scholarly journals CamRegBase: a gene regulation database for the biofuel crop, Camelina sativa

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Fabio Gomez-Cano ◽  
Lisa Carey ◽  
Kevin Lucas ◽  
Tatiana García Navarrete ◽  
Eric Mukundi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Close Relative ◽  
Jet Fuels ◽  
Genome Wide ◽  
Reference Plant ◽  
Winter Cover Crop ◽  
One Stop ◽  
New Gene ◽  
Brassicaceae Family

Abstract Camelina is an annual oilseed plant from the Brassicaceae family that is gaining momentum as a biofuel winter cover crop. However, a significant limitation in further enhancing its utility as a producer of oils that can be used as biofuels, jet fuels or bio-based products is the absence of a repository for all the gene expression and regulatory information that is being rapidly generated by the community. Here, we provide CamRegBase (https://camregbase.org/) as a one-stop resource to access Camelina information on gene expression and co-expression, transcription factors, lipid associated genes and genome-wide orthologs in the close-relative reference plant Arabidopsis. We envision this as a resource of curated information for users, as well as a repository of new gene regulation information.

scholarly journals Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 492 ◽  
Author(s):  
Buchberger ◽  
Reis ◽  
Lu ◽  
Posnien
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Evolutionary Biology ◽  
Phenotypic Evolution ◽  
Specific Expression ◽  
Expression Studies ◽  
Genome Wide ◽  
Key Driver ◽  
Context Dependent ◽  
Genome Wide Expression

Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic evolution. An exceptional contribution of cis-regulatory divergence has been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and stage-specific expression. We argue that the regulatory context must be considered in comparative expression studies.

scholarly journals Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for the Evolution of Gene Expression

2019 ◽  
Author(s):  
Elisa Buchberger ◽  
Micael Reis ◽  
Ting-Hsuan Lu ◽  
Nico Posnien
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Evolutionary Biology ◽  
Expression Data ◽  
Regulatory Evolution ◽  
Specific Expression ◽  
Genome Wide ◽  
Key Driver ◽  
Context Dependent ◽  
Genome Wide Expression

Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic variation. An exceptional contribution of cis-regulatory evolution has for instance been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and developmental stage-specific expression. We argue that the regulatory context must be considered when studying evolution of gene expression.

scholarly journals Co-expression Networks From Gene Expression Variability Between Genetically Identical Seedlings Can Reveal Novel Regulatory Relationships

2020 ◽  
Vol 11 ◽  
Author(s):  
Sandra Cortijo ◽  
Marcel Bhattarai ◽  
James C. W. Locke ◽  
Sebastian E. Ahnert
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
New Approach ◽  
Biologically Relevant ◽  
Expression Variability ◽  
Environmental Perturbation ◽  
Environmental Perturbations ◽  
In The Wild ◽  
New Gene ◽  
And Function

Co-expression networks are a powerful tool to understand gene regulation. They have been used to identify new regulation and function of genes involved in plant development and their response to the environment. Up to now, co-expression networks have been inferred using transcriptomes generated on plants experiencing genetic or environmental perturbation, or from expression time series. We propose a new approach by showing that co-expression networks can be constructed in the absence of genetic and environmental perturbation, for plants at the same developmental stage. For this, we used transcriptomes that were generated from genetically identical individual plants that were grown under the same conditions and for the same amount of time. Twelve time points were used to cover the 24-h light/dark cycle. We used variability in gene expression between individual plants of the same time point to infer a co-expression network. We show that this network is biologically relevant and use it to suggest new gene functions and to identify new targets for the transcriptional regulators GI, PIF4, and PRR5. Moreover, we find different co-regulation in this network based on changes in expression between individual plants, compared to the usual approach requiring environmental perturbation. Our work shows that gene co-expression networks can be identified using variability in gene expression between individual plants, without the need for genetic or environmental perturbations. It will allow further exploration of gene regulation in contexts with subtle differences between plants, which could be closer to what individual plants in a population might face in the wild.

scholarly journals Stress-responsive and metabolic gene regulation are altered in low S-adenosylmethionine

2018 ◽  
Author(s):  
Wei Ding ◽  
Daniel P Higgins ◽  
Dilip K. Yadav ◽  
Read Pukklia-Worley ◽  
Amy K Walker
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Stress Responses ◽  
Chromatin Modification ◽  
Metabolic Gene ◽  
C Elegans ◽  
Genome Wide ◽  
Heat Shock Responses ◽  
Pathogen Response ◽  
H3k4 Methyltransferases

