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Stephen J Gaunt - One of the best experts on this subject based on the ideXlab platform.
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possible rules for the ancestral origin of hox gene Collinearity
Journal of Theoretical Biology, 2016Co-Authors: Stephen J Gaunt, Alexander L GauntAbstract:The Hox gene cluster is believed to have formed from a single ProtoHox gene by repeated cycles of the following events: tandem gene duplication, mutation to generate a new expression boundary along the embryonic axis, and acquisition of a new Hox patterning function. The Hox cluster in Bilateria evolved in compliance with the so-called Collinearity rule. That is, the order of the genes along the chromosome corresponds with the order of their embryonic expression domains along the head-tail axis. Gaunt (2015) suggested that Collinearity may have arisen as a mechanism to minimise the incidence of boundaries between active and inactive genes within the Hox cluster. We now attempt to clarify the model by presenting it in the form of three rules: 1) no two Hox genes may persist in the same cluster with the same anterior boundary of activity in the same tissue; 2) an inactive Hox gene must not be flanked by two active Hox genes; 3) an active Hox gene must not be flanked by two inactive genes. We provide evidence and illustrative computer simulations to show that these rules, which can apply only to partially overlapping patterns of Hox activity, may account for the ancestral origin of Hox gene Collinearity.
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The significance of Hox gene Collinearity.
The International journal of developmental biology, 2015Co-Authors: Stephen J GauntAbstract:Arthropods and vertebrates inherited their Hox clusters from an ancestral cluster of at least six genes already present in their last common ancestor, Urbilateria. Clustering and a common transcriptional direction are both likely features of the way that the gene complex first arose in a process of tandem gene duplication. Spatial Collinearity (correspondence between ordering of Hox genes along the chromosome and their expression patterns along the head-tail axis) has been conserved in many animal groups and is likely to have been already present in Urbilateria. It is not known why the Hox cluster evolved with spatial Collinearity. Four models are discussed. These vary in the significance they place upon Hox chromatin structure, and also on whether they propose that Collinearity is primarily concerned with establishment or maintenance of Hox expression. Published proposals to explain spatial Collinearity, which invoke enhancer sharing, chromatin closing or chromatin opening, are either problematic or can offer only partial explanations. In an alternative proposal it is suggested here that spatial Collinearity evolved principally to maximise physical segregation, and thereby minimise incidence of boundaries, between active and inactive genes within the Hox cluster. This is to minimise erroneous transfer of transcriptional activity, or inactivity, between adjacent Hox genes.
Michael J Zickar - One of the best experts on this subject based on the ideXlab platform.
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some common myths about centering predictor variables in moderated multiple regression and polynomial regression
Organizational Research Methods, 2012Co-Authors: Dev K Dalal, Michael J ZickarAbstract:Additive transformations are often offered as a remedy for the common problem of Collinearity in moderated regression and polynomial regression analysis. As the authors demonstrate in this article,...
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some common myths about centering predictor variables in moderated multiple regression and polynomial regression
Organizational Research Methods, 2012Co-Authors: Dev K Dalal, Michael J ZickarAbstract:Additive transformations are often offered as a remedy for the common problem of Collinearity in moderated regression and polynomial regression analysis. As the authors demonstrate in this article, mean-centering reduces nonessential Collinearity but not essential Collinearity. Therefore, in most cases, mean-centering of predictors does not accomplish its intended goal. In this article, the authors discuss and explain, through derivation of equations and empirical examples, that mean-centering changes lower order regression coefficients but not the highest order coefficients, does not change the fit of regression models, does not impact the power to detect moderating effects, and does not alter the reliability of product terms. The authors outline the positive effects of mean-centering, namely, the increased interpretability of the results and its importance for moderator analysis in structural equations and multilevel analysis. It is recommended that researchers center their predictor variables when thei...
Dev K Dalal - One of the best experts on this subject based on the ideXlab platform.
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some common myths about centering predictor variables in moderated multiple regression and polynomial regression
Organizational Research Methods, 2012Co-Authors: Dev K Dalal, Michael J ZickarAbstract:Additive transformations are often offered as a remedy for the common problem of Collinearity in moderated regression and polynomial regression analysis. As the authors demonstrate in this article,...
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some common myths about centering predictor variables in moderated multiple regression and polynomial regression
Organizational Research Methods, 2012Co-Authors: Dev K Dalal, Michael J ZickarAbstract:Additive transformations are often offered as a remedy for the common problem of Collinearity in moderated regression and polynomial regression analysis. As the authors demonstrate in this article, mean-centering reduces nonessential Collinearity but not essential Collinearity. Therefore, in most cases, mean-centering of predictors does not accomplish its intended goal. In this article, the authors discuss and explain, through derivation of equations and empirical examples, that mean-centering changes lower order regression coefficients but not the highest order coefficients, does not change the fit of regression models, does not impact the power to detect moderating effects, and does not alter the reliability of product terms. The authors outline the positive effects of mean-centering, namely, the increased interpretability of the results and its importance for moderator analysis in structural equations and multilevel analysis. It is recommended that researchers center their predictor variables when thei...
Alexander L Gaunt - One of the best experts on this subject based on the ideXlab platform.
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possible rules for the ancestral origin of hox gene Collinearity
Journal of Theoretical Biology, 2016Co-Authors: Stephen J Gaunt, Alexander L GauntAbstract:The Hox gene cluster is believed to have formed from a single ProtoHox gene by repeated cycles of the following events: tandem gene duplication, mutation to generate a new expression boundary along the embryonic axis, and acquisition of a new Hox patterning function. The Hox cluster in Bilateria evolved in compliance with the so-called Collinearity rule. That is, the order of the genes along the chromosome corresponds with the order of their embryonic expression domains along the head-tail axis. Gaunt (2015) suggested that Collinearity may have arisen as a mechanism to minimise the incidence of boundaries between active and inactive genes within the Hox cluster. We now attempt to clarify the model by presenting it in the form of three rules: 1) no two Hox genes may persist in the same cluster with the same anterior boundary of activity in the same tissue; 2) an inactive Hox gene must not be flanked by two active Hox genes; 3) an active Hox gene must not be flanked by two inactive genes. We provide evidence and illustrative computer simulations to show that these rules, which can apply only to partially overlapping patterns of Hox activity, may account for the ancestral origin of Hox gene Collinearity.
Denis Duboule - One of the best experts on this subject based on the ideXlab platform.
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Chromatin Architectures and Hox Gene Collinearity
Current topics in developmental biology, 2013Co-Authors: Daan Noordermeer, Denis DubouleAbstract:Ever since the observation that Collinearity, that is, the sequential activity of Hox genes based on their relative positions within their gene clusters, is conserved throughout most of the animal kingdom, the question has been raised as to what are the underlying molecular mechanisms. In recent years, technological advances have allowed to uncover changes in chromatin organization that accompany Collinearity at Hox gene clusters. Here, we discuss insights in the dynamics of histone modifications and 3D organization in Drosophila and mammals and relate these findings to genomic organization of Hox gene clusters. Using these findings, we propose a framework for Collinearity, based on five components: clustering, coating, compaction, compartmentalization, and contacts. We argue that these five components may be sufficient to provide a mechanistic ground for the readout of Collinearity in Drosophila and vertebrates.