Crop epigenetics and the molecular hardware of genotype × environment interactions

King, Graham J.

doi:10.3389/fpls.2015.00968

Cited by 24 publications

(13 citation statements)

References 241 publications

(326 reference statements)

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“…Finally, while incorporating TF binding, chromatin accessibility, and epigenetic mark data into our models of the cis-regulatory codes improved their performance, these data were not ideally suited for this study because they were generated from plants at different developmental stages and under different conditions than those used to generate the transcriptomic data (14). This is an important consideration as TF binding, chromatin accessibility, and epigenetic marks change over the course of development and in response to environmental conditions (45,77,78).…”

Section: Discussionmentioning

confidence: 99%

Thecis-regulatory codes of response to combined heat and drought stress inArabidopsis thaliana

Azodi

Lloyd

Shiu

2020

Preprint

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Plants respond to their environment by dynamically modulating gene expression. A powerful approach for understanding how these responses are regulated is to integrate information about cis-regulatory elements (CREs) into models called cis-regulatory codes. Transcriptional response to combined stress is typically not the sum of the responses to the individual stresses. However, cis-regulatory codes underlying combined stress response have not been established. Here we modeled transcriptional response to single and combined heat and drought stress in Arabidopsis thaliana. We grouped genes by their pattern of response (independent, antagonistic, synergistic) and trained machine learning models to predict their response using putative CREs (pCREs) as features (median F-measure = 0.64). We then developed a deep learning approach to integrate additional omics information (sequence conservation, chromatin accessibility, histone modification) into our models, improving performance by 6.2%. While pCREs important for predicting independent and antagonistic responses tended to resemble binding motifs of transcription factors associated with heat and/or drought stress, important synergistic pCREs resembled binding motifs of transcription factors not known to be associated with stress. These findings demonstrate how in silico approaches can improve our understanding of the complex codes regulating response to combined stress and help us identify prime targets for future characterization.in nature and elicit both overlapping and conflicting physiological responses in plants (36). Moreover, TFs and TF binding motifs are known for these stresses individually (37,38). To better understand the regulatory logic underlying single and combined stress, first, we grouped genes likely to be co-regulated based on their shared pattern of transcriptional response under single and combined heat and drought stress (14) (Step 1, Fig. 1). Then, we used known TFBMs and enrichment based pCREs (Step 2, Fig. 1) to generate models of the cis-regulatory codes controlling these different patterns of responses to single and combined heat and drought stress using machine learning. To improve our models of the cisregulatory codes and therefore our understanding of how response to single and combined stress is regulated in A. thaliana, we modeled regulatory interactions (Step 3A, Fig. 1), used a deep learning approach to integrate additional omics information (i.e. chromatin accessibility, sequence conservation, and histone marks) into our models (Step 3B, Fig. 1), and expanded the scope of our models by including pCREs identified outside of the promoter region ( Step 3C, Fig. 1). In addition to providing a comprehensive overview of the cis-regulatory codes of response to single and combined heat and drought stress in A. thaliana, this study also exemplifies how a data-driven approach can be used to make novel discoveries in a complex system like gene regulation (Step 4, Fig.1). MATERIALS AND METHODS Expression data processing, response group classificat...

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Section: Discussionmentioning

confidence: 99%

Thecis-regulatory codes of response to combined heat and drought stress inArabidopsis thaliana

Azodi

Lloyd

Shiu

2020

Preprint

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“…Epigenetic modifications comprise DNA methylation, histone modifications, and the production of microRNA ( Yaish et al, 2011 ). As environmental stress factors can cause epigenetic modification of the genome, which provides an important mechanism for mediating gene-environment interplay ( King, 2015 ). Recent studies suggest that epigenetic modification plays a significant role in plant response to abiotic stresses such as drought, salinity, heat, and cold ( Kim et al, 2015 ).…”