AbstractS-adenosylmethionine (SAM) is the methyl donor that modifies proteins such as histones, nucleic acids and produces phosphatidylcholine. Thus variations in SAM levels could affect processes from lipogenesis to epigenetic gene regulation. SAM is hypothesized to link metabolism and chromatin modification, however, its role in acute gene regulation is poorly understood. We recently found that Caenorhabditis elegans with reduced SAM had deficiencies in bacterial-induced H3K4 trimethylation at selected pathogen-response genes, decreasing their expression and limiting survival on the pathogen Pseudomonas aeruginosa. This led us to the hypothesis that SAM may be generally required stress-responsive transcription. Here we show that C. elegans with low SAM fail to activate genome-wide transcriptional programs when exposed to bacterial or xenotoxic stress. However, heat shock responses were unaffected. We also investigated the role of two H3K4 methyltransferases that use SAM, set-2/SET1, and set-16/MLL and found that set-2/SET1 has a specific requirement in bacterial stress responses, whereas set-16/MLL was required for survival in all three stresses. These results define a role for SAM and H3K4 methyltransferases in the acute genome-wide remodeling of gene expression in response to stress. Finally, we find that the ability to modify metabolic gene expression correlates with enhanced survival in stress conditions.

scholarly journals Histone acylation marks respond to metabolic perturbations and enable cellular adaptation

2020 ◽  
Vol 52 (12) ◽  
pp. 2005-2019
Author(s):  
Chanhee Jo ◽  
Seokjae Park ◽  
Sungjoon Oh ◽  
Jinmi Choi ◽  
Eun-Kyoung Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Gene Activation ◽  
Metabolic Stress ◽  
Atp Citrate Lyase ◽  
Cellular Adaptation ◽  
Genome Wide ◽  
Metabolic States ◽  
Citrate Lyase ◽  
Chain Acyl

AbstractAcetylation is the most studied histone acyl modification and has been recognized as a fundamental player in metabolic gene regulation, whereas other short-chain acyl modifications have only been recently identified, and little is known about their dynamics or molecular functions at the intersection of metabolism and epigenetic gene regulation. In this study, we aimed to understand the link between nonacetyl histone acyl modification, metabolic transcriptional regulation, and cellular adaptation. Using antibodies specific for butyrylated, propionylated, and crotonylated H3K23, we analyzed dynamic changes of H3K23 acylation upon various metabolic challenges. Here, we show that H3K23 modifications were highly responsive and reversibly regulated by nutrient availability. These modifications were commonly downregulated by the depletion of glucose and recovered based on glucose or fatty acid availability. Depletion of metabolic enzymes, namely, ATP citrate lyase, carnitine acetyltransferase, and acetyl-CoA synthetase, which are involved in Ac-CoA synthesis, resulted in global loss of H3K23 butyrylation, crotonylation, propionylation, and acetylation, with a profound impact on gene expression and cellular metabolic states. Our data indicate that Ac-CoA/CoA and central metabolic inputs are important for the maintenance of histone acylation. Additionally, genome-wide analysis revealed that acyl modifications are associated with gene activation. Our study shows that histone acylation acts as an immediate and reversible metabolic sensor enabling cellular adaptation to metabolic stress by reprogramming gene expression.

scholarly journals Genome-wide analysis of the association of transposable elements with gene regulation suggests that Alu elements have the largest overall regulatory impact

2017 ◽  
Author(s):  
Lu Zeng ◽  
Stephen M. Pederson ◽  
Danfeng Cao ◽  
Zhipeng Qu ◽  
Zhiqiang Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Transposable Elements ◽  
Regulatory Sequences ◽  
Alu Elements ◽  
Genome Wide ◽  
A Genome ◽  
Regulatory Impact ◽  
Species Specific ◽  
Regulated Gene Expression

ABSTRACTNearly half of the human genome is made up of transposable elements (TEs) and there is evidence that TEs are involved in gene regulation. Here, we have integrated publicly available genomic, epigenetic and transcriptomic data to investigate this in a genome-wide manner. A bootstrapping statistical method was applied to minimize the confounder effects from different repeat types. Our results show that although most TE classes are primarily associated with reduced gene expression, Alu elements are associated with up regulated gene expression. Furthermore, Alu elements had the highest probability of any TE class of contributing to regulatory regions of any type defined by chromatin state. This suggests a general model where clade specific SINEs may contribute more to gene regulation than ancient/ancestral TEs. Finally, non-coding regions were found to have a high probability of TE content within regulatory sequences, most notably in repressors. Our exhaustive analysis has extended and updated our understanding of TEs in terms of their global impact on gene regulation, and suggests that the most recently derived types of TEs, i.e. clade or species specific SINES, have the greatest overall impact on gene regulation.

New gene expression switches

Nature India ◽  
2009 ◽  
Keyword(s):  
Gene Expression ◽  
New Gene

Genome Wide Transcriptional Analysis of Gene Expression Signatures and Pathways on Neoplastic Pancreatic Cancer

2012 ◽  
Vol 2 (8) ◽  
pp. 43-44
Author(s):  
Anusha.B.N Anusha.B.N ◽  
◽  
Shambu.M.G Shambu.M.G ◽  
Kusum Paul
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Transcriptional Analysis ◽  
Genome Wide ◽  
Gene Expression Signatures
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