Susceptibility to Heat Stress and Aberrant Gene Expression Patterns in Holocarboxylase Synthetase-Deficient Drosophila melanogaster Are Caused by Decreased Biotinylation of Histones, Not of Carboxylases

Abstract Embryonic gene expression patterns are an indispensable part of modern developmental biology. Currently, investigators must visually inspect numerous images containing embryonic expression patterns to identify spatially similar patterns for inferring potential genetic interactions. The lack of a computational approach to identify pattern similarities is an impediment to advancement in developmental biology research because of the rapidly increasing amount of available embryonic gene expression data. Therefore, we have developed computational approaches to automate the comparison of gene expression patterns contained in images of early stage Drosophila melanogaster embryos (prior to the beginning of germ-band elongation); similarities and differences in gene expression patterns in these early stages have extensive developmental effects. Here we describe a basic expression search tool (BEST) to retrieve best matching expression patterns for a given query expression pattern and a computational device for gene interaction inference using gene expression pattern images and information on the associated genotypes and probes. Analysis of a prototype collection of Drosophila gene expression pattern images is presented to demonstrate the utility of these methods in identifying biologically meaningful matches and inferring gene interactions by direct image content analysis. In particular, the use of BEST searches for gene expression patterns is akin to that of BLAST searches for finding similar sequences. These computational developmental biology methodologies are likely to make the great wealth of embryonic gene expression pattern data easily accessible and to accelerate the discovery of developmental networks.

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Microarray data uncover the genome-wide gene expression patterns in response to heat stress in rice post-meiosis panicle

Journal of Plant Biology ◽

10.1007/s12374-014-0177-z ◽

2014 ◽

Vol 57 (6) ◽

pp. 327-336 ◽

Cited By ~ 15

Author(s):

Xianwen Zhang ◽

Hairong Xiong ◽

Ailing Liu ◽

Xiaoyun Zhou ◽

Yan Peng ◽

...

Keyword(s):

Gene Expression ◽

Heat Stress ◽

Microarray Data ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Genome Wide ◽

Genome Wide Gene Expression

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Comparative assessment of heat stress induced changes in carcass traits, plasma leptin profile and skeletal muscle myostatin and HSP70 gene expression patterns between indigenous Osmanabadi and Salem Black goat breeds

Meat Science ◽

10.1016/j.meatsci.2018.03.015 ◽

2018 ◽

Vol 141 ◽

pp. 66-80 ◽

Cited By ~ 19

Author(s):

P.R. Archana ◽

V. Sejian ◽

Wilfred Ruban ◽

M. Bagath ◽

G. Krishnan ◽

...

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Heat Stress ◽

Expression Patterns ◽

Comparative Assessment ◽

Gene Expression Patterns ◽

Hsp70 Gene ◽

Induced Changes ◽

Plasma Leptin ◽

Black Goat

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Adaptive divergence in transcriptome response to heat and acclimation in Arabidopsis thaliana plants from contrasting climates.

10.1101/044446 ◽

2016 ◽

Cited By ~ 3

Author(s):

Nana Zhang ◽

Elizabeth Vierling ◽

Stephen Tonsor

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Heat Stress ◽

High Temperature ◽

Expression Patterns ◽

High Elevation ◽

Adaptive Divergence ◽

Gene Expression Patterns ◽

Direct Exposure ◽

Small Hsps

Phenotypic variation in stress response has been widely observed within species. This variation is an adaptive response to local climates and is controlled by gene sequence variation and especially by variation in expression at the transcriptome level. Plants from contrasting climates are thus expected to have different patterns in gene expression. Acclimation, a pre-exposure to sub-lethal temperature before exposing to extreme high temperature, is an important adaptive mechanism of plant survival. We are interested to evaluate the gene expression difference to heat stress for plants from contrasting climates and the role of acclimation in altering their gene expression pattern. Natural Arabidopsis thaliana plants from low elevation mediterranean and high elevation montane climates were exposed to two heat treatments at the bolting stage: a) 45 oC: a direct exposure to 45oC heat; b) 38/45 oC: an exposure to 45oC heat after a 38oC acclimation treatment. Variation in overall gene expression patterns was investigated. We also explored gene expression patterns for Hsp/Hsf pathway and reactive oxygen species (ROS) pathway. In both heat treatments, high elevation plants had more differentially expressed (DE) genes than low elevation plants. In 45 oC, only Hsp/Hsf pathway was activated in low elevation plants; both Hsp/Hsf and ROS pathways were activated in high elevation plants. Small Hsps had the highest magnitude of change in low elevation plants while Hsp70 and Hsp90 showed the largest magnitude of fold in high elevation plants. In 38/45 oC, Hsp/Hsf and ROS pathways were activated in both low and high elevation plants. Low elevation plants showed up-regulation in all Hsps, especially small Hsps; high elevation plants showed down-regulation in all Hsps. Low elevation and high elevation also adopted different genes in the ROS pathway. We also observed genes that shifted expression in both low and high elevation plants but with opposite directions of change. This study indicates that low and high elevation plants have evolved adaptive divergence in heat stress response. The contrasting patterns of temperature variation in low and high elevation sites appears to have played a strong role in the evolution of divergent patterns to high temperature stress, both pre-acclimation and direct exposure gene expression responses.

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