Section: Aba Signaling Response At Gene Expression Levelsmentioning

confidence: 99%

Abscisic Acid and Abiotic Stress Tolerance in Crop Plants

2016

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Abiotic stress is a primary threat to fulfill the demand of agricultural production to feed the world in coming decades. Plants reduce growth and development process during stress conditions, which ultimately affect the yield. In stress conditions, plants develop various stress mechanism to face the magnitude of stress challenges, although that is not enough to protect them. Therefore, many strategies have been used to produce abiotic stress tolerance crop plants, among them, abscisic acid (ABA) phytohormone engineering could be one of the methods of choice. ABA is an isoprenoid phytohormone, which regulates various physiological processes ranging from stomatal opening to protein storage and provides adaptation to many stresses like drought, salt, and cold stresses. ABA is also called an important messenger that acts as the signaling mediator for regulating the adaptive response of plants to different environmental stress conditions. In this review, we will discuss the role of ABA in response to abiotic stress at the molecular level and ABA signaling. The review also deals with the effect of ABA in respect to gene expression.

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“…TEs can disrupt promoter regions or other regulatory sequences internal to genes [27,28]. In addition, epigenetic silencing, as a defense against TE proliferation, can tighten local chromatin structure and inhibit access of transcriptional machinery [74,75]. In this study, the differences between alleles in DE genes in the number of TE insertions were a significant predictor of differential expression.…”

Section: Discussionmentioning

confidence: 81%

Differential gene expression is associated with degeneration of mating-type chromosomes in the absence of sexual antagonism

Carpentier

Giraud

et al. 2019

Preprint

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50In animals and plants, differential expression of genes on sex chromosomes is widespread 51 and it is usually considered to result from sexually antagonistic selection; however differential 52 expression can also be caused by asymmetrical sequence degeneration in non-recombining sex 53 chromosomes, which has been very little studied. The anther-smut fungus Microbotryum 54 lychnidis-dioicae is ideal to investigate the extent to which differential gene expression is 55 associated with sequence degeneration because: 1) separate haploid cultures of opposite mating 56 types help identify differential expression, 2) its mating-type chromosomes display multiple 57 evolutionary strata reflecting successive events of gene linkage to the mating-type loci, and 3)58 antagonistic selection is unlikely between isogamous haploid mating types. We therefore tested 59 the hypothesis that differential gene expression between mating types resulted from sequence 60 degeneration. We found that genes showing differential expression between haploid mating types 61 were enriched only on the oldest evolutionary strata of the mating-type chromosomes and were 62 associated with multiple signatures of sequence degeneration. We found that differential 63 expression between mating types was associated with elevated differences between alleles in 64 non-synonymous substitution rates, indels and premature stop codons, transposable element 65 insertions, and altered intron and GC content. Our findings strongly suggest that degenerative 66 mutations are important in the evolution of differential expression in non-recombining regions. 67 Our results are relevant for a broad range of taxa where mating compatibility or sex is determined 68 by genes located in large regions of recombination suppression, showing that differential 69 expression should not be taken as necessarily arising from antagonistic selection. 70 71 Key words: sex chromosomes, differential gene expression, sequence degeneration, haploid 72 culture, transposable elements, dN, premature stop codon, GC content, intron, Microbotryum 73 fungus 74 3 75 Author Summary 76Differences between males and females, from morphology to behavior and physiology, are 77 considered to largely reflect differential expression of genes that maximize fitness benefits 78 relative to costs that are specific to one sex. However, there is an unexplored alternative to such 79 'sexually antagonistic selection' to explain differential expression. Reproductive compatibility is 80 often determined by genes located in large non-recombining chromosomal regions, where 81 degenerative mutations are expected to accumulate and may separately affect the expression of 82 alternate alleles of genes. We tested the role of genetic degeneration in determining differential 83 expression between the isogamous haploid mating types of the anther-smut fungus,84 Microbotryum lychnidis-dioicae, where sexually antagonistic selection is not a confounding 85 factor. We show that differentially expressed genes are highly enriched in t...

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Crop epigenetics and the molecular hardware of genotype × environment interactions

Cited by 24 publications

References 241 publications

Thecis-regulatory codes of response to combined heat and drought stress inArabidopsis thaliana

Thecis-regulatory codes of response to combined heat and drought stress inArabidopsis thaliana

Abscisic Acid and Abiotic Stress Tolerance in Crop Plants

Differential gene expression is associated with degeneration of mating-type chromosomes in the absence of sexual antagonism

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