cis acting sequences that regulate a gene locus. “Strong” domain models propose that the domain is a spatially isolated entity consisting of a region of extended accessible chromatin bordered by insulators that have evolved to act as functional boundaries. However, the observation that independently regulated loci can overlap partially or completely raises questions about functional requirements for physically isolated domain structures. An alternative model, the “weak” domain (...)
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  39.  23
    Clocked gene expression in somite formation.Claudio D. Stern & Daniel Vasiliauskas - 1998 - Bioessays 20 (7):528-531.
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  40.  15
    Modulation of gene expression by auxin.Joe L. Key - 1989 - Bioessays 11 (2-3):52-58.
    Auxin, a class of plant hormones which affects a wide array of growth and developmental processes including cell elongation and cell division, alters gene expression in a very rapid, selective, and dramatic way. The relative level of some mRNAs decreases several fold, while that of other mRNAs increases many fold. These changes are mediated, at least in some cases, by very fast (within 5–10 min) modulation by auxin of transcription as measured by run‐off transcription assays using nuclei isolated (...)
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  41.  13
    Introns and gene expression: Cellular constraints, transcriptional regulation, and evolutionary consequences.Patricia Heyn, Alex T. Kalinka, Pavel Tomancak & Karla M. Neugebauer - 2015 - Bioessays 37 (2):148-154.
    A gene's “expression profile” denotes the number of transcripts present relative to all other transcripts. The overall rate of transcript production is determined by transcription and RNA processing rates. While the speed of elongating RNA polymerase II has been characterized for many different genes and organisms, gene‐architectural features – primarily the number and length of exons and introns – have recently emerged as important regulatory players. Several new studies indicate that rapidly cycling cells constrain gene‐architecture toward (...)
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  42.  45
    Control involving metabolism and Gene expression.Hans V. Westerhoff & Daniel Kahn - 1993 - Acta Biotheoretica 41 (1-2):75-83.
    Control of DNA supercoiling by the free-energy of hydrolysis of ATP that involves gene expression is analyzed in terms of three levels of unconnected metabolic pathways. These are synthesis and breakdown of topoisomerase mRNAs, synthesis and breakdown of topoisomerase proteins and supercoiling and relaxation of DNA. The so-called square-matrix method previously developed for the control of metabolic pathways, is extended to deal with this hierarchical control system. It turns out that also in this case, the matrix of control (...)
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  43.  14
    The kinetics of mammalian gene expression.James L. Hargrove, Martin G. Hulsey & Elmus G. Beale - 1991 - Bioessays 13 (12):667-674.
    When rates of transcription from specific genes change, delays of variable length intervene before the corresponding mRNAs and proteins attain new levels. For most mammalian genes, the time required to complete transcription, processing, and transport of mRNA is much shorter than the period needed to achieve a new, steady‐state level of protein. Studies of inducible genes have shown that the period required to attain new levels of individual mRNAs and proteins is related to their unique half‐lives. The basis for this (...)
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  44.  19
    Regulation of Gene Expression and Replication Initiation by Non‐Coding Transcription: A Model Based on Reshaping Nucleosome‐Depleted Regions.Julien Soudet & Françoise Stutz - 2019 - Bioessays 41 (11):1900043.
    RNA polymerase II (RNAP II) non‐coding transcription is now known to cover almost the entire eukaryotic genome, a phenomenon referred to as pervasive transcription. As a consequence, regions previously thought to be non‐transcribed are subject to the passage of RNAP II and its associated proteins for histone modification. This is the case for the nucleosome‐depleted regions (NDRs), which provide key sites of entry into the chromatin for proteins required for the initiation of coding gene transcription and DNA replication. In (...)
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  45.  20
    Serial analysis of gene expression (SAGE): unraveling the bioinformatics tools.Renu Tuteja & Narendra Tuteja - 2004 - Bioessays 26 (8):916-922.
    Serial analysis of gene expression (SAGE) is a powerful technique that can be used for global analysis of gene expression. Its chief advantage over other methods is that it does not require prior knowledge of the genes of interest and provides qualitative and quantitative data of potentially every transcribed sequence in a particular cell or tissue type. This is a technique of expression profiling, which permits simultaneous, comparative and quantitative analysis of gene‐specific, 9‐ to (...)
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  46.  27
    On gene expression patterns in mammalian hibernation.Katharine M. Brauch - 2008 - Bioessays 30 (9):920-920.
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  47.  44
    Lens development and crystallin gene expression: many roles for Pax‐6.Aleš Cvekl & Joram Piatigorsky - 1996 - Bioessays 18 (8):621-630.
    The vertebrate eye lens has been used extensively as a model for developmental processes such as determination, embryonic induction, cellular differentiation, transdifferentiation and regeneration, with the crystallin genes being a prime example of developmentally controlled, tissue‐preferred gene expression. Recent studies have shown that Pax‐6, a transcription factor containing both a paired domain and homeodomain, is a key protein regulating lens determination and crystallin gene expression in the lens. The use of Pax‐6 for expression of different (...)
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  48.  16
    Mechanism of gene expression by the glucocorticoid receptor: Role of protein‐protein interactions.Iain J. McEwan, Anthony P. H. Wright & Jan-Åke Gustafsson - 1997 - Bioessays 19 (2):153-160.
    The glucocorticoid receptor belongs to an important class of transcription factors that alter the expression of target genes in response to a specific hormone signal. The glucocorticoid receptor can function at least at three levels: (1) recruitment of the general transcription machinery; (2) modulation of transcription factor action, independent of DNA binding, through direct protein‐protein interactions; and (3) modulation of chromatin structure to allow the assembly of other gene regulatory proteins and/or the general transcription machinery on the DNA. (...)
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    Mitochondrial content is central to nuclear gene expression: Profound implications for human health.Rebecca Muir, Alan Diot & Joanna Poulton - 2016 - Bioessays 38 (2):150-156.
    We review a recent paper in Genome Research by Guantes et al. showing that nuclear gene expression is influenced by the bioenergetic status of the mitochondria. The amount of energy that mitochondria make available for gene expression varies considerably. It depends on: the energetic demands of the tissue; the mitochondrial DNA (mtDNA) mutant load; the number of mitochondria; stressors present in the cell. Hence, when failing mitochondria place the cell in energy crisis there are major effects (...)
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  50.  3
    Regulation of gene expression in developing epidermal epithelia.Carolyn Byrne - 1997 - Bioessays 19 (8):691-698.
    Skin is one of the most thoroughly studied epithelia and can be used as a model for transcriptional control of epithelial differentiation. In particular, the stages of epidermal development and differentiation from a simple epithelium are well characterized. Temporal gene expression during development can be used to assign roles for transcription factors in epidermal differentiation. Approaches to understanding transcriptional regulation in epidermis include extensive promoter analysis and expression studies, in some cases coupled to functional studies. This work (...)
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