<scp>erefinder</scp>: Genome‐wide detection of oestrogen response elements

Anderson, Andrew P; Jones, Adam G.

doi:10.1111/1755-0998.13046

Cited by 6 publications

(6 citation statements)

References 49 publications

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“…We then ran the exactmatch feature to produce a list of coordinates from the investigated AREs. We used a previously published custom R script (Anderson et al, 2020, Anderson andJones, 2019) that matches AREs to genes based on a predetermined distance from the transcription start and end sites. In this case, we search 25-kb upstream of the transcription start site, 10-kb downstream of the transcription end site, and the entirety of the gene (both introns and exons).…”

Section: Responsiveness and Ares In Humansmentioning

confidence: 99%

“…There is evidence that sex-biased gene expression is altered as physically proximal cis-regulatory elements are gained or lost (Matthews et al, 2021). In the human genome, there is a correlation between the number of estrogen-mediated genes and the number of putative estrogen binding sites across chromosomes (Anderson and Jones, 2019). In the Gulf pipefish, there is an excess of estrogen binding regions near putative sex-biased and estrogen-mediated genes involved in ornament expression (Anderson et al, 2020).…”

mentioning

confidence: 99%

“…As genomic information becomes more readily available, the genome‐wide effects of sexual selection may become detectable without a priori knowledge of the strength of sexual selection or phenotypic characteristics. Because sexual selection often drives the evolution of sexually dimorphic traits, the extent of sexual dimorphism across species can be used as an indicator of the relative strength of sexual selection, especially in systems where the mating competition is well understood (Dines et al., 2014, Fitzpatrick et al., 2012, Morris and Carrier, 2016). In primates, for example, body mass and canine tooth length are sexually dimorphic in strongly sexually selected species (Plavcan and van Schaik, 1997, Thorén et al., 2006).…”

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confidence: 99%

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The relationship between sexual dimorphism and androgen response element proliferation in primate genomes

Anderson

Jones

2022

Evolution

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In the males of many vertebrate species, sexual selection has led to the evolution of sexually dimorphic traits, which often are developmentally controlled by androgen signaling involving androgen response elements (AREs). Evolutionary changes in the number and genomic locations of AREs can modify patterns of receptor regulation and potentially alter gene expression. Here, we use recently sequenced primate genomes to evaluate the hypothesis that the strength of sexual selection is related to the genome‐wide number of AREs in a diversifying lineage. In humans, we find a higher incidence of AREs near male‐biased genes and androgen‐responsive genes when compared to randomly selected genes from the genome. In a set of primates, we find that gains or losses of AREs proximal to genes are correlated with changes in male expression levels and the degree of sex‐biased expression of those genes. In a larger set of primates, we find that increases in indicators of sexual selection are correlated with genome‐wide ARE counts. Our results suggest that the responsiveness of the genome to androgens in humans and their close relatives has been shaped by sexual selection that arises from competition among males for mating access to females.

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Section: Responsiveness and Ares In Humansmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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The relationship between sexual dimorphism and androgen response element proliferation in primate genomes

Anderson

Jones

2022

Evolution

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“…A variant of this gene regulatory mechanism is employed to control numerous physiologic functions in all higher organisms. To demonstrate the power of data unification achieved with our G-Dash-min application, we have identified estrogen response elements (EREs) using ERE-Finder (51). These informatics data are displayed as the ERE Track in Fig.…”

Section: Informatics To Physical Structurementioning

confidence: 99%

Genome Dashboards: Framework and Examples

Sun

Bishop

2020

Biophysical Journal

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Genomics is a sequence-based informatics science and a three-dimensional-structure-based material science. However, in practice, most genomics researchers utilize sequence-based informatics approaches or three-dimensional-structure-based material science techniques, not both. This division is, at least in part, the result of historical developments rather than a fundamental necessity. The underlying computational tools, experimental techniques, and theoretical models were developed independently. The primary result presented here is a framework for the unification of informatics-and physics-based data associated with DNA, nucleosomes, and chromatin. The framework is based on the mathematical representation of geometrically exact rods and the generalization of DNA basepair step parameters. Data unification enables researchers to integrate computational, experimental, and theoretical approaches for the study of chromatin biology. The framework can be implemented using model-view-controller design principles, existing genome browsers, and existing molecular visualization tools. We developed a minimal, web-based genome dashboard, G-Dash-min, and applied it to two simple examples to demonstrate the usefulness of data unification and proof of concept. Genome dashboards developed using the framework and design principles presented here are extensible and customizable and are therefore more broadly applicable than the examples presented. We expect a number of purpose-specific genome dashboards to emerge as a novel means of investigating structure-function relationships for genomes that range from basepairs to entire chromosomes and for generating, validating, and testing mechanistic hypotheses.

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“…A variant of this gene regulatory mechanism is employed to control numerous physiologic functions in all higher organisms. To demonstrate the power of data unification achieved with our G-Dash-min application, we have identified estrogen response elements (ERE) using ERE-Finder (50). This informatics data is displayed as the ERE Track in Fig 3. All experimentally determined nucleosome positions for the human genome (51) are also displayed in Fig 3 as the Nuc-Pos Track.…”

Section: Informatics To Physical Modelunclassified

Genome dashboards: Framework and Examples

Sun

Bishop

2019

Preprint

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Genomics is a sequence-based informatics science and a 3D structure-based material science. Here we describe a framework for developing genome dashboards specifically designed to unify informatics with studies of chromatin structure and dynamics. The framework is based on the mathematical representation of geometrically exact rod models and the generalization of DNA base pair step parameters. A Model-View-Controller software design approach is proposed to implement genome dashboards as finite state machines either as desktop or web based applications. Two examples are demonstrated using our minimal genome dashboard called G-Dash-min. The data unification achieved with a genome dashboard supports the bi-directional exchange of data between informatics and structure. Thus any experimentally or theoretically determined sequence based informatics track can inform DNA, nucleosome or chromatin modeling (e.g. nucleosome positions) and structure features can be analyzed as informatics tracks in a genome browser (e.g. DNA base pair step parameters: Roll, Tilt, Twist). Here the framework is applied to chromatin, but genome dashboards are more broadly applicable. Genome dashboards are a novel means of investigating structure-function relationships for regions of the genome ranging from base pairs to entire chromosomes and for generating, validating, and testing mechanistic hypotheses.

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erefinder: Genome‐wide detection of oestrogen response elements

Cited by 6 publications

References 49 publications

The relationship between sexual dimorphism and androgen response element proliferation in primate genomes

The relationship between sexual dimorphism and androgen response element proliferation in primate genomes

Genome Dashboards: Framework and Examples

Genome dashboards: Framework and Examples

